Table of contents

Subject

Page #

Anatomy and
physiology

Body organization & tissues

Circulatory systems
Digestive systems
Cell signalling
Excretory systems
Immune systems
Integumentary systems
Muscular systems
Nervous systems
Respiratory systems
Sensory systems
Skeletal systems

1
5
14
24
28
39
45
48
56
67
76
78
82
85
89
95

Cell and molecular

biology

Carbohydrates
Cell cycle
Cell signalling
Molecular biology lab
techniques
Diffusion and osmosis
Substance transport
Glycolysis
Mitosis and meiosis
Nucleic acids
Organelles
Origins of life
Oxidative phosphorylation
Photosynthesis
Prokaryotes vs eukaryotes
Amino acids
TCA, citric acid cycle
Viruses
Water

97
99
102
106
112
117
124
129
136
140
145
154
159
162

Developmental
biology

Animal reproduction
Embryonic development

165
175

Diversity of
life

Archaea and bacteria

Eukarya

184
185

Evolution and
ecology

Behavior
Biogeochemical cycles
Community ecology
Ecosystems
Evolution
Population ecology

212
214
215
217
219
223

Genetics

225

1
Body organization and types of tissues
Hierarchical organization of body plans
Cells are organized into tissues, groups of cells with a similar appearance and a common
function.
Different types of tissues are further organized into functional units called organs.
Organs are generally made up of 4 types of tissue:
Nervous tissue
Epithelial tissue
Muscle
Connective tissue
Groups of organs that work together, providing an additional level of organization and
coordination, make up an organ system.
Types of animal tissues
Epithelial cells or epithelia cover the outside of the body and line organs and cavities
within the body.
Epithelial cells are closely packed, often with tight junctions.
They function as a barrier against mechanical injury, pathogens, and fluid loss.
Also form active interfaces with the environment.
Different cell shape and arrangements correlate to distinct functions.
They are polarized, meaning that they have two different sides.
The apical surface faces the lumen (cavity) or outside of the organ and is therefore
exposed to fluid or air. Specialized projections often cover this surface.
The opposite side of each epithelium is the basal surface.
Connective tissue consists of a sparse population of cells scattered through an extracellular
matrix. It holds many tissues and organs together and in place.
Three different types of connective tissue fibers:
Collagenous fibers provide strength and flexibility
Reticular fibers join connective tissue to form adjacent tissues
Elastic fibers make tissues elastic
Loose connective tissue is the most common tissue: binds epithelia to underlying
tissues and holds organs in place.
Fibrous connective tissues is dense with collagenous fibers.
Bone generates the skeleton of animals.
Adipose tissue stores fat in adipose cells.
Blood carry nutrients from one place to another.
Cartilage contains collagenous fibers embedded in chondroitin sulfate. Very strong.
cartilage tissue is surrounded by a dense fibrous connective tissue called
Perichondrium
Muscle tissue is the tissue responsible for nearly all types of body movement.
Skeletal muscle is responsible for voluntary movements.
Smooth muscle, which lacks striations, is responsible for involuntary body movements.
Cardiac muscle forms the contractile wall of the heart and is involuntary.
Nervous tissue functions in the receipt, processing, and transmission of information.
Contains neurons, which transmits nerve impulses, and support cells called glial cells.
Peritoneum is the tissue that covers all the digestive organs and lines in the body cavity.
Homeostasis
Regulating and conforming

An animal is a regulator for an environmental variable if it uses internal mechanisms to

control internal change in the face of external fluctuation.
An animal is a conformer for a particular variable if it allows its internal conditions to
change in accordance with external changes in the variable.
An animal may regulate some processes and conform to other processes.
Homeostasis
Homeostasis means steady state, referring to the maintenance of internal balance.
In achieving homeostasis, animals maintain a relatively constant internal environment even
when the external environment changes significantly.
Mechanisms of homeostasis
An animal achieves homeostasis by maintaining a variable at a particular value, or set
point.
A fluctuation in the variable above or below the set point serves as the stimulus detected by
a sensor.
Upon receiving a signal from the sensor, a control center generates an output that triggers a
response, a physiological activity that helps return the variable to the set point.
Feedback control in homeostasis
Negative feedback is a control mechanism that reduces the stimulus.
For example, you sweat to decrease the effects of heat (increase body temperature).
Positive feedback (e.g. orgasm) is a control mechanism that amplifies, rather than reduces,
the stimulus.
Does not play a major role in homeostasis, but helps drive processes to completion.
Alterations in homeostasis
A circadian rhythm is a set of physiological changes that occur roughly every 24 hours.
One way in which homeostasis may be altered is through acclimatization, the gradual
process by which an animal adjusts to changes in its external environment.
Acclimatization is a temporary change during an animal's lifetime and does not bring
about any changes within the genetic code.

Thermoregulation
Endothermy and Ectothermy
Endothermic means that the organism is warmed by internal mechanisms.
Can maintain a stable body temperature in the face of large fluctuations in the
environmental temperature.
Ectothermic means that the organism gains heat from external sources.
Mainly adjust their body temperature by behavioral means.
Ectotherms generally need to consume much less food than endotherms of equivalent
size.
Organisms may be both ectothermic and endothermic in some way.
Variation in body temperature
A poikilotherm is an animal whose body temperature varies with its environment.
A homeotherm has a relatively constant body temperature.
There is no fixed relationship between endothermy, homeothermy, poikilothermy, and
ectothermy.
Balancing heat loss and gain
The essence of thermoregulation is maintaining a rate of heat gain that equals the rate of
heat loss.

Many of these mechanisms involve the integumentary system, the outer covering of
the body, consisting of the skin, hair, and nails.
Radiation is the emission of electromagnetic waves by all objects warmer than absolute
zero.
Evaporation is the removal of heat from the surface of a liquid that is losing some of its
molecules as gas.
Convection is the transfer of heat by the movement of air or liquid past a surface.
Conduction is the direct transfer of thermal motion (heat) between two molecules of
objects in contact with each other.
Insulation
A major thermoregulatory adaptation is insulation, which reduces the flow of heat between
an animal's body and its environment.
Insulation may include hair or feathers, as well as layers of fat formed by adipose tissue.
Circulatory adaptations
Nerve signals that relax the muscles of vessel walls result in vasodilation, a widening of
superficial blood vessels. As a result, blood flow of the skin increases. Done in hot
temperatures.
Vasodilation warms the skin and increases the transfer of body heat to the environment.
Vasoconstriction reduces blood flow and heat transfer by decreasing the diameter of
superficial vessels. Done in cold temperatures.
In many birds and mammals, reducing heat loss from the body comes from countercurrent
heat exchange, the transfer of heat between fluids that are flowing in opposite directions.
Arteries and veins are located adjacent to each other. As warm blood moves from the
body to the core in the arteries, it transfers heat to the colder blood returning from the
extremities in the veins.

Cooling by evaporative heat loss

Many terrestrial animals lose water by evaporation from their skin and respiratory surfaces.
Water absorbs considerable heat when it evaporates (high specific heat); this heat is carried
away from the body surface with water vapor. This is evaporative heat loss.

Behavioral responses
Many ectotherms maintain a nearly constant body temperature by engaging in relatively
simple behaviors.
When cold, they seek warm places, orienting themselves toward heat sources and
expanding their portion of body surface exposed to the heat source.
When hot, they bate, moving to cool areas, or turn in another direction, minimizing their
absorption of heat form the sun.
Adjusting metabolic heat production
Endotherms can vary heat production, thermogenesis, to match changing rates of heat loss.
It is increased by such muscle activity as moving or shivering.
Nonshivering thermogenesis occurs in brown adipose tissues. The breakdown of the
adipose tissues eventually generates a proton gradient. Instead of using the gradient to
synthesize ATP, the gradient is used to generate heat.
Physiological Thermostats
The sensors for thermoregulation are concentrated in the hypothalamus
within the hypothalamus, a group of nerve cells functions as a thermostat, responding to
body temperatures outside the normal range by activating mechanisms that promote heat
loss or gain.

5
Circulatory systems in other animals
Gastrovascular cavities
Gastrovascular cavity is a digestion and circulatory system with only one opening
usually seen in Cnidarians.
Fluid bathes both the inner and outer tissue layers, facilitating exchange of gases and
cellular waste. Only the cells lining the cavity have direct access to nutrients released by
digestion. However, the body wall is 2 cells thick so the diffusion distance is really
small.
In a hydra, thin branches of the gastrovascular cavity extend into the animal's tentacles.
In jellies and other cnidarians, the gastrovascular cavity has a much more elaborate
branching pattern.
Flatworms and planarians survive without a circulatory system due to the combination of a
gastrovascular cavity and a flat body.
Flat body optimizes exchange with environment by increasing surface area and
minimizing diffusion distances.
Open and closed circulatory systems
A circulatory system has 3 basic components:
circulatory fluid
set of interconnecting vessels
a muscular pump, the heart
In an open circulatory system, the circulatory fluid, called hemolymph is also the
interstitial fluid that bathes body cells.
Arthropods have open circulatory systems.
Heart contraction pumps hemolymph through the circulatory vessels into
interconnected sinuses, spaces surrounding the organs.

Within the sinuses, chemical exchange occurs between the hemolymph and body cells.
In a closed circulatory system, a circulatory fluid called blood is confined to vessels and is
distinct from the interstitial fluid.
One or more hearts pump blood into large vessels that branch off into smaller ones that

6
infiltrate the organs.
Chemical exchange occurs between the blood and the interstitial fluid, as well as
between the interstitial fluid and the body cells.
Annelids, cephalopods, and all vertebrates have closed circulatory systems.

Open circulatory systems require less energy input than closed circulatory systems.
Closed circulatory systems allows animals to be larger.
Organization of vertebrate circulatory systems
The closed circulatory system of humans and other vertebrates is called the cardiovascular
system.
Blood flow through blood vessels is unidirectional
Blood vessels are only distinguished by the direction in which they carry blood
Arteries carry blood from the heart to organs throughout the body.
Within organs, arteries branch into arterioles.
Arterioles convey blood to capillaries, microscopic vessels with very thin, porous walls.
Networks of capillaries, called capillary beds, infiltrate tissues, passing within a few
cell diameters of every cell in the body. Exchange of gases and nutrients occur between
the interstitial fluid and capillary beds.
At their downstream end, capillaries converge into venules, and venules converge into
veins, the vessels that carry blood back to the heart.
Portal veins (exception to the general rule) carry blood between pairs of capillary beds
in the digestive system to capillary beds in the liver.
The hearts of all vertebrates contain two or more muscular chambers.
The chambers that receive blood entering to the heart are called atria (singular, atrium)
and the chambers responsible for pumping blood out of the heart are called ventricles.
Single circulation
In bony fishes, rays, and sharks, the heart consists of two chambers: an atrium and a
ventricle.
The blood passes through the heart once in each complete circuit through the body, an

arrangement called single circulation.

Blood pumped out from the ventricles go to the capillary bed in the gills, where oxygen
diffuses into the blood and carbon dioxide diffuses out of the blood.
As blood leaves the gills, the capillaries converge into a vessel that carries oxygen-rich
blood to capillary beds throughout the body.
Deoxygenated blood then travels back to the heart (atria).
Double circulation
The circulatory systems of amphibians, reptiles, and mammals have two circuits, an
arrangement called double circulation.
The pumps for the two circuits are combined into a single organ, the heart (allows for
coordination of both circuits).
One pump, the right side of the heart, delivers oxygen-poor blood to the capillary beds of
the gas exchange tissues where oxygen/carbon dioxide exchange occurs. This is called the
pulmonary circuit if the capillary beds are all in the lungs. It is called a pulmocutaneous
circuit if it includes capillaries in both the lungs and the skin, as in many amphibians.
After oxygen-enriched blood leaves the gas exchange tissues, it enters the other pump, the
left side of the heart. The heart will propel the blood to capillary beds in organs and tissues
throughout the body, where appropriate exchanges will occur between capillaries and the
interstitial fluids. Deoxygenated blood then travels back to the heart, completing the
systemic circuit.

Mammals and birds have 4 chambered hearts

Repitles and amphibians have 3 chambered hearts
Fish have 2 chambered hearts
Crocodiles and alligators have 4 chambered hearts

The heart
Mammalian circulation

Contraction of the right ventricle pumps blood to the lungs via pulmonary arteries.
As blood flows through capillary beds in the left and right lungs, it loads oxygen and
unloads carbon dioxide.
Oxygen-rich blood returns to the lungs via the pulmonary veins to the left atrium of the
heart.
Oxygen-rich blood flows into the left ventricle.
Blood leaves the left ventricle via the aorta, which conveys blood to arteries leading
throughout the body.
The first branches leading from the aorta are the coronary arteries, which supply blood to
the heart muscle itself.
Then branches lead to capillary beds in the head and arms, where the appropriate exchanges
occur.
The aorta descends into the abdomen, supplying oxygen-rich blood leading to capillary beds
in the abdominal organs and legs, where the appropriate exchanges occur.
Deoxygenated blood in the upper half of the body is channeled into a large vein, the
superior vena cava. The inferior vena cava drains blood form the bottom half of the body.
The two venae empty their blood into the right atrium, for which oxygen-poor blood flows
into the right ventricle and restarts the cycle.
Mammalian heart structure
The two atria have relatively thin walls and serve as collection chambers for blood
returning to the heart from the lungs or other body tissues.
The two ventricles have thicker walls and contract much more forcefully. The left ventricle
contracts with more force than the right ventricle since it needs to pump blood to the entire
body.

The heart contracts and a rhythmic cycle called the cardiac cycle.
When the heart contracts, it pumps blood; when it relaxes, its chambers fill with blood.
The contraction phase is called systole, and the relaxation phase is called diastole.
The volume of the blood each ventricle pumps per minute is called the cardiac output. Two
factors:
Rate of contraction, or heart rate (beats per minute)
stroke volume, the amount of blood pumped by a ventricle in a single contraction.
Stroke volume = end diastole volume end systolic volume
Four valves prevent backflow and keep blood moving in the right direction. Made up of
connective tissue, valves open when pushed from one side and close when pushed from the
other.
Atrioventricular (AV) valves lie between each atrium and ventricle.
Pressure generated by contraction of the ventricles closes the AV valves, preventing
blood from flowing back into the atria.
Papillary muscles are located in the ventricles and bind to the AV valve to prevent
inversion of these valves during systole.
Valve on the right side of the heart has 3 cusps and is called the tricuspid valve
The valve on the left side has 2 cusps and is called the mitral valve.
Semilunar valves are located at the two exits of the heart: where the aorta leaves the left
ventricle and where the pulmonary artery leaves the right ventricle.
Pushed open by pressure generated from contraction of ventricles.
Relaxation of ventricles closes the semilunar valves and prevents backflow.
If blood squirts backward through a defective valve, it may produce an abnormal sound
called a heart murmur.
Maintaining the heart's rhytmic beat
Some cardiac muscle cells are autorhythmic, meaning they can contract and relax
repeatedly without any signal from the nervous system.
The sinoatrial (SA) node sets the rate and timing at which all cardiac muscle cells contract.
It is autorhythmic and is located in the wall of the right atrium, near where the superior
vena cava enters the heart.
Some arthropods have SA nodes located in the nervous system, outside the heart.
Produces electrical impulses. Since cardiac muscle cells are electrically coupled through
gap junctions, impulses from the SA node spread rapidly throughout heart tissue.
Impulses from the SA node spread rapidly through the walls of the atria, causing both atria
to contract in unison.
When the atria contracts, the impulses originating at the SA node reach other autorhythmic
cells located in the wall between the left and right atria. The cells form a relay point called
the atrioventricular (AV) node.
The impulses at the AV node are delayed by about 0.1 seconds before spreading to the
heart so that the atria can completely empty.
The signals from the AV node are sent through the bundle of His, nodal tissue that passes
down between both ventricles and then branches into the ventricles through the Purkinjie
fibers. This impulse results in the contraction of the ventricles.
Physiological cues can later heart tempo by regulating the SA node.
The parasympathetic and sympathetic nervous systems are largely responsible for this.
Sympathetic nervous system speeds up SA node and heartbeat, and the
parasympathetic nervous system slows down SA node and heartbeat.
Body temperature affects SA node.

10

An increase in 1 degree Celsius increases heart rate by 10 beats per minute.

Blood Vessels
Blood vessel structure
Blood vessels contain a central lumen (cavity) lined with an endothelium, a single layer of
flattened epithelial cells.
The smooth surface of the endothelium minimizes resistance to the flow of blood
Capillaries are the smallest blood vessels and have very thin walls, which consist of an
endothelium and a surrounding extracellular layer called the basal lamina.
Exchange of substances between blood and the interstitial fluid only occurs in capillaries
because the walls are thin enough to permit this exchange.
The walls of arteries and veins have more complex organization than those of capillaries.
The outer layer is connective tissue that contains elastic fibers, that provides strength.
The layer next to the endothelium contains smooth muscle.
The walls of arteries are thick and strong, accommodating blood pumped at high
pressure by the heart and are elastic.
Veins have a thinner wall than arteries. Also contain valves which maintains a
unidirectional flow of blood.
Blood flow velocity
The velocity of blood slows as it moves from arteries to arterioles to the much narrower
capillaries.
TOTAL cross sectional area is inversely proportional to velocity.
As capillaries have the highest total cross sectional area, velocity is lowest.
The larger the blood vessel, the lower the total cross sectional area, and the higher the
velocity (arteries > arterioles and veins > venules)
Note: the greatest resistance to blood flow is located in the arterioles.
Blood pressure
Contraction of a heart ventricle generates blood pressure, which exerts a force in all
directions.
Arterial blood pressure is highest when the heart contracts during ventricular systole. The
pressure at this time is called systolic pressure.
The rhythmic bulging of the artery is the pulse.
During diastole, the elastic walls of the artery snap back. As a consequence, there is a lower
but still substantial blood pressure when the ventricles are relaxed. This is the diastolic
pressure.
Regulation of blood pressure
As the smooth muscles in the arteriole walls contract, the arterioles narrow, a process called
vasoconstriction. This increases the artery blood pressure.
When the smooth muscles in the arteriole relax, the arterioles undergo vasodilation, an
increase in diameter that causes blood pressure in the arteries to fall.
Nitric oxide is the major inducer of vasodilation and endothelin, a peptide, is the major
potent inducer of vasoconstriction.
Capillary function
Given that capillaries lack smooth muscle, how is blood flow in the capillary beds altered?
One mechanism is constriction or dilation of the arterioles that supply capillary beds.
A second mechanism involves precapillary sphincters, rings of smooth muscle located
at the entrance to each capillary bed.
These sphincters regulate and redirect the passage of blood into particular sets of

11
capillaries.
Two opposing forces control the movement between the capillaries and the surrounding
tissues:
Blood pressure tends to drive fluid out of the capillaries
the presence of blood proteins tend to pull fluid back. The dissolved proteins in the
blood generates osmotic pressure
Blood pressure > osmotic pressure, so this leads to a let loss of fluid from the capillaries.
The net loss is generally greatest at the arterial end of these vessels, where the blood
pressure is highest.

Double capillary beds occur in the glomerulus, around the loop of henle, small intestine,
liver, hypothalamus, and anterior pituitary gland. The capillary bed pools into another
capillary bed without first going to the heart (transports products in high concentration
without spreading to the rest of the body)
Capillary bed 1 drains into the portal vein and capillary bed 2 drains into vein that
returns to the heart
Fluid return by the lymphatic system
The lost fluid and proteins return to the blood via the lymphatic system, which includes a
tiny network of vessels intermingled among capillaries of the cardiovascular system, as well
as larger vessels into which small vessels empty.
After entering the lymphatic system by diffusion, the fluid lost by capillaries is called
lymph; its composition is about the same as that of the interstitial fluid.
The lymphatic system drains into large veins of the cardiovascular system at the base of
the neck.
Lymph vessels have valves to prevent backflow
Along a lymph vessel are small, lymph-filtering organs called lymph nodes, which play an
important role in the body's defense.
Contains phagocytic cells (leukocytes) that filter the lymph and serve as immune
response centers.
The spleen is an organ that makes lymphocytes, filters the blood, stores blood cells, and
destroys old blood cells.

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Blood components
Blood composition and function
Blood is 55% plasma and 45% other cellular components.
Vertebrate blood is a connective tissue of consisting of cells suspended in a liquid matrix
called plasma.
Many of the dissolved solutes are inorganic ions sometimes referred to as electrolytes.
Some ions buffer the blood
Some ions maintain the osmotic balance of blood
Affects the composition of the intersitial fluid
Plasma proteins acts as buffers against pH and helps maintain the osmotic balance
Contains nutrients, metabolic wastes, respiratory gases, and hormones.
Has a much higher protein concentration than interstitial fluid, although the two fluids
are otherwise similar.
Cellular elements
Red blood cells, or erythrocytes, are by far the most numerous blood cells. The main
function is oxygen transport.
Contains hemoglobin, an iron-containing protein that transports oxygen (up to 4
molecules per molecule).
Lacks organelles and a nucleus to maximize hemoglobin content.
NOTE that erythrocytes derive their energy from glycolysis and not from the TCA
cycle and oxidative phosphorylation!
erythropoietin is a hormone released from the kidneys and will stimulate red blood
cell formation in the bone marrow
White blood cells are leukocytes. Their function is to fight infections.
Diapedesis is the process by which white blood cells become part of the interstitial
fluid (slip through endothelial lining)
Platelets are pinched-off cytoplasmic fragments of specialized bone marrow cells.
Functions in blood clotting. Do not contain a nucleus.
Derived from megakaryocytes.
Maintenance of body pH
body fluid is relatively constant at 7.4 this consistency is attained by the removal of CO2
by the lungs and hydrogen ions by the kidneys.
Disorders:
Respiratory: affects the blood acidity by causing changes in PCO2 (high CO2 = acidic)
Metabolic: affects the blood acidity by cuasing changes in HCO3- (High HCO3- =
basic)
Blood clotting
Platelets adhere to exposed collagen of damaged vessel and cause neighboring platelets to
form the platelet plug (temporary sealing the break in the vessel wall).
Both the platelets and damaged tissue release clotting factor called thromboplastin.
Thromboplastin converts inactive plasma protein prothombrin to thrombin
Thrombin converts fribrinogen into fibrin
Fibrin threads coat damaged area and trap blood cells to form a clot. Serum is the fluid left
after blood clotting.
A thrombus is a blood clot that forms in a vessel abnormally.
Fetal circulation
oxygenated, nutrient-rich blood from placenta is carried to fetus via umbilical vein

13
Blood bypasses the liver through the ductus venosus. The ductuc venosus provides a direct
communication between the umbilical vein and the inferior vena cava. Oxygenated blood
from the ductus venosus combines with the deoxygenated blood in the inferior vena cava
and continues to the heart.
Blood travels to the fetus heart through the inferior vena cava and mixes with deoxygenated
blood returning from the superior vena cava. Blood then enters the right atrium of the
heart.
Because fetal lungs are not functional, most blood will bypass the right ventricle and be
shunted to the left atrium via the foramen ovale. Blood will then travel into the left
ventricle and be distributed throughout the fetal body via the aorta.
Some blood will enter the right ventricle from the right atrium and proceed to the
pulmonary trunk. However, most of this blood will be shunted away from the
pulmonary arteries and into the aorta via the ductus arteriosus.
Blood circulates through the fetal body and returns to the placenta via the umbilical
arteries. These arteries are also carrying deoxygenated blood back to the placenta.
The placenta re-oxygenates blood returning from the umbilical arteries and repeats the
fetal cardiovascular cycle by recycling the newly oxygenated blood to the fetus through the
umbilical vein.
Click the link below, and select fetal system for an excellent animation to understand this!
http://www.indiana.edu/~anat550/cvanim/fetcirc/fetcirc.html

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Features of diet
Essential Nutrients
Some cellular processes require materials that an animal cannot assemble from simpler
organic precursors.
These materialspre-assembled organic molecules and mineralsare called essential
nutrients.
Essential nutrients include essential amino acids and fatty acids, vitamins and minerals.
Essential nutrients serve key functions in cells such as serving as substrates of enzymes
(as coenzymes), and as cofactors in biosynthetic pathways.
Essential amino acids are the 8 amino acids that cannot be synthesized within the body.
Essential fatty acids are fatty acids that contain double bonds that cannot be normally
synthesized within the body.
Vitamins are organic molecules that are required in the diet in very small amounts.
Are either fat-soluble or water-soluble.
Minerals are inorganic nutrients that are usually required in small amounts.
Dietary deficiencies
A diet that lacks one or more essential nutrients or consistently supplied less chemical
energy than the body requires results in malnutrition, failure to obtain adequate nutrition.
A diet that fails to provide adequate sources of energy results in undernutrition.
Digestion in other animals
Main stages of food processing
The first stage, ingestion, is the act of eating or feeding.
During digestion, the second stage of food processing, food is broken down into molecules
small enough for the body to absorb.
Mechanical digestion breaks food into smaller pieces, increasing the surface area
available for chemical processes.
Chemical digestion is necessary because animals cannot directly use the proteins,
carbohydrates, nucleic acids, fats, and phospholipids in foods.
Enzymatic hydrolysis breaking macromolecules into smaller components through
breaking bonds by adding water.
In the third stage, absorption, the animal's cell take up (absorb) small molecules.
Elimination completes the process as undigested material passes out of the digestive
system.
4 main feeding mechanisms of animals
Many aquatic animals are filter feeders (whale), which strain small organisms or food
particles from the surrounding medium.
Substrate feeders (caterpillar) are animals that live in or on their food source.
Most animals, including humans, are bulk feeders (humans), which eat relatively large
pieces of food.
Fluid feeders (mosquito) suck nutrient rich fluid from a living host.
Intracellular digestion
Food vacuoules, cellular organelles in which hydrolytic enzymes break down food, are the
simplest digestive compartments. The hydrolysis of food inside vacuoules is called
intracellular digestion.
This usually occurs after phagocytosis or pintocytosis.
Amoeba captures food via phagocytosis. The engulfed food becomes a food vacuoule. A
lysosome fuses with the food vacuoule, and its enzymes breakdown the food.

15

The cilia of paramecium sweeps food into its cytopharynx. The food vacuoule forms and
moves toward the anterior of the cell, where it will fuse with a lysosome and become
degraded.
Extracellular digestion
In most animal species, hydrolysis occurs largely by extracellular digestion, the f body.
Many animals with relatively simple body plans have a digestive compartment with a single
opening called a gastrovascular cavity. It functions in digestion as well as in the
distribution of nutrients throughout the body.
A hydra uses its tentacles to stuff captured prey through its mouth into its
gastrovascular cavity. Specialized gland cells of the hydra's gastrodermis, the tissue
layer that lines the cavity, then secretes digestive enzymes that break the soft tissues of
the prey into tiny pieces. Other cells of the gastrodermis engulf these food particles, and
most of the hydrolysis of macromolecules occur intracellularly.

Most animals have a digestive tube extending between two openings, a mouth and an anus.
This is a complete digestive tract, or more commonly, an alimentary canal.
The alimentary canal of an earthworm includes a muscular pharynx that sucks food
through the mouth. Food passes through the esophagus and is stored and moistened in

16
the crop. Mechanical digestion occurs in the muscular gizzard, which pulverizes food
with the aids of small bits of sand and gravel. Further digestion and absorption occurs in
the intestine. The intestine contains typholosole which helps increase surface area for
absorption.
A grasshopper has several digestive chambers grouped into three main regions: a
foregut, with an esophagus and a crop; a midgut; and a hindgut. Food is stored and
moistened in the crop, but most digestion occurs in the midgut. Pouches called gastric
cecae extend from the beginning of the midgut and function in digestion and absorption.

Many birds have a crop for strong food and a stomach and gizzard for mechanically
digesting it. Chemical digestion and absorption of nutrients occurs in the intestine.

Digestion in plants and fungi

Plants do not have a digestive system. Most of digestion occurs intracellularly. The
processes are similar to animals.
Plants store starch primarily in seeds, stems, and roots
When nutrients are required, polymers are broken down into the appropriate monomers
by enzymatic hydrolysis.
Some plants use extracellular digestion
Venus flytrap enzymes diggest trapped flies (serves as nitrate source). However, it is
still autotrophic.
Fungi rhizoids of bread mold secrete enzymes into bread, producing simple digestive
products which are then absorbed by diffusion into rhizoid.

17

Human Digestive System

Introduction
In mammals, the digestive system consists of the alimentary canal and various accessory
glands that secrete digestive juices through the ducts into the canal.
Accessory glands are salivary galnds, pancreas, liver, and the gallbladder.

Food is pushed along the alimentary canal by peristalsis, alternating waves of contraction
and relaxation in the smooth muscles lining the canal.
At some junctions between specialized compartments, the muscular layer forms ringlike
valves called sphincters. They regulate passage of material between compartments.
The oral cavity, pharnyx, and esophagus
Ingestion and the initial steps of digestion occur in the mouth, or oral cavity.
Mechanical digestion occurs through chewing of food.
The salivary glands deliver saliva through ducts to the oral cavity. Saliva initiates
chemical digestion while also protecting the oral cavity.
The enzyme amylase hydrolyzes starch into smaller polysaccharides and maltose.
The protective effect of saliva is provided by mucus, which protects the lining of the
mouth from abrasion and lubricates food for easier swallowing.
The tongue aids digestive processes by evaluating ingested material to determine if
it should be ingested and then enabling its further passage if it is deemed okay. It
also helps manipulate the mixture of saliva and food into a ball shape called a bolus.
papillae are projections on the tongue surface and are involved in the sensation
of taste.
The pharynx, or throat region, opens to two passageways: the trachea (windpipe) and
the esophagus.
The esophagus connects to the stomach. When a food bolus arrives at the pharynx,
the larynx tips a flap of tissue called the epiglottis down, preventing food from
entering the trachea. The upper esophageal sphincter (blocks esophagus) relaxes,
allowing the bolus to pass through. Once food enters here, peristaltic contractions of

18

smooth muscle move each bolus to the stomach.

Digestion in the stomach
The stomach, which is located just below the diaphragm, stores foods and begins digestion
of proteins.
Secretes a digestive fluid called gastric juice and mixes with the food. This mixture of
ingested food and gastric juice is called chyme.
Components of gastric juice:
Hydrochloric acid which disrupts the ECM that binds cells together. Also creates a low
pH environment in the stomach (pH = 2), which kills most bacteria, and denatures
proteins in food.
Pepsin, a protease, cleaves peptide bonds to turn proteins into smaller polypeptides.
Works best in a very acidic environment.
The interior surface of the stomach wall is highly folded and dotted with pits leading into
tubular gastric glands. The gastric glands have all three types of cells that secrete the
different components of the gastric juice.
Parietal cells use an ATP-driven pump to expel hydrogen ions into the lumen. Also
pumps out chloride ions. Only in the lumen the H+ and the Cl- ions combine to form
HCl.
G cells secrete gastrin, a large polypeptide hormone which is absorbed into the
blood. It stimulates parietal cells to secrete HCl.
Gastrin also stimulates ECL cells, neuroendocrine cells in the digestive tract.
They release histamine which in turn stimulates parietal cells to produce
hydrochloric acid.
Chief cells release pepsin into the lumen in an inactive form called pepsinogen. HCl
converts pepsinogen into active pepsin. Then pepsin itself activates the remaining
pepsinogens. Example of positive feedback.
Mucous cells secrete mucus, which lubricates and protects the cells lining the stomach.
Peptic ulcers are caused by failure of mucosal lining to protect stomach. Can also
be caused by excess stomach acid or H. pylori as well.

19
Chemical digestion by gastric juice is facilitated by the churning action of the stomach.
Churning is the coordinated series of muscle contractions and relaxations that mixes the
stomach contents about every 20 seconds.
The lower esophageal sphincter, or cardiac sphincter, is the sphincter between the
esophagus and the stomach that normally opens only when bolus arrives.
Occasionally, a person experiences acid reflux, a backflow of chyme from the stomach
into the lower end of the esophagus.
The controlled release of chyme into the small intestine is controlled by the pyloric
sphincter.

Digestion in the small intestine

The small intestine is the alimentary canal's longest compartment and most of the
enzymatic hydrolysis of macromolecules from food occurs here.
The first section of the small intestine forms the duodenum. Most of the digestion is
completed in this section. It is here that chyme from the stomach mixes with the digestive
juices from the pancreas, liver, and gallbladder, as well as gland cells of the intestinal wall
itself.
The pancreas aids chemical digestion by producing an alkaline solution rich in
bicarbonate as well as several enzymes.
The bicarbonate neutralizes the acidity of the chyme and acts as a buffer.
Pancreatic enzymes secreted are trypsin and chemotrypsin, proteases secreted into
the duodenum in inactive forms. Trypsin gets activated first by enteropeptidase
(enzyme secreted from intestinal glands when food passes through duodenum), and
then it activates the other enzymes.
Pancreas also secretes lipases (digestion of fats) and pancreatic amylase (digestion
of starch).
Liver produces bile, a substance that helps digest fats and other lipids. Bile contains
salts, which acts as emulsifiers. Bile is stored and concentrated in the gallbaldder.
The epithelial lining of the duodenum is a source of several digestive enzymes. Some
are secreted into the lumen of the duodenum, whereas others are bound to the surface of
epithelial cells.
Peristalisis moves the mixture of chyme and digestive juices along the small intestine.

20

The remaining regions of the small intestine, the jejunum and the ilenum, are the major
sites for absorption of nutrients.
Absorption in the small intestine
Most of the absorption occurs at highly folded surface of the small intestine.
Large folds in the lining encircle the intestine and are studded with finger-like
projections called villi. In turn, each epithelial cell of a villus has on its apical surface
many microscopic projections called microvilli.
This confers extremely high surface area, which greatly increases the rate of
absorption.
Depending on the nutrient, transport across epithlial cells can be passive or active.
Goblet cells secrete mucus to lubricate and protect epithelial cells from
mechanical/chemical damage.
The capillaries and veins that carry nutrient-rich blood away from the villi converge into
the hepatic portal vein, a blood vessel that leads directly to the liver.
By channeling all nutrients through the liver, it allows it to regulate the distribution
of nutrients to the rest of the body.
Also allows liver to remove toxic substances.

Some products of fat digestion take a different path.

Hydrolysis of fats by lipase in the small intestine generates fatty acids and
monoglycerides.
They are absorbed by epithelial cells and then recombined into triglycerides.
They are then coated with phospholipids, cholesterol, and proteins, forming globules
called chylomicrons.
Chylomicrons are first transported from an epithelial cell in the intestine to a lacteal, a
lymph filled vessel at the core of each villus. The lacteal passes the chylomicrons to the
heart.
Small intestine also absorbs water and ions.

21

Functions of the liver

Blood storage
Blood filtration kupfer cells (macrophages) phagocytize bacteria picked up in intestines
Carbohydrate metabolism liver maintains normal blood glucose levels via
gluconeogenesis (generation of glucose) and glycogenesis (generation of glycogen)
All carbohydrates absorbed into the blood are carried by the hepatic portal vein into the
liver.
Protein metabolism liver deaminates amino acids, forms urea from ammonia in blood,
synthesizes plasma proteins, synthesizes nonessential amino acids.
Detoxification detoxidifes chemicals, secreted by liver as part of bile
Erythrocyte destruction kupfer cells destroy irregular erythrocytes (most are done by
spleen)
Vitamin storage and iron storage
if blood glucose levels are high glycogenesis
if blood glucose levels are low
glycogenolysis
Produces bile
Jaundice is yellowing of the skin due to excess bilirubin (typically liver failure).
Processing in the large intestine

22
The alimentary canal ends with the large intestine, which includes the colon, cecum, and
rectum. The small intestine connects to the large intestine at a T-shaped junction.
One long arm is the colon, which leads to the rectum and anus.
The other arm is a pouch called the cecum, which is important for fermenting ingested
material.
The appendix, a finger-like extension of the human cecum, has a minor and dispensable
role in immunity.
The colon completes reabsorption of water that began in the small intestine. What remain
are the feces, the wastes of the digestive system, which becomes increasingly solid by the
end.
If less water than normal is reabsorbed by the colon, the result is diarrhea
If too much water is reabsorbed by the colon, the result is constipation.
A rich community of mostly harmless bacteria lives on the unabsorbed organic material in
the colon. The main source of vitamin K and vitamin B come from these symbiotic
bacteria.
The terminal portion of the large intestine is the rectum, where the feces are stored until
they can be eliminated.
Between the rectum and anus are two sphincters, the inner one being involuntary
and the outer one being voluntary.
Regulation of digestion
Hormonal control of digestion
A branch of the nervous system called the enteric division is dedicated to regulating
digestive events and peristalisis in the small and large intestines.
Gastrin is produced by the stomach lining, and the effects have been discussed above.
Secretin is produced by cells lining duodenum when food enters; this stimulates pancreas
to produce bicarbonate (neutralizes the chyme).
Enteropeptidase is produced by cells lining the duodenum when food enters; this
stimulates the pancreas to deposit its mass of digestive enzymes into the duodenum.
Somatostatin is produced by delta cells of the pancreas. It will suppress the release of
gastrointestinal hormones such as gastrin, secretin, and cholecystokinin. This suppression
will decrease the rate of gastric emptying along with reducing blood flow within the
intestines.
Cholecystrokinin is produced by small intestine in response to fats; stimulates gallbladder
to release bile and pancreas to release its enzymes.
If the chyme is rich in fats, high levels of secretin and cholecystrokinin released act on
the stomach to inhibit peristalsis and secretion of gastric juices, thereby slowing down
digestion.
Gastric inhibitory peptide is produced in response to fat/protein digestates in the
duodenum; mild decrease of stomach motor activity.
Glucose homeostasis
When the blood glucose level rises above the normal range, the secretion of insulin triggers
the uptake of glucose from the blood into body cells, thereby decreasing the blood glucose
concentration.
Insulin does not act on the brain.
When the blood glucose level drops below the normal range, the secretion of glucagon
promotes the release of glucose into the blood by breaking down storage carbohydrates

23

(glycogen).
Both hormones are produced in the pancreas.
Alpha cells within the pancreatic islets create glucagon and beta cells create insulin.
Diabetes Mellitus
Diabetes mellitus is caused by a deficiency of insulin or a decreased response to insulin in
target tissues.
Cells do not take in glucose to break down for energy; instead the cells mainly use fat.
Type 1 diabetes is when the immune system destroys the beta cells within the pancreas and
thus destroys the person's ability to synthesize insulin.
Type 2 diabetes is characterized by a failure of target cells to respond normally to insulin.
Insulin is produced, but target cells fail to take up glucose from the blood, and blood
glucose levels remain elevated.
Regulation of appetite and consumption
Secreted by the stomach wall, ghrelin is one of the signals that triggers feelings of hunger
as mealtimes approach.
A rise in blood sugar level after a meal stimulates the pancreas to secrete insulin. Among
other functions, insulin suppresses appetite by acting on the brain.
Produced by adipose tissue, leptin suppresses appetite. When the amount of body fat
decreases, leptin levels fall, and apetite increases.
The hormone PYY, secreted by the small intestine after meals, acts as an appetite
suppressant that counters the appetite stimulant ghrelin.

24
Signaling
Intracellular communication
In endocrine signaling, hormones secreted into extracellular fluid by endocrine cells reach
target cells via the bloodstream or hemolymph.
Local regulators are molecules that act over short distances and reach their target cells
solely by diffusion.
In paracrine signaling, the local regulator targets cells that lie near the secreting cell.
In autocrine signaling, the local regulator targets the secreting cell itself.
In synaptic signaling, neurons form specialized junctions called synapses with target cells,
such as other neurons and muscle cells.
At most synapses, neurons secrete neurotransmitters.
In neuroendocrine signaling, specialized neurons called neurosecretory cells secrete
neurohormones, which diffuse from nerve cell endings into the bloodstream.
Members of a particular animal species sometimes communicate with each other via
pheromones, chemicals that are released into the external environment.
Types of local regulators
Prostaglandins are local regulators that promote inflammation and the sensation of pain
in response to injury. They are modified fatty acids.
Cytokines and growth factors are typically local regulators.
Nitrous oxide (NO) is a gas that functions as a local regulator and a neurotransmitter.
When the level of oxygen in the blood falls, endothelial cells in blood vessel walls
synthesize and release NO.
NO causes vasodilation, which increases blood flow to the tissues.
Classes of hormones
Hormones are transported throughout the body in blood. A small amount generates a large
impact. They tend to have slower effects.
Many hormones elicit more than one type of response in the body.
These molecules bind to receptors that are highly specific to their structure.
Some hormones have receptors on almost all cells, some have receptors only on specific
tissues.
Peptide hormones are synthesized in the rough ER as a larger preprohormone (precursor
to one or more prohormones), cleaved in the ER lumen to a prohormone (committed
precursor of a single hormone) and then cleaved again (and possibly modified with carbs) in
the golgi body to the final form.
Includes: FSH, LH, ACTH, HGH, TSH, prolactin, ADH, oxytocin, PTH, glucagon and
insulin
They are water-soluble hormones, so they cannot diffuse through the plasma membrane.
They attach to a membrane receptor and initiate signal transduction pathways.
Secondary messengers are created along the pathways; which create the actual effects.
This is indirect stimulation.
Steroid hormones are synthesized from cholesterol in the smooth ER.
Includes: glucocorticoids, mineralocorticoids, cortisol, aldosterone, esterogen,
progesterone, and testosterone.
They are lipid-soluble hormones, so they are able to diffuse through the plasma
membrane.
Steroid hormones attaches to a receptor in the cytoplasm or the nucleus. The
hormone+receptor binds to an active portion of DNA and alters the transcription rate.
This is an example of direct stimulation since the hormone itself is generating the

25
effects.
Tyrosine derivatives are formed by enzymes in the cytosol or on the rough ER.
Includes: catecholamines, T3, T4
They are either water-soluble or lipid-soluble.
Feedback regulation and coordination with the nervous system
Simple pathways
In a simple endocrine pathway, endocrine cells respond directly to an internal or
environmental stimulus by a secreting a particular hormone. The hormone will travel in the
bloodstream to the target cells, where it will elicit the appropriate responses.
In a simple neuroendocrine pathway, the stimulus is received by a sensory neuron, which
stimulates a neurosecretory cell. The neurosecretory cell then secretes a neurohormone,
which will diffuse into the bloodstream and travel to target cells.
Feedback regulation
Regulation often involves negative feedback, in which the response reduces the initial
stimulus.
Positive feedback reinforces a stimulus, leading to an even greater response.
Organs of the endocrine system
Endocrine glands vs. exocrine glands
Endocrine glands synthesizes and secretes hormones into the bloodstream.
Exocrine glands secrete substances by way of a duct to the exterior of the body.
Hypothalamus
The hypothalamus monitors the external environment and internal conditions of the body.
Contains neurosecretory cells that link the hypothalamus to the pituitary gland.
Synthesizes ADH (vasopressin) and oxytcin to be stored in the posterior pituitary.
Synthesizes releasing and inhibiting hormones to regulate the anterior pituitary.
Synthesizes gonadotropin releasing hormone (GnRH) from neurons, which stimulates the
anterior pituitary to secretes FSH and LH.
Anterior pituitary
The anterior pituitary mainly regulates hormone production by other grands.
The anterior pituitary is regulated by the hypothalamus.
Releasing hormones are produced by neurosecretory cells in the hypothalamus and are
secreted into the blood. This blood flows directly into the anterior pituitary, where the
releasing hormones stimulate the release of tropic or direct hormones produced/stored and
secreted in the anterior pituitary.
Direct hormones directly stimulate target organs. Types of direct hormones
produced/stored in the anterior pituitary:
Somatotropin (HGH), which stimulates bone and muscle growth.
Prolactin stimulates milk production in females.
Endorphins inhibit perception of pain (technically a neurohormone).
Tropic hormones stimulate other endocrine glands. Types of tropic hormones
produced/stored in the anterior pituitary:
Adrenocrticotrophic hormone (ACTH) stimulates the adrenal cortex to release
glucocorticoids, which are involved in regulation of metabolism of glucose.
Thyroid-stimulating hormone (TSH) stimulates the thyroid gland (increases size

26

and cell number) to release thyroid hormone.

Lutenizing hormone (LH) in females stimluates the formation of the corpus luteum.
In males, leutinzing hormone stimulates leydig cells of the testes to produce
testosterone.
Follicle-stimulating hormone (FSH) in females stimulates maturation of ovarian
follices to secrete estrogen. In males, FSH stimulates sertoli cells to help mature
sperm cells.
Posterior pituitary
The posterior pituitary does not synthesize hormones, it stores hormones produced by the
hypothalamus. Hormones that it stores/secretes:
Antidiuretic hormone (ADH/vasopressin) increases the reabsorption of water by
increasing the amount of aquaporins in the epithelium cells in the collecting duct.
Coffee and alcohol blocks ADH.
Oxytocin is secreted during childbirth. It increases the strength of uterine contractions
and stimulates milk ejection.
Pineal gland
Pineal gland secretes melatonin, a hormone that participates in regulation of biological
rhythms.
Thyroid
Thryoid glands are located on the ventral surface of the trachea. Hormones that it
produces/secretes:
Achondroplasia is dwarfism of the thyroid.
Progeria is premature aging of the thyroid.
Thyroxine (T4) and Triiodothyronine (T3) are necessary for the growth and
neurological development in children and increase basal metabolic rate in body.
Provide a negative feedback on TSH, meaning high amounts of T3 and T4 will
decrease production of TSH.
Hypothyroidism means undersecretion of T3 and T4; results in low heart and
respiratory rate.
Hyperthryoidism means oversecretion of T3 and T4; results in increased metabolic
rate and sweating.
Hypo- and hyperthyroidism lead to goiter, the abnormal enlargement of the thyroid
gland.
Calcitonin tones down Ca2+ in blood.
It decreases plasma Ca2+ by inhibiting its release from bone
Decreases osteoclast activity and number.
Parathyroid
The Parathyroid is four pea-shaped structures attached to the back of thyroid. Hormones
that it produces/secretes:
Parathyroid hormone (PTH) is antagonistic to calcitonin.
Raises Ca2+ concentrations in the blood by stimulating release from bone.
Increases osteocyte absorption of Ca + P from bone; stimulates osteoclast
proliferation
Increases renal Ca absorption
Thymus
Thymus is involved in the immune response. Hormones that it produces/secretes:

27

Thymosins stimulate lymphocytes (WBCs) to become T-cells

Adrenal gland
Adrenal gland is located on the top of kidneys and consists of two main parts:
Adrenal cortex secretes only steroid hormones. Hormones that it produces/secretes:
Glucocorticoids (cortisol and cortisone) raise blood glucose levels (stimulates
gluconeogenesis in liver); affect fat and protein metabolism; stress hormones
Mineralocorticoids (aldosterone) increaes reabsorption of Na+ and secretion of K+.
Causes passive reabsorption of water in the nephron, which will cause a rise in blood
volume/pressure.
Androgenic steroids these hormones are converted elsewhere in the body to form
estrogens and androgens; however, these steroid hormones are produced in much
larger amounts by the gonads.
Adrenal medulla. Hormones that it produces/secretes:
Epinephrine and norepinephrine fight or flight hormones.
These hormones are catecholamines they are water soluble, bind to receptors
on target tissue membranes, and mainly act via a second messenger.
Glycogen glucose, vasoconstrictor to internal organs and skin but vasodilator
to skeletal muscle, increased heartbeat.
Pancreas
Pancreas (exocrine and endocrine) has bundles of cells called islets of Landerhans which
contains two cell types:
Alpha cells secrete glucagon: catabolic, released when energy charge low; raises blood
glucose levels. Stimulates liver to break down glycogen into glucose.
Beta cells secrete insulin: anabolic, released when energy charge is high; lower blood
glucose levels. Stimulates liver and most other body cells to absorb glucose. Provokes
liver and muscles to turn glucose into glycogen and fat cells to turn glucose into fat.
Somatostatin is released by delta cells of pancreas; inhibits both insulin and glucagon.
Possibly increases nutrient absorption time
Testis and Ovaries
Testis produces and secretes testosterone, a hormone that induces spermatogenesis and
secondary male sex characteristics.
Ovaries produces and secretes estrogen and progesterone:
Estrogen is involved in the menstrual cycle and produces secondary female sex
characteristics.
Progesterone is involved in the menstrual cycle and pregnancy.
Gastrointestinal hormones
Gastrin secretes stimulation of HCl when food is in the stomach.
Secretin, secreted from the small intestine, neutralizes the acidity of chyme by enhancing
the secretion of alkaline bicarbonate.
Cholecystokinin, secreted from the small intestine, causes the contraction of the gallbladder
to release bile in the presence of high fatty food.

28
Osmoconformers vs. osmoregulators
Osmoregulatory challenges and mechanisms
An osmoconformer has its internal osmolarity isoosmotic with its surroundings.
Marine animals are all osmoconformers.
An osmoregulator has its internal osmolarity independent compared to its surroundings.
Enables animals to live in environments that are unhabitable fo rosmoconformers, such
as freshwater and terrestrial habitats, or to move between marine and freshwater
environments.
Many marine vertebrates and some marine invertebrates are osmoregulators. Their body is
hypotonic to the environment and water will naturally flow out. Mechanisms:
Gain of water and salt ions from eating food and drinking seawater.
Osmotic water loss through gills and other pats of the body surface.
Excretion of salt ions from gills.
Excretion of salt ions and small amounts of water in scanty urine from kidneys.
Freshwater fish are osmoregulators. Their body is hypertonic to the environment, meaning
water will naturally flow in.
Gain of water and some ions in food. NO DRINKING.
Uptake of salt ions by gills.
Osmotic water gain through gills and other parts of body surface.
Excretion of salt ions and large amounts of water in dilute urine form kidneys.

Transport epithelia in osmoregulation

In most animals, osmoregulation and metabolic waste disposal rely on transport epithelia
one or more layers of epithelial cells specialized for moving particular solutes in
controlled amounts in specific directions.
Typically arranged into complex tubular networks with extensive surface areas.
In birds, the transport epithelium are the pair of nasal salt glands.
Salt glands use active transport to secrete excess salts. They maintain salt balance and
allow for saltwater to be drank.

Nitrogen waste
Forms of Nitrogenous Waste
Animals that secrete nitrogenous wastes as ammonia need access to lots of water because
ammonia can be tolerated at very low concentrations. Most common in aquatic species.
Most terrestrial animals and many marine species secrete urea. The advantage is that urea
has very low toxicity. The disadvantage is that it requires tremendous amounts of energy.

29
Insects, land snails, and many reptiles, including birds, create uric acid as their primary
nitrogenous waste. The advantage is that uric acid is not toxic and it can be disposed with
minimal water loss. Disadvantage is that it requires lots of energy.
Structure of excretory systems
Excretory processes
Hydrostatic pressure drives a process of filtration, where a tubule collects a filtrate from
the blood. Proteins and other large molecules can't be filtered out of the blood while small
solutes can.
The transport epithelium then reclaims valuable substances from the filtrate and returns
them to body fluids. This is reabsorption.
Other substances, such as toxins and excess ions, are extracted from body fluids and added
to the contents of the excretory tubule. This is called secretion
The altered filtrate (urine) leaves the system and the body. This is called excretion.
Protonephridia
Platyhelminthes and Rotifera have units called protonephridia, which form a network of
dead-end tubules.
The tubules, which are connected to external openings, branch throughout the flatworm
body.
Cellular units called flame bulbs cap the branches at each protonephridium.
During filtration, the beating of the cilia draws water and solutes from the interstitial
fluid through the flame bulb, releasing filtrate into the tubule netowrk.
The filtrate then moves outward through the tubules and empties as urine into the
environment.

30

Metanephridia
Annelids have metanephridia, excretory organs that collect fluid directly from the coelom.
Each segment of an annelid has a pair of metanephridia, which are immersed in
coleomic fluid and enveloped by a capillary network.
A ciliated funnel surrounds the internal opening of each metanephridium.
As the cilia beat, fluid is drawn into a collecting tubule, which includes a storage
bladder that opens to the outside.

Malphagian tubules
Arthropods have organs called malphagian tubules that remove nitrogenous wastes and
also function in osmoregualtion.
They extend from dead-end tips immersed in the hemolymph to openings in the
digestive tract.
There is NO filtration step.
The transport epithelium that lines the tubules secretes certain solutes from the
hemolymph into the lumen of the tubule.
Water follows the solutes into the tubule by osmosis, and the fluid then passes into the
rectum.
There, most solutes are pumped back into the hemolymph, and water reabsorption by
osmosis follows.
Wastes are eliminated as dry matter along with feces.

31

Mammalian Excretory system

Excretory organs
In the lungs, CO2 and water vapor diffuse from the blood and are continually exhaled.
The liver produces nitrogenous wastes, blood pigment wastes, and other chemical
wastes.
excess bilirubin causes jaundice (usually a liver issue)
The skin sweat glands excrete water and dissolved salts to regulate body temperature.
The excretory system consists of kidneys, a pair of organs for transporting and storing
urine.
Urine produced by each kidney exits through a duct called the ureter; the two ureters
drain into a common sac called the urinary bladder.
During urination, urine is expelled from the bladder through a tube called the urethra
Sphincter muscles near the junction of the urethra and bladder regulate urination.
Kidney structure
Each kidney has an outer renal cortex and an inner renal medulla. Both regions are
supplied with blood by a renal artery and drained by a renal vein.
Within the cortex and the medulla lie tightly packed excretory tubules and associated
blood vessels.
The fluid that will be excreted as urine is collected in the inner renal pelvis, and exits
the kidney via the ureter.
Nephron Types
Weaving back and forth across the renal cortex and medulla are the nephrons, the
functional units of the vertebrate kidney.

32
85% of the nephrons are cortical nephrons, which reach only a short distance into the
medulla.
The remainder, the juxtamedullary nephrons, extend deep into the medulla.
They are essential for production of urine that is hyperosmotic to body fluids, a key
adaptation for water conservation in mammals.

Nephron organization
Each nephron consists of a single long tubule as well as a ball of capillaries called the
glomerulus. The blind end of the tubule forms a cup-shaped swelling, called Bowman's
capsule, which surrounds the glomerulus.
Filtrate is formed when blood pressure forces fluid from the blood in the glomerulus
into the lumen of Bowman's capsule.
Processing occurs as the filtrate passes through three major regions of the nephron: the
proximal tubule the loop of Henle, and the distal tubule.
A collecting duct receives processed filtrate from many nephrons and transports it to the
renal pelvis.
Each nephron is supplied with blood by an afferent arteriole an offhsoot of the renal
artery that branches and forms the capillaries of the glomerulus. The capillaries
converge as they leave the glomerulus, forming an efferent arteriole.
Branches of this vessel form the peritubular capillaries, which surround the proximal
and distal tubules. Other branches extend downward and form the vasa recta, hairpinshaped capillaries that serve the renal medulla, including the long loop of Henle of
juxtamedullary nephrons.
How the whole excretory process occurs
From blood filtrate to urine
The porous capillaries and specialized cells of Bowman's capsule are permeable to water
and small solutes, but not blood cells or large molecules.
The filtrate produced in the capsule contains salts, glucose, amino acids, vitamins,
nitrogenous wastes, and other small molecules.
Concentration of these substances in the initial filtrate are the same as those in blood
plasma.

33

Reabsorption in the proximal tubule is critical for the recapture of ions, water, and valuable
nutrients from the huge volume of the initial filtrate.
NaCl gets reabsorbed. Epithelial cells pump Na+ into interstitial fluid, and this transfer
of positive charge out of the tubule drives the passive transport of Cl-.
Glucose, amino acids, and K+ ions are reabsorbed through active or passive
transportation from the filtrate interstitial fluid peritubular capillaries.
Water gets reabsorbed through passive transport.
Processing of filtrate in proximal tubule help remains constant pH in body fluids:
Cells in transport epithelium secrete H+ and NH3 into the tubule, which then
combines to form NH4+ in the tubule. The more acidic the filtrate is, the more
ammonia the cells secrete into the tubule.
Proximal tubules also reabsorb the buffer HCO3- (bicarbonate) from the filtrate,
contributing further to balance pH.
Reabsorption of water continues as the filtrate moves into the descending loop of hemle.
Numerous water channels formed by aquaporins make the transport epithelium freely
permeable to water.
The osmolarity of the interstitial fluid of the kidney increases progressively from the
outer cortex to the inner medulla. As a result, the kidney osmolarity makes it favorable
to water to be reabsorbed.
The filtrate reaches the tip of the loop and then returns to the cortex in the ascending loop
of Henle.
Two specialized regions: a thin segment near the loop tip and a thick segment adjacent
to the distal tubule.

34

As filtrate ascends in the thin segment, NaCl diffuses out passively into the
interstitial fluid. This helps maintains the osmolarity of the interstitial fluid of the
medulla.
In the thick segment of the ascending limb, NaCl must be pumped out actively into
the epithelium.
The distal tubule plays a key role in regulating K+ and NaCl concentration of body fluids
and pH regulation.
K+ is actively secreted from the epithelium and into the distal tubule. The amount
secreted will regulate the K+ concentration in body fluids.
Water is passively reabsorbed.
NaCl is actively reabsorbed from the filtrate. The amount reabsorbed will regulate NaCl
concentration in body fluids.
Contributes to pH regulation by actively secreting H+ into the tuubule and actively
reabsorbing HCO3-.
The collecting duct carries the filtrate through the medulla to the renal pelvis. Final
processing of the filtrate by the transport epithelium of the collecting duct forms the urine.
Hormonal control determines the extent to which the urine becomes concentrated.
When kidneys are conserving water, aquaporin channels in the collecting duct allow
H2O molecules to be reabsorbed passively. At the same time, the epithelium remains
impermeable to salt and urea. This creates a hyperosomotic urine. In the inner
medulla, the duct becomes permeable to urea. Since the urine is hyperosmotic, urea
passively gets reabsorbed.
When kidneys are producing dilute urine, the kidney actively reabsorbs NaCl
without allowing water to follow by osmosis.
Solute gradients and water conservation
The primary solutes affecting osmolarity are NaCl and urea.
The nephron uses countercurrent system to maximize the activities it wants to do.
The nephron uses a countercurrent multiplier system in which it expends energy to
create concentration gradients.
The countercurrent multiplier system makes the medulla very salty which facilitates
water reabsorption.
Types of urine produced in other animals
Mammals can produce hyperosmotic urine.
Birds can produce hyperosmotic urine, but their main water conservation adaptation is uric
acid. birds have a long loop of henle, thus concentrated urine
Reptiles can only produce isoosmotic or hypoosmotic urine.
Freshwater fishes cannot produce hyperosmotic urine.
Amphibians cannot produce hyperosmotic urine.
Homeostatic regulation of the kidney
Hormonal control
The hypothalamus in the brain controls hormones that regulate osmolarity.
Antidiuretic hormone (ADH) or vasopressin helps increase the reabsorption of water in
the collecting duct.
ADH is produced in the posterior pituitary gland.
When blood osmolarity rises, the hypothalamus trigger release of ADH from the
posterior pituitary.

35
ADH brings about changes that make the epithelium more permeable to water (recruits
more aquaporins to the epthelium) and thus able to reabsorb more water.
The increase in water reabsorption concentrates urine, reduces urine volume, and lowers
blood osmolarity back toward the set point.
As the osmolarity of the blood falls, a negative-feedback mechanism reduces the activity
of osmoreceptor cells in the hypothalamus, and ADH secretion is reduced.
The second regulatory mechanism that helps maintain homeostasis by acting upon the
kidney is the renin-angiotensisn-aldosterone system (RAAS).
The RAAS system involves the juxtaglomerular apparatus (JGA), a specialized tissue
consisting of cells of and around the afferent arteriole, which supplies blood to the
glomerulus.
When blood pressure or volume drops in the afferent arteriole (for instance, as a result
of dehydration), the JGA releases the enzyme renin.
Renin initiates a sequence of steps that cleave a plasma protein secreted from the liver
called angiotensinogen ultimately yielding a peptide called angiotensin II.
Angiotension II stimulates the adrenal glands to release a hormone called aldosterone.
Aldosterone causes the nephrons' distal tubules and collecting duct to excrete K+ and
reabsorb more Na+ and water, increasing blood volume and pressure.
Atrial natriuretic peptide (ANP) opposes the RAS.
The walls of the atria of the heart release ANP in response to an increase in blood
volume and blood pressure.
ANP inhibits the release of renin from the JGA.

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Innate immunity
Innate immunity of invertebrates
Innate immunity provides an immediate defense against infection. Cells of innate system
recognize and responds to pathogens in a generic way, but, unlike the adaptive immune
system, does not confer long-lasting or protective immunity to the host. Nonspecific
immune system.
Binding of an innate immune receptor to a foreign molecule activates internal defenses,
enabling responses to a very broad range of pathogens.
Found in all animals
Innate immunity in invertebrates
Insects rely on their exoskeleton as a first line of defense against infection.
Composed largely of the polysaccharide chitin, the exoskeleton provides an effective
barrier defense against most pathogens.
Chitin also lines insect's intestine, where it blocks infection by many pathogens ingested
with food.
Lysozyme, an enzyme that breaks down bacterial cell walls, further protects the insect's
digestive system.
Any pathogen that breaches the barrier defenses encounters a number of internal immune
defenses.
Hemocytes travel throughout the body in the hemolymph, the circulatory fluid.
They ingest and break down bacteria and other foreign substances through
phagocytosis.
Also release chemicals that kill pathogens and entrap large parasites.
Encounters with pathogens in the hymolymph can cause hemocytes and other cells to
secrete antimicrobial peptides, which are short chains of amino acids that circulate
throughout the body of the insect and inactivate or kill fungi and bacteria by disrupting
their plasma membranes.
Immune cells of insects bind to molecules found only on the outer layers of fungi or
bacteria.
Innate immune responses are distinct for different classes of pathogens.
Innate immunity in vertebrates
Barrier defenses block the entry of pathogens.
They include the skin and the mucous membranes lining the digestive, respiratory,
urinary, and reproductive tracts. The mucous membranes produce mucus, a viscous
fluid that traps pathogens and other particles.
Lysozymes in tears, saliva, and mucous secretions destroys the cell walls of susceptible
bacteria as they enter the openings around the eyes or the upper respiratory tract.
Microbes that go through the digestive tract must contend with the acidic environment
of the stomach, which kills most pathogens.
Secretions from oil and sweat glands give huma
Symbiotic bacteria in the digestive tract and vagina out-competes many other
organisms.
Many pathogens that get through barrier defenses are engulfed by phagocytic cells that use
several types of receptors to detect pathogens.
Toll-like receptors can detect a broad range of human pathogens, as well as a variety of
other molecules that activate tissue damage, by a process called pattern recognition.
These receptors initiate the innate and the adaptive immune response.

37
Types of phagocytic cells:
Neutrophils, which circulate in the blood, are attracted by signals from infected
tissues and then engulf and destroy the infecting pathogens.
Are the most common WBC.
Move into tissues via diapedesis.
Monocytes move into tissues (diapedesis) where they develop into macrophages,
which phagocytize cell debris and pathogens.
Are also antigen-presenting cells.
Dendritic cells mainly populate tissues, such as skin, that contact the environment.
They stimulate adaptive immunity against pathogens as they encounter and engulf.
Antigen-presenting cells.
Eosinofils, often found beneath mucosal surfaces, are important in defending against
multicellular invaders.
Basophils store histamine and work in inflammatory response. Are the least common
WBC.
Mast cells secrete histamine and work in the allergic and inflammatory response.
Natural killer cells circulate through the body and detect the abnormal array of surface
proteins characteristic of some virus-infected and cancerous cells.
They do not engulf cells; instead, they secrete chemicals that lead to cell death.
Many cellular innate defenses in vertebrates involve the lymphatic system, a network
that distributes lymph throughout the body.
Some macrophages reside in lymph nodes.
Dendritic cells can migrate to the lymph nodes after interacting with pathogens. Also
stimulates adaptive immunity within the lymph nodes.
In mammals, pathogen recognition triggers the production and release of a variety of
peptides and proteins that attack pathogens or impede their production.
Interferons are proteins that provide innate defense by interfering with viral infections.
They limit the cell-to-cell spread of viruses in the body.
The complement system consists of roughly 30 proteins in blood plasma.
These proteins circulate around the blood in an inactive form and are activated by
substances on the surfaces of pathogens.
Activation leads to lysis of the cells.
Functions in the inflammatory response as well as the adaptive defenses.
The inflammatory response is the changes brought about by signaling molecules released
upon injury or infection.
One important inflammatory molecule is histamine, which is stored in densely packed
vesicles of mast cells, found in connective tisuse.
Histamine released at sites of damage triggers nearby blood vessels to dilate and become
more permeable. The dilation causes capillaries to leak fluid into the neighboring
tissues, causing localized swelling.
Complement system helps phagocytes engulf foreign cells and help lyse foreign cells.
Phagocytes are attracted to injury by chemical gradients of complement, engulf
pathogens and damaged cells.
When macrophages and neutrophils are activated, the cells discharge cytokines,
signaling molecules that modulate immune responses.
Cytokines promote blood flow to the injury site or infection.

38
The result in the of the increased blood flow is the accumulation of pus, a fluid rich in
white blood cells, dead pathogens, and cell debris from damaged tissue.
Fever is a systemic inflammatory response.
In response to certain pathogens, substances released by activated macrophages cause
the body's thermostat to reset to a higher temperature.
Higher temperature is beneficial to help fighting off infections.

Adaptive immunity players

Introduction
In adaptive immunity, molecular recognition relies on a vast arsenal of receptors, each of
which recognizes a feature typically found on only a particular part of a particular molecule
in a particular pathogen.
Recognition and response occurs with tremendous specificity.
Is activated after the innate immune response and develops more slowly.
Receptors provide pathogen-specific recognition
The adaptive response relies on T and B cells, which are types of white blood cells called
lymphocytes.
Lymphocytes originate from stem cells in the bone marrow.
Lymphocytes that go to the thymus (an organ above the heart) mature into T cells.
Lymphocytes that remain and mature in the bone marrow develop as B cells.
Lymphocytes of a third type remain in the blood and become natural killer cells
active in innate immunity.
Any substance that elicits a B or T cell response is called an antigen. They are typically
foreign and are large molecules, either proteins or polysaccharides that protrude from the
surface of foreign cells or viruses.
In adaptive immunity, recognition occurs when a B or T cell binds to an antigen via a
protein called an antigen receptor.
All of the antigen receptors made by a single B or T cell are identical.
Each antigen receptor binds to just one part of one molecule from a particular pathogen.
The small, accessible portion of an antigen that binds to an antigen receptor is called an
epitope.
A single antigen usually has several epitopes, each binding to a receptor with

39

different specificity.
Each B or T cell displays specificity for a particular epitope, enabling it to respond
to any pathogen that produces molecules containing that epitope.
The antigen receptors of the B cells can bind to epitopes of intact antigens on pathogens
or circulating free in body fluids.
Antigen recognition by B cells and Antibodies
Each B cell antigen receptor is a Y-shaped molecule consisting of 4 polypeptide chains:
two identical heavy chains and two identical light chains, with disulfide bridges linking the
chains together. A transmembrane region anchors the receptor. A short tail region at the end
of the transmembrane region extends into the cytoplasm.
The light and heavy chains each have a constant region, where amino acid sequences
vary very little among the receptors.
Within the two tips of the Y shape, each chain has a variable region, so named because
its amino acid sequence varies extensively from one B cell to another. The combination
of the V region makes up the antigen binding site. Note that the antigen-binding site is
at the N-terminus!

Binding of a B cell antigen receptor to an antigen is an early step in B cell activation,

leading to the formation of cells that secrete a soluble form of the receptor. The secreted
protein is called an antibody.
Antibodies have the same Y-shaped structure as B cell antigen receptors but are secreted
rather than membrane bound.
Antibodies bind to intact antigens in the blood and the lymph.
in a typical antibody, heavy and light chains are linked by hydrogen bonds
Antigen recognition by T cells
The T cell antigen receptor consists of two different polypeptide chains, an alpha and beta
chain, linked by a disulfide bridge. At the base of the T cell antigen receptor is a
transmembrane region that anchors the receptor. At the outer tip of the molecule, the
variable regions o the alpha and beta chains together form a single-antigen binding site.
The remainder of the molecule is made up of the constant regions.
T cells can bind only to fragments of antigens that are displayed, or presented, on the

40
surface of host cells, unlike B cells.

The host protein that displays the antigen fragment on the cell surface is called the major
histocompatibility complex (MHC) molecule. Most body cells only have MHC II but
antigen presenting cells have MHC II and I.
Recognition of a protein antigens by T cells begin when a pathogen or part of a
pathogen either infects or is taken by a host cell.
Inside the host cell, enzymes cleave the antigen into smaller peptides and then the
antigen fragments bind to the MHC molecules inside the cell.
Movement of the MHC molecule and the bound antigen fragment up to the cell surface
results in antigen presentation, display of the antigen fragment in an exposed groove of
the MHC protein.
The appropriate T cell can then bind to the antigen fragment and the MHC molecule.
B and T cell development
4 major characteristics of adaptive immunity:
immense diversity of lymphocytes and receptors, enabling immune system to detect
pathogens never encountered
adaptive immunity normally has self-tolerance, the lack of reactivity against an animal's
own molecules and cells
cell proliferation triggered by activation greatly increases number of B and T cells
specific for the antigen
there is a stronger and more rapid response to an antigen encountered previously
The capacity to generate diversity in B and T cells is built into the structure of Ig genes.
A receptor light chain is encoded by three gene segments: a variable (V) segment, a
joining (J) segment, and a constant (C) segment.
The V and J segments together encode the variable region of the receptor chain while
the C segment encodes for the constant region.
Assembling a functional Ig gene requires rearranging the DNA. Early in B cell
development, an enzyme complex called recombinase links one light-chain V segment
to one J segment. This leads to the creation of many different types of short and long
chains, and thus many different types of antigen-binding sites. This is called VJ
recombination.

41
Mutations in VJ recombination can add additional variation.

Origin of self-tolerance
As lymphocytes mature in the bone marrow or thymus, their antigen receptors are tested for
self-reactivity. If this fails the test, they are destroyed by apoptosis.
Proliferating of B and T cells
An antigen is presented to a steady stream of lymphocytes in the lymph nodes until a match
is made.
Once the match is made, the B or T cell undergoes multiple cell divisions. The daughter
cells are clones of the original cell.
Some of the clones become effector cells, short-lived cells that take effect immediately
against the antigen and any pathogens producing that antigens.
The effector forms of B cells are plasma cells, which secretes antibodies.
The effector forms of T cells are helper T cells and cytotoxic T cells.
The remaining cells in the clone become memory cells, long-lived cells that can give
rise to effector cells if the same antigen is encountered later in the animal's life.
This whole process is called clonal selection because an encounter with an antigen selects
which lymphocyte will divide to produce a clonal population for a particular epitope.
Primary vs. secondary immune response
Immunological memory is responsible for the long-term protection that a prior infection
provides against many diseases.
The production of effector cells from a clone of lymphocytes during the first exposure to an

42
antigen is the basis for the primary immune response
If an individual is exposed again to the same antigen, the response is faster, of greater
magnitude, and more prolonged. This is called the secondary immune response.
Adaptive immunity mechanism
Humoral vs. cell-mediated response
The humoral immune response occurs in the blood and lymph. In the humoral response,
antibodies help neutralize or eliminate toxins in the blood and lymph.
In the cell-mediated immune response, specialized T cells destroy infected host cells.
Helper T cells: A response to nearly all antigens
A type of T cell called a helper T cell triggers the humoral and cell-mediated immune
responses. They secrete signals which help initiate productions of antibodies that neutralize
pathogens and activate T cells that will kill the infected cells. Two requirements for helper T
cells to activate:
A foreign molecule must be present that can bind specifically to the antigen receptor of
the T cell
The antigen must be displayed on the surface of an antigen-presenting cell.
Can be a dendritic cell, macrophage, or B cell.
Most body cells have class I MHC molecules, but antigen-presenting cells have
class I and class II molecules.
An accessory protein called CD4 helps the helper T cell bind to the class II MHC
molecule. When the helper T cell binds to the antigen-presenting cell cytokines are
exchanged.
Once the helper T cell has been activated, they produce interleukins to stimulate
proliferation of T cells, B cells and macrophages.
Cytotoxic T cells
Cytotoxic T cells use toxic proteins to kill cells infected by viruses or other intracellular
pathogens before fully mature.
To become active, cytotoxic T cells require signals from helper T cells and interaction
with an antigen-presenting cell.
The accessory protein CD8 binds to the class I MHC molecule to keep the 2 cells in
contact.
The cytotoxic T protein kills the host cell by secreting proteins that disrupt membrane
integrity and trigger cell death.
T suppressor cells
T suppressor cells serve to town down the T cell response to self cells or following an
infection.
Activation and function of B cells
Activation of B cells involve both helper T cells and proteins on the surface of pathogens.
When an antigen first binds to receptors on the surface of a B cell, the cell takes in a few
foreign molecules by receptor-mediated endocytosis.
The class II MHC protein of the B cell presents an antigen fragment to a helper T cell. The
T cell attaches to that antigen. The direct cell-to-cell contact is usually critical to B cell
activation.
A single activated B cell gives rise to thousands of clones. These clones begin producing
and secreting antibodies.
Antibody function

43
Antibodies do not actually kill pathogens, but by binding to pathogens, they interfere with
pathogen activity or mark pathogens in various ways for inactivation or destruction.
Types of antibodies:
IgG is most abundant antibody
IgM is the first antibody to appear in response to an antigen
IgA is present in mucosal secretions
IgE is present in the allergic response
IgD crosses the placenta and activates T-cells
Neutralization is a process in which antibodies bind to proteins on the surface of a virus
and makes it impossible for the virus to infect the cell.
In opsonization, antibodies bound to antigens on bacteria do not block infection, but instead
present a readily recognized structure for macrophages or neutrophils.
Antibodies can also work with proteins of the complement system.
Binding of complement protein to an antigen-antibody complex on a foreign cell
triggers the generation of a membrane attack complex that forms a pore in the
membrane of the cell and causes lysis.

Active vs. passive immunity

Active immunity are the defenses that arise when a pathogen infects the body and prompts
a primary or secondary immune response.
Passive immunity is when the antibodies in the blood of a pregnant female cross the
placenta to her fetus.
Newborn infants are protected by passive immunity also by drinking breast milk. Breast
milk contains antibodies.
Antibiotics are chemicals derived from bacteria or fungi that are harmful to other
microorganisms.
Vaccines are substances that stimulate the production of memory cells. Inactivated viruses
or fragments of viruses, bacteria, or other microorganisms are used as vaccines. Once
memory cells have formed, the introduction of a live microorganism will stimulate a swift

44

response by the immune system before any disease can become established.
vaccine = active immunity that is artificially acquired
Transplant rejection (immune system)
Transplanted tissues or organs are detected as nonself by the recpient's immune system
because the antigens on the donated organ are those of the donor, not the recipient.
As a result, the recipient's immune system will attack the transplanted organ.
Take immunosuppressing drugs to help prevent transplant rejection. They work by lowering
the body's immune response to antigens.
The recipient who is taking these drugs are immunocompromised because the immune
system is not functioning at full capacity.

45
Functions of the skin
Functions
Thermoregulation: helps regulate body temperature
Protection: skin is a physical barrier to abrasion, bacteria, dehydration, many chemicals,
and UV radiation.
Environmental sensory input: skin gathers information about environment by sensing
temperature, pressure, pain and touch
Excretion: water and salts excreted through skin
Immunity: specialized cells of the epidermis are components of the immune system
Blood reservoir: Vessels in the dermis hold up to 10% of the blood in resting adult
Vitamin D synthesis: UV radiation on skin catalyzes the synthesis of vitamin D from a
precursor molecule
Structure of the skin
Epidermis
Epidermis is the superficial epithelial tissue.
It is avascular, meaning it has no blood vessels linking to it.
It depends on the dermis for oxygen and nutrients.
Layers from top to bottom:
Stratum corneum 25 to 30 layers of dead cells.
Filled with keratin (fibrous protein responsible for protective properties of the
epidermis) and surrounded by lipids.
Lamellar granulues makes it water repellent
Stratum lucidum 3-5 layers of clear, dead cell.
Only located in the palms, soles of feet, and finger tips
Stratum granulosum 3-5 layers of dying cells
lamellar bodies release hydrophobic lipids
the stratum granulosum is that layer containing granules which can easily strain
Stratum spinosum 8-10 layers of cells
Cells are held together by desmosomeskeratin involving adhesion proteins
Provides strength and flexibility
Stratum basale (germinativum) contains merkel cells and stem cells that divide to
produce keratinocytes; attached by basement membrane.

46

Melanocytes are most likely found in the stratum germinativum

The keratinocytes are pushed from this layer to the stratum corneum. As they rise,
they accumulate keratin and die. When they die, they lose cytoplasm, nucleus, and
other organelles. At the outermost layer of the skin, they slough off the body.
Cells of the epidermis
Keratinocytes produce the protein keratin that helps waterproof the skin
Melanocytes transfer skin pigment melanin to keratinocytes
Melanin protects the cell nucleus from the destructive effects of UV radiation.
Individual and racial differences in skin coloring are probably due to differences in
melanocyte activity.
Langerhans cells interact with helper T-cells of the immune system. They are
macrophages.
Merkel cells attach to sensory neurons and function in touch sensation
Dermis
Dermis is the primary connective tissue of the skin.
Contains collagen and elastic fibers
Contains hair follicles, glands, nerves, and blood vessels
Layers of the dermis
Papillary region makes up the top 20% of the dermis
Reticular region is the dense connective tissue that is made up of collagen and elastic
fibers
Provides strength and elasticity (stretch marks are dermal tears!)
Packed with oil glands, sweat gland ducts, fat, and hair follicles
Hypodermis (subcutaneous)
The hypodermis is not part of the skin. It is the innermost and the thickest layer.
Mainly composed of adipocytes, cells that are specialized in accumulating and storing
fats. These cells are grouped together in lobules separated by connective tissue. Acts as
energy reserve and as a thermoregulatory insulator.
Has pressure sensing nerve endings
Passage for blood vessels

47

Glands of the skin

Sebaceous (oil) glands are connected to hair follicles except on the palms and soles.
Secrete an oily secretion called sebum.
Sebum is usually ducted into a hair follicle where it softens and lubricates the hair and
skin and has a bactericidal action.
Ceruminous glands secrete ear wax
Mammary glands secrete milk
Sudoriferous glands are sweat glands. Two types:
Eccrine glands are on most of the body. They regulate temperature through perspiration
and eliminate urea.
Apocrine glands are on the armpits, pubic region, and nipples. They secrete viscous
secretions with an unknown function. Activated by the sympathetic nervous system.

48
Vertebrate skeletal muscle structure and function
Structure of skeletal muscle
Vertebrate skeletal muscle, which moves bones and body, has a hierarchy of smaller and
smaller units.
fascia is loose connective tissue that covers the surface of muscle
Within a typical skeletal muscle is a bundle of muscle fibers that run parallel to the length
of the muscle.
Each fiber is a single cell with multiple nuclei.
Each nucleus is derived from one of the embryonic cells that fused to form the muscle
cell.
Sarcoplasm is the cytoplasm of a fiber cell.
Sarcolemma is the plasma membrane of muscle cells.
It can propagate an action potential
It is invaginated by transverse tubules
It wraps several myofibrils together to form a muscle cell/muscle fiber
Mitochondria is present in large amounts for ATP synthesis
Inside a muscle cell lies a longitudinal bundle of myofibrils, which contain the thick and
thin filaments.
Thin filaments is comprised of two strands of actin that are coiled around each
other.
Thick filaments, which are staggered arrays of myosin molecules.
The interaction between thick and thin filaments produces muscle cell contraction.
the alternating between the thin actin filaments and the thick myosin filaments is
responsible for striations in the skeletal muscle.
The myofibrils in muscle fibers are made up of repeating sections called sarcomeres, which
are the basic contractile units of skeletal muscle.
Thin filaments attach at Z lines which are located at the boundary of a single sarcomere,
while thick filaments are anchored at M lines centered in the sarcomere.
The I band is the region containing thin filaments.
The H zone is the region containing thick filaments.
The A band is the region of actin and myosin overlapping.
The H zone and I band reduce during contraction, but the A band does NOT.

49

The sliding-filament model

According to the well-accepted sliding-filament model, the thin and thick filaments ratchet
past each other, powered by myosin muscles.
1) The myosin head is bound to ATP and it is in its low-energy configuration.
2) The myosin head hydrolyzes ATP to ADP and phosphate and is now in its high-energy
conformation.

50
3) The myosin head binds to actin on its myosin-binding site, forming a cross-bridge.
4) Releasing ADP and Pi, myosin returns to its low-energy configuration, sliding the thin
filament toward the center of the sarcomere.
5) Binding of a new molecule of ATP releases the myosin head from actin, and a new cycle
begins.
Without new ATP, the cross bridges remain attached to the myosin head. This is why dead
corpses are stiff.
At rest, most muscle fibers contain only enough ATP for a few contractions. Powering
repetitive contractions requires two other storage compounds:
Creatine phosphate, which will transfer a group from phosphocreatine to ADP in an
enzyme-catalyzed transphosphorylation reaction.
Glycogen can be broken down into glucose, which can be metabolized quickly to create
ATP.
During intense muscle activity, oxygen becomes a limiting reagent and ATP is instead
generated by lactic acid fermentation.
This generates much less ATP per glucose molecule and creates the burning sensation in
the muscles.

The role of calcium and regulatory proteins

Tropomyosin, a regulatory protein, and the troponin complex, a set of additional
regulatory proteins, are bound to the actin strands of thin filaments.
In a muscle fiber at rest, tropomyosin covers the myosin-binding sites on the actin (thin)

51

filaments, preventing actin from interacting.

When Ca2+ ions accumulates in the cytosol, it binds to the troponin complex, causing
tropomyosin bound along the actin strands to shift position and expose the myosinbinding sites. When the Ca2+ concentration falls, the binding sites are covered, and
contraction stops.
Whereas contraction of a single skeletal muscle fiber is a brief all-or-none twitch,
contraction of a whole muscle is graded; you can voluntarily alter the extend and strength
of its contraction.
The nervous system produces graded contractions of whole muscles by varying (1) the
number of muscle fibers that contract and (2) the rate at which muscle fibers are
stimulated.
The strength of a contraction of a single muscle fiber cannot increase but the strength of
overall contraction can be increased by recruiting more muscle fibers.
A motor unit consists of a single motor neuron and all the muscle fibers it controls.
Usually small motor units are activated first, then larger ones are activated as needed.
This creates a smooth increase in force.
Fine movement uses small motor units only.
1) Acetylcholine (Ach) is released at the synaptic terminal of a motor neuron. It diffuses
across the synaptic cleft and binds to the receptor proteins on the muscle fiber's plasma
membrane, triggering an action potential in the muscle fiber.
2) The action potential is propogated along the plasma membrane and down transverse
tubules.
3) The action potential propogating down the T tubules make close contact with the
sarcoplasmic reticulum (SR), a specialized endoplasmic reticulum. Close contact of the
AP with the SR triggers the release of Ca2+ ions from the SR.
4) Ca2+ ions bind to the troponin complex in the thin filament, exposing the myosin binding
sites.
5) Cycles of myosin cross-bridge formation and the breakdown, coupled with ATP
hydrolysis, slide thin filament toward center of sacromere. The muscle contracts.
6) Cytosolic Ca2+ is removed by active transport into the SR after the action potential ends.
7) Tropomyosin blockage of myosin-binding sites is restored; contraction ends, and the
muscle fiber relaxes.

52

Types of muscles
Types of muscle responses
Simple twitch is the response of a single muscle fiber to a brief stimulus. Three phases:
Latent period is the time between stimulation and onset of contraction. During this
time, the action potential propagates along the sacrolemma and Ca2+ ions are released
to open up the myosin-binding sites.
Contraction
Relaxation is the absolute refractory period. The muscle is now unresponsive to a
stimulus during this time.
Summation occurs when two contractions combine additively and become stronger. They
are more prolonged than a simple twitch.
This occurs when a second action potential arrives before the muscle fiber has
completely relaxed.
Tetanus is the continuous sustained contraction because the rate of muscle stimulation is so
fast that the twitches blur into one smooth constant.
Tonus is the unconscious low level contraction of your muscles while they are rest. It is a
state of partial contraction.

53

Your muscles are never completely relaxed.

This is what makes your muscles feel somewhat firm while you are resting and not
intentionally tesning them.
5 types of muscle contractions
Isotonic contraction is when a muscle shortens against a fixed load while the tension on the
muscl eremians constant
A concentric contraction is a type of dynamic contraction wher ehte muscle fibers hsorten
and the tension on the muscle fiber increases.
An eccentric contraction ia type of dynamic contraction wher eht emuscle fiber lengthens
and the tension on the muscle increases.
Dynamic contraction involves both concentric and eccentric type of contractions.
An isometric contraction occur when both ends of the muscle are fixed and nochange in
length occurs during the contraction, but the tension increases.
Types of muscle fibers
Skeletal muscle is voluntary, striated, and moves bone. It is multi-nucleated. They generally
don't undergo mitosis to create new cells (hyperplasia), but will increase in size
(hypertrophy). There are multiple types:
Fibers that rely mostly on aerobic respiration are called oxidated fibers.
They have many mitochondria for ATP synthesis.
They have a rich blood supply for easy access to nutrients.
Have a large amount of the oxygen-storing protein myoglobin.
Slow oxidative muscle fibers have a low rate of myosin ATPase activity. They have
the smallest diameter and are the most highly resistant to fatigue. Red color. Are
slow-twitch fibers, meaning that they contract slowly but they contract for a much
longer period of time than fast-twitch fibers. Muscles that need to be active
continuously have many of these fibers.
Fast oxidative muscle fibers have a high rate of myosin ATPase activity. They have
an intermediate diameter and are intermediate in resistance to fatigue. Red to pink
color. They are fast-twitch fibers, meaning that they contract very fast. Fast-twitch
fibers enable brief, rapid, powerful contractions.
In contrast, glycolytic fibers rely on glycolysis as their major source of ATP production.
They have the largest diameter and the low concentrations of myoglobin.
They have high myosin ATPase activity.
Fast-twitch fiber
Typically white color.
Usually used for power.
Cardiac muscle is only found in the heart. It is striated and involuntary. They are mononucleated or bi-nucleated.
High amounts of mitochondria
NO summation or tetanus due to long refractory period
Ion channels in the plasma membrane of cardiac muscle cells cause rhythmic
depolarizations that trigger action potentials WITHOUT nervous system input
(myogenic). Action potentials last much longer than skeletal muscles.
Adjacent cardiac muscle cells are electrically coupled by specialized regions called
intercalated disks. This enables the action potential generated by specialized cells in
one part of the heart to spread, causing the whole heart to contract.
Smooth muscle is found mainly in hollow organs such as the digestive tract and blood

54
vessels. They lack striations, are mono-nucleated, and are involuntary.
Thick filaments are scattered throughout the cytoplasm and thin filaments are attached
to structures called dense bodies, some of which are tethered to the plasma membrane.
There is less myosin than in skeletal muscle and the myosin is not associated with
specific actin strands.
The contraction of the thin and thick filaments causes the dense bodies to move closer,
which causes the shortening of the intermediate filaments found throughout the cell.
This causes the cell to get smaller and contract as a whole.
These muscles are stimulated by the autonomic nervous system.
Smooth muscle can respond to hormones, change in pH, oxygen and carbon dioxide
levels, temperatures on top of neuronal responses.
Two main types:
Single unit (visceral) smooth muscle is connected by gap junctions and contract as
a single unit (stomach uterus, urinary bladder).
In multiunit smooth muscle, each fiber is directly attached to neurons and can
contract independently (iris, bronchioles).
Vertebrate skeleton
Organization
Axial skeleton is the part of the skeleton that consists of the bones of the heat and the trunk
of a vertebrate.
The appendular skeleton supports the attachment and functions of the upper and lower
limbs of the human body. Consist of pectoral girdle, pelvic girdle, upper limbs (arms) and
lower limbs (legs).
Joints are areas where different bones meet:
Stutures are immovable joints that holds together the bones of the skull.
Moveable joints are bones that move relative to each-other.
Ligaments are bone-to-bone connectors that strengthen joints.
Tendons are muscle-to-bone connectors that bend skeleton at moveable joints.
Origin is the point of attachment of muscle to stationary bone.
Insertion is the point of attachment of muscle to bone that moves.
Extension is the straightening of a joint.
Flexion is the bending of a joint.
A fibrous joint connect bones without allowing any movement.
Cartilaginous joints are bones that are attached by cartilage that allow for little
movement.
Synovial joints allow for much more movement. They are most common.
They are filled with synovial fluid which acts as a lubricant.
Movement in lower forms
Unicellular locomotion
Protozoans and primitive algae use flagella by means of power stroke or recovery stroke.
Amoeba extend pseudopodia; advancing the cell membrane as it extends forward.
Invertebrate locomotion
A hydrostatic skeleton consists of fluid held under pressure in a closed body
compartments. Invertebrates with these skeletons control their form and movement by using

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muscles to change the shape of the fluid filled compartments.
Flatworms uses bi-layered longitudinal and circular muscles to contract against the
hydrostatic skeleton. Contraction causes hydrostatic skeleton to flow longitudinally,
lengthening the animal
Segmented worms (annelids) advance by action of muscles on hydrostatic skeleton.
Bristles in the lower part of each segment setae, anchor the worm in the earth while
muscles push ahead.

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Neuron structure and organization
Neuron structure and function
Neurons are cells that transformation within the body.
Most of a neuron's organelles, including its nucleus, are located in the cell body.
A typical neuron has numerous highly branched extensions called dendrites.
The dendrites receive signals from other neurons.
A neuron as a single axon, an extension that transmits signals to other cells.
Axons are much longer than dendrites.
The axon divides into many branches at its end.
The greater the diameter of the axon, the faster impulses will propagate. This is because
larger diameter axons have less resistance to flow of ions.
Each branched end of an axon transmits information to another cell at a junction called a
synapse.
The part of each axon branch that forms this specialized junction is a synaptic terminal.
At most synapses, chemical messengers called neurotransmitters pass information
from the transmitting neuron to the receiving cell.
In describing a synapse, we refer to the transmitting neuron as the presynaptic cell and
the neuron, muscle, or gland cell that receives the signal as the postsynatpic cell.
The connection shaped base of an axon connected to the cell body is called the axon
hillock. This is typically where signals that travel down the axon are generated.
Mylein sheath is an electrically insulating material (made of lipid) that forms around the
axon of a neuron. This increases the speed at which an action potential moves down the
axon.
Mylein sheath is created by glial cells:
Central nervous system neuronal mylein sheath is created by glial cells called
oligodendrocytes.
Peripheral nervous system neuronal mylein sheath is created by glial cells called
Schwann cells.
In myleinated axons, voltage-gated sodium channels are restricted to gaps in the mylein
sheath called nodes of Ranvier.
The extracellular fluid is only in contact with the axon membranes at the nodes.
Depolarization occurs at the nodes of Ranvier.
The mechanism for propagating action potentials along an axon is called saltatory
conduction, because the action potential appears to jump along the axon from
node to node.
The neurons of vertebrates and most invertebrates require supporting cells called glial cells,
or glia.
They nourish neurons, insulate the axons of neurons, and regulate the extracellular fluid
surrounding neurons.
Nissl bodies are areas of the rough ER that are involved in neuron protein synthesis.
Microglia are the phagocytic cells of the CNS.
Glia sometimes function in replenishing certain groups of neurons and in transmitting
information.
Glial cells vastly outnumber neurons.
Special cells in the CNS:
Astrocytes maintain the integrity of the blood-brain barrier, regulate nutrient and

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dissolved gas concentrations, and absorb and recycle neurotransmitters.
Ependymal cells line the brain ventricles and aid in the production circulation, and
monitoring of cerebrospinal fluid.
Introduction to information processing
Introduction
Information processing by a nervous system occurs in three stages:
sensory input
integration
motor output
In all but the simplest animals, specialized populations of neurons handle each stage of
information processing.
Sensory neurons transmit information about external stimuli or internal conditions
Neurons in the brain or ganglia integrate (analyze and interprate) the sensory input. The
vast majority of the neurons in the brain are interneurons, which form the local circuits
connecting neurons in the brain.
Neurons that extend out of the processing centers trigger output in the form of muscle or
gland activity.
In many animals, the neurons that carry out integration are organized in a central nervous
system (CNS).
These constitute all nerves DIRECTLY inside the brain and spinal cord.
The neurons that carry information into and out of the CNS constitute the peripheral
nervous system (PNS).
These constitute all nerves that ARE NOT DIRECTLY inside the brain and spinal cord.
Satellite cells surround the neuron cell bodies in the ganglia.
When bundled together, the axons of neurons form nerves.
A plexus is a network of nerve fibers.
The vagus nerve is one very important parasympahetic nerve that innverates many of
the thoracic and abdominal viscera.
Depending on its role in information processing, a neuron can vary from simple to quite
complex.

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Ion pumps and channels establish resting potential
Formation of resting potential
There is a charge gradient between the interior of a neuron and the extracellular space. This
charge difference is called a membrane potential.
For a resting neuron, one that is not sending a signal, the membrane potential is called the
resting potential and is typically between -60 and -80 mV.
The sodium-potassium pump plays a key role in establishing the resting potential.
This pump uses the energy of ATP hydrolysis to actively transport out 3 Na+ and
actively pump in 2 K+ into the cell.
The concentration gradients of ions across the plasma membrane represent a form of
potential energy that can be harnessed for cellular processes.
Some ion channels along the membrane of the neuron are always open. These ion channels
are called leak channels and only allow the passive movement of potassium ions.
Since the internal [K+] is greater than the external [K+], there will be a net movement of
potassium ions out of the cell. This helps generate the internal negative charge of the
neuron.
As there are no leak channels for Na+, sodium cannot move in or out of the neuron
freely.
Action potentials basics
Hyperpolarization and depolarization
Changes in membrane potential occur because neurons contain gated ion channels, ion
channels that open or close in response to stimuli.
When the gate opens, ions flow the channel, changing the membrane potential.
Hyperpolarization is an increase in the absolute value of Vm. The membrane potential
moves farther from 0.
Depolarization is a decrease in the absolute value of Vm. The membrane potential moves
closer to 0.
Graded potentials and action potentials
Threshold is the membrane potential to which an action potential will occur if reached.
In many mammalian neurons, the threshold is -55 mV.
Graded potentials are shifts in the membrane potential that do not reach the threshold
needed for an action potential.
Can be a hyperpolarization or a depolarization.
An action potential occurs when a depolarization causes the membrane potential to reach
the threshold.
Action potentials are all-or-nothing, meaning that if the membrane potential hits the
threshold, an action potential will occur.
Action potentials arise because some of the ion channels in neurons are voltage-gated ion
channels, opening or closing when the membrane potential passes a particular level.
Once a certain membrane potential is experienced, the voltage-gated ion channels will
open, causing further depolarization.
This positive-feedback mechanism explains the all-or-nothing phenomenon of action
potentials.
Sub-maximal vs. maximal stimulus
A sub-maximal stimulus is the amount of voltage necessary to elicit a response between
the threshold and the maximum response.

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Maximal stimulus is the amount of voltage necessary to elicit a maximal response.
Mechanism of action potential
Mechanism
When the membrane of the axon is at the resting potential, most voltage-gated sodium and
voltage-gated potassium channels are closed.
A stimulus opens up some sodium channels. Na+ inflow through those channels
depolarizes the membrane. If the depolarization reaches the threshold, it triggers an action
potential.
Once threshold is crossed, the positive-feedback cycle of the voltage-gated ion channels
rapidly brings the membrane potential close to ENa. This is called the rising phase
ENa is the equilibrium value of sodium. The sodium-potassium pump generates an
electrochemical gradient between inside the neuron and the extracellular space via
active transport. Higher concentration of Na+ outside than inside.
When the voltage-gated ion channels open, Na+ are allowed to passively diffuse to
either side. Since an electrochemical gradient is generated at the resting potential, there
is a net movement of Na+ ions into the neuron. This causes the neuron to become
positively charged.
Two events prevent the membrane potential from actually reaching ENa: (1) Voltage-gated
Na+ channels inactivate soon after opening, halting Na+ inflow and (2) Most voltage-gated
potassium channels open, causing a rapid outflow of K+. Both events quickly bring the
membrane potential back toward EK. This stage is called the falling phase.
EK is the equilibrium value for potassium. The sodium-potassium pump generates an
electrochemical gradient between the inside of the neuron and the extracellular space via
active transport. Higher concentration of K+ inside than outside.
When the voltage-gated ion channels open, K+ can passively diffuse to either side. K+
will spontaneously move out into the extracellular space. This brings the internal
membrane potential down toward EK.
In the final phase of an action potential, called the undershoot, the membrane's
permeability to K+ is higher than at rest, so the membrane potential is closer to EK than it is
to the resting potential. The gated potassium channels eventually close and the membrane
potential returns to resting potential.
This is also called the refractory period, where a second action potential cannot be
initiated. This limits the maximum frequency at which an action potential can be
generated. It is due to inactivation of sodium channels.
Conduction of action potential across axon
Action potential that starts at the axon hillock moves along the axon only toward the
synaptic terminals.
At the site where the action potential is imitated, usually the axon hillock, Na+ inflow
during the rising phase creates an electrical current that depolarizes the neighboring
region of the axon membrane (zone of depolarization). The depolarization is large
enough to reach threshold, causing an action potential in the neighboring region. This
process is repeated across the axon.

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Behind the zone of depolarization is the zone of repolarization caused by K+ outflow.
In this zone, sodium channels remain activated. Therefore, an action potential cannot be
generated here.

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The rate at which action potentials are produced conveys information about the strength of
the input signal.
Synaptic communication
Introduction
Information is transmitted at the synaptic terminals. Basic steps:
At the terminal of the presynaptic neuron, the neuron synthesizes the neurotransmitter
and packages it in multiple membrane-enclosed compartments called synaptic vesicles.
The arrival of an action potential at the presynaptic terminal depolarizes the plasma
membrane, opening voltage-gated channels that allow Ca2+ ions to diffuse into the
terminal.
The resulting rise in Ca2+ concentration in the terminal causes the neurotransmitter to
be released.
Once released, the neurotransmitter diffuses across the synaptic cleft, the gap that
separates the presynaptic and the postsynaptic neurons.
Upon reaching the postsyanptic membrane, the neurotransmitter binds binds to an
activates a specific response in the membrane.

Generation of postsynatpic potentials

The receptor protein that binds and responds to neurotransmitters is a ligand-gated ion
channel, often called an ionotropic receptor.
Binding of the neurotransmitter to a particular part of the receptor opens the channel and
allows specific ions to diffuse across the postsynaptic membrane.
The result is a postsynaptic potential, a graded potential in the postsyanptic cell.
At some synapses, the ionotropic receptor is permeable to Na+ and K+. When this receptor

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opens, the membrane potential depolarizes to a value midway between EK and ENa.
This depolarization brings the postsynaptic neuron above the threshold. This is called a
excitatory postysynaptic potential (EPSP).
At other synapses, the ionotropic receptor is selectively permeable for only K+ and Cl-.
When this receptor opens, the postsynatpic membrane hyperpolarizes.
The hyperpolarization produce din this manner is called an inhibitory postysnaptic
potential (IPSP) because it moves the membrane potential further from threshold.
Neurotransmitters can also bind to metabotropic receptors, a receptor that activates a
signal transduction pathway in a postsynaptic neuron that creates a second messenger.
The second messenger can alter the postysnaptic neuron in diverse ways, such as
altering the number of open potassium channels.
Metabotropic receptors have a slower onset than ionotropic receptors but last longer.
Metabotropic receptors do not directly pump ions like ionotropic receptors!
Summation of postsynaptic potentials
One postsyanptic potential usually isn't strong enough to produce an effect.
One neuron is linked up to many other neurons, so it can receive multiple postsynaptic
potentials in rapid succession from different presynaptic neurons. When this happens, the 2+
postysnaptic potentials add up in effect to produce one main effect.
EPSPs produced nearly simultaneously by DIFFERENT synapses on the same
postysynaptic neuron can add together, an effect called spatial summation.
In addition, two EPSPs can occur at a single synapse in such a rapid succession that the
postysynaptic neuron's membrane potential hasn't returned to resting potential before the
arrival of the second EPSP.
When this happens, the EPSPs add together, an effect called temporal summation.

Neurotransmitters
Types
Acetylcholine is vital for nervous system function that includes muscle stimulation,
memory formation, and learning. Two main acetylcholine receptors:
One is a ligand-gated ion channel, which functions at the vertebrate neuromuscular
junction, the site where a motor neuron forms a synapse with a skeletal muscle cell.
When acetylcholine is released by a motor neuron binds to this receptor, the ion channel
opens forming an EPSP. This is excitatory.
The second is a metabotropic receptor found in locations that include the vertebrate
CNS and heart. Acetylcholine released by neurons activate a G protein signal
transudction pathway that leads to open potassium channels. This is an IPSP, or an
inhibitory effect.
Gamma-aminobutyric acid (GABA) is the neurotransmitter at most inhibitory synapses in
the brain.
Binding of GABA to receptors in postsynatpic cells increases membrane permeability to
Cl-, resulting in an IPSP.
Norepinephrine is an excitatory neurtornasmiter in the autonomic nervous system, a branch
of the PNS.
Dopamine and seratonin are released at many sites in the brain and affect sleep, mood,
attention, and learning.
Nervous systems

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Vertebrate central nervous system

During embryonic development, the central nervous system develops from the notochord
a hallmark of chordates.
Meninges cover around the brain and spinal cord.
The brain is made up of outer gray matter and inner white matter. Surrounded by
cerebrospinal fluid.
There are 12 pairs of cranial nerves that are sensory, motor, and mixed. Most cranial
nerves are mixed.
The forebrain has activities that include the processing of olfactory input (smells),
regulation of sleep, learning, and any complex processing.
telencephalon = cerebral cortex + olfactory bulb
diencephalon = thalamus + hypothalamus
The cerebrum is the largest part of the brain.
Divided into the left and right cerebral hemispheres. Left hemisphere controls
right side of body and vice versa.
Divided into 4 lobes:
Frontal lobe concerned with reasoning, planning, parts of speech,
movement, emotions and problem solving.
Parietal lobe concerned with perception of stimuli such as touch, pressure,
temperature and pain.
Temporal lobe concerned with perception and recognition of auditory
stimuli (hearing) and memory.
Occipital lobe concerned with many aspects of vision.
A thick band of axons called the corpus calossum enables the right and left
cerebral cortices to communicate.
The outer layer of the cerebrum is called the cerebral cortex and is vital for
perception, voluntary movement, and learning. The inner portion is called the
medulla.
Olfactory bulb controls smell.
The thalamus is the main input center for sensory information going to the
cerebrum. Takes in sensory information and relays it to the correct areas.
The hypothalamus constitutes the control center that includes the body's thermostat
as well as the central biological clock.
The midbrain, located centrally in the brain, coordinates routing of sensory input.
The hindbrain controls involuntary activities, such as blood circulation.
The cerebellum coordinates movement and balance and helps in learning and
remembering motor skills. Controls muscular coordination.
The pons is a relay center to allow communication between the cortex and the
cerebllum.
Medulla oblongata controls breathing, heart rate ,and gastrointesitnal activity.
The midbrain and portions of the hindbrain give rise to the brainstem, the part of the
brain that is connected to the spinal cord.
It controls the flow of messages between the brain and the rest of the body, and
controls basic body functions such as breathing, swallowing, heart rate, blood
pressure, consciousness, and whether one is awake or sleepy.
Consists of the midbrain, pons, and the medulla oblongata.

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The spinal cord runs lengthwise inside the vertebral column, known as the spine. It
conveys information to and from the brain and generates basic patterns of locomotions.
The central canal is the space that runs longitudinally through the length of the entire
spinal cord. It is filled with cerebrospinal fluid, which supplies the CNS with nutrients
and hormones and carrying away wastes.
Made up of grey and white matter:
Gray matter is primarily made up of neuron cell bodies.
White matter consists mainly of bundled axons.
Makes up the outer layer of the spinal cord.
Acts independently of the brain as part of simple nerve circuits that produce reflexes,
the body's automatic responses to certain stimuli. Does NOT travel through brain!
Sensory information enters through the dorsal horn and motor information exits
through the ventral horn.
Peripheral nervous system
Sensory information reaches CNS along PNS neurons designated as afferent neurons.
Following processing within the CNS, instructions travel to muscles glands, and endocrine
cells along PNS neurons called efferent neurons.
PNS has two different components:
The motor system consists of neurons that carry signals to skeletal muscles. Can be
voluntary or involuntary.
The autonomic nervous system consists of neurons that carry signals to smooth and
caridac muscles. It is generally involuntary. 3 subdivisions:
The enteric division of the autonomic nervous system are active in controlling the
digestive tract, pancreas, and gallbladder.
The sympathetic division corresponds to the fight-or-flight response. Major
neurotransmitter is norepinephrine.
The paraympathetic division causes the opposite response of the sympathetic
division and promotes calming and a return to self-maintenance functions. Major
neurotransmitter is acetylcholine.

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Respiratory system
Partial pressure gradients in gas exchange
Partial pressure is the pressure exerted by a particular gas in a mixture of gasses. A gas
always undergoes net diffusion from a region of higher partial pressure to a region of lower
partial pressure.
Respiratory media
The conditions for gas exchange vary considerably, depending on whether the respiratory
mediumthe source of oxygenis air or water.
Gas exchange with air is much easier than gas exchange with water due to differing
diffusional coefficients. Do2 in air is higher than DO2 in water.
Aquatic animals that need to extract oxygen out of water have developed special adaptations
to do this.
Respiratory surfaces
The respiratory surface is the part of an animal's body where gas exchange occurs.
The cells that carry out gas exchange have a plasma membrane that must be in contact with
an aqueous solution. Respiratory surfaces are always moist.
The movement of oxygen and carbon dioxide across respiratory surfaces takes place by
diffusion.
Respiratory surfaces tend to be large and thin to maximize surface area to maximize the
flux of these gases.
In sponges, cnidarians, and flatworms, every cell in the body is close enough to the external
environment so that gases can diffuse quickly between any cell and the environment. The
skin serves as the respiratory organ.
In other animals, the bulk of the body's cells lack immediate access to the environment.
External vs internal respiration
External respiration refers to the entrance of air into the lungs and the gas exchange
between the alveoli and the blood
Internal respiration includes the exchange of gas between blood and the cells and the
intracellular processes of respiration.
Gills in aquatic animals
Gills are outfoldings of the body surface that are suspended in the water. They often have a
total surface area much greater than that of the rest of the body's exterior.
Movement of the respiratory medium over the respiratory, a process called ventillation,
maintains the partial pressure gradients of oxygen and carbon dioxide across the gill that are
necessary for gas exchange.
In fishes, the efficiency of gas exchange is maximized by countercurrent exchange, the
exchange of a substance or heat between two fluids moving in opposite directions.
In a fish gill, the two fluids are blood and water.
As blood enters a gill capillary, it encounters water that is completing its passage
through the gill (almost depleted of oxygen). The partial pressure of oxygen in the water
is greater than that of the blood in the capillaries, and oxygen transfer takes place.
Because blood flows in the direction opposite to that of water passing over the gills,
at each point in its travel blood is less saturated with oxygen than the water it meets.
Even as the blood continues its passage, its partial pressure of oxygen steadily
increases, but so does that of the water it encounters, since each successive position
in the blood's travel corresponds to an earlier position in the water's passage over the
gills.

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Tracheal systems in insects

The tracheal system is a network of airtubes that branch throughout the body.
The largest tubes, called tracheae, open tot he outside.
The finest branches, tracheoles, extend close to the surface of nearly every cell, where

gas is exchanged by diffusion across the moist epithelium that lines the tips of tracheal
branches.
Lungs
Lungs are localized respiratory organs. They are an infold of the body surface that are
typically subdivided into numerous pockets. It is the largest internal organ.
In humans, the right lung is larger than the left lung. The right lung has 3 lobes whereas the
left lung has 2 lobes.

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Pleurae is the thin, smooth membranous outer covering of the lungs.

Because the respiratory surface of a lung is not in direct contact with all other parts of the
body, the gap must be bridged by the circulatory system.
Book lungs are stacks of flattened membranes enclosed in an internal chamber.
Mammalian respiratory systems

Air enters through the nostrils. The air is then filtered by hairs, warmed, humidified, and
sampled for odors through the nasal cavity.
Mucus secreted by goblet cells traps large dust particles, pollen, and other particulate
contaminants.
The nasal cavity leads to the pharynx, an intersection where the paths for air and food
cross.
All the contaminants and mucus are swept back here by cilia for disposal via spitting or
swallowing. Called the mucus escalator.
smoking can damage the cilia of the respiratory cells and allow toxins to remain in
lungs
The larynx is the upper part of the respiratory pathway. It is the voice-box; if non-gas
enters, cough reflex activates.
Also controls action of the epiglottis. If food is moving down the pharynx, the larynx
will tip the epiglottis over the glottis, which is the opening of the trachea so food can
move down through the esophagus. If air is moving through, the epiglottis is covering
the esophagus, so air can travel down through the glottis.

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The trachea is the windpipe.
The walls of the trachea is reinforced by ringed cartilage that is C-shaped (for strength
and to keep the airway open).
Covered by ciliated mucus cells.
The trachea branches into two bronchi, one leading to each lung. Within each lung, the
bronchi branch repeatedly into finer and finer tubes called bronchioles.
Gas exchange in mammals occur in alveoli, air sacs clustered at the tips of the thinnest
bronchioles.
emphysema is a pathology marked by destruction of alveoli
Oxygen diffuses through the alveolar wall through the pulmonary capillary wall, into
blood, and into red blood cells. Carbon dioxide moves in the opposite direction starting
at the red blood cells and moving into the alveoli.
Alveoli lack cilia or significant air currents to remove particles from the surface so they
are highly susceptible to contamination.
White blood cells patrol the alveoli, engulfing foreign particles.
Alveoli produces a mixture of phospholipids and proteins called surfactant, which coats
the alveoli and reduces surface tension which prevents collapse.
Breathing
How an amphibian breathes
An amphibian such as a frog ventilates its lungs by positive pressure breathing, inflating
the lungs with forced airflow.
Muscles lower the floor of an amphibian's oral cavity, drawing in air through its nostrils.
With the nostrils and the mouth closed, the floor of the oral cavity rises, forcing air
down the trachea and into the lungs.
During exhalation, air is forced back out by the elastic recoil of the lungs and by
compression of the muscular body wall.
How a bird breathes
To bring fresh air into their lungs, birds use eight or nine air sacs situated on either side of
the lungs.
The air sacs do not function directly in gas exchange but acts as bellow that keep air
flowing through the lungs.
Instead of having alveoli, sites of gas exchange in bird lungs are tiny channels called
parabronchi.
Two cycles of inhalation and exhalation are required to pass one breath through the system:
First inhalation: air fills the posterior air sacs
First exhalation: posterior air sacs contract, pushing air into the lungs
Second inhalation: air passes through the lungs and fills the anterior air sacs
Second exhalation: as anterior air sacs contract, air that entered the body at first
inhalation is pushed out of the body.

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How a mammal breathes

Tidal breathing is breathing in and out through the same tubing, inhibiting gas exchange
during exhalation.
Deoxygenated air is mixed with some fresh air during inhalation, some of it is rebreathed
Much less efficient than birds as a result
Mammals employ negative pressure breathingpulling, rather than pushing, air into their
lungs.
Using muscle contraction to expand their thoracic cavity, mammals use lower air
pressure in their lungs below the air outside the body. The pressure gradient causes air to
flow into the lungs.
During exhalation, the muscles controlling the thoracic cavity relax, and the volume of the
cavity is reduced. The increased air pressure in the alveoli forces air up into the breathing
tubes and out of the body.
Expanding the thoracic cavity during inhalation involves the animal's rib muscles and the

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diaphragm, a sheet of skeletal muscle that forms the bottom wall of the cavity.
The diaphragm is a skeletal muscle and is controlled by the phrenic nerve It is also the
only organ which only and all mammals have, and without which no mammal can live.
Inhalation is an active process diaphragm and the intercostal muscles (between ribs)
contract and flattens. This causes an increase in volume and a decrease in pressure in the
lungs. The pressure gradient is created and there is a bulk flow of air into lungs.
Exhalation is a passive process decrease in lung volume causes an increase in air
pressure. Air then rushes out and the diaphragm relaxes and expands.

The volume of air inhaled and exhaled with each breath is called tidal volume.
The tidal volume during maximal inhalation and exhalation is called vital capacity.
The air that remains after a forced exhalation is called the residual volume.
As you get older, residual volume increases while vital capacity decreases.
Control of breathing in humans
Most of the time your breathing is regulated by involuntary mechanisms.
The neurons mainly responsible for regulating breathing are in the medulla oblongata, near
the base of the brain. Neural circuits in the medulla form a pair of breathing control
centers that establish the breathing rhythm.
chemoreceptors located on the aorta and carotid arteries are involved in blood gas content
monitoring.
When you breathe deeply, a negative-feedback mechanism prevents the lungs from over
expanding: during inhalation, sensors that detect stretching of the tissue send nerve impulses
to control circuits in the medulla, inhibiting further inhalation.
In regulating breathing, the medulla uses the pH of the surrounding tissue fluid as in
indicator as blood carbon dioxide concentration.
Blood carbon dioxide is the main determinant of the pH of cerebrospinal fluid, the fluid
surrounding the brain and the spinal cord.
Carbon dioxide diffuses from the blood and into the cerebrospinal fluid, where it reacts
with water to form carbonic acid. Carbonic acid then dissociates into bicarbonate
anion and hydrogen ion.
In response to decreasing pH, the medulla will increase the depth and rate of breathing

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until the pH returns to a normal value.
Respiratory pigments
coordination and circulation of gas exchange
During inhalation, fresh air mixes with air remaining in the lungs.
The resulting mixture formed in the alveoli has a higher Po2 and a lower PCO2 than the blood
through the alveolar capillaries.
As a result, there is a net diffusion of oxygen out of the alveoli and there is a net
diffusion of carbon dioxide into the alveoli.
By the time leaves the lungs in the pulmonary veins, its Po2 and Pco2 match the values for
those gases in the alveoli (because they are in equilibrium).
In the systemic capillaries, the partial pressure gradients favor oxygen to diffuse out of the
blood and carbon dioxide to diffuse into the blood.
After the blood unloads oxygen and loads carbon dioxide, it is return to the heart and
pumped to the lungs again. And the cycle re-begins.
Respiratory pigments
Animals transport most of their oxygen bound to proteins called respiratory pigments.
Respiratory pigments greatly increase the amount of oxygen that can be carried within
the circulatory fluid.
The main respiratory pigment of all most all vertebrates and many invertebrates is
hemoglobin.
In vertebrates, it is contained in erythrocytes (RBCs) and has 4 subunits, each with a
cofactor called a heme group with an iron atom at its center.
Each heme binds one molecule of oxygen, so 1 hemoglobin molecule can carry 4
molecules of oxygen.
Hemolgobin binding to oxygen is reversible, allowing it to load O2 in one area and
unload it elsewhere.
Binding for O2 is cooperative, meaning that when one oxygen molecule binds, the
other subunits conformations change, increasing their affinities for oxygen.
As we have seen, high amounts of carbon dioxide lowers the pH of its surroundings by
reacting with water to form carbonic acid. Low pH decreases the affinity of hemoglobin
for oxygen, an affect called the Bohr shift. This is to facilitate hemoglobin to release
oxygen to offset the increased carbon dioxide concentrations.
2,3-diphosphoglycerate (2,3-DPG) is produced from an intermediate compound in
glycolysis and decreases the affinity of hemoglobin for oxygen.
Produced when there are low oxygen levels so that hemoglobin can be stimulated to
release its bound oxygen molecules.
During high levels of oxygen, oxyhemoglobin inhibits the enzyme that synthesizes
2,3-DPG.
Chloride shift: carbonic anhydrase is in red blood cells so charge must be maintained
when bicarbonate ions (negative charge) leaves the cell. When bicarbonate diffuses out
into the plasma, chloride anions enter.
Haldane effect: Deoxygenation of the blood increases hemoglobin's ability to carry carbon
dioxide whereas oxygenated blood decreases hemoglobin's ability to carry carbon dioxide.
CO2 does not dissolve in blood well, so we need to convert it into H2CO3 to increase the
dissolving ability.
At tissues we have high concentrations of carbon dioxide (from respiration). It will

74
diffuse into the blood cell, where carbonic anhdyrase will turn it into H2CO3, which
then becomes bicarbonate and H+. This explains why high [CO2] lead sot low pH.
At the lungs, CO2 wants to leave the blood and into the alveoli while oxygen wants to
leave the alveoli and into the blood cells. However, the CO2 is in the bicarbonate form,
so it will have to re-enter the RBC where the carbonic anhydrase will reverse the
reaction and turn it back into CO2. It will then diffuse out of the lungs.
Consider hemoglobin: hemoglobin is going to interact with H+ (Bohr shift) to form an
alternative version of hemoglobin that doesn't bind to oxygen as well and therefore will
end up binding to CO2 instead. So in the presence of high [CO2] and [H+], the
hemoglobin structure is altered to the alternative form that will release oxygen and will
bind to CO2.
Bigger picture: tissues are high [CO2] and [H+] and they are not getting a lot of oxygen
so we want to oxygenate them. When hemoglobin arrives at these tissues, the low pH
causes Bohr shift which stimulates the hemoglobin to release its oxygen molecules to
the tissues and will stimulate the hemoglobin to attach to CO2 molecules. When
Hemoglobin binds to CO2, it prevents the CO2 from forming carbonic acid. In this
sense, hemoglobin is acting as a buffer by binding to CO2 molecules to prevent more
CO2 molecules from turning into carbonic acid and decreasing the pH. At the lungs,
carbonic acid will be re-converted back into CO2. This will raise the pH and cause the
hemoglobin molecule to return back to its normal form with higher affinities for oxygen.
CO2 leaves to the alveoli while oxygen diffuses in and becomes bound to the
hemoglobin.

Factors that affect dissociation curve of hemoglobin:

75
the dissociation curve of hemoglobin is sigmodial.
Curve is shift right (oxygen is released easier, lower oxygen affinity) increase of CO2
pressure, H+ concentrations, temperature, and exercise. CADET face right!
Myoglobin is the oxygen binding pigment in muscles.
It has a hyperbolic dissociation curve.
No cooperative binding
single subunit
Saturates very quickly and releases in very low oxygen emergency muscle situations
Fetal hemoglobin has a dissociation curve shifted to the left compared to an adult.
By shifting the curve to the left, the fetal hemoglobin has a higher binding affinity to
grab oxygen from maternal blood.

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Sensory receptors
Types
Mechanoreceptors sense physical deformation caused by forms of mechanical energy such
as pressure, touch, stretch, motion and sound.
Chemoreceptors include both general receptors, those that transmit information about total
solute concentration and specific receptors, those that respond to individual kinds of
molecules (Taste and smell).
Electromagnetic receptors detect forms of electromagnetic energy such as light, electricity,
and magnetism.
Thermoreceptors detect heat and cold.
Nociceptors detect pain.
Important information
Sensory receptors respond strongly to own stimuli and weakly to others.
The neural pathways separate for each type of receptor and all terminate somewhere in the
CNS.
The Eye
Pathway of light stimuli
Cornea (focuses light) pupil (controls amount of light that enters the eye; diameter
controlled by iris) lens (focuses image; controlled by cilliary muscles) Retina
(location of rods and cones).
Cones detect high-intensity illumination and are sensitive to color.
Rods detect low intensity illumination, are important in night vision, and do not detect
color.
Rod pigment rhodopsin is struck by photons from light, causing hyperpolarization
transduction into neural action potential sent to brain.
Photoreceptor cells synapse to bipolar cells ganglion cells axons of ganglion
cells bundle to optic nerve.
Point at which optic nerve exits is called the blind spot (no photoreceptors here)
Eye has virtrous and aqueous humor:
Virtrous humor is the clear gel that fills the space between the lens and retina of the
eyeball. It is jelly like, maintains eye shape and optical properties.
Aqueous humor is the thin, watery fluid that fills the space between the cornea and the
iris. This fluid nourishes the cornea and the lens and give the eye its shape. \

77

Eye disorders
Myopia nearsightedness
Hyperopia farsightedness
Astigmatism irregularly shaped cones. Causes blurred vision at any distance.
Cataracts lens becomes opaque and light cannot enter
Glaucoma increase in pressure of eye due to blocking of outflow of aqueous humor.
Causes blurred vision, distorted vision, or vision loss.

The ear
Structure
The Ear transduces sound energy into impulses.
Outer ear auricle/pinna (what we think of as the ear) and the auditory canal; direct
sound into external auditory canal
Middle ear amplifies sound; tympanic membrane (eardrum) begins the middle ear and
vibrates at the same frequency as incoming sound ossicles: malleus, incus, and stapes
(transmit sounds from the air to the cochlea)
Inner eat wave moves through the cochlea as the vibration of ossicles exert pressure on
fluid. As waves move through the ear the pressure alternates, moving the vestibular
membrane in and out; this movement is detected by hair cells (sensory receptors of the
ear) that are located in the organ of Corti transduced neural signal action potential
The inner ear also has semicircular canals that are responsible for balance (fluid + hair
cells sense orientation + motion)

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DAT destroyer info

upon stressing a bone, bone forming cells called osteoblasts deposit collagen and release
calcium phosphate to strengthen the bone. The mineral hydroxyapetite is produced.
During osteoporosis, bones become fragile and more likely to fracture. Estrogen can help
maintain bone density. Prevention of osteoporosis includes calcium and vitamin D.
bone growth occurs at the epiphyseal plates of long bones
ACL ligament limits rotational knee movement and connects femur and tibia
Invertebrate sekeletons
Arthorpods have an exoskeleton composed of hart chitin. Chitin helps necessitate molting
for growth.
Vertebrate sekeleton
vertical column: cervical, thoracic, lumbar, sacrum, coccyx
upper limbs: humerous, radius, ulna, carpal, metacarpal
lower limbs: femur, tibia, fibula patella, tarsal, metatarsal
Cartillage avascular connective tissue (supplied with nutrients via diffusion) and it is
softer and more flexible.
Made up of specialized cells called chondrocytes that produce a ground substance
(supports the cells and fibers and helps determine the consistency of the ECM).
Made up of mostly collagen
Found on the ear, nose, larynx, trachea, and joints
In fetal development, the greater part of the skeleton is cartilaginous. The cartilage is
replaced by bone, a process that ends at puberty.
3 types (differ in the amount of cartillage):
hyaline is most common reduced friction/absorbs shock in joints
fibrocartilage
elastic
How cartilage is made (chondrogenesis):
1) Condensed mesenchyme tissue differentiates into chondroblasts
2) Chondroblasts secrete collagen, hydroxylysine, ground substance, and elastin
fiber. Chondroblasts that get trapped in the ECM are called chondrocytes.
Bone is connective tissue that is hard and strong, while elastic and lightweight.
Functions: supports soft tissue, protects internal organs, assists in body movement,
stores minerals (mainly calcium), produces blood cells, and stores energy in the form of
adipose cells in bone marrow.
Contains blood and nerves.
4 different types of cells:
Osteoprogenitor/Ostreogenic cells differentiate into osteoblasts
Osteoblasts (Bone Building) secrete collagen and organic compounds upon which
bone is formed.
Incapable of mitosis
As matrix is released around them, they are enveloped by the matrix and
differentiate into osteocytes.
Osteocytes are incapable of mitosis and exchange nutrients and waste material with
the blood.
Osteoclasts reabsorb (destroy) bone matrix, releasing minerals back into the blood.
Develop from monocytes.
Structure:
Areas of the bone:

79
The epipheysis is the is one of the rounded ends of the long bones of the body
which makes up a joint.
Metaphysis is the area of the bone which grows during childhood
Below the metaphysis is the diaphysis, or the shaft of the bone, which makes up
the main section of the bone.

Compact bone is highly organized, dense bone that doesn't appear to have cavities
from the outside.
Osteoclasts burrow tunnels called Haversian canals throughout. They contain
blood and lymph vessels and are connected by Volkmann's canals.
Osteoclasts are followed by osteoblasts, which lay down new matrix onto tunnel
walls, forming concentric rings called lamellae.
Osteocytes traped between the lamella in spaces called lacunae exchange
nutrients via canaliculi, small canals between the lacunae of bone.
An entire system of haversian canals and lamellae is called an osteon, or a
Haversian system.
Also filled with yellow bone marrow that contains adipose cells for fat storage.

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Spongy (cancellous) bone is less dense and consists of an interconnecting lattice of

bony spicules called trabeculae. Filled with red bone marrow, which is the site of
RBC development.
Bone growth occurs at cartilaginous epiphyseal plates (occurs at the metaphysis)
that are replaced by bone in adulthood. Bone increases in length but also in diameter
along the diaphysis as well. When a person reaches full maturity, the new bone
slowly hardens and the plate turns into the epiphyseal line
Most of the Ca2+ in body is stored in bone matrix as hydroxyapatite.

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Bones can be made from a combination of compact and spongy bone.

Bone formation occurs during the fetal stage of development in a developing human.
Endochondral ossification is when existing cartilage is replaced by bone (long
bones, limbs, fingers, toes)
Intramembranous ossification is when undifferentiated connective tissue is
replaced by bone (flat bones, skull, sternum, mandible, clavicles)

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A. Monosaccharides and Disaccharides )
I. The two families of monosaccharides are aldoses and ketoses
a. The backbones of common monosaccharides are unbranched carbon chains in which all
the carbon atoms are linked by single bonds. In this form, one of the carbon atoms is
double-bonded to an oxygen atom to form a carbonyl groups; each of the other carbon
atoms has a hydroxyl group.
i. If the carbonyl group is at the end of a carbon chain, the monosaccharide is an
aldose (aldehyde).
ii. If the carbonyl group is at any other position, the monosaccharide is a ketose
(ketone).

II. Monosaccharides have asymmetric centers

a. All of the monosaccharides contain one or more chiral carbon atoms.
b. D/L configuration is based on the chiral center most distant from the carbonyl carbon.
Those with the OH on the left is the L-stereoisomer and those with the OH on the right
is the D-stereoisomer. (The molecules shown above are both D-stereoisomers)
c. Two sugars that differ only in the configuration around one carbon atom are called
epimers. Note that the carbon that differs among the two molecules is NOT the
anomeric carbon.
III. The common monosaccharides have cyclic structures
a. In aqueous solution, all monosaccharides with five or more carbon atoms in the
backbone occur predominantly as cyclic structures in which the carbonyl group has
formed a covalent bond with the oxygen of a hydroxyl group along the chain.
b. The formation of these ring compounds is the result of a general reaction between
alcohols and aldehydes or ketones to form derivatives called hemiacitals or hemiketals.
i. hemi meaning that the alcohol and the aldehyde or ketone are all in the same
molecule.
c. The reaction with the first molecule of alcohol creates an additional chiral center (the
carbonyl carbon). The alcohol can add in either one of two ways, attacking either the
front or the back of the carbonyl carbon, meaning that two stereoisomeric
configurations (denoted alpha and beta) can be produced.
d. Isomeric forms of monosaccharides that differ only in their configuration about the
hemiacital or hemiketal carbon are called anomers, and the carbonyl carbon is called
the anomeric carbon.
i. If an anomeric carbon has an -OH on it, it is a reducing carbon. If the anomeric
carbon has an -OR attached to it, then it is non-reducing.
e. Six-membered ring compounds are called pyranoses (formed from aldohexoses) and 5membered ring compounds are called furanoses (formed from aldopentoses and
ketohexoses).

83
IV.Disaccharides contain a glycosidic bond
a. Disaccharides consist of two monosaccharides joined covalently by an O-glycosidic
bond, which is formed when a hydroxyl group of one sugar molecule reacts with the
anomeric carbon of the other.
i. This reaction represents the formation of an acetal from a hemiacetal and an alcohol,
and the resulting compound is a glycoside.

B. Polysaccharides
I. Introduction
a. Polysaccharides, also called glycans, differ from each other in the identity of their
recurring monosaccharide units, in length of their chains, in the types of bonds linking
the units, and in the degree of branching.
i. Homopolysaccharides contain only a single monomeric species.
ii. Heteropolysaccharides contain two or more different kinds.
b. Polysaccharides do not have defining molecular weights.
II. Some homopolysaccharides are stored forms of fuel
a. Starch in plant cells and glycogen in animal cells are the most important storage
polysaccharides.
i. They are both heavily hydrated, because they have many exposed OH groups
available to hydrogen-bond with water.
b. Starch contains two types of glucose polymer, amylose and amylopectin.
i. Amylose consists of long, unbranched chains of D-glucose residues connected by
alpha14 linkages.
ii. Amylopectin consists of highly branched chains (branch points occurring every 24
to 30 residues). The glucose residues are connected by alpha14 linkages and the
branch points are connected by alpha16 linkages.
c. Glycogen is the main storage polysaccharide of animal cells. Glycogen is a polymer of
alpha14 linked subunits of glucose, with alpha16 linked branches, but glycogen is
more extensively branched (every 8-12 residues) and more compact than starch.
i. A glycogen molecule with n branches has n+1 nonreducing ends, but only one
reudcing end.
ii. When glycogen is used as an energy source, glucose units are removed one at a time
from the nonreducing ends.
iii. Reacts positively with iodine to turn purple.
III. Some homopolysaccharides serve structural roles
a. Cellulose is a fibrous, tough, water-insoluble substance, found in the cell walls of

84
plants.
i. It is a linear, unbranched homopolysaccharide. All the glucose residues have a beta
configuration.
ii. Each monomer is turned 180 degrees around the glycosidic bond; this gives the
polymer a linear, extended chain.
iii. Cellulose contains many intrachain and interchain hydrogen bonds, but no interchain
covalent bonds.
iv. The supermoleuclar structure has high tensile strength and low water content (no
place for water hydogen bonds)
b. Chitin is a lnear homopolysaccharide composed of N-acetylglucosamine residues in a
(beta14) linkage.
i. The only chemical difference from cellulose is the replacement of the hydroxyl
group C-2 with an acetylated amino group.
ii. It is the principal component of the hard exoskeletons of arthropods.
IV.Bacterial and algal cell walls contain structural heteropolysaccharides
a. The rigid component of bacterial cell walls, peptidoglycan, is a heteropolymer of
alternating beta14 linked N-acetylglucosamine and N-acetylmuramic acid residues.
i. The linear polymers lie side by side in the cell wall, cross-linked by short peptides,
the exact structure depends on species.
ii. Penicillin and related antibiotics kill bacteria by preventing synthesis of the cross
links, leaving the cell wall to weak to resist osmotic lysis.
V. Glycosaminoglycans are heteropolysaccharides of the extracellular matrix
a. The extracellular space in the tissues of multicellular animals is filled with a gel-like
material, the extracellular matric (ECM), which holds cells together and provides a
porous pathway for the diffusion of nutrients and oxygen to individual cells.
i. The ECM is composed of an interlocking network of heteropolysaccharides and
fibrous proteins. These heteropolysaccharides are called glycosaminoglycans
(GAG); they are unique to animals and are not found in plants.
C. Glycoconjugates: Proteoglycans, Glycoproteins, and Glycophingolipids
I. Types of glycoconjugates
a. A glycoconjugate is a carbohydrate covalently joined to a protein or a lipid (these
molecules are biologically active).
b. Proteoglycans are macromolecules of the cell surface or ECM where one or more
sulfated GAG chains are joined covalently to a membrane protein or a secreted protein.
i. They bind to ECM proteins through electrostatic interactions (GAGs are very
negative).
c. Glycoproteins have one or more several oligosaccharides of varying complexity joined
covalently to a protein. They are usually found on the outer face of the plasma
membrane.
d. Glycosphingolipids are plasma membrane components in which the hydrophilic head
groups are oligosaccharides.
II. Proteoglycans are glycoasminoglcyancontaining macromoleucles of the cell surface and
ECM
a. Some proteoglycans can form proteoglycan aggregates, enormous supramolecular
assemblies of many core proteins bound to a single moleucle of hyaluronan.

85

4 main phases of the cell cycle

G1 = growth and preparation of chromosomes for replication (2n). Longest phase
S = synthesis of DNA (DNA replication) a duplication of the centrosome (2 x 2n)
G2 = preparation for mitosis (2x2n)
M = mitosis/meiosis (2x2n 2n if mitosis. 2X2n n if meiosis). Around 10% of cycle.

G0 phase
Many times a cell will leave the cell cycle, temporarily or permanently.
It exits at the G1 and enters a stage called G0. They are busy carrying out their other
functions (secretion, attacking pathogens, etc.).
Checkpoints: quality control of the cell cycle
G1 checkpoint is the most important checkpoint. At the end of G1 phase, if the cell is not
ready to divide, the next phase will be temporarily suspended. The cell could possibly arrest
in the G0 phase and never proceed, or wait until it is ready. When the cell is ready to divide,
it will move on to the S phase.
G2 Checkpoint is at the end of G2 phase. It evaluates the accuracy of DNA replication and
determines whether the cell is ready to begin mitosis.
M checkpoint is at the end of metaphase. It checks to see if the microtubules are properly
attached to kinetochores. If not, anaphase is suspended.

86

Other features of cell cycle control

Growth factors attach to plasma membrane receptors. They stimulate the cell for division.
Density-dependent inhibition: Cells stop dividing when the surrounding density becomes
too high.
Anchorage dependence: Most cells only divide when they are attached to an external
surface such as a neighboring cell.
Cyclin dependent kinases (CDKs) are enzymes that activate proteins that regulate the cell
cycle via phosphorylation. CDKs are activated by the protein cyclin.

87

Alternation of generations
In most plants, meiosis and fertilization divide the life of an organism into two distinct
phases or generations.
The gametophyte generation begins with a spore produced by meiosis. The spore is
haploid, and all the cells derived from it (by mitosis) are also haploid. In due course, this
multicellular structure produces gametesby mitosisand sexual reproduction then
produces the sporophyte generation.
The sporophyte generation begins with a zygote. Cells contain diploid number of
chromosomes. Cells will divide and grow. Eventually through, certain cells will undergo
mitsosi, forming spores and starting a new gametophyte generation.
The gametophyte is an inconspicuous structure in angiospersm and other higher plants.

88

Cancer
Cancer refers to uncontrollable cell division as a result of cell cycle regulatory mechanisms
become inactive.
A cancerous cell will exhibit defective cell differentiation.
a cancerous cell known as myeloma may be cultured indefinitely
a lymphocyte may be fused with myeloma cell to produce a hybridoma
sarcoma only occurs in connective tissue
carcinoma occurs in epithelial tissue

89

5 common features of signal transducing systems

Specificity: signal molecule fits binding site on its own complementary receptor; other
signals do not fit. Particular receptor in a cell may listen to one signal but not the other. In
addition, the receptor may not be present in every cell so a cell may not be able to listen to
a certain signal. A signal will not be heard in each and every cell type.
Amplification: when enzymes activate systems, the number of affected molecules increases
geometrically in an enzyme cascade. A single signaling molecule can activate a large
number of target molecules.
Modularity: proteins with multivalent affinities from diverse signaling complex form
interchangeable parts. Phosphorylation provides reversible proteins of interaction.
Adaptation/desensitization: Receptor activation triggers a feedback circuit that shuts off
the receptor or moves it from the cell surface.
Integration: when two signals have opposite effects on a metabolic characteristic, the
regulatory outcomes results from the integrated input of both receptors. Integrated means at
some point, both receptor pathways will converge on the same molecule and will cause a
common response.
Signal transduction generalizations
Signal transduction pathways have unique features:
differ between cell types, even closely related ones
they change with cellular and environmental conditions
Gated ion channels
generally found in excitable cells
Usually move ions by facilitated diffusion very quickly (these channels cannot be saturated)
Gated ion channels are one of two signaling systems which actually move molecules
through the membrane
The membrane has a very asymmetric ion distribution (creates membrane potential)
Sodium-potassium pump
energy source: ATP hydrolysis
3 Na+ leaves, 2 K+ comes in (moves one positive charge to the outside)
Generates a membrane potential (electrochemical gradient)

90

Membrane potential definitions

polarization: a difference in charge across a membrane, results in a positive or negative Vm
depolarization: a decrease in the absolute value of Vm (membrane potential moves closer
to 0)
hyperpolarization: an increase in absolute value of Vm (membrane potential moves farther
from 0)
Three types of cell signals
Paracrine signals: A secreting cell acts on nearby target cells by secreting molecules of a
local regulator.
Synaptic signaling: A nerve cell releases neurotransmitter molecules into a synapse,
stimulating the target cell.
Endocrine (hormonal) signaling: specialized endocrine cells secretes hormones into body
fluids. Hormones reach virtually all body cells.
G protein-coupled receptors
A G protein-coupled receptor is a cell-surface trans membrane receptor that works with
the help of a G protein, a protein that binds the energy-rich molecule GTP. When GDP is
bound to the protein, the protein is inactive. When GTP is bound to the protein, the protein
becomes active.
Step 1: When the appropriate signaling molecule binds to the extracellular side of the
receptor, the receptor is activated and changes shape. Its cytoplasmic side binds an
inactive G protein, causing a GTP to displace the GDP. This activates the G protein.
Step 2: The activated G protein dissociates from the receptor, diffuses along the
membrane, and then binds to the enzyme, altering the enzyme's conformation. Once
activated, the enzyme can trigger the next step leading to a cellular response. (Binding is
reversible).
Step 3: The changes in the enzyme and G protein are only temporary because the G
protein also functions as a GTPase enzymeit then hydrolyzes GTP to GDP and Pi. It
now is available for reuse.

91

Receptor tyrosine kinases

Receptor tyrosine kinases catalyzes the transfer of phosphate groups from ATP to the
amino acid tyrosine on a substrate proteins.
Step 1: before the signaling molecule binds, the receptors exist as individual units refer
to as monomers.
Step 2: the binding of a signaling molecule causes two receptor monomers to associate
closely with each other, forming a complex known as a dimer.
Step 3: Dimerization activates the tyrosine kinase region of each monomer; each
tyrosine adds a phosphate from an ATP molecule to a tyrosine on the tail of the other
monomer.
Step 4: Now that the receptor is fully activated, it is recognized by specific relay
proteins inside the cell. Each protein binds to a specific phosphorylated tyrosine, thus
activating the protein. Each activated protein triggers a transduction pathway, leading to
a cellular response.

92

Ligand-gated ion channel

Ligand-gated ion channel is a type of membrane receptor containing a region that can act
as gate when the receptor changes shape.
Step 1: Ligand-gated ion channel receptor remains closed until a ligand binds to the
receptor.
Step 2: when the ligand binds to the receptor and the gate opens, specific ions flow
through the channel and rapidly change the electrochemical gradient of the cell.
Step 3: when the ligand dissociates from the receptor, the gate closes and ions no longer
enter the cell.

Steroid hormones
Steroid hormones are nonpolar: they can diffuse through the plasma membrane without a
problem. They have a different pathway than other ligands:
Step 1: hormone diffuses into the cell through the plasma membrane
Step 2: hormone binds to an intracellular receptor in the cytoplasm or nucleus. This
binding activates the protein.
Step 3: the bound protein acts as a transcription factor, stimulating the transcription of
the gene into mRNA

93

cyclic AMP and second messengers

Second messengers are small, non-protein, water-soluble molecules that act in a signal
transduction pathway.
Binding of epinephrine to the plasma membrane elevates the cytosolic concentration of
cyclic AMP (cAMP).
A membrane-bound enzyme called adenylyl cyclase, converts ATP to cAMP in response to
an extracellular-signal.
Phosphodiesterase is the enzyme that breaks down cAMP.
The effect of increased cAMP levels is the activation of protein kinase A.
IP3 and Ca2+ pathway
Step 1: signaling molecule binds to a receptor, leading to activation of phospholipase C
Step 2: Phospholipase C cleaves a plasma membrane phospholipid called PIP2 into DAG
(diacylglycerol) and IP3 (inositol triphoshoate). /DAG functions as a 2nd messenger in other
pathways.
Step 3: IP3 quickly diffuses through the cytosol and binds to an IP3-gated calcium channel
in the ER membrane, causing it to open.
Step 4: Calcium flows out of the ER (down the concentration gradient), raising cytosolic
Ca2+ levels.
Step 5: The calcium ions activate the next protein in one or more signaling pathways.

94

95

Studying cells
Stereomicroscope: Uses visible light to view surface of sample, but only at low resolutions.
Compound microscope: Uses visible light to view a thin section of sample. May require
staining for increased viability.
Phase-contrast: Uses light phases and contrast to allow for detailed observation of living
organisms if thin.
Confocal laser scanning + fluorescence: Can look at thin slices while keeping sample
intact; can look at specific parts of cell via fluorescent tagging. Can look at living cells, but
only fluorescently tagged parts. Used to observe chromosomes during mitosis.
Scanning elctron microscope (SEM): Look at surface of (3D) objects with high resolution.
Cant use on living specimens as sample needs to be dried and coated.
CryoSEM: Like SEM but no dehydration so you can look at samples in more natural
form. Cant use on living samples.
Transmission electron microscope (TEM): look at very thin cross-sections in high detail.
Can look at internal structures, very high resolution, but cant be used on living things.
Electron tomography: 3D-Electron tomography: 3D model buildup using TEM data.
Cell fractionalization (centrifugion): cells whose membranes have been centrifuged at
various speeds for varying lengths to separate components of different sizes, densities, and
shapes. Due to differences in density.
Fastest to pellet out = nucleus
then mitochondria, chloroplats, lysosomes, peroxisomes
then ER, vesicles
then ribosomes, viruses, larger macromolecules

Freeze fracture: split lipid bilayer of a frozen specimen. Used to study cell membranes and

96
organelles.
Gram straining: common technique used to distinguish gram positive from gram negative
bacteria.
Gram positive bacteria strain violet due to the presence of a thick layer of
peptidoglycan.
Gram negative bacteria strain red because of the thinner peptidoglycan wall.

97

Facilitated diffusion
Diffusion is the spontaneous movement of particles from an area of high concentration to
low concentration.
Diffusion can also occur if there is a difference in charge between two different areas
this is called an electrochemical gradient.
Facilitated diffusion is the process of moving polar, large, and ionic molecules through the
plasma membrane via protein channels.
Can be done without the input of energy passive diffusion. Molecules can only move
in the direction of the concentration gradient.
Can be done with input of energy (coupled with ATP hydrolysis) active diffusion.
Molecules can move against the concentration gradient.

Cotransport
A cotransport protein can couple the downhill diffusion of a solute to the uphill
transport of a second substance against its own concentration gradient.
Osmosis
Osmosis is the spontaneous movement of water from areas of low osmolarity to high
osmolarity.
Osmolarity is defined as the total amount of solutes in moles divided by liters of solution.
Tonicity is the ability of a surrounding solution to cause a cell to gain or lose water.
Depends on solute concentration and membrane permeability.
In an isotonic enviornment, the external osmolarity is equal to the internal osmolarity of
the cell. There will be no net movement of water across the plasma membrane. Volume of
the cell is stable.
In a hypertonic environment, the external osmolarity is greater than the internal osmolarity
of the cell. There will be a net movement of water out of the cell. The cell may shrivel up an
die.
In a hypotonic environment, the external osmolrity is lower than the internal osmolarity of
the cell. There will be a net movement of water into the cell. The shell may get too big and
lyse.
Plant cells have a cell wall, so that changes how the cell responds to changes in osmolarity.
When in a hypotonic solution, the cell becomes turgid (normal state).

98
When in an isotonic solution, the cell becomes flaccid.
When in a hypertonic solution, the cell becomes plasmolyzed.

Types of transport molecules

Uniport transports one solute at a time.
Co-transport involves moving two different molecules.
Symport transports the solute and another molecule in the same direction at the same time.
Antiport transports the solute and another moelcule in different directions at the same time.

99

Endocytosis
In endocytosis, the cell enguls some of its extracellular fluid including material dissolved or
suspended in it. A portion of the plasma membrane is invaginated and pinched off forming a
membrane-bounded vesicle called an endosome.
Clathrin participates in endocytosis by forming a polyhedral lattice around coated pits.
Three types: phagocytosis, pintocytosis, and receptor mediated endocytosis
Receptor mediated endocytosis
Receptor mediated endocytosis is an endocytotic mechanism in which specific molecules
are ingested into the cell. The specificity results from a receptor-ligand interaction.
Receptors on the plasma membrane of the target tissue will specifically bind to ligands on
the outside of the cell. An endocytotic process occurs and the ligand is ingested.
Phagocytosis
Phagocytosis results in the ingestion of living matter (i.e. bacteria) from the extracellular
fluid. The endosome is called a phagosome.
Occurs in certain specialized cells such as neutrophils, macrophages, amoeba, etc.
Happens sporadically.
Pintocytosis
Pintocytosis, cell drinking, is a mode of endocytosis in which small particles are brought
into the cell, forming an invagination, and then suspended within small vesicles.
Primarily used for absorption of extracellular fluids.

Exocytosis
Exocytosis is the energy-consuming process by which a cell directs the contents of
secretory vesicles out of the cell membrane and into the extracellular space.

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Autophagy
Autophagy is a normal physiological process in the body that deals with destruction of cells
in the body.
It maintains homeostasis or normal functioning by protein degradation and turnover of the
destroyed cell organelles for new cell formation.
During cellular stress the process of Autophagy is upscaled and increased. Cellular stress is
caused when there is deprivation of nutrients and/or growth factors.
Thus Autophagy may provide an alternate source of intracellular building blocks and

substrates that may generate energy to enable continuous cell survival.

Intracellular circulation
Brownian movement is the movement due to the kinetic energy of particles. It causes
spreading of particles throughout the cytoplasm.
Cyclosis (cytoplasmic streaming) is the circular motion of cytoplasm around cell transport

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molecules. Active process that requires ATP.
Endoplasmic Reticulum provides a direct continuous channel from the plasma membrane
to the nuclear membrane.

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Metabolic pathways in eukaryotic cells occur in specific compartments

reason behind this is that different metabolites can operate in different locations and in
different pathways
in eukaryotic cells:
mitochondrion: citric acid cycle, electron transport oxidative phosphorylation, fatty
acid oxidation, amino acid breakdown
cytosol: glycolysis, pentose phosphate pathway, fatty acid biosynthesis, gluconeogenesis
rough ER: protein synthesis
smooth ER: lipid and steroid biosynthesis
central importance of glucose
glucose is an excellent fuel
yields good amount of energy upon oxidation
can be sufficiently stored in polymeric form (starch, glycogen)
many organisms and tissues can meet their energy needs on glucose only
glucose is a versatile biochemical precursor
Four major pathways of glucose utilization
(1) storage
can be stored in the polymeric form (starch, glycogen)
when there is plenty of excess energy
(2) glycolysis
generates energy via oxidation of glucose
short-term energy needs
(3) pentose phosphate pathway
generates NDAPH via oxidation of glucose
for detoxification and the bio synthesis of lipids and nucleotides
(4) synthesis of structural polysaccharides
Glycolysis: overview
in the evolution of life, glycolysis probably was one of the earliest energy-yielding pathways
it was developed before photosynthesis, when the atmosphere was still anaerobic.
It is the anaerobic conversion of glucose into pyruvate by a sequence of enzyme-catalyzed
reactions
pyruvate can be further aerobically oxidized
pyruvate can be used as a precursor in biosynthesis
STEP 1: Phosphorylation of Glucose
Glucose + ATP Glucose-6-phosphate
nucleophilic oxygen at C6 of glucose attacks the last (gamma) phosphate of ATP
uses up the energy of ATP
hexokinase in eukaryotes, and glucokinase in prokaryotes
hexokinase = induced fit (binding of glucose and Mg*ATP induces a large conformational
change which brings the active site residues together)
Rationale:
traps glucose inside the cell (adding phosphate gives molecule negative charge)
lowers intracellular glucose concentration to allow further uptake of glucose
ATP-bound Mg2+ facilitates this process by shielding the negative charges on ATP
highly thermodynamically favorable/irreversible (regulated by substrate inhibition)
STEP 2: phosphohexose isomerization
Glucose-6-phosphate Fructose-6-phosphate
catalyzed by phosphohexose isomerase

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Rationale:
C1 of fructose is easier to phosphorylate by PFK
Allows for symmetrical cleavage by aldolase
Converts the aldose glucose into the ketose fructose
Slightly thermodynamically unfavorable/reversible
product concentration kept low to drive forward
STEP 3: 2nd priming phosphorylation
Fructose 6-phosphate + ATP Fructose 1,6-biphosphate
catalyzed by phosphofructokinase-1 (PFK-1)
Rationale:
further activation of glucose
allows for 1 phosphate/3-carbon sugar after step 4
First commited step of glycolysis
fructose 1,6-biphosphate is comitted to become pyruvate and yield energy
this process uses the energy of ATP
highly thermodynamically favorable/irreversible
phosphofructokinase-1 is highly regulated
STEP 4: Aldol Cleavage of F-1,6-bP
Fructose 1,6-biphosphate dihydorxyacetone phosphate (DHAP)+ glyceraldehyde 3phosphate (GAP)
catalyzed by aldolase
Rationale:
cleavage of a six-carbon sugar into two three-carbon sugars
high-energy phosphate sugars are three-carbon sugars
cleave of Frc 1,6-bisP is highly unfavorable under standard conditions, but only slightly under
physiological conditions
GAP (glyceraldehyde 3-phosphate) concentration is kept low to pull reaction forward
STEP 5: triose phosphate interconversion
dihydroxyacetone phosphate glyceraldehyde 3-phosphate
catalyzed by: triose phosphate isomerase
rationale:
allows glycolysis to proceed by one pathway
GAP is the substrate for the next enzyme, so DHAP must be converted to GAP
thermodynaically unfavorable/reversible
GAP concentration kept low to pull reaction forward
****NOTE steps 6-10 happen twice since 2 GAP molecules are generated*********
STEP 6: Oxidation of GAP
glyceraldehyde 3-phosphate + Pi + NAD+ 1,3-bisphosphoglycerate + NADH + H+
catalyzed by: glyceraldehyde 3-phosphate dehydrogenase (GAPDH)
rationale:
generation of a high-energy phosphate compound
incorporates Pi which allows for net production of ATP via glycolysis
first energy-yielding step in glycolysis (forms NADH)
thermodynamically unfavorable/reversible
coupled to next reaction to pull forward

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STEP 7: 1st production of ATP

1,3-bisphosphoglycerate + ADP ATP + 3-phosphoglycerate
catalyzed by phosphoglycerate kinase
Rationale: substrate-level phosphorylation to make ATP
catalyzed by phosphoglycerate kinase (kinases transfer phosphate groups from ATP to various
substrates)
1,3-bisphosphoglycerate is a high energy compound. It can donate the phosphate group to ADP
to make ATP
Highly thermodnamically favorable/reversible
Is reversible because of coupling to GAPDH reaction
STEP 8: Migration of the phosphate
3-phosphoglycerate 2-phosphoglycerate
catalyzed by phosphoglycerate mutase (mutases catalyze migration of functional groups)
rationale: be able to form high-energy phosphate compound
thermodynamically unfavorable/reversible
reactant concentration kept high by PGK to push forward
STEP 9: dehydration of 2-PG to PEP
2-phosphoglycerate phosphoenolpyruvate + H2O
catalyzed by enolase
rationale: generate a high-energate phosphate compound
2-phosphoaglycerate is not a good enough phosphate donor this is why step 8 happens
slightly thermodynamically unfavorable/reversible
product concentration kept low to pull forward
STEP 10: phosphotransfer from PEP
phosphoenolpyruvate + ADP pyruvate + ATP
catalyzed by pyruvate kinase (requires divalent metals for activity)
second substrate level phosphorylation: generates another ATP molecule
rationale:
substrate-level phosphorylation to make ATP
produces 2 ATP
Loss of phosphate from PEP yields an enol that tautomerizes into ketone
Tautomerization:
effectively lowers the concentration of the reaction product
drives the reaction toward ATP formation
highly thermodynamically favorable/irreversible
Balanced equation of glycolysis
C6H12O6 + 2 ADP + 2 Pi + 2NAD+ 2 pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H2O
Pyruvate has 3 fates:
TCA cycle (oxygen is present)
2) lactic acid fermentation (no oxygen is present)
pyruvate + NADH + H+ l-lactate + NAD+
rationale: NAD+ is regenerated by transferring e- to pyruvate and reducing it to lactate. By
regenerating NAD+, it can be re-used in glycolysis.
Done in humans (muscles)
lactate builds up in muscle during strenuous exercise the acidification of muscle prevents

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its continuous strenuous work
the lactate can be transported to the liver and converted back to glucose (cori cycle)
ethanol fermentation (no oxygen is present)
Done in yeast
rationale: NAD+ is regenerated by transferring e- to acetaldehyde and reducing it to ethanol.
By regenerating NAD+, it can be re-used in glycolysis.
Pyruvate acetyldehyde + CO2
catalyzed by pyruvate decarboxylase
Acetaldehyde + NADH + H+ ethanol + NAD+
catalyzed by alcohol dehydrodgenase
two-step reduction of pyruvate to ethanol, irreversible
Note that acetaldehyde is the final electron acceptor
humans do not have pyruvate dehydrogenase for ethanol metabolism
CO2 is responsible for carbonation in beer, rising in bread

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Mitosis
Karyokinesis is nuclear division (occurs first)
Cytokinesis is cell division (occurs second)
G2 of interphase
Nuclear envelope encloses the nucleus
The nucleus contains DNA
Two centrosomes have formed by duplication of a single centrosome. Centrosomes are
regions in the animal cells that organize the microtubule of the spindle. Each centrosome
contains two centrioles.
Prophase
chromatin fibers become more tightly coiled, condensing into discrete chromosomes
Each duplicated chromosome appears as two identical sister chromatids joined at their
centromeres.
Mitotic spindle begins to form. It is composed of two centrosomes and the microtubules
that extend from them. The radial arrays of shorter microtubules that extend from the
centrosomes are called asters.
Prometaphase
Nuclear envelop fragments
Microtubules extending from each centrosome can now invade the nuclear area
Each two of the chromatids of each chromosome now has a kinetochore, a specialized
protein structure at the centromere.
Some of the microtubules attach to the kinetochores, which jerk the chromosomes back
and forth.
Nonkinetochore microtubules interact with those from the opposite pole of the spindle.
Metaphase
The centrosomes are now at opposite poles of the cell
The chromosomes have all arrived at the metaphase plate, a plane that is equidistant
between the spindle's two poles. The chromosomes' centromeres lie at the metaphase
plate.
For each chromosome, the kinetochores of the sister chromatids are attached to
kinetochore microtubules coming from opposite poles.
Anaphase
Anaphase is the shortest stage of mitosis.
Begins when the cohesin proteins are cleaved. Allows the sister chromatids of each pair
to part suddenly. Each chromatid becomes a full-fledged chromosome.
The two liberated daughter chromosomes begin moving toward opposite ends of the cell
as their kinetochore microtubules shorten.
By the end of anaphase, the two ends to he cell have equivalentand complete
collections of chromosomes.
Telophase
Two daughter nuclei form in the cell. Nuclear envelops re-arise.
Chromosomes become less condensed.
Mitosis is now complete.
Cytokinesis
Division of the cytoplasm is well under way by late telophase, so the two daughter cells
appear shortly after the end of mitosis.
In animal cells, cytokinesis involves the formation of a cleavage furrow, which pinches
the cell in two.
In plants, a cell plate forms.

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Meiosis
Prophase I
Centromere movement, spindle formation, and nuclear breakdown occur as in mitosis.
Chromosomes condense progressively throughout prophase I
Homologous pairs of chromosomes line up (synapsis), forming tetrads (4 chromatids).
Crossing over occurs between sister chromatids here. Each homologous pair has one or
more X-shaped regions called chiasmata, where crossovers have occurred.
Synaptonemal complex is a protein structure that temporarily forms between
homologous chromosomes. It gives rise to the tetrad with chiasmata and crossing over.
Later in prophase I, microtubules from one pole or the other will attach to the two
kinetochores, one at each centromere.
5 steps:
leptotene chromosomes start condensing
zygotene synapsis begins and the synaptonemal complex begins to form

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pachytene synapsis is complete and crossing over occurs

diplotene synaptonemal complex disappears but the chiasmata still present
diakinesis nuclear envelope fragments, chromosomes complete condensing, and
tetrads are ready for metaphase
Metaphase I
Pairs of homologous chromosomes are now arranged at the metaphase plate, with one
chromosomes in each pair facing each pole.
Both chromatids of one homolog are attached to kintochore microtubules from one pole.
Anaphase I
Breakdown of the proteins that are responsible for sister chromatid cohesion along
chromatid arms.
Homologs move toward opposite poles, guided by the spindle apparatus.
Sister chromatid cohesion persists at the centromere, causing chromatids to move as a
unit toward the same pole.
Telphase I and cytokinesis
When telophase I begins, each half of the cell has a complete haploid set of duplicated
chromosomes. Each chromosome is composed of two sister chromatids; one or both
chromatids chormatids include regions of nonsister chromatid DNA.
Cytokinesis usually occurs simultaneously with telophase I, forming two haploid
daughter cells.
In animal cells, a cleavage furrow forms. In plants, a cell plate forms.
Prophase II
Spindle apparatus forms.
In late prophase II, chromosomes, each still composed of two chromatids, associated at
the centromere, move toward the metaphase II plate.
Metaphase II
Chromosomes are positioned at the metaphase plate as in mitosis.
Anaphase II
Breakdown of proteins holding the sister chromatids together at the centromere allows
the cromatids to separate. The chromatids move toward the opposite poles as individual
chromosomes.
Telophase II and cytokinesis
Nuclei form, the chromosomes begin decondensing and cytokinesis occurs
Meiotic division of parent cell produces 4 daughter cells, each with a haploid set of
chromosomes.
The 4 daughter cells are geneticlaly distinct from one another.
Sources of genetic Variation FROM MEIOSIS
Crossing over during prophse I
Independent assortment of homologues during metaphase 1 (which chromosome goes to
which cell)
Random joining of gametes during fertilizations
Functional limitations of cell cycle
Surface area-to-volume ratio: volume gets much large when cells grow vs SA. When S/V
is large, exchange becomes much easier. When S/V is small, exchange is hard, leads to cell
death, or cell division to increase SA.
Genome-to-volume ratio: genome size remains constant throughout life; as cell grows,

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only volume increases. G/V will be small and thus exceed the ability of its genome to
produce sufficient amounts of regulator of activities. Some large cells are multinucleated to
deal with this.

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112
A. Some basics
I. Introduction
a. A segment of DNA that contains the information required for the synthesis of a
functional biological product, whether protein or RNA, is referred to as a gene.
b. RNAs have a broader range of functions, and several types are found in cells:
i. Ribosomal RNAs are components of ribosomes, the complexes that carry out the
synthesis of proteins.
ii. Messenger RNAs are intermediaries, carrying genetic information from one or a
few genes to a ribosome, where the corresponding proteins are synthesized.
iii. Transfer RNAs are adapter molecules that faithfully translate the information in
mRNA into a specific sequence of amino acids.

II. Nucleotides and nucleic acids have characteristic bases and pentoses
a. Nucleotides have three characteristic components: (1) a nitrogenous base, (2) a pentose,
and (3) one or more phosphates.
i. The molecule without a phosphate group is called a nucleoside.
ii. The nitrogenous bases are derivatives of two parent compounds, pyrimidine and
purine.
b. The base of a nucleotide is joined covalently (at N-1 of pyrimidines and N-9 of purines)
in an N-B-glycosyl bond to the 1' carbon of the pentose, and the phosphate is esterified
to the 5' carbon.
i. N-B-glycosyl bond is formed by the removal of the elements of water (OH from the
pentose and the H from the base).
c. Both DNA and RNA contain two major purine bases, adenine and guanine, and two
major pyrimidines. In both DNA and RNA one of the pyrimidines is cytosine, but the
second common pyrimidine is not the same in both: it is thymine in DNA and uracil in
RNA.

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d. Nucleic acids have two kinds of pentoses.

i. DNA contains 2'-deoxy-D-ribose and RNA contains D-ribose. Both types of
pentoses are in their B-furanose (closed five-membered ring) form.
ii. The pentose ring is not planar but occurs in one of a variety of conformations
generally described as puckered.
e. Deoxyribonucleotides are the structural units of DNA (base + phosphate +
deoxyribose) and ribonucleotides are the structural units of RNA (base + phosphate +
ribose).

III. Phosphodiester bonds link successive nucleotides in nucleic acids

a. Nucleotides in both DNA and RNA are covalently linked together through phosphategroup bridges, in which the 5'-phosphate group of one nucleotide unit is joined to the
3'-hydroxyl group of the next nucleotide, creating a phosphodiester linkage.
i. Thus, backbones of nucleic acids consist of alternating phosphate and pentose
residues. The backbones of both DNA and RNA are hydrophilic.
b. All phosphodiester linkages have the same orientation giving the nucleic acid a specific
directionality which goes from a 5' to a 3' direction (refers to the end of the strand).
i. The 5' end lacks a nucleotide at the 5' position and the 3' end lacks a nucleotide at
the 3' position.

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IV.The properties of nucleotide bases affect the 3D structure of nucleic acids
a. Pyrimidines and purines are weakly basic compound and are thus called bases.
b. Electron delocalization among atoms in the ring gives most of the bonds partial doublebond character.
i. One result of this is that pyrimidines and purines are nearly to very planar.
c. All nucleotide bases absorb UV light, and nucleic acids are characterized by a strong
absorption at wavelengths near 260 nm.
d. Purine and pyrimidine bases are hydrophobic and relatively insoluble in water at nearneutral pH of the cell.
e. Hyrophobic stacking interactions in which two or more bases are positioned with the
planes of their rings parallel (like a stack of coins) helps create the 3D structure.
i. The stacking provides a combination of van der Waals and dipole-dipole interactions
and helps minimize contact of the bases with water.
f. The bases hydrogen bond with one another: this is the most important mode of
interaction between two complementary strands of nucleic acid.
i. A bonds to T = 2 hydrogen bonds
ii. G bonds to C = 3 hydrogen bonds
B. Nucleic acid structure
I. DNA is a double helix that stores genetic information
a. Chargaff's rules
i. The base composition of DNA generally varies from one species to another.
ii. DNA specimens isolated from different tissues of the same species have the same
base composition.
iii. The base composition of DNA in a given species does not change with an organism's
age, nutritional state, or changing environment.
iv. A = T
G=C
A+G=T+C
b. Two helical DNA chains are wound around the same axis to form a right-handed double
helix.
c. The hydrophilic backbones are on the outside of the double helix, facing the surrounding
water. These strands are antiparallel to one another (one in 5' to 3' direction and the
other is in 3' to 5' direction).
d. The pairing of the two strands creates a major groove and minor groove on the surface
of a duplex.
e. 10.5 base pairs per helical turn when in aqueous solution.
f. The sequence of DNA from each strand is complementary to each other (wherever
adenine occurs in one chain, thymine is found in the other).

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II. DNA can occur in different 3D forms

a. Structural variation in DNA reflects 3 things: (1) different possible conformations of the
deoxyribose, (2) rotation about the contiguous bonds that make up the
phosphodeoxyribose backbone, and (3) free rotation about the C-1'-N glycosyl bond.
b. The b-form DNA is the most stable structure for DNA molecule under physiological
conditions.
c. A-form DNA is favored in solutions that are devoid of water. It is a right-handed
double helix, but the helix is wider and their number of base pairs per helical turn is 11.
d. Z-form DNA has 12 base pairs per helical turn and the structure appears more slender
and elongated. The backbone takes on a zigzag appearance. Z-DNA is a left-handed
helix and there is barely a minor groove. Z-DNA have been found in bacteria and
eukaryotes. It may play a role in regulating the expression of some genes.

III. Certain DNA sequences adopt unusual structures

a. A common type of DNA sequence is a palindrome: the sequence is spelled identically
when read either forward or backward. Palindromes are repeats in opposite strands.
They create special structures:
i. When only a single DNA (or RNA) strand is involved, the structure is called a
hairpin.
ii. When both strands of duplex DNA are involved, it is called a cruciform.
b. When an inverted repeat occurs within each individual strand of the DNA (on the same
strand), the sequence is called a mirror repeat.

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IV.Many RNAs have more complex 3D structures
a. The product of transcription of DNA is always single-stranded RNA.
b. The single strand tends to assume a right-handed helical conformation dominated by
base-stacking interactions.
c. RNA can base-pair with complementary regions of either DNA or RNA.
d. Double stranded RNA is usually found in the A-form. (B-form is not observed, Z-form
has been synthesized in the lab)
e. The 3D structure of RNA is very complex. Weak interactions, especially base-stacking
interactions help stabilize RNA structures.
V. Nucleic acids from different species can form hybrids
a. Hybrid duplexes are which segments of one species DNA strand form base-paired
regions with segments of another species DNA strand.
i. It reflects a common evolutionary heritage; the closer the evolutionary relationship
between two species, the more extensively their DNAs will hybridize.
C. Other functions of nucleotides
I. Nucleotides carry chemical energy in cells
a. The phosphate group covalently linked at the 5' hydroxyl of a ribonucleotide may have
one or two additional phosphates attached.
i. The resulting molecules are referred to as nucleoside mono-, di-, and triphosphates.
ii. Hydrolysis of the nucleoside phosphates provides the chemical energy to drive many
cellular reactions.
II. Some nucleotides are regulatory molecules
a. Second messengers tend to be nucleotides.
i. One of the most common is cyclic AMP or cAMP, formed from ATP in a reaction
catalyzed by adenylyl cyclase.
ii. Another regulatory nucleotide, ppGpp, is produced in bacteria in response to a
slowdown in protein synthesis during amino acid starvation. It inhibits the synthesis
of rRNA and tRNA molecules needed for protein synthesis, preventing the uncessary
production of nucleic acids.

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Cellular membranes
Introduction
Fluid mosaic model of membranes because it is a patchwork of different types of
molecules and these molecules move rapidly within the lipid bilayer
permeable for non-poolar compounds, but not for polar
made up of sterols, sphingolipids, and glycerophospholipids
non-polar elements face each other internally and polar head groups face outward
Hydrophobic interactions in water
Glycerophospholipids and sphingolipids spontaneously form bilayers when placed in a
polar solution like water. This is done to minimize the surface area of contact between
the nonpolar areas of the molecule and the polar liquid.
In a bilayer, polar head groups are on the outside, whereas the hydrophobic tales on are
on the inside, pointing down to one another. The tails on the end of the bilayer are
exposed to water, so they form a (liposome) vescile.
It can be thought that cells and organelles are big vesicles

Membrane fluidity
Membrane fluidity depends on temperature
At low temperatures, the lipids solidify into a paracrystal
At higher temperatures, lipids adopt a fluid state
Most stable state is called liquid ordered state (this is at intermediate temps). It is
becomes too hot, it turns into the liquid disordered state (not as stable).
Sterols broaden the transition range between paracrystal and liquid disordered state.
Sterols increase ordering of unsaturated fatty acids and decrease ordering of
saturated fatty acids
If the membrane has more unsaturated fatty acids, the transition temperature is
lowered.
Lipids in the plasma membrane are free to move around across.
Membrane proteins
Channel proteins: provide passageway through membrane for hydrophilic substances.
Recognition proteins (glycoproteins) are peripheral proteins on the extracellular side of
the plasmamembrane that helps other cells distinguish it from foreign cells. The

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oligosaccharide chain attached to the protein serves as this recognition tag.

Ion channels help move ions across the membrane. Two different types:
Voltage gated ion channels respond to differences in membrane potential
Ligand gated ion channels require a chemical to bind to a receptor site, which will
cause the channel to open.
Mechanically-gated ion channels respond to environmental stimuli such as
pressure, vibration, temperature, etc.
Porins allow passage of certain ions and small polar molecules through the membrane.
Tend to not be specific, they are just large passages. If you can fit you can go through
Aquaporin increase rate of H2O passing.
Carrier proteins bind to specific molecules, change shape, then allow the passage of
certain molecules through.
Transport proteins help move molecules (ions, large molecules, polar molecules) move
through the passive membrane. Can be done passively, or actively by coupling
movement with the hydrolysis of ATP. It is a very broad category of proteins.
Adhesion proteins attach cells to neighboring cells, providing anchors for internal
filaments and tubules (stability)
Receptor proteins are the binding sites for hormones and other trigger molecules.
Cell Wall
Cell Wall found in plants, fungi, protists, and bacteria
cellulose in plants; chitin in fungi; peptidoglycans in bacteria; polysaccharides in
archaea.
Provides support to the cell. Sometimes, a secondary structure develops beneath the primary
one.
Glycocalyx: a carbohydrate coat that covers the outer face of cell wall of some bacteria and
outer face of plasma membrane of some animal cells. Consists of glycolipids (attached to
plasma membranes) and glycoproteins (such as recognition proteins). May provide adhesive
capabilities, a barrier to infection, or markers for cell-cell recognition.

Extracellular matrix
Found in animals: areas between adjacent cells occupied by fibrous structural proteins,
adhesion proteins, and polysaccharides secreted by cells.
Common structures: collagen, integrin + fibronectin, laminin
Provides mechanical support and helps bind adjacent cells.

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Cells adhere to the ECM in two ways:

focal adhesions connection of the ECM to actin filaments in the cell
hemidesmosomes connection of ECM to intermediate filaments
Cytoskeleton
Cytoskeleton is a network of specialized proteins that provides a framework for
maintenance of cell shape. Involved in cell movement and movement of organelles.
Protein filaments are the basic units for maintenance of cell's shape. Three types:
microfilaments: made up two intertwined strands of actin. Thinnest of the three types.
Involved in muscle contraction, and cell motility.
Microtubules: made up of the protein tubulin, provide support and motility for cellular
activities. Thickest of the three types. Spindle fibers for mitosis and meiosis are made up
of microtubules.
Colchinine inhibits microtubule activity, and will interfere with mitosis.
If a person is born with a genetic defect that produces abnormal microtubules, sperm
cells, cells of the larynx, and trachea would be greatly effected.
Intermediate filaments: provide support for maintaining cell shape (keratin)
Locomotion
Microtubule organizing enters (MTOCs) Structures from which microtubules
emerge.include centrioles and basal bodies (are at the base of each flagellum and cillium
and organize their development). Are in a 9x3 array. Plants, although they lack centrioles,
do have MTOCs.
Some types of cell motility involve the cytoskeleton. Cell motility generally requires
interaction of the cytoskeleton with motor proteins.
Flagella and cilia are microtubule-containing extensions that project from some cells.
Both are in a 9+2 array; 9 pairs + 2 singlets in center
Microtubule assembly of cilium or flagellum is anchored in the cell by a basal body.
Fagella are usually limited to just one or a few per cell, and are longer than cillia.
Dyenin is a protein associated with a flagellum. Converts chemical energy from ATP
into mechanical energy of movement.
Motile cillia usually occur in large numbers on the cell surface.
Cell Junctions
Plant cell walls are perforated with plasmodermata: channels that connect plant cells.
These connections unify most of the plant into one living continuum.
There are three main types of cell juntions in animal cells:
Tight junctions: Plasma membranes of the neighboring cells are tightly pressed against
each other, bound together by specific proteins.
Desmosomes (adhesion junction): function like rivets, fastening cells together into
strong sheets.
Gap Junctions: provide direct connection between cytoplasm of one cell and cytoplasm
of neighboring cell via channels called connexins.

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Nucleus
The nucleus contains the DNA, the genetic material of the cell.
The nuclear envelope surrounds the nucleus with a double membrane with multiple pores.
Separates the contents of the nucleus from the cytoplasm.
Regulate the passage of macromolecules (proteins, RNA), but permit free passage of
water, ions, ATP, and other small molecules.
Inside the nuclear envelope is the chromatin, which consists of DNA tightly twisted around
proteins. They form long strands called chromosomes.
When a cell is not dividing, chromatin appears as a diffuse mass and you can't determine
one chromosome from another. As the cell prepares to divide, the chromosomes move
farther away to the point where they can be distinguished from one another.
The nucleolus is the central portion of the cell nucleus and is composed of chromosomal
RNA, proteins, and DNA. The nucleolus accomplishes the manufacture of ribosomes.
The nuclear side of the envelope is lined by the nuclear lamina. This is the dense fiber
network of most cells. Composed of intermediate filaments and membrane associated
proteins. Provides mechanical support and regulates cellular events such as DNA replication
and cell division. Participates in chromatin organization.
There is much evidence for a nuclear matrix, a framework of protein fibers extending
throughout the nuclear interior.

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Cytosol vs Cytoplasm
Cytoplasm is the streaming movement within a cell. It includes everything suspended
between the cell wall and the nucleus. Cytoplasm = veggie-stew. Cytosol + organelles +
everything else that is suspended.
Cytosol is the aqueous substance that everything is suspended in. IT JUST DESCRIBES
THE FLUID. Cytosol = broth.
Ribosomes
Ribosomes are complexes made up of ribosomes RNA and protein. They carry out protein
synthesis.
Cells that have high rates of protein synthesis have large numbers of ribosomes.
Ribosomes build proteins in to cytoplasmic locations:
free ribosomes are suspended in the cytosol. Proteins made from these types of
ribosomes function within the cytosol.
bound ribosomes are attached to the outside of the endoplasmic reticulum or the
nuclear envelope. Proteins made from these types of ribosomes are usually destined for
insertion into membranes or for export from the cell.
Endoplasmic Reticulum
The Endoplasmic reticulum (ER) is an extensive network of membrane tubules and sacs
called cisternae. Internal compartment of the ER surrounded by the membranes is called the
ER lumen. ER runs adjacent to the nucleus.
Two distinct types of ER:
The smooth ER outer surface lacks ribosomes. Functions of the smooth ER include:
lipid and sterol synthesis, detoxification of drugs and poisons, and storage of calcium
ions.
The rough ER outer surface is studded with ribosomes. The rough ER is continuous
with the outer nuclear membrane. The main function of the rough ER is to generate
proteins and package them for secretion. Many of these secretory proteins are
glycoproteins. Another function of the rough ER is to build parts that add to the plasma
membrane.

Golgi Apparatus
Many transport vesicles travel to the Golgi apparatus after leaving the ER. The golgi
apparatus is like a warehouse for receiving, sorting, and shipping, and some modifications

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of the vesicles.
Consists of flattened membranous sacscisternae. The membrane of each cisterna in a
stack separates its internal space from the cytosol.
The two sides of a Golgi stack are referred to as the cis and trans face; these act,
respectively, as the receiving and the shipping departments of the Golgi apparatus.
Vesicles adds its comments to the Golgi apparatus on the cis side and the vesicles leave
the Golgi apparatus on the trans side.

Lysosomes
A lysosome is a membarnous sac of hydrolitic enzymes that many eukaryotic cells use to
digest marocmolecules and damaged organelles.
Glycosidases, aryl sulfatases, and phosphatases are found in lysosomes.
Lysosomes internal evironment is acidic because its enzymes function best in those pH
levels.
Functions in phagocytosis. When a cell engulfs good, the lysosome fuses with the food
vacoule and then catalyzes digestion.
Functions in autophagy. A damaged organelle becomes surrounded by a double membrane,
and the lysosome fusees with the vesicle, catalyzing digestion.
Vacuoules
Vacuoules are large vesicles derived from the ER or Golgi apparatus. Perform a variety of
functions in different kinds of cells.
Food vacuoules are formed by phagocytosis.
Many unicellular eukaryotes in living in fresh water have contractile vacuoules that pump
out excess water out of the cell, thereby maintaining the appropriate internal osmolarity.
Mature plant cells generally contain a large central vacuoule, which develops by the
coalescence of smaller vacuoules. Solution inside the central vacuoule is called cell sap, and
it is the main repository of inorganic ions.

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Peroxisomes
The peroxisome is a specialized metabolic compartment bounded by a single membrane.
They contain enzymes that remove hydrogen atoms from various substrates and transfer
them to oxygen, producing hydrogen peroxide as a by-product.
Specialized peroxisomes called glyoxysomes are found in fat-storing tissues of plant seeds.
Contain enzymes that initiate the conversion of fatty acids to sugar, which seedlings use as
source of energy.
Mitochondria
Exceptions to the universality of the genetic code is seen with mitochondria.

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We know there was life by 3.45 billion years ago

Sulfur isotopes of organic matter preserved in 3.45-billion-year-old stromatolites reveal
microbial metabolism
Stromatolite: layered calcareous structures formed by bio-films (microorganisms adhered
together) binding sedimentary gains

LUCA
Last universal common ancestor (LUCA): the population of organisms at the base of the
tree of life. All living things today are descended from this one lineage. Is there really a
LUCA?
LUCA is by far the most probable theory than the closest competing hypothesis even
when counting for exchanging material between organisms (horizontal gene transfer)
There was probably more than one self-replicating early life form. One population was
successful enough to establish itself

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What are the properties of life?

Organization: maintenance of parts (whether cells or more complex)
metabolism: control of chemical reactions to sustain life
Growth and reproduction: creation of offspring
homeostasis: the ability to regulate one's internal environment
external response: response to external environment and stimuli
What are some critical steps required for life?
Generation of simple organic molecules from inorganic molecules
origin of self replication
genotype and phenotype linkage and natural selection
moving from RNA to DNA
creation of cells (compartmentalization)
Prebiotic soup hypothesis
Prebiotic soup hypothesis: the idea that the earliest life emerged in a soup-like liquid
environment, drawing energy from the cosmic rays, volcanic eruptions, and the Earth's
internal heat
Organic from Inorganic
Many experiments have shown that life related molecules can be synthesized from simple
inorganic components
1828 urea (organic) created from inorganic salts, ammonium chloride, and cilver
cyanate
helped disprove that the chemistry of living systems were fundamentally different
from nonliving systems

Oparin and Haldane's organic soup theory

If there was oxygen, no organic molecules would have formed.
The original Earth environment was very reducing (allowing chemical parts to turn
into more complex ones)
Miller-Urey experiments
simulated ocean and atmosphere interface
methane, ammonia, and hydrogen mixed with boiling water and simulated lighning
reactions produced amino acids
these were done in reducing environments (without compounds with oxygen). This
may not be accurate.

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Reducing environments exist in hydrothermal sites.

The discovery of chemosynthesis at vents in 1977 gave some credence to deep sea
origins.

Reducing environments exist in space as well.

Amino acids were found on a 4.6 billion year old meteorite

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Could extreme pressure and heat of impact destroy amino acids?

Goldman et al. 2010 suggests glancing strikes would allow survival. Also suggested
that heat could encourage more complex amino acid complexes.
Problems with organic from inorganic
some compounds have still never been produced (nucleotides)
low quantities are produced
Origin of self replication
chicken egg problem: DNA encodes information for proteins; proteins can't replicate'
proteins are required for replication of DNA
Solution: RNA world
RNA was the information carrier and catalyst
RNA has diverse roles that include catalyst and temporary information carrier
Ribozymes = RNA enzymes
RNA world: a hypothetical early stage in the history of life in which RNA was the
fundamental unit upon which life was based, fulfilling both an information role and a
catalytic role.
DNA replaces RNA
RNA was replaced by DNA around 3.5 billion years ago as the genotype
DNA is more stable whereas RNA is more reactive
DNA have repair mechanisms (proofreading, error correction)
lower mutation rates better storage
proteins were used for catalytic functions (phenotype).
They can be more complex and diverse than RNA
Molecular bridge from RNA to DNA still unknown
Reverse transcriptase can convert from RNA to DNA today
Precursors to first organisms
Protobionts are precursors of cells. They are like cells and metabolically active but are
unable to reproduce.
Microspheres, spontaneously formed lipid or protein bilayer bubbles, are experimentally
produced protobionts that have some selective permeable qualities.
What were the first organisms like?
The first single celled life was prokaryotic (they have no nucleus or organelles)
Organisms were compartmentalized
If functions are delegated, you need to contain the parts
Also, a self replicating system, if not compartmentalized, might be coopted by other
organisms
Metabolism
Primitive heterotrophic prokaryotes: obtained materials by consuming other organic
substances (pathogenic bacteria)
Primitive autotrophic prokaryotes: mutation, heterotroph gained ability to produce its
own food cyanobacteria.
Reproduction
Reproduction may have resulted from overproduction. the cell expands so large that
splitting is more stable.
Minimal gene sets
Minimal gene set is the hypothetical minimal number of genes thought necessary to

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allow for cellular based life. Around 206 genes (done by comparing genomes)
Early population of these organisms exchanged material most likely
Horizontal gene transfer: the transfer of genetic material from one organisms to
another that is not its offspring. This was more prevalent in the early tree of life.
Basically, early cells may have swapped DNA frequently.

Where do viruses fit in here?

Hypotheses
Escaped gene hypothesis: escaped selfish genes that have evolved protein coatings and
self replication
Reduction hypothesis: extremely reduced cellular organisms
Remnants of the RNA world
viruses may have predated or coexisted with LUCA
Oxygen and ozone layer ended abiotic chemical evolution
O2 and O3 formed by production of photosynthetic activity of autotrophs (cyanobacteria).
Ozone layer formed, which absorbs UV light, blocking energy for abiotic synthesis of
organic materials.
This terminated primitive cells.
Formation of the first eukaryotes
Endosymbiosis: a mutually beneficial relationship in which one organism lives within the
body, often within the cell, of another.
It has been shown that mitochondria and chloroplasts formed through this process
Evidence for symbiosis (commonly asked on DAT):
http://evolution.berkeley.edu/evolibrary/article/_0_0/endosymbiosis_04 (READ THIS
PAGE)

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Overview
oxidative phosphorylation:
catabolism of carbohydrates, lipids, amino acids converge on cellular respiration
oxygen is reduced to H2O; electrons are donated by NADH and FADH2
takes place in mitochondria for eukaryotes
Brief review of universal electron carriers
oxidative phosphorylation is based on electron carriers
dehydrogenases collect electrons from catabolic pathways and transfer them to:
nicotamide nucleotides: NAD+ and NADP+
Flavin nucleotides: FAD and FMN
Universal electron carriers 1: Ubiquinone
Ubiquinone (coenzyme Q)
remains in lipid bilayer
very mobile
shuttles electrons between various carriers
Accepts 1 or 2 electrons
Universal electron carriers 2: Cytochromes
Electron carrier proteins
most are integral proteins of inner mitochondrial membrane
Accepts 1 electron only
complex 1- NADH:Ubiquinone Oxidoreductase
Structural features:
transfers electrons from NADH ubiquinone
Embedded in membrane
one domain extends into matrix (docking station for NADH)
Mechanistic features:
couples 2 reactions: electron transfer and proton translocation across inner mitohondrial
membrane
(1) Transfers 2 electrons from NADH to ubiquinone
(2) Transfers 4 protons through inner mitochondrial membrane per 2 electrons
Exergonic (1) drives endergonic (2)
complex 2 succinate dehydrogenate
Transfers electrons from succinate FADH2 ubiquinone
Succinate dehydrogenase is the only membrane-bound enzyme in the Krebs Cycle
Electrons from succinate do not have enough energy to allow proton pumping cannot be
funneled through complex 1
Other bypasses of complex 1
first step of fatty acid breakdown (formation of -C=C- bond) passes electrons from acylCoA to electron transfer flavoprotein (ETF)
ETF will eventually complete electron transfer to Q:
FAD electron transfer flavoprotein ETF:ubiquinone oxidoreductase ubiquinone
(Q)
Other bypasses of complex 1
glycerol-3-phosphate from fat degradation or reduction of dihydroxyacetone phosphate
(glycolysis)
oxidized by glycerol 3-phosphate dehydrogenase (outer surface of membrane)

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dehydrogenase channels electrons to ubiquinone (Q) via FAD

complex 3 cytochrome bc1

structure:
also known as ubiquinone:cytochrome c oxidoreductase
transfers electrons from ubiquinone cytochrome c
transports 2 protons through inner membrane
mechanism:
Function: switch from 2-electron carrier (NADH, FADH2, QH2) to 1-electron carrier
(cytochromes, Cu+)
Pumps 4H+ through the membrane for every pair of electrons passed to cytochrome c (2
needed)
Cytochrome c passes electrons to complex IV
Net equation: QH2 + 2 cyt c1 (oxidized) + 2H+ (inside) ---> Q + 2 cyt c1 (reduced) + 4H+
(outside)
2 H+ comes from the conversion of QH2 back to Q

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cytochrome IV cytochrome oxidase

structure
transfers electrons from cytochrome c O2
reduces 1 O2 to 2 H2O
mechanism
for every 4 electrons passing through complex IV:
One O2 is converted to 2 H2O using 4 H+ from matrix
involves single-electron transfers (cytochrome c)
all intermediates remain bound to complex
all intermediates are highly reactive radicals and can cause damage if released

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ETC balance sheet

For each electron pair:
4 H+ are pumped out by complex I
4 H+ are pumped out by complex III
2 H+ are pumped out by complex IV
10 H+ total using NADH
pumping out H+ generates electrochemical gradient. Energy is stored as a proton-motive
force
2 components:
1) chemical potential due to [H+] gradient across membrane
2) electrical potential due to separation of charge (H+)
protons spontaneously flow down electrochemical gradient driving ATP synthesis
ATP synthesis
proton motive force provides energy to drive ATP synthesis (ADP + Pi ATP)
Requires ~50 kJ/mol under cellular conditions
ATP synthesis results from coupling proton flux to phosphorylation
The ATP synthase paradox
Proton motive force is required to released tightly bound ATP rather than to synthesize
it!!!!!
ATP synthase consists of two functional domains
Fo: contains a passive proton pore
F1 containts nine subuints (5 types)
'head' consists of altering alpha and beta subunits
beta subunits contain catalytic site
stator connects Fo and F1

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F1 structure and dynamics

Each beta subunit adopts a different conformation
each conformation binds different ligands (none, ADP/Pi, ATP)
gamma subunit binds only 1 Beta subunit
rotation of gamma subunit (driven by PMF) forces beta subunits to cycle through
conformations
rotational catalysis model for ATP synthesis

movement of protons down electrochemical gradient through c ring induces rotation of ring
and gamma stalk in plane of membrane (green circle in middle)
rotation of gamma stalk causes beta subunits to associate with gamma in a cyclic fashion
FOCUS ON THE PURPLE UNIT ONLY:
1) Subunit begins in the Loose conformation. This is the conformation that will bind the
ADP and Pi. (step 1)
2) Gamma stalk rotates and changes the conformation of the subunit from the Loose
conformation to the Tight conformation. In the tight conformation, ADP and Pi bind to
form ATP. (step 2 and Step 3)
3) Gamma stalk rotates and changes the conformation of the subunit from the Tight
conformation to the Open conformation. This causes ATP to be released from ATP
synthase. (step 4)
Note that there are three different subunits per ATP synthase (purple subunit, blue subunit,
and yellow subunit). In one 360 degree rotation, each different color subunit goes through
all different conformations (as described above). This means that in one 360 degree rotation,
3 ATP is formed.
direction of rotation determines outcome:
direction 1: PMF-driven ATP synthesis
direction 2: ATP-driven H+ pump

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ATP hydrolysis
ATP breakdown to ADP is a hydrolysis reaction!
stoichiometry of ATP synthesis historical view
number of electrons moved and number of ATP molecules formed are whole numbers
(integers)
values of these numbers are derived from P/O ratios
Phosphates transferred (P) : oxygen oxidized (O)
Ratios were NADH = 3, succinate = 2 (Numbers you need to know for DAT)
Prokatyotes vs. eukaryotes
In eukaryotes, the total energy from glucose is about 36 ATP. However, in eukaryotes, the
total energy from glucose is about 38 ATP. Why?
Prokaryotes have no mitohcondria so they do not need to transfer pyruvate into the
mitochondrial matrix, which is done via active transport, thus costing ATP. They use cell
membrane for respiration.
Note that prokaryotes does not do TCA cycle because they don't have mitochondria.

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The two stages of photosynthesis

(1) light dependent
energy from light is absorbed by chlorophyll and other pigments
absorbed energy is used: to generate ATP and to transfer electrons from water to
NADP+ (oxygen is produced)
(2) carbon assimilation/carbon fixation
uses products of light reactions
NADPH and ATP reduce CO2
new organic carbon is converted into triose phosphates, sucrose, and starch
Structure of plant chloroplasts
chloroplasts are surrounded by two membranes, an outer membrane that is permeable to
small molecules and ions, and an inner membrane that encloses the internal compartment.
This compartment contains many flattened, membrane-surrounded vesicles or sacs, the
thylakoids, usually arranged in stacks called grana.
Embedded in the thylakoid membrane are the photosynthetic pigments and enzyme
complexes that carry out the light reactions and ATP synthesis.
The stroma, the aqueous phase enclosed by the inner membrane, contains most of the
enzymes for the carbon-assimilation reactions.

Chromophores: Light-absorbing molecules

light absorption: absorbing a photon raises chromophore (electrons) to a higher energy level
Photon energy must match exactly energy gap between ground state and excited state
excited state is unstable and short-lived
Excited chromophore eventually returns to ground state
energy is released as light (emission), heat, or (biological) work
This is the idea behind photosynthesis
Primary Photosynthetic Pigments 1: chlorophylls
Green pigments in thylakoid membranes
Contain polycylic, planar rings resembling heme w/ phytol side-chain
Mg 2+ (not iron) is at center of tetrapyrrol ring
strongly absorb light due to conjugated double bonds in ring
spectra of chlorophylls a and b are not identical
chlorophylls are always associated with binding proteins
chlorophyll + binding protein = light harvesting complexes (LHCs)

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proteins orient chlorophyll in 3D space

Energy transfer requires contact between pigments, binding proteins and membrane
components
Accessory (secondary) pigments: carotenoids
present in thylakoid membranes
secondary pigments absorb light outside the range of chlorophylls
Primary and secondary photopigments
spectra are complimentary: each 'antenna' absorbs in a specific wavelength range
pigments cover whole visible spectrum
Chlorophylls channel energy from sunlight to reaction centers
photosystems: pigments/proteins arranged into functional units
all pigments absorb light as photons
only a few chlorophylls convert light energy into chemical energy
these are part of photochemical reaction centers
rest of pigments transmits light energy to reaction centers light-harvesting (antenna)
molecules
Energy transfer from antennas to reaction centers: exciton transfer
one pigment absorbs a photon and is excited
energy is randomly transferred to a neighboring light-harvesting molecule, exciting it
first one returns to the ground state
exciton transfer continues until it reaches a specialized pair of chlorphyll a at reaction center
energy passed to chlorophyll a in reaction center causes one electron to be promoted to next
orbital
this electron is passed to an electron acceptor molecule initiates plant electron transport
leaves an electron hole (+) in the donor chlorophyll a
Electron acceptor gains a negative charge (-)
electron is replaced through transfer from a neighboring electron donor, which becomes
positively charged

Reaction centers of higher plants

chloroplast thylakoids: two distinct reaction center types, P680 and P700
are complementary

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resemble the two bacterial systems

each chloroplast has hundreds of each system in thylakoid membranes
Photosystem 2 (PSII):
contains equal amounts of chlorophylls a and b
P680 reaction center
contributes to proton gradient across thylakoid membrane
Photosystem 1 (PSI):
P700 reaciton center
high amounts of chlorophylls a and b
reaction center transfers electrons to Fd
electrons from Ferredoxin are used to reduce NADP+
Reaction centers act in tandem to move electrons from H2O to NADP+ using sunlight
Plastocyanin (Cu) moves electrons between PSII and PSI (one electron at a time)
H2O is oxidized to O2 replaces electrons transferred from PSII to PSI
Plants: oxygenic photosynthesis
Bacteria: anoxygenic photosynthesis
Oxygen evolving complex
Oxygen evolving complex breaks down 2 H2O molecules into 4 H+ ions and 4 e-.
The 4 e- are then used to replace the electrons that were excited by photons in P680.
Note that for this reason photosynthesis is non-cyclic electron flow!
The 4H+ are used to create the electrochemical gradient for ATP synthesis.

PSI and PSII are physically separated

PSII is located in grana stacks
PSI and ATP synthase are located in unstacked stromal thylakoids access to stroma
Cytochrome b6f distribution is more uniform
Association of PS I and PS II with LSCHII is regulated by
sunlight
protein phosphorylation
cytochrome b6f complex
function = proton pumping as electrons are transported: moves 4 H+ per pair of electrons

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from stroma into thylakoid lumen. Establishes electrochemical gradient (PMF)

volume of thylakoid lumen in chloroplasts is small moving a small number of protons
has large effect
result: 3 unit pH difference, i.e. 1000-fold difference in [H+]
PMF drives ATP synthesis
ATP synthesis in photophosphorylation: overview
mechanism for ATP synthesis is analogous to that in mitochondria
ATP synthesis is catalyzed by CF1/Cfo ATPase on outer surface of thylakoid membranes
ATP is produced by rotational catalysis
Balance sheet for photophosphorylation: we have a model but all is not known
About 12 H+ move from stroma to thylakoid lumen per 4 electrons (i.e. per O2 formed)
4 H+ by oxygen-evolving complex
up to 8 + by cytochrome b6f complex
electrochemical potential: change in pH = 3 across thylakoid membrane
but: most of electrical potential is lost due to counterion movement unlike mitochondria
where little is lost
Energy stored in proton gradient per pole of proton: G = -17 kJ/mol
12 moles of protons translates to ~200 kJ
enough free energy to drive synthesis of several ATP
ATP yield is about 3 per mole of O2 (experimental value)
Photorespiration
Photorespiration is fixation of oxygen by rubisco instead of carbon dioxide. This is a
problem because rubsico will fix both CO2 and O2 at the same time if both are present.
This feature of rubsico probably arose because in the early earth atmosphere, there was
not much O2 so it didn't matter.
The products of photorespiration are useless and are broken down by the peroxisome.
C4 photosynthesis
Purpose is to move CO2 from the mesophyll to the bundle sheath cell to maximize
photosynthesis and minimize photorespiration and water loss from stomata.
Found in hot dry, dry climates (think of corn and sugar cane!!!!)
Requires one additional ATP, which becomes AMP This is like using up 2 ATP
Structure of a C4 leaf is called the kranz anatomy (shown below).

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Mechanism is called the hatch-slack pathway (shown below).

CAM photosynthesis
Function is to allow the calvin cycle to proceed during the day when the stomata are closed.
This in turns reduces H2O loss.
Found in hot, dry climates (think of cactus and pineapple!!!)
Special feature is that the stomata open during the night. Usually, the stomata opens during
the day!
Mechanism shown below. Note that Malic acid is created and stored in the vacuole at night.
During the day, malic acid is transported back into the vacuoule and broken down to release
CO2.

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DNA replication
Prokaryotes
Only one origin of replication per DNA molecule
Occurs inside the cytoplasm
Eukaryotes
Multiple origin of replication sites per DNA molecule
Occurs inside nucleus
Transcription/Translation
Prokaryotes
Transcription and translation occur simultaneously
Eukaryotes
Transcription occurs in nucleus, translation occurs in cytoplasm
Cellular respiration
Prokaryotes
Occurs on plasma membrane
Eukaryotes
Occurs in mitochonrida

Cell theory
all living things are composed of cells
the cell is the basic functional unit of life
the chemical reactions of life take place inside the cell
cells only arise from pre-existing cells
cells carry genetic information in the form of DNA (passed from parent cell to daughter
cell)

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Cell wall
Prokaryotic cell walls give structural integrity and shape and serve to anchor flagellae.
Cell walls are typically made up of peptidoglycan in eubacteria and polysaccharides in
archaebacteria.
Peptidoglycan is a polymer composed of modified sugars cross-linked by short
polypeptides.
Two main types:
Gram positive bacteria have a thick peptidoglycan wall. Contain teichoic acid chains.
Gram negative bacteria have a thin peptidoglycan wall and are structurally more
complex, with an outer membrane that contains lipopolysaccharides. Outer membranepeptidoglycan layer-plasma membrane.

Cell wall of many prokaryotes is surrounded by a sticky layer of polysaccharide or protein.

Called a capsule if it is dense and well-defined or a slime layer if it is not well
organized.
Both structures help prokaryotes to adhere to their substrate or to other individuals.
Certain bacteria have developed resistant cells called endospores to withstand hard
conditions.
The original cell produces a copy of its chromosome and surrounds that copy with a
tough, mulitlayered structure, forming the endospore.
Endospore can live in harsh conditions. When conditions get better, it turns back into a
normal cell.

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Some prokaryotes stick to their substrate or to one another by hairlike appendages called
fimbriae.
Fimbriae are usually shorter than more numerous than pili.

Motility
About half of all prokaryotes are capable of taxis, a directed movement toward or away
from a stimulus.
Chemotaxis means changing movement in response to chemicals.
Organization of DNA
genome of prokaryote usually has considerably less DNA.
1 chromosome that is circular, whereas eukaryotes have linear chromosomes.
Chromosomes of prokaryotes are associated with many fewer proteins than are the
chromosomes of eukaryotes.
Chromosome is located in the nucleoid, a region of the cytoplasm that is not enclosed by a
membrane.
A typical prokaryotic cell have much smaller rings of independently replicating DNA
molecules called plasmids, most carrying only a few genes.
Prokaryotic ribosomes are slightly smaller than eukaryotic ribosomes.
restriction endonuclease is a bacterial protein that cleaves foreign DNA at specific sites
Reproduction
Reproduce by binary fission.
They are small and have short generation times.
Differences between binary fission and mitosis:
Binary fission occurs among prokaryotes (cells that do not have a nucleus) whereas
Mitosis occurs among eukaryotes (cells that do have a nucleus)
binary fission does not include spindle formation and sister chromatids in its process
making it faster means of cell division than mitosis
Binary fission does not have the 4 distinct cellular phases that are seen in mitosis
Transformation, transduction, conjugation = how to introduce variation in prokaryotes
In transformation, the genotype and possible phenotype of a prokaryotic cell are altered by
the uptake of foreign DNA from its surroundings.

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In transduction, phages carry prokaryotic genes from one host cell to another. This results
from accidents that occur during the phage replication cycle. When the phage replicate its
own DNA in a host cell and then packages new phages, some phages may have accidentally
uptook non-viral DNA or DNA that is partially viral or partially host. When that virus
injects the DNA into a new host, the DNA cannot replicate but now is injected into the
prokaryote.

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In conjugation, DNA is transferred between two prokaryotic cells. Ability to do this results
from a piece of DNA on the plasmid called the F factor. (F- cell, Hfr cell, F+ cell). (Look at
picture for more information)

Prokaryotes are diverse in metabolism

Obligate aerobes must use oxygen for cellular respiration and cannot grow without it.
Appear in top of test tube.
Obligate anaerobes cannot use O2, they are poisoned by it. Appear at very bottom of test
tube.
Facultative anaerobes use O2 if it is present but also can carry out fermentation or
anaerobic respiration if it is an anaerobic environment. Appear mostly at top because
aerobic respiration is better.
Microaerophiles need oxygen because they cannot ferment or respire anaerobically but are
poisoned at very high O2 concentrations. Appear in upper part of test tube but not very top.
Aerotolerant organisms do not require oxygen because they metabolize energy
anaerobically. Can be found spread evenly throughout the test tube.

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1. Amino acids
a) Amino acids share common structural features
All 20 of the common amino acids are alpha-amino acids. They have a carboxyl group
and an amino group bonded to the same carbon atom (the alpha carbon).
They differ from each other in their side chains, or R groups, which influence the
solubility of the amino acids in water.
For all amino acids except glycine, the alpha carbon is bonded to four different groups.
This means that the alpha-carbon is a chiral center and thus, amino acids have two
possible stereoisomers.
The two forms are enantiomers and the stereoisomers are optically activethat is,
they rotate plane-polarized light.
The absolute configurations of simple sugars and amino acids are specified by the D,
L system.
L-amino acids are those with an alpha-amino group on the left whereas D-amino
acids have the alpha-amino group on the right.
b) The amino acid residues in proteins are L stereoisomers
The amino acid residues in protein molecules are exclusively L stereoisomers.
c) Amino acids can be classified by R group
Amino acids can be simplified by grouping the amino acids into 5 main classes based on
the properties of their R groups, particularly their polarity, or tendency to interact with
water at biological pH.
Nonpolar, Alipathic R Groups
The R groups in this class of amino acids are nonpolar and hydrophobic.
These proteins tend to stabilize protein structure by means of hydrophobic
interactions.
Aromatic R groups
All of the aromatic amino acids are relatively nonpolar and can participate in
hydrophobic interactions.
Can absorb UV light.
Polar, Uncharged R Groups
These amino acids contain functional groups that form hydrogen bonds with water.
Cysteine is readily oxidized to form a covalently linked dimeric amino acid called
cystine, in which two cysteine molecules or residues are joined by a disulfide bond.
The S-S bond is strongly hydrophobic. These bonds play a special roles of many
proteins by forming covalent links between parts of a polypeptide molecule or
between two polypeptide chains.
Positively charged (basic) R groups
Histidine has an ionizable side chain with a pKa near neutrality, histidine may be
positively charged or uncharged at 7.0
Negatively charged (acidic) R groups
Aspartate + glutamate
Random important information
Most flexible amino acid = glycine
Most constrained amino acid = proline
d) Amino acids can act as acids or bases
When an amino acid lacking an ionizable R group is dissolved in water at neutral pH, it
exists in solution as the dipolar ion, or zwitterion, which can act as either an acid or

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base. Amino acids are thus amphoteric.
e) Titration curves predict the electric charge of amino acids
An important piece of information derived from the titration curve of an amino acid is
the relationship between its net charge and the pH of the solution.
The characteristic pH at which the net electric charge is zero is called the isoelectric
point or isoelectric pH, designated pI. pI = 0.5(pKa1 + pKa2)
pH > pI, molecule will have a negative charge (amino acid will act like acid and
donate H+ into the more basic solution)
pH < pI, molecule will have a more positive charge (amino acid will act like base
and accept H+ from the more acidic solution)
At its isoelectric point, the Amino acid is least soluble in water and does not migrate in
an electric field.
The the farther the pH of the solution is from the isoelectric point, the greater the net
electric charge of the amino acid.
2. Peptides and proteins
a) Peptides are chains of amino acids
A peptide is two or more amino acid molecules covalently linked together.
The amino acids are held together by a peptide bond.
In a peptide, the amino acid residue at the end with a free alpha-amino group is the
amino-terminal (or N-terminal) residue; the residue at the other end, which has a free
carboxyl group, is the carboxyl terminal (C-terminal) residue.

b) Biologically active peptides and polypeptides occur in a vast range of sizes and
compositions
Some proteins consist of a single polypeptide chain, but others, called multisubunit
proteins, have two or more polypeptides associated noncovalently.

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If at least two polypeptide chains are identical, then the protein is said to be
oligomeric, and the identical units are referred to as protomers.
3. Working with proteins
a) Proteins can be separated and purified
It is important to purify proteins before the protein's properties and activities can be
determined.
The first step in purification is to break open the cells, releasing the proteins into a
solution called a crude extract.
The extract is subjected to treatments that separate the proteins into different fractions
based on a property such as size or charge, a process referred to as fractionization.
A solution containing the protein of interest usually must further be altered before
subsequent purification steps are possible.
Dialysis is a procedure that separates proteins from small solutes by taking
advantage of the proteins' larger size. The purified extract is placed in a bag or tube
made up of some semipermeable membrane. When this is suspended in a much
larger volume of buffered solution, the membrane allows the exchange of salt but
not proteins.
Column chromatography takes advantage of differences in protein charge, size,
binding affinity, and other properties. A porous solid material with the appropriate
chemical properties (the stationary phase) is held in a column, and a buffered
solution (the mobile phase) migrates through it. The protein, dissolved in the same
buffered solution that was used to establish the mobile phase, is layered on top of the
column. The protein then percolates through the solid matrix. Individual proteins
migrate faster or more slowly through the column depending on their properties.
Ion-exchange chromatographyexploits differences in the sign and magnitude
of the net electric charge of proteins at a given pH. The column matrix is a
synthetic polymer (resin) containing bound charged groups; those bound with
anionic groups are called cation exchangers, and those with bound cationic
groups are called anion exchangers. The affinity of each protein for the charged
groups on the column is affected by the pH (which determines the ionization
state of the molecule) and the concentration of completing free salt ions in the
surrounding solution. Separation can be optimized n band in the mobile phase
(the protein solution) is caused both by separation of proteins with different
properties and by diffusional spreading. As the length of the column increases,
the resolution of two types of proteins with different net charges generally
improves.
In cation-exchanged chromatography, the solid matrix has negatively
charged groups. In the mobile phase, proteins with a net positive charge
migrate through the matrix more slowly than those with a net negative
charge, because the migration of the former is retarded more by interaction
with the stationary phase. The expansion of the protein band in the mobile
phase is caused by both separation of proteins with different properties and
by diffusional spreading.
Size-exclusion crhomatography separates proteins according to size. Large
proteins emerge fro the column sooner than small ones. The solid phase consists of
cross-linked cavities of a particular size. Large proteins cannot enter the cavities and
so take a shorter path through the column. Small proteins enter the cavities and are
slowed by their more labyrinthine path through the column.

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Affinity chromatography is based on binding affinity. The beads in the column

have a covalently attached chemical group called a liganda group or molecule that
binds to a macromolecule such as a protein. When a protein mixture is added to the
column, any protein with affinity to the ligand binds to the beads, and its migration
through the matrix is retarded.
b) Proteins can be separated and characterized by electrophoresis
Electrophoresis helps separate proteins based on the migration of charged proteins in an
electric field.
Proteins can be visualized meaning a researcher can quickly estimate the number of
different proteins in a mixture or the degree of purity of a particular protein preparation.
Can be also sued to determine isoelectric point and molecular weight.
Carried out in a gel that helps slow the migration of proteins approximately in
proportion to their charge-to-mass ratio.
An electrophoretic method commonly employed for estimation of purity and molecular
weight makes use of sodium dodecyl sulfate (SDS).
A protein will bind about 1.4 times its weight of SDS. SDS bound contributes a large
net negative charge, rendering the overall charge from the protein insignificant and
conferring on each protein a similar charge-to-mass ratio.
Electrophoresis in the presence of SDS therefore separates proteins almost
exclusively
After electrophoresis, the proteins are visualized by adding a blue color dye.
Position on the band is used to determine molecular weight.
Isoelectric focusing is a procedure used to determine the isoelectric point (pI) of a
protein. A pH gradient is established by allowing a mixture of low molecular weight
organic acids and bases to distribute themselves in an electric field across the gel. When
a protein mixture is applied, each protein migrates until it reaches the pH that matches
its pI so proteins will be at different points on the gel.
Two-dimensional electrophoresis is combining isoelectric focusing and SDS
electrophoresis sequentially. Proteins are first separated by isoelectric focusing in a thin
strip gel. The gel is then laid horizontally on a second gel, and the proteins are separated
by SDS gel electrophoresis. Horizontal separation reflects differences in pI; vertical
separation reflects differences in molecular weight.
c) Protein chemistry is enriched by methods derived from classical polypeptide sequencing
The Edman degradation procedure labels and removes the only amino-terminal residue
from a peptide, leaving all other peptide bonds intact.
d) Mass spectrometry offers an alternative method to determine amino acid sequences
Mass spectrometry can provide a highly accurate measure of the molecular weight of a
protein.
4. Overview of Protein Structure
a) Introduction
The spatial arrangement of atoms in a protein or any part of a protein is called its
conformation.
The possible conformations a protein include any structural state it can achieve
without breaking covalent bonds.
Proteins must have multiple stable conformationsthis reflects the changes that
must take place in most proteins as they bind to other molecules or catalyze
reactions.
The most stable conformation is the one that is the most thermodynamically stable,

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also known as having the lowest Gibbs free energy.
Proteins in any of their functional, folded conformations are called native proteins.
b) A protein's conformation is stabilized largely by weak interactions
Stability is defined as the tendency to maintain a native conformation.
The chemical interactions that stabilize the native conformation include disulfide bonds
and weak interactions.
Disulfide bonds are typically found in extracellular proteins because the
environment is more oxidizing (inside the cell it is more reducing).
Disulfide bridges are NOT broken down during allosteric interactions.
Weak interactions that predominate as a stabilizing force in a protein structure because
there are so many.
In general, the protein conformation with the lowest free energy (the most stable
conformation) is the one with the maximum number of weak interactions.
On carefully examining the contribution of weak interactions to protein stability, we find
that hydrophobic interactions generally predominate.
When water surrounds a hydrophobic molecule, the optimal arrangement of the
hydrogen bonds results in a highly structured shell, or solvation layer, of water
around the molecule. This creates an unfavorable decrease in entropy. When
nonpolar groups cluster together, the extent of the solvation layer decreases, because
each group no longer presents its entire surface to the solution. This results an a
favorable increase in entropy.

Hydrophobic amino acid side chains therefore tend to cluster in a protein's interior,
away from water. Amino acid sequences of most proteins contain a significant
content of hydrophobic amino acid side chains.
It is also important that any polar or charged groups in the protein interior have suitable
partners for hydrogen bonding or ionic interactions. The presence of hydrogen-bonding
groups without partners in the hydrophobic core of a protein can be destabilizing.

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Most of the structural patterns reflect two simple rules: (1) hydrophobic residues are
largely buried in the protein interior, away from water, and (2) the number of hydrogen
bonds and ionic interactions within the protein is maximized, thus reducing the number
of hydrogen-bonding and ionic groups that are not paired with a suitable partner.
5. Protein secondary structure
a) Introduction
Secondary structure is the chosen segment of a polypeptide chain and describes the
local spatial arrangement of its main-chain atoms, without regard to positioning of its
side chains or its relationship to other segments.
A regular secondary structure occurs when each dihedral angle, phi and psi, remains the
same or nearly the same throughout the segment.
Where a regular pattern is not found, the secondary structure is sometimes referred to as
undefined or a random coil.
b) The alpha helix is a common protein secondary structure
In the alpha helix, the polypeptide backbone is wound around an imaginary axis drawn
longitudinally through the middle of the helix, and the R groups of the amino acid
residues protrude outward from the helical backbone.
Each helical turn includes 3.6 amino acid residues.
Why does the alpha helix form more readily than many other possible conformations?
The structure is stabilized by a hydrogen bond between the hydrogen atom attached
to the electronegative nitrogen atom of a peptide linkage and the electronegative
nitrogen atom of a peptide linkage.
Within the alpha helix, every peptide bond participates in such hydrogen bonding.
c) Amino acid sequence affects stability of the alpha helix
Each amino acid residue in a polypeptide has an intrinsic propensity to form an alpha
helix, reflecting the properties of the R group and how they affect the capacity of the
adjoining main-chain atoms to take up the characteristic phi and psi angles.
Alanine shows the greatest tendency to form alpha helices.
The position of an amino acid residue relative to its neighbors is also important. The
order of the amino acid side chains can stabilize or destabilize the alpha-helical
structure.
The twist of an alpha helix ensures that the critical interactions occur between an amino
acid side chain and the side chain three to four residues away on either side of it.
Positively charged amino acids are often found three residues away from negatively
charged amino acids, permitting the formation of an ion pair.
A final factor affecting the stability of an alpha helix is the identity of the amino acid
residues near the ends of the alpha-helical segment of the polypeptide.
A small electric dipole exists in each peptide bond. These dipoles are aligned
through the hydrogen bonds of the helix, resulting in a net dipole across the helical
axis that increases with helix length.
For this reason, negatively charged amino acids are often found near the amino
terminus of the helical segment, where they have a stabilizing interaction with the
positive charge of the helix dipole; a positively charged amino acid at the aminoterminal end is destabilizing.
The opposite is true at the carboxyl-terminal end of the helical segment.

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d) The beta conformation organizes polypeptide chains into sheets

The beta conformation is defined by backbone of a polypeptide chain extending into a
zigzag rather than a helical structure. Hydrogen bonds form between adjacent segments
of the polypeptide within the sheet.
The arrangement of several segments side by side, all of which are in the beta
conformation, is called a beta sheet.
The individual segments that form a beta sheet are usually nearby on the polypeptide
chain but can also be quite distant from each other in the linear sequence of the
polypeptide; they may be in different polypeptide chains.
The adjacent polypeptide chains in a Beta sheet can be either parallel or antiparallel.
Hydrogen bonds are linear in the antiparallel conformations

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6. Protein tertiary and quaternary structures

a) Introduction
The overall three-dimensional arrangement of all atoms in a protein is referred to as the
protein's tertiary structure.
Amino acids that are far apart in the polypeptide sequence and are in different types of
secondary structure may interact within the completely folded structure of a protein.
The location of bends in the polypeptide chain and the direction and angle of these
bends are determined by the number and location of specific bend-producing residues,
such as Pro, Thr, Ser, and Gly.
Some proteins contain multiple subunits. The arrangement of these protein subunits in
three-dimensional complexes constitutes quaternary structure.
There are two major groups in which many proteins are classified: fibrous proteins,
with polypeptide chains arranged in long strands or sheets, and globular proteins, with
polypeptide chains folded into a spherical or globular shape.
b) Fibrous proteins are adapted for a structural function.
Fibrous proteins share properties that give strength and/or flexibility to the structures in
which they occur.
They are all insoluble in water.

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Alpha-keratin
Alpha-keratin is found only in mammals (make up hair, nails, etc.). The alphakeratin helix is a right-handed alpha helix. Two strands of alpha-keratin, oriented in
parallel (with the same amino termini at the same end, are wrapped about each other
to form a supertwised coiled coil. The supertwists are left-handed, opposite in the
sense to the alpha helix. The surfaces where the two alpha helices touch are made up
of hydrophobic amino acids, which permits close packing.
The strength of fibrous proteins is enhanced by covalent cross-links between
polypeptide chains and between adjacent chains in a supramolecular assembly.
These cross-links are disulfide bonds.
Collagen
Collagen helix is a unique secondary structure (like an alpha helix with key
differences). It is left-handed and has three amino acid residues per turn.
Three separate polypeptides, called alpha chains, are supertwisted about each other.
The twisting is right-handed. The tight wrapping provides a lot of strength.
c) Methods for determining 3-D structure of a protein
X-ray diffraction
The spacing of atoms in a crystal lattice can be determined by measuring the
intensities and locations of spots produced on photographic film by a beam of x rays
of given wavelength, after the beam has been diffracted by the electrons of the
atoms.
The physical environment in a crystal is not like in a living cell, so the protein can
look different.
X-ray diffraction is done best in tandem with NMR.
Nuclear magnetic resonance
Advantages: NMR is carried out on macromolecules in solution and it can illustrate
the dynamic side of protein structure.
Only certain atoms have the kind of nuclear spin that gives rise to an NMR signal.
d) Protein Quaternary Structures range from simple dimers to large complexes
Many proteins have multiple polypeptide subunits. A multisubunit protein is referred to
as a multimer. A multimer with just a few subunits is often called an oligomer.
Most multimers have identical subunits in symmetrical arrangements.
The repeating structural unit in a multimeric protein is called a protomer.
e) Some proteins or protein segments are intrinsically disordered
Intrinsically disordered proteins have properties that are distinct from classical
structured proteins. They lack a hydrophobic core, and instead are characterized by high
densities of charged amino acid residues. Pro residues are also prominent, as they tend
to disrupt ordered structures.

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in eukaryotes, citric acid cycle occurs in mitochondria

glycolysis occurs in cytoplasm
citric acid cycle occurs in the mitochondrial matrix
oxidative phosphorylation occurs in the inner membrane

(Pyruvate decarboxylation) conversion of pyruvate to acetyl co-a

net reaction: oxidative decarboxylation of pyruvate
Rationale: acetyl-CoA can enter the citric acid cycle and yield energy. Acetyl-CoA can
also be used to synthesize storage lipids.
Pyruvate + CoA-SH + NAD+ ----> Acetyl-CoA + NADH + CO2
enzyme: pyruvate dehydrogenase complex (PDC) (E1 + E2 + E3)
PDC is a large multi-enzyme complex
short distance between catalytic sites all channeling of substrates from one catalytic
site of another. This minimizes side reactions.
TPP, lipoyllysine and FAD are prosthetic groups
structure of Coenzyme A
recall that coenzymes or co-substrates are not a permanent part of the enzyme's
structure; they associate, fulfill a function, and dissociate
the function of CoA is to accept and carry acetyl groups
Step 1: Condensation
Acetyl-CoA + Oxaloacetate + H2O ----> CoA-SH + Citrate
enzyme: citrate synthase (induced fit = wont be active until all substrates bind to it)
rate-limiting step of citric acid cycle
activity largely depends on concentration of oxaloacetate
highly thermodynamically favorable/irreversible
regulated by substrate availability and product inhibition
Step 2: transformation of 6 carbon unit to isocitrate
citrate ----> cis-Aconitate + H2O
enzyme = aconitase
cis-aconiate +H2O ----> Isocitrate

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enzyme: aconitase
citrate, a tertiary alcohol, is a poor substrate for oxidation. However, isocitrate is a
secondary alcohol and is a good substrate for oxidation.
Addition of H2O to cis-aconitate is stereospecific
thermodynamically unfavorable/reversible
product concentration kept low to pull forward
step 3: decarboylation #2 and formation of NADH
Isocitrate + NADP+ ----> alpha-ketoglutarate + NADPH + H+ + CO2
NADPH + NAD+ ---> NADH + NADP+
enzyme: isocitrate dehydrogenase
oxidative decarboxylation: lose a carbon as co2 and generate NADH
oxidation of the alcohol to a ketone: transfers a hydride to NAD
cytosolic isozyme uses NADP+ as a cofactor
highly thermodynamically favorable/irreversible
regulated by product inhibition and atp
step 4: decarboxylation #3 and formation of NADH
alpha-ketoglutarate + CoA-SH + NAD+ Succinyl-CoA + NADH + H+ + CO2
enzyme: alpha-ketuoglutarate dehydrogenase
last oxidative decarboxylation:
net full oxidation of all carbons of glucose
after two turns of the cycle
carbons not directly from glucose because carbons lost came from oxaloacetate
succinyl-CoA is another high-energy thioester bond
highly thermodynamically favorable/irreversible
regulated by product inhibition
Step 5: formation of GTP
succinyl-CoA + GDP + Pi ---> GTP + CoA-SH + Succinate
enzume: succinyl-CoA synthetase
synthases catalyze condensation reactions where no nucleotides are involved
synthetases: condensation reactions that use nucleotides
substrate level phosphorylation
energy of thioester allows for incorporation of inorganic phosphate
Produces GTP, which can be converted to ATP
slightly thermodynamically favorable/reversible
product concentration kept low to pull forward
Step 6: the third oxidation
succinate + FAD -----> fumarate + FADH2
enzyme: succinate dehydrogenase
bound to mitochondrial inner membrane
part of complex II in the electron-transport chain
near equilibrium/reversible
product concentration kept low to pull forward
step 7: hydration
Fumarate + OH- ----> carbanion transition state
carbanion transition state + H+ ---> L-malate
enzyme: fumarase
stereospecific:

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addition of water is always trans and forms L-malate

OH- adds to fumarate... then H+ adds to the carbanion
slightly thermodynamically favorable/reversible
product concentration kept low to pull reaction forward
last step
L-malate + NAD+ ---> NADH + H+ + Oxaloacetate
enzyme: malate dehydrogenase
final step of cycle
regenerates oxaloacetate for citrate synthase
highly thermodynamically unfavorable/reversible
oxaloacetate concentration kept VERY low by cytrase synthase
pulls the reaction forward
CAC intermediates are amphibolic (Anaplerotic reactions)
intermediates in citric acid cycle can be used in biosynthetic pathways (removed form
cycle)
must replenish intermediates in order for the cycle and central metabolic pathway to
continue
4-carbon intermediates are formed by carboxylation of 3-carbon precursors

Calvin's experiments
Calvin: incubated green algae with 14CO2 isotope and traced the metabolic fate of 14C
isotope

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Observation 1: within less than a minute, 14C-labeled amino acids and sugars found
explanation: green algae are able to convert CO2 into small organic compounds
(CO2 assimilation)
Observation 2: within 5 sec of incubation of 14CO2, labeled 3-phosphoglycerate (3PG)
was detected
explanation: 3PG is a stable intermediate and is formed by carboxylation of carbon
intermediate
Carbon assimilation pathway: the calvin cycle (dark reaction)
autotrophic organisms use CO2 as sole source for biosynthesis of starch, cellulose, lipids,
and proteins and other organic molecules
use reducing equivalents of NADPH and energy (ATP), which is generated during
photosynthesis to reduce CO2 to carbon intermediates!!!!
Calvin cycle doesn't happen in the dark because reducing equivalents and ATP are not
provided in the absence of photosynthesis
3 turns of calvin cycle consume: 3 CO2, 9 ATP, 6 NADPH and make 1 GAP
Calvin cycle step 1: CO2-fixation
3 ribulose 1,5 bisphosphate + 3 CO2 ----> 6 3-phosphoglycerate
enzyme: rubisco (ribulose 1,5B-P carboxylase) (most abundant protein in biosphere)
carboxylation of ribulose 1,5 BisP to generated 3 molecules of 3-phosphoglycerate
calvin cycle step 2: reduction
6 3-phosphoglycerate + 6 ATP + 6 NADPH + 6 H+ ----> 6 Glyceraldehyde-3-phosphate + 6
ADP + 6 NADP+ +6 Pi
mechanism: reversal of glycolysis with the exception that NADPH is used instead of NADH
Unlike GAPDH from cytoplasmic gluconeogenesis, stromal enzyme uses NADPH as
co-factor
fates of GAP:
Used to regenerate ribulose 1,5 bisphosphate (most do this)
stored as starch in chloroplast for later use
translocated to cytosol and converted to sucrose (transported to non-photosynthesizing
parts)
Calvin cycle step 3: regeneration
5 Glyceraldehyde-3-phosphate + 3 ATP ----> 3 Ribulose 1,5-bisphosphate + 3 ADP
very similar to the non-oxidative part of the pentose phosphate pathway except that it
proceeds in the opposite direction. Called reductive pentose phosphate pathway (from
hexose to pentose)
A stoichiometry problem:
3 CO2 + 9 ATP + 6 NADPH + 6 H+ ---> 1 GAP + 9 ADP + 8 Pi + 6 NADP+ (calvin cycle)
But you are short 1 Pi from balancing!
The 9th Pi is added from the cytosol

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Pi/Triose antiporter
DHAP (produced from calvin cycle) leaves stroma into cytosol through the Pi-triose
antiporter. DHAP gets dephosphroylated when it eventually turns into sucrose. The stripped
Pi then moves back into the stroma via the same transporter and this balances out the calvin
cycle.
Antiport is also used to transfer NADPH and ATP produced by photosystems into the
cytosol

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Viruses introduction
Viruses are infectious particles consisting of little more than genes packed in a protein coat.
Viruses are nonliving because they cannot reproduce on their own.
Structure of viruses
Virus genomes can be double stranded DNA, single stranded DNA, double stranded RNA,
or single stranded RNA.
The genome is usually organized as a single linear or circular molecule of nucleic acid.
The protein shell enclosing the viral genome is called a capsid. Could be rod-shaped,
polyhedral, or more complex in shape.
Capsids are built from a large number of protein subunits called capsomeres.
Viral envelopes are membranes surrounding viruses that contain host cell phospholipids
and glycoproteins. This aids the virus in entering the host cell.
Viruses that infect bacteria are called bacteriophages. These viruses usually bind to
teichoic acid chains as means to cell attachment.
Viruses only replicate in host cells. The number of species a particular virus can infect is
called the host range of the virus.
Phages that can reproduce by lytic and lysogenic cycle are called temperate phages.

Lytic cycle
A phage that replicates only by the lytic cycle is called a virulent phage.
Stage 1: Virus attaches to the host cell.
Stage 2: Virus injects DNA into host cell. Host cell's DNA is hydrolyzed.
Stage 3: Viral DNA directs production of viral proteins and copies of the viral genome by
host and viral enzymes.
Step 4: New viruses are put together.

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Step 5: Virus directs production of an enzyme that damages the cell wall, allowing to fluid
and enter. The cell swells and bursts, releasing new virus particles.

Lysogenic cycle
A prophage is a virus who has injected its DNA into the host cell and the DNA
incorporated itself into the host chromosome.
Phage injects DNA into the host cell. The host cell incorporates itself into the host DNA and
lays dormant. Bacterium reproduces normally, copying the prophage DNA long with it.
Certain stress factors activates the prophage DNA to begin the lytic cycle. When this
happens, the phage DNA will begin creating itself and will follow the lytic cycle from hereon out, until it re-enters the lysogenic cycle.

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RNA viruses
RNA viruses are called retroviruses.
These viruses are equipped with an enzyme called reverse transcriptase, which transcribes
an RNA template into DNA.

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1. Weak Interactions in Aqueous Systems
a) Hydrogen bonding gives water its unusual properties
Each hydrogen atom of a water molecule shares an electron pair with the central oxygen
atom. The H-O-H bond angle is 104.5 degrees.
The oxygen nucleus attracts electrons more strongly than does the hydrogen nucleus;
that is, oxygen is more electronegative. The result of this unequal electron sharing is two
electric dipoles in the water molecule, one along each of the H-O bonds; each hydrogen
atom bears a partial positive charge and the oxygen atom bears a partial negative charge
equal in magnitude.
As a result, there is an electrostatic attraction between the oxygen atom of one water
molecule and the hydrogen of another, called a hydrogen bond. It is a weak bond, about
10% covalent and 90% electrostatic.
Hydrogen bonds in water have a very short lifetime, but they are constantly breaking
and forming. The sum of all the hydrogen bonds between water molecules confers great
internal cohesion on liquid water.
The nearly tetrahedral arrangement of the orbitals about the oxygen atom allows each
water molecule to form hydrogen bonds with as many as four neighboring water
molecules.
Hydrogen bonds account for a higher melting point because much thermal energy is
required to break a sufficient portion of hydrogen bonds to destabilize the crystal lattice
of ice.
During melting or evaporation, the entropy of the system increases as the water
molecules become less orderly.
b) Water forms hydrogen bonds with polar solutes
Hydrogen bonds form between an electronegative atom (the hydrogen acceptor, usually
oxygen or nitrogen) and a hydrogen atom covalently bonded to another electronegative
atom (the hydrogen donor) in the same or another molecule.
Hydrogen bonded to carbons do not participate in hydrogen bonding.
4 important hydrogen bonds in our body:
Between the hydroxyl group of an alcohol and water
Between the carbonyl group of a ketone and water
Between peptide groups in polypeptides
Between complementary bases of DNA

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Hydrogen bonds are strongest when the bonded molecules are oriented to maximize
electrostatic reaction, which occurs when the hydrogen atom and the two atoms that
share it are in a straight linethat is, when the acceptor atom is in line with the covalent
bond between the donor atom and H.
c) Water interacts electrostatically with charged solutes
Compounds that dissolve easily in water are hydrophilic whereas nonpolar solvents that
does not dissolve easily in water are hydrophobic.
Water easily dissolves charged molecules; it destabilizes the charge by surrounding the
individual ions. Water has a very high dielectric constant, a physical property that
reflects the number of dipoles in a solvent. By this being high, it is effective in screening
electrostatic reactions between dissolved ions.
d) Nonpolar gasses are poorly soluble in water
e) Nonpolar compounds force energetically unfavorable changes in the structure of water
When water is mixed with a nonpolar compound, two phases form; neither liquid is
soluble in the other.
The nonpolar compounds interfere with the hydrogen bonding among water molecules.
Dissolving hydrophobic molecules in water produces a measurable decrease in entropy.
Water molecules in the immediate vicinity of a nonpolar solute are constrained in their
possible orientations as they form a highly ordered cage-like shell around each solute
molecule. The number of ordered water molecules, and therefore the magnitude of of
the entropy decrease, is proportional to the surface area of the hydrophobic solute
enclosed within the cage of water molecules.
Amphipathic compounds contain regions that are polar and regions that are nonpolar.
When an amphipathic compound is mixed with water, the polar, hydrophilic region
interacts favorably with water and tends to dissolve, but the nonpolar, hydrophobic
region tends to avoid contact with water. The nonpolar regions cluster together to
present the smallest hydrophobic area to the aqueous solvent, and the polar regions
are arranged to maximize their interaction with the solvent. These structures are
called micelles. The forces that hold the nonpolar regions of the molecules together
are called hydrophobic interactions.
2. Ionization of Water, Weak acids, and weak bases
a) Pure water is slightly ionized
When any acid is dissolved in water, they contribute H+ by ionizing; bases consume H+
by becoming protonated. The total hydrogen ion concentration from all sources is
measurable and is expressed as the pH of the solution.
Hydrogen ions formed in water are immediately hydrated to form hydronium ions
(h3o+). Hydrogen bonding between water molecules makes the hydration of
dissociating protons virtually instantaneous.
No individual proton moves very far through the solution, but a series of proton hops
between hydrogen-bonded water molecules causes the net movement of a proton over a
long distance in a remarkably short time.
As a result of the high ionic mobility of H+, the acid-base reactions in aqueous solutions
are exceptionally fast.
b) The pH and blood
When the pH of the blood often falls below the normal value of 7.4, this condition is
called acidosis. When the pH of the blood is higher than normal, the condition is called
alkalosis.
3. Cohesion vs Adhesion and Capillary Action

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a) Cohesion
Cohesion water is attracted to other water molecules. Defined as the stickiness that
water molecules have for eachother.
Cohesion makes a water droplet a drop.
b) Adhesion
Adhesion water is attracted to other substances (namely polar ones).
c) Capillary action
Capillary action is the movement of water within the spaces of a porous material
against the flow of gravity. This is due to adhesion and cohesion.

4. Specific heat of water

a) Water's high specific heat
The ability of water to stabilize temperature stems from its relatively high specific heat.
The specific heat of a substance is defined as the amount of heat that must be absorbed
for 1g of that substance to change its temperature by 1 degree Celsius.
This means that water will change its temperature less than other liquids when it absorbs
or loses a given amount of heat.
The high specific heat of water can be due to its hydrogen bonding. Heat must be
absorbed to break hydrogen bonds. Since hydrogen bonds are strong, lots of heat is
required to make this happen.

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Section 46.1
Asexual and sexual reproduction
In sexual reproduction, the fusion of haploid gametes form a diploid cell, the zygote.
Eventually, the animal that develops from a zygote can give rise to gametes by meiosis.
In humans:
The female gamete, the egg, is large and non-motile
The male gamete, the sperm, is much smaller and motile
In asexual reproduction, new individuals are generated without the fusion of egg and
sperm.
Reproduction relies entirely on mitotic cell division

Mechanisms of asexual reproduction

Budding is when new individuals arise from outgrowths of existing ones (reef building
coral)
Common among invertebrates is fission, the separation of a parent organism into two
individuals of approximately equal size (similar to mitosis).
Parthenogenesis is when an egg develops without being fertilized (bees, wasps, ants, etc.)
Progeny can be haploid or diploid
Asexual reproduction can be a two-step process:
fragmentation: breaking of the body into several pieces
regeneration: regrowth of lost body parts
If more than one piece grows and develops into a complete animal, the effect is
reproduction
reproductive cycles
Most animals exhibit cycles in reproductive activity, often related to changing seasons.
Found in asexully and sexually reproducing animals
Cycles controlled by hormones. Secretion of hormones is regulated by environmental
cues.
Because reproductive cycles are regulated by environmental cues, global climate change
can affect reproduction.
Ovulation, the release of mature eggs, occurs at the midpoint of a cycle.
Variation in patterns of sexual reproduction
Hemaphroditisim is when an individual has both male and female reproductive systems.

Section 46.2

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Introduction
the union of sperm and egg, fertilization, can be either internal or external.
In external fertilization, t he female releases eggs into the environment where the male
fertilizes them.
Moist habitat is almost always required for external fertilization, to prevent gametes
from dying out and allow the sperm to swim to the eggs
Other species have internal fertilization, where sperm is deposited in or near the female
reproductive tract, and fertilization occurs within that tract.
It is an adaptation that enables sperm to reach en egg even when the environment is dry
Non-placental internal development: certain animals (e.g. marsupials, tropical fish)
have no placenta. There is limited exchange of food and oxygen between mother and
young.
Placental internal development: lots of exchange of food and oxygen between mother
and young.
Ensuring the survival of offspring
Internal fertilization is typically associated with the production of fewer gametes than
external fertilization but results in the survival of a higher fraction of zygotes.
This is because the environment of internal fertilization is shielded from predators and
also contains mechanisms that provide greater protection and care of the embryos.
Gamete production and delivery
Sexual reproduction in animals relies on sets of cells that are precursors for eggs and sperm.
These precursor cells are created very early in life and remain inactive until later in life,
where they are amplified to increase production of gametes.
Animals also employ a variety of reproductive systems
Gonads are organs that produce gametes.
More elaborate reproductive systems include sets of structures that carry, nourish, and
protect the gametes.
In many insect species, the female reproductive system contains one or more
spermathecae, sacs in which sperm may be stored for extended periods.
Vertebrate reproductive systems display limited but significant variations.
Some vertebrates have a 2 chamber uterus, others only have a 1 chamber uterus.
In many nonmammalian vertebrates, the digestive, excretory, and reproductive systems
have a common opening to the outside, the cloaca.
Animals often mate with more than one member of the other sex.

Section 46.3
Male reproductive anatomy
Testes
The male gonads, or testes produce sperm in highly coiled tubes called seminiferous
tubules.
Sertoli cells are the nurse cells of the testes that helps in the process of
spermatogenesis. Activated by follicle-stimulating hormone (FSH).
Intersticial cells (leydig cells) produce male sex hormones (testosterone) in the
presence of luteinizing hormone (LH).
The scrotum is the small muscular sac that contains and protects the testicles. Keeps the
testes cooler than the rest of the body for proper production of sperm.

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Ducts (path of sperm is SEVEnUP)
From the seminiferous tubules of a testis, the sperm pass into the coiled duct of an
epidiymis. Takes 3 weeks for sperm to pass through this (enough time for it to grow and
mature).
During ejaculation, the sperm are propelled from each epidiymis through a muscular
duct, the vas deferens.
Each vas deferens, one from each epididymis (one for each testes), extends around
and behind the urinary bladder, where it joins a duct from the seminal vesicle,
forming a short ejaculatory duct.
The ejaculatory duct opens to the urethra, the outlet tube for both the excretory
system and the reproductive system.
Penis
The human penis contains the urethra as well as three cylinders of spongy erectile
tissue.
During sexual arousal, the erectile tissue fills with blood from the arteries and the
increased pressure blocks of the veins. This causes an erection.
The main shaft of the penis is covered by relatively thick skin.
The head, or glans, of the penis has a much thinner outer layer and is more sensitive to
stimulation
the human glans is surrounded by a fold of skin called the prepuce, which is removed
during circumcision.
Accessory glands
three sets of accessory glandsthe seminal vesciles, the prostate glands, and the
bulbourethral glandsproduce secretions that combine with sperm to form semen, the
fluid that is ejaculated.
Two seminal vesicles contribute about 60% of the volume of the semen. Provides
mucus (liquid for sperm), fructose as ATP, and prostaglandins
The prostate gland secretes its products directly into the urethra through the small
ducts. Neutralizes acidity of urine that may still be in urethra, vagina acidity, and
seminal fluid.
Bulbourethral glands secrete small amount of fluid of unknown function into the
urethra.

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Human Female reproductive anatomy

Ovaries
The female gonads are a pair of ovaries that flank the uterus and are held in place by
ligaments.
Outer layer is packed with follicles, each consisting of an oocyte, a partially developed
egg, surrounded by support cells.
Support cells nourish and protect oocyte during development.
Oviduct and uterus
Oviduct, or fallopian tube, extends from the uterus to each ovary.
The cilia that lines the oviduct helps facilitate movement of the egg.
The uterus is a thick, muscular organ that can expand during pregnancy to
accommodate a fetus.
The inner lining of the uterus is the endometrum (richly supplied with blood vessels).

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The neck of the uterus, the cervix opens up to the vagina.
Vagina
Vagina is a muscular but elastic chamber that is the site of insertion of the penis. Also
serves as the birth canal where a baby is born.
The clitoris consists of erectile tissue supporting a rounded glans.

Mammary glands
Mammary glands (only in mammals) are present in both sexes, but they normally produce
milk only in females.
Spermatogenesis
The father cell of sperm is clalled the spermatogonia cells primary spermatocytes

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(mitosis) (meiosis I) 2 secondary spermatocytes (meiosis II) 4 spermatids

Sertoli cells nourish the newly formed sperm cells and help make them motile.
Sperm
Sperm are compact packages of DNA specialized for effective male genome delivery
Sperm head: contains chromosomes and the acrosome.
Acrosome is at the tip of the sperm head and contains enzymes which are used to
penetrate the egg
Midpiece: flagellum and lots of mitochondria for ATP generation
Tail: remainder of flagellum

Oogenesis
Oogonia (fetal cells) (mitosis) primary oocytes (meisosis) and remain at prophase I

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until puberty menstural cycle releases 1 egg per month released egg continues
development through remainder of meiosis I in a follicle (protects and nourishes oocyte)
(completion of meiosis I) secondary oocyte and polar body (meiosis) and remains at
metaphase II until sperm enters the egg completion of meiosis II at fertilization

Section 46.4
Hormones from multiple glands govern reproduction in males and females.
The hypothalamus secretes gonadotropin-releasing hormone (GnRH), which then directs the
anterior pituitary to secrete the gnoadotropins, follicle stimulating hormone (FSH) and

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lutenizing hormones (LH).

Are called gonadotropins because they act on male and female gonads, and they support
gametogenesis by stimulating sex hormone production, among with other mechanisms.
Sex hormones:
androgens = testosterone
estrogens = estradiol and progesterone
gonads are major source of sex hormones
Sex hormones regulate gametogenesis both directly and indirectly, but they also have other
actions.
Hormonal control of the male reproductive system
FSH and LH, released by the anterior pituitary in response to GnRH from the hypothalamus,
direct spermatogenesis by acting on different types of cells in the testis.
Hormonal upregulation:
FSH stimulates sertoli cells, located within the seminiferous tubules, to nourish
developing sperm.
LH causes leydig cells, to produce testosterone and other androgens, which promote
spermatogenesis.
Negative feedback routes:
Testosterone regulates blood levels of GnRH, FSH, and LH.
Inhibin, a hormone that in males is produced by sertoli cells, acts on the anterior
pituitary gland to reduce FSH secretion.
Hormonal control of female reproductive cycles
The cyclic shredding of the blood-rich endometrium from the uterus, a process that occurs
in a flow through the cervix and vagina, is called menstruation.
Menstrual cycle refers to the changes that occur about once a month in the uterus
The cyclic changes in the uterus is called the ovarian cycle.
Menstrual cycle
menarche is a girl's first menstrual period
Hypothalamus and anterior pituitary initiate the reproductive cycle. Low levels of estrogen
and progesterone lead to the secretion of GnRH, which in turn, stimulates production of
FSH and LH.
FSH stimulates the development of the follicle and the oocyte.
FSH also stimulates the secretion of estrogen from the follicle.
The rising levels of estrogen stimulate the anterior pituitary to create lots of LH. The surge
of LH triggers ovulation.
After ovulation, the follicle, now called the corpus luteum, continues to develop under the
influence of LH and secretes both estrogen and progesterone.
Estrogen and progesterone stimulate the development of the endometrium.
Negative feedback from the high levels of estrogen and progesterone cause the anterior
pituitary to crease production of FSH and LH through the hypothalamus.
In absence of FSH and LH, the corpus luteum deteriorates. The deterioration stops
production of estrogen and progesterone. When estrogen and progesterone stop getting
produced, the growth of the endometrium cannot be supported. As a result, the endometrium
disintegrates; sloughing off during menstruation.
If implantation of the embryo occurs, the implanted embryo will secrete human chorionic
gonadotropin (HCG) to sustain the corpus luteum. As a result, the corpus luteum will

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produce estrogen and progesterone to maintain the endometrium. Estrogen and progesterone
production will then be maintained by the placenta later on.
Ovarian cycle
follicular phase: development of the egg and secretion of the estrogen from the follicle.
Ovulation: the midcycle release of the egg
Luteal phase: the secretion of estrogen and progesterone from the corpus luteum after
ovulation.
the menstrual cycle consists of the menstrual flow phase, proliferative phase, and secretory
phase
menstrual phase is when the endometrium is shed
proliferative phase is when estrogens allow the endometrium to thicken as allow glands
and arteries to grow during the secretory phase
secretory phase is when the corpus luteum produces progestrone which allows the
endometrium to be receptive to implantation of the blastocyst. Progesterone levels are at the
highest during this phase.
Birth control pills contain synthetic estrogen and progestin. Estrogen and progestin stops
pituitary gland from releasing FSH and LH.

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Fertilization
1a) Capacitation: Secretions from the uterus wall and uterine tube destabilize the plasma
membrane surrounding the head of the sperm, making the head more fluid which helps it
prepare for fertilization, and makes the sperm hyperactive (Faster and wiggle more)
1b) Contact: The sperm contacts the egg's jelly coat, triggering exocytosis of the sperm's
acrosome.
2) Acrosomal reaction: the hydrolytic enzymes make a hole in the jelly coat. Actin
filaments extend from the sperm onto sperm-binding receptors (ZP3) on the plasma
membrane (zona pellucida) of the egg. The binding to the ZP3 receptors triggers the
acrosome reaction during which the enzymatic contents of the acrosome are released. Helps
the sperm create a hole through the zona pellucida.
3) contact and fusion of sperm and egg membranes: fusion triggers depolarization of the
membrane, which acts as a fast block to polyspermy (prevents other sperm from fusing)
4) cortical reaction: cortical granules in the egg fuse with the plasma membrane. The
secreted contents clip off the sperm-binding receptors and cause the fertilization envelope to
form. This acts as a slow block to polyspermy.
5) Entry of sperm nucleus. This triggers meiosis II
6) fusion of nuclei and replication of DNA: sperm and ovum nuclei fuse to create the
zygote

Cleavage
The zygote undergoes a succession of rapid cell divisions that characterize the cleavage
stage of early development.

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during cell cleavage the nuclear to cytoplasmic ratio increases

G1 and G2 phase of cell cycle basically skipped, cells are in S and M phase.
No increase in mass
Cleavage partitions of the cytoplasm of the larged fertilized egg into many smaller cells
called blastomeres.
Pattern of cleavage divisions differs among species.

Common characteristics of early cleavage:

Embryo polarity (asymmetric cleavage): Egg has an upper, animal pole, and a lower,
vegetal pole. The yolk (stored nutrients) will be distributed unequally, pooling at the
vegetal pole.
Polar and equatorial cleavages: The yolk begins to affec the relative size of cells
produced in the two hemispheres. This division is equatorial if the line is perpentiduclar
to the line connecting the poles. The division can also be polar if the line is the same line
connecting the poles.
Holoblastic vs meroblastic: Holoblastic is when the cleavage furrow passes entirely
through the egg whereas meroblastic means when the cleavage furrow does not pass
entirely through the egg.
Radial and spiral cleavages: In duterostomes, early cleavages are radial, forming cells
at the animal and vegetal poles that are aligned together, the top cells directly above the
bottom cells. In protosomtes, cleavages are spiral, forming cells that are shifted with
respect to those below them.
Indeterminate and determinate cleaves: A cleavage is said to be indeterminate if it
produces blastomeres that, if separated, can individually complete normal development.
Blastomeres produced by a determinate cleavage cannot develop into a complete
embryo if separated from other blastomeres.
Radial cleavages in duterostomes are usually indeterminate, whereas spiral
cleavages in protostomes are usually determinate.
Successive cleavage dvisions result in a solid ball of cells called a morula (8 cell stage, the
cells are totipotent).
As cell divisions continue, liquid fills the morula and pushes cells out to form a circular
cavity surrounded by a single layer of cells. The hollow sphere of cells is called the blastula
(128 cell stage) and the cavity is called the blastocel.
Formation of the gastrula occurs when a group of cells invaginate (move inward) into the
blastula, forming a two layered embryo with an opening from the outside into a center

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cavity. Special features:
Archentron: The center cavity formed by gastrulation. Completely surrounded by
endoderm cells. Develops into the digestive tract of an animal.
Blastopore: opening into the archentron. Becomes the mouth (in protostomes) or the
anus (in duterostomes).
Three germ layers: A third cell layer forms in between the outer and inner layers of the
invaginated embryo. These three cell layers, the ectoderm, mesoderm, and endoderm
(outside, middle, and inside layer, respectively) are the three primary germ layers from
which all subsequent tissues develop.
Ecotderm: forms epidermis skin, nervous and sensory systems, pituitary gland, jaws
and teeth, germ cells
Mesoderm: muscle, bone, kidneys, blood, gonads, and connective tissues
Endoderm: epithelial lining of most organs, thymus, thyroid, and parathryoid
glands, liver, and the lungs

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Embryonic membrane development

In birds, reptiles, and humans, called the amniotes, extraembryonic (outside the embryo)
membranes develop, as follows:
Chorion: The chorion is the outer membrane that surrounds the embryo. In birds and
reptiles, it acts as a membrane for gas exchange. In mammals, the chorion implants into
the endometrium. Later, the chorion forms the placentaa blaned of maternal and
embryonic tissues across which gases, nutrients, and wastes are exchanged.
Amnion: The amnion is a membrane encloses the amniotic cavity, a fluid-filled cavity
that cushions the developing embryo.
Allantois: A sac that buds off from the archentron. Eventually, it encircles the embryo,
forming a layer below the chorion. In birds and reptiles, it initially stores waste
products. Later in development, it fuses with the chorion, and together they act as one
membrane for gas exchange. In mammals, the allantois transports waste product to the
placenta. Eventualy forms the umbilical cord.
In birds and reptiles, a yolk sack membrane digests enclosed yolk. Yolk is a part of an
egg that feeds the developing embryo. Blood vessels transfer nutrients to the embryo. In
placental mammals, the yolk sack is empty as the umbilical cord/placenta delivers
nutrients.
Organogenesis
The development of organs is called organogenesis. Features characteristic of chordates:
Notochord: cells along the dorsal surface of the mesoderm germ layer form the
notochord, a stiff rod that provides support in lower order chordates. In most vertebraes,
a more complex, joined skeleton develops around the ancestral notochord, and the adult
retains only remnants of the embryonic notochord.
Neutral tube: In the ecotderm layer directly above the notochord, a layer of cells form
the neural plate. The plate indents, forming the neural groove, and then rolls up into a
cylinder, the neural tube. The neural tube develops into the nervous system. Additional
cells roll off the top of the developing neural tube and form the neural crest. These cells
form various tissues: including teeth, bone, and muscles of the skull, etc.

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Important variations in other animals in development

Frog (an amphibian)
When the sperm penetrates a frog egg, a reorganization of the cytoplasm results in the
appearance of a gray, crescent-shaped region, called the gray crescent.
The dorsal lip, which forms at the site of the grey crescent, is the site of initiation of
gastrulation in the amphibian embryo. The bottom and sides of the blastopore edge are
called the ventral and lateral lips.
Cells from the vegetal pole rich in yolk material form a yolk plug near the dorsal lip.

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Bird
Most of the yolk in the bird is not involved in cleavages. Instead, the cleavages occur in
a blastula that consists of a flattened, disk-shaped region that sits on top of the yolk. This
is called a blastodisc. When gastrulation occurs, invagination occurs along a line called
the primitive streak. As cells migrate into the primitive streak, the crevice formed
becomes an elongated blastopore.

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Humans
At the end of cleavage, the embryo is a blastocyst, the mammalian version of a blastula.
Clustered at one end of the blastocyst cavity is a group of cells called the inner cell
mass (embryonic disk) and at the other end is another ring of cells called the
trophoblast.
The trophoblast have several functions. First, it accomplishes implantation by
embedding into the endometrium of the uterus. It produces human chorionic
gonadotropin, which maintains progesterone production of the corpus luteum (which,
in turn, will maintain the endometrium). Later, the trophoblast forms the chorion, the
extraembryonic membrane that will eventually turn into the placenta.
Within the trophoblast, a bundle of cells called the inner cell mass (embryonic disk)
clusters at one end and flattens into the embryonic disk. This is analogous to the
blastodisk of birds and reptiles. A primitve streak develops, gastrulation follows, and
development of the embryo and the extraembryonic membranes ensues.

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Factors that influence development and differentiation

Influence of the egg cytoplasm. Cytoplasmic material is distributed unequally in the egg
and subsequent daughter cells during cleavage (i.e. yolk and gray crescent). Nonuniform
distribution of the cytoplasm results in embryonic axes. When cleavages divide the egg, the
quality of cytoplamic substances will vary among daughter cells. Substances unique to
certain daughter cells may influence their subsequent development.
Embyronic induction is the influence of one cell group or group of cells over neighboring
cells. Cells that exert this influence are called organizers; they do this by secreting
chemicals that diffuse to neighboring cells, influencing their development.
The dorsal lip functions as an organizer for the notochord.
Homeotic genes contribute to the control of development by turning on and off other genes
that code for substances that directly affect development. A homeobox is an 180 nucleotide
sequence that is highly conserved between many species that are homeotic genes.
Apoptosis, programmed cell death, is a normal part of development. Damaged cells
undergo apoptosis; if not, cancer may develop.
During embyronic development, the individual digits separate after being fused. This
best illustrates apoptosis.
The fate of a cell is said to be determined if its final form cannot be changed. Cells are
more likely to be determined later in the developmental sequence than earlier.
By tracing the fates of cells during development, a lineage map can be built (tells you
which cells arose from which cells).
Stem cells
Many early animal embryos contain stem cells capable of giving rise to differentiated cells
of any type (embryonic stem cells).
Stem cells can be isolated from early embryos at the blastula stage, or the blastocyst stage in
humans. These cells can differentiate into many different types of cells.
Adult body has stem cells (adult stem cells), but they can only generate a few different
types of cells.
Totipotent stem cells are the most versatile of stem cell types. Can give rise to ANY and
ALL human cells. Can give rise to an entire organism. First few divisions in embryonic
development produce totipotent cells.
Pluripotent stem cells can give rise to all tissue types, but CANNOT give rise to an entire
organism.
Multipotent stem cells give rise to a limited range of cells within a tissue type.
Types of reproducing animals
monotremes are egg laying mammals (platypus)
marsupials are mammals where the young is carried in a pouch
a viviparous mammal is one in which the offspring develop within the uterus
an oviparous mammal is one in which the parent lays eggs (birds, some amphibians, most
repitles)
oviviparous animal is a combination. The young are hatched from eggs, but the eggs are
kept in the mother's body until they are ready to hatch.
Fertilization, pregnancy, and labor
fertilization (syngamy) of the egg normally occurs in the fallopian tubes
Fraternal twins result from more than one egg being fertilized; identical twins result from
indeterminate cleavage

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Ectopic pregnancy results when the zygote makes contact and starts to grow in improper
places.
Tubal pregnancies are when the zygote implants itself into the fallopian tube
erythroblastosis fetalis = Rh+ fetus; Rh- mother (google this if you don't understand this)
first trimester of pregnancy is where organs are formed
at approximately 8 weeks, the embryo is called a fetus
at 5 weeks, eyes, heart, liver, pancreas, and limb buds have begun development
Labor (three stages) a series of strong uterine contractions
1. Cervix thins out and dilates, amniotic sac ruptures and releases fluids
2. Rapid contractions followed by birth
3. Uterus contracts and expels umbilical cord and placenta
Insect development
In insects, molting and metamorphosis are regulated by the hormone ecdysone

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Archaea
Archaea are prokaryotes but differ from bacteria.
Archael cell walls (different from bacteria) contain various polysaccharides and proteins,
but not peptidoglycan.
Phospholipid components (different from eukaryotes and bacteria): glycerol is different
and the hydrocarbon chains are branched with ether-linkages instead of ester-linkages.
Similarity with eukaryotes:
DNA of both archaea and eukaryotes are associated with histones, but bacterial DNA is
not.
Ribosome activity is not inhibited by certain antibiotics such as streptomycin and
chloramphenicol unlike bacteria.
Various groups of archaea
Methanogens: obligate anaerobes that produce methane as a by-product of obtaining
energy from hydrogen gas to fix carbon dioxide.
Extremophiles: live in extreme environments
Halophiles (salt lovers): live in extremely salty environments; most are aerobic and
heterotrophic whereas others are anaerobic and photosynthetic with the pigment
bacteriorhodopsin.
Thermophiles (heat lovers): sulfur-based chemoautoroph in very hot places.
Acidophile is an organism with an optimal growth at pH levels 3 or below. Aklaliphile
is an organism with optimal growth at pH levels 9 or above.
Bacteria
Distinct from archaea and eukaryotes by these features:
cell wall made up peptidoglycan
bacterial DNA not associated with histones
ribosome activity is inhibited by streptomycin and chloramphenicol
How bacteria are classified
Mode of nutrition/how they metabolize resources
Ability to produce endospores (resistant bodies that contain DNA and a small amount
of cytoplasm surrounded by a durable wall)
Means of motility: flagella, corckscrew motion, or gliding through slime material
Shapes: cocci (spherical), bacilli (rod-shaped), spirilla/spirochetes (spiral)
Thick peptidoglycan cell wall (gram-positive), thin peptidoglcyan cell wall covered
with lipopolysaccharides (gram-negative).
Common groups of bacteria
cyanobacteria: photosynthetic bacteria (contain accessory pigment phycobillins; some
are specialized cells called heterocysts that produce nitrogen-fixing enzymes). Known
as blue-green algae.
Chemosynthetic: autotrophs; some are nitrifying bacteria NO2- NO3 Nitrogen-fixing: heterotrophs that fix nitrogen, lives in nodules of plants (mutualism)
Spirochetes: coiled bacteria that move with corkscrew motion, internal flagella between
cell wall layers.

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Kingdom Protista
Protista is an artificial kingdom used mainly for convenience; poorly understood. Features
shared by two or more groups may represent convergent evolution. (arose independently). Most
are unicellular.
Algaelike (plant-like): members of protista that all obtain energy by photosynthesis. All have
chlorophyll a, some have others plus accessory pigments. Mainly categorized via the form of
carbohydrate used to store energy.
phytoplankton are autotrophic organisms that float near the surface of the ocean, lakes, and
ponds.
Eugleniods
Have one to three flagella at their apical (leading) end.
Instead of cellulose cell wall, they have thin, protein strips called pellicles that wrap
over their cell membranes.
Heterotrophic in absence of light
some have an eyespot that permits phototaxis (ability to move in response to light)
Dinoflagellates
Have two flagella: one is posterior, while the second is transverse (across the body) and
rests in an encircling mid groove perpendicular to the first flagellum.
Some of these are bioluminescent.
Others produce nerve toxins that concentrate in filter-feeding shellfish, which can cause
illness in humans.
the red tide is a harmful algal bloom caused predominantly by dinoflagellates
Diatoms
Have tests (shells) that fit together like a box with a lid.
Shells made out of silica dioxide (SiO2)
Brown algae
Multicellular
Flagellated sperm cells
some are giant seaweeds, or kelps
Rhodophyta (red algae)
Contain red accessory pigments called phycobilins.
Multicellular
Gametes do not have flagella
Chlorophyta (green algae)
Have chlorophyll a and b
Have cellulose cell walls
Store carbohydrates as starch
Some species have isogamous gametes, where both sperm and egg are motile and equal
in size
Some species have ansiogamous, where the sperm and egg differ in size
Some species are oogamous, where a large egg cell remains with the parent and is
fertilized by a small, motile sperm.
A lineage of Chlorophytes, the charophytes, are believed to be the ancestors of plants
Protozoa (animal-like): heterotrophs that consume either living cells or dead organic mater.
Rhizopoda
Amoebas that move by extension of their cell body called pseudopodia.
Pseudopodia encircle food and absorb it by phagocytosis.
Foraminifera

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Tests usually made up of calcium carbonate (CaCO3)

Many ancient marine sediments consisting of certain foram tests are good indicators of
underlying oil deposits.
Apicomplexans
Parasites of animals
Characterized by apical complex, a complex of organelles located at each end (apex) of
the cell.
No physical means of motility
Form spores that are dispersed by one or more hosts
Ciliates
Distinguished by their cilia, which they use for moving.
Have specialized features such as mouths, anal pores, contractile vacuoules, two kinds
of nuclei (one large and one small), and other features.
Perhaps the most complex of all cell.
Paramecium
Fungi-like protists resemble fungi because they form either filaments or spore-bearing bodies
similar to the fungi.
Cellular slime molds
exhibit both funguslike and protozoalike characteristics during their life cycle.
Spores germinate into amoebas which feed on bacteria
When food sources are depleted, the amoebas aggregate into a single unit, which
migrates as a slug. The individual cells of the slug mobilize to form a stalk with a
capsule at the top similar to the spore-bearing bodies of many fungi. Spores are then
released, which repeat the cycle.
The stimulus for aggression is cyclic AMP, which is secreted by the amoebas that
experience food deprivation first.
Plasmodial slime molds
Grow as a single, spreading mass (plasmodium) feeding on decaying vegetation.
When food becomes unavailable or when the environment desiccates (dries up), stalks
bearing more capsules form.
Haploid spores released from the capsule germinate into haploid amoeboid or flagellated
cells, which fuse to form a diploid cell.
The diploid cell grows into the spreading plasmodium.
Oomycota
Either parasites or saprobes
They form filaments (hyphae) which secret enzymes that digest the surrounding
substances. The breakdown products are then absorbed.
The filaments of Oomycota lack septa, or cross walls, which in many of the true fungi
have.
Because they lack septa, they are coenocytic, containing many nuclei within a single
cell.
Cell walls made up of cellulose, not chitin like fungi

Kingdom fungi
Properties of fungi
fungi grow as filamments called hyphae

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A mass of hyphae is called mycellium

Some fungi have septum which divides the filament into compartments containing single
nucleus.
Those without septa are coenocytic, or multinucleated.
Cell walls contain chitin, a nitrogen containing polysaccharide
Are either parasites or saprobes.
Many parasitic fungi have hyphae called haustoria that penetrate their host.
A fungus not only attacks dead matter, but may attack living tissue such as in athlete's foot
fungi are more similar to human cells than bacterial cells
Sexual reproduction
Fungi are primarily haploid, but most form temporary diploid structures for sexual
reproduction.
3 primary stages:
Plasmogamy is the fusing of cells from two different fungal strains to produce a single
cell with nuclei from both strains. A pair of haploid nuclei, one from each strain, is
called a dikaryon.
Karyogamy is the fusing of the two haploid nuclei of a dikaryon to form a single
diploid nucleus.
Meiosis of the diploid nucleus restores the haploid condition. Daughter cells develop
into haploid spores, which germinate and form haploid hyphae.
Asexual reproduction
Fungi reproduce asexually by various means:
fragmentation of the hyphae and regeneration
budding the pinching off a small hyphal outgrowth
asexual spores (2 types):
sporangiospores are produced in sacklike capsules called sporangia that are born
on a stalk called a sporangiophore.
Conidia are formed at the tips of specialized hyphae, not enclosed inside sacks.
Hyphae bearing conidia are called conidiophores.
Fungal groups
Zygomycota (bread mold)
lack septa, except when filaments border reproductive filaments
reproduce sexually by fusion of hyphae from different strains
Haploid zygospores are produced, which germinate into new hyphae.
Glomeromycota (symbiotic fungi)
Lack septa, but do not produce zygospores.
Occur only in mutualistic associations with roots of plants
Mycorrhizae plant provides carbohydrates to fungus and the fungus increases the
ability of plant roots to absorb nutrients, especially phosphorus
Ascomycota (yeast)
Have septa and reproduce sexually by producing haploid ascospores.
After plasmogamy of hyphae from unlike strains, a dikaryotic hypha produces more
filaments by mitosis.
Karyogamy and meiosis subsequently occur in terminal hyphal cells producing 4
haploid cells.
These 4 cells divide by mitosis to produce 8 haploid ascospores in a sac called an ascus.

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8 ascospores grouped together into fruiting bodies called ascocarps.
Basidiomycota (mushrooms)
Have septa and reproduce sexually by producing haploid basidiospores.
Plasmogamy between two unlike hyphae is followed by mitosis and the growth of
dikaryotic hyphae to form a fruiting body is called a basidiocarp.
Duteromycota
No sexual reproduction
Lichens (mutualistic)
mutualistic associations between fungi and algae
the algae, which is usually a chlorophyta or cyanobacteria, provides sugar from
photosynthesis. If the algae is nitrogen-fixing, then nitrogen is also provided.
The fungus, which is most often an ascomycete, provides water and protection from the
environment.
Some fungi produce pigments that shield algae from UV radiation or excess light.
Kingdom Plantae
Major plant adaptations for survival on land:
Except for primitive bryophytes, the dominant generation of all plants is the diploid
sporophyte generation. A diploid structure is more apt to survive genetic damage because
two copies of each chromosome allow recessive mutations to be masked.
All plants possess a cuticle, a waxy covering on aerial parts that reduces desiccation.
Development of a vascular system allows the plant to distribute water and nutrients
throughout all parts. Leaves developed as centers for photosynthesis. Stems developed to
provide a framework to support leaves. Roots developed to obtain water and anchor the
plant.
In the more primitive plant divisions, flagellated sperm require water to swim to eggs. In the
more advanced divisions (Coniferophyta and Anthophyta), the sperm, packaged as pollen,
are adapted for delivery by wind or animals.
In the most advanced divisions, the Anthophyta, the gametophytes are enclosed (and thus
protected) inside an ovary.
Plants of the Coniferophyta and Anthophyta have developed adaptations to seasonal
variations in the availability of water and light.
For example, some trees are deciduous; that is, they shed their leaves to minimize water
loss during slow-growing seasons.
Following plant divisions is of increased comlexity:
1) Bryophytes - (mosses, liverworts, hornworts)
Gametes are produced in protective structures called gametangia
The haploid gametophyte stage is the dominant stage of the life cycle of bryophytes
The male gametangium, or antheridium (plural, antheridia), produces flagellated sperm
that swim through water to fertilize eggs produced by the female gametangium, or
archegonium (plural, argegonia).
Resulting zygote grows into a diploid structure, still connected to the gametophyte.
Bryophytes do not have a vascular system
Must remain small and water must be readily available for absorption through surface
tissues and as a transport medium for sperm.
Tracheophytes or vascular plants. Contain a vascular system. Similar reproduction cycle to

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the Bryophytes where the gametophytes produce antheridia and archegonia and the flagellated
sperm must swim to the archegonia to fertilize the eggs. However, the sporophyte is the
dominant generation.
2) Lycophyta (club mosses, spike mosses, quillworts)
Produce clusters of spore-bearing sporangia in conelike structures called strobili.
3) Pterophyta
Ferns
Produce clusters of sporangia called sori that develop on the under-surface of fern
fronds (leaves).
Horsetails
Have hollow, ribbed stems that are joined at nodes. Nodes occur at intervals along
the stem and produce small leaves and, in some species, branches.
Stems, branches, and leaves are green and photosynthetic and have a rough texture
to the presence of silicon dioxide.
Sporangia are called strobili.
Whisk ferns
Branching stems without roots
Leaves are very small or absent
The absence of roots and leaves is considered a secondary lossthat is, these
structures were lost as whisk ferns diverged from their ancestors.
Seed plants: two kinds of spores are produced, male spores and female spores.
Microsporangia produce the microspores (male spores), and the macrosporangia produce the
macrospores (female spores). Summary of reproduction in seed plants:
Microsporangium produces numerous microspore mother cells, which divide by meiosis to
produce 4 haploid cells, the microspores.
Microscpores mature into pollen grains. A pollen grain represents the male
gametophyte generation.
The pollen grain further divides into three cells (in flowering plants) or four cells (in
conifers). One of these cells is a vegetative, or tube, cell that controls the growth of the
pollen tube. Other cells become the sperm cells.
The megasporangium, called the nucellus, produces a macrospore mother cell, which
divides by meiosis to produce 4 haploid cells. One of these cells survives to become the
megaspore and represents the female gametophyte generation.
Megaspore divides by mitosis to produce one egg (in flowering plants) or two eggs (n
conifers).
Other accessory cells, in addition to the egg may be produced: one of two tissue layers
called integuments surround the megasporangium.
The integuments, nucellus, and megaspore daughter cells are collectively called the
ovule.
An opening through the integruments for pollen access to the egg is called the
micropyle.
When a pollen grain contacts the megasporangium, the tube cell directs the growth of a
pollen tube through the micropyle and toward the egg.
After fertilization by the sperm cells, the zygote forms an embryo, the beginning of the
sporophyte generation. The integuments develop into the seed coat.
4) Coniferophyta (conifers)
Cone bearing plants

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Male and female reproductive structures are borne in pollen-bearing male cones and ovulebearing female cones.
Vast majority do not have flagellated sperm
Conifers + other minor divisions make up the gymnosperms. Gymnosperms have seeds
produced in unprotected megaspores near the surface of the reproductive structure.
Fertilization and seed development are lengthy: 1-3 years.
5) Anthophyta, or angiosperms, are flowering plants.
No flagellated sperm
More specialized vascular tissues
Numerous variations in habitat in growth
Can survive in a variety of environmental conditions
Major parts of the flower:
Pistil is the female reproductive structure and consists of 3 parts: egg-bearing ovary, a
style (tube on top of the ovary), and a stigma (receives pollen during fertilization).
The stamen is the male reproductive structure and consists of a pollen-bearing anther
and its stalk, the filament (holds the anther).
Petals, and sodmetimes sepals (smaller leaves under the flower), function to attract
pollinators.
Flower is an evolutionary advancement for the following reasons:
Flower is a special adaptation to attract pollinators, such as insects and birds
The ovules are protected inside an ovary
The ovary develops into a fruit which fosters the dispersal of seeds by wind, insects,
mammals, and other animals.
Fertilization in angiosperms:
Pollen lands on the sticky stigma. A pollen tube, an elongating cell that contains the
vegetative nucleus, grows down the style toward an ovule. There are two sperm cells
inside the pollen tube.
Ovules within the ovary consist of a megaspore mother cell surrounded by the nucellus
and integuments. The megaspore mother cell divides by meiosis to form 4 haploid cells,
the megaspores. One surviving megaspore divides 3 times by mitosis to produce 8
nuclei. 6 of the nuclei undergo cytokinesis and form plasma membranes. The result is an
embryo sac. At the micropyle end of the embryo sac are the three cells, an egg cell and
two synergids. At the opposite end of the micropyle are the three antipodal cells (play a
part in embryo nutrition). In the middle are the two haploid nuclei, the polar nuclei.
When the pollen tube enters the embryo sac through the micropyle, one sperm fertilizes
the egg, forming a diploid zygote. The nucleus of the second sperm fuses with both
polar nuclei, forming a triploid nucleus. The triploid nucleus divides by mitosis to
produce the endospore, which provides the nourishment for subsequent development of
the embryo and seedling. The fertilization of the egg and the polar nuclei each by a
separate sperm nucleus is called double fertilization.

Kingdom Animalia
5 shared characteristics
Multicellular
Heterotrophic
Dominant generation in the life cycle is the diploid generation
Most animals are motile during at least some point in the life cycle

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Undergo a period of embryonic development during which 2 or 3 layers of tissue form

7 characteristics that generate diversity
Most animals, collectively called the eumetazoa, have closely functioning cells organized
into tissues. They have two (diplopblastic) or three (triploblastic) layers of tissue called
germ layers. In another group of animals, the parazoa, cells are not organized into true
tissues, and organs do not develop.
Animals have radial symmetry, the type of symmetry found in a flowerpot. There is a top
and bottom side, but not front, back, left, or right sides. Other animals have bilaterial
symmetry, the type of symmetry found in a shovel. Have 2 axes of orientation: front to
back and top to bottom. Have a dorsal (top) side and a ventral (bottom) side, a left and a
right side, an anterior (front) end and a posterior (back) end.
Cephalization. In animals with bilateral symmetry, there is a progressively greater increase
in nerve tissue concentration at the anterior end as organism increase in complexity.
Gastrovascular cavities, or guts, are areas where food is digested. If they have one opening,
they are saclike, and the type of processes that can occur are limited. Two openings
designate a digestive tract, allowing specialized activities to occur as food travels from
beginning to end.
During embryonic development in more advanced animals, a cavity called a coleom
develops from tissue derived from the mesoderm. The fluid-filled coleom cushions the
internal organs and allows for their expansion and contraction. Acoelomate animals lack a
coleom, while pseudocoelomate animals have a cavity that is not completely lined by
mesoderm-derived tissue.
Many animals have segmented body parts. In some cases, the body parts are the same and
repeat, while in other cases the body parts are modified and adopt specialized functions.
Two markedly different cleavage patterns occur to produce two groups of animals, the
protostomes and duterostomes.
Protostomes have spiral, determinate cleavages. Solid masses of the mesoderm split
and form the coleom. The blastopore turns into the mouth.
Duterostomes have radial and indeterminate cleavages. Folds of the archentron form
the coleom. The anus develops from the blastopore.
10 main animal phyla
Porifera (sponges)
Feed by filtering water drawn through the sponge wall by flagellated cells called
choanocytes. Water exits through an opening called the osculum.
Choanocytes pass food to the amoebocytes, which wander between the two cell layers
of the sponge wall, digesting and distributing nutrients. Amoebocytes carry out
digestion.
The sponge wall contains spicules, skeletal muscles made from either CaCO3 or SiO2.
Classified with the parazoa because the cells of Porifera are not organized in a
coordinated fashion to form tissues.
Reproduces asexually via budding or sexually (hermaphrodites).
No body symmetry.
No respiratory system.
No ciruclatory system.
No excretory system.
Cnidaria (jellyfish, comb jellies, corals)
Radial symmetry, 1 gut opening, 2 germ layers, eumetazoa

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Some have stinging cells called nemocysts.

Nervous system: nerve net, no brain
Asexual or sexual reproduction
Two body forms:
Medusa which is a floating, umbrella-shaped body with dangling tentacles (typical
of jellyfish)
Polyp: a sessile, cylinder-shaped body with rising tentacles (typical of sea
anemones).
In some Cnidaria, both body forms alternate throughout the life cycle.
Platyhelminthes (flatworms, tapeworms, flukes)
Bilaterial symmetry, 1 gut opening, 3 germ layers, eumetazoa, acoelomates
No circulatory system relies on diffusion
No respiratory system relies on diffusion
Nervous system: two nerve cords (anterior centralized ganglia brain). Some have eye
spots.
Excretory system protonephridia and flame cells
Reproduction asexual (fragmentation and regeneration) or sexual (hermpahroditism)
Free-living flatworms are carnivores or scavengers that live in marine or freshwater.
Flukes are internal animal parasites or external animal parasites that suck tissue fluids
or blood.
Tapeworms are internal parasites that often live in the GI tract of vertebrates. They have
segments called proglottids but they develop secondarily for reproduction so
tapeworms are not truly segmented. Do not have a GI tract themselves and must digest
pre-digested food.
Nematoda (roundworms)
Free-living soil dwellers that help decompose and recycle nutrients.
Some have a cuticle to prevent degradation by host digestive system
Bilateral symmetry, triploblast (eumetazoa)
Pseudocoelomate
No circulatory system
Nervous system nerve cord and ring
Digestive system 2 gut openings (alimentary canal)
No excretory system
Rotifera (rotifers)
Multicellular with specialized organs enclosed in a pseudocoelom.
Bilateral symmetry
Triploblasts, eumetazoa
No circulatory system
Nervous system: cerebral ganglia (brain) w/ some nerves extending through body
No respiratory system
Digestive system filter-feeders, drawing water and food into the mouth by the beating
action of cilia. Alamentary canal (2 gut openings)
Mollusca (snails, octupuses, squids)
Most molluscs have shells made up of calcium carbonates
Have tongues called radula.
Bivalves: shell has two parts

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Squids: shell is reduced in internal
Octopuses: shell is absent entirely
Bilateral symmetry
Triploblasts, eumetazoa
Ceolmate
Open circulatory system
Nervous system Ventral nerve chords and brain
Respiratory system Gills
Digestive system 2 gut openings (alimentary canal)
Excretory system nephridia
Embryonic development protostome
Annelida (segmented worms leeches, earthworms, polychaete worms)
Leeches are either predators of small animals or blood sucking parasites. Two suckers at
opposite ends that are used for attachment and movement.
Asexual reproduction (fragmentation and regeneration) and sexual reproduction
(hermaphrodites)
Bilateral symmetry
triploblasts, eumetazoa
ceolomate
closed
nervous system nerve cord and brain
respiratory system none (diffusion)
digestive system alimentaray canal (2 openings)
excratory system metanephridia
embryonic development protostome
Arthropoda (insects, crustaceans, spiders)
Two different types of life cycles:
Some arthropods are born as nymphs, or small versions of the adult and change
shape gradually as they grow to adult size and proportions.
Other arthropods are born as larvae, maggots specialized for eating. When they
reach a certain size, they enclose themselves within a pupa (cocoon) and undergo a
dramatic change in body form, a process called metamorphosis. They emerge from
their pupae as adults, specialized for dispersal and reproduction.
Bilateral symmetry
triploblasts, eumetazoa
ceolomate
circulatory system open with hemolymph
nervous system fused ganglia, ventral nerve chord
respiratory system tracheal system with cuticles and spiracles, gills, book lungs
digestive system alimentary canal (2 openings)
excretory system malphagian tubules
embryonic system protostomes
Echinodermata (sea stars, sea urchins, sand dollars)
sexual or asexual reproduction
larvae have bilateral symmetry, adults have radial symmetry

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triploblasts, eumetazoa
ceolomate
open circulatory system
nervous system nerve ring and radial nerves
respiratory system none
digestive system alimentary canal (2 openings)
excretory system none
duterostome
Chordata
4 main shared features:
Notochord provides a dorsal, flexible rod as a support.
Dorsal hollow nerve cord forms the basis of the nervous system. In some
chordates, the nerve cord becomes the brain and spinal cord.
Pharyngeal gill slits provide channels across the pharynx (a muscular structure at
the beginning of the digestive tract) to the outside of the body. In some chordates,
the slits become gills for oxygen exchange or filter feeding, while in others, the slits
disappear during embryonic development.
A muscular tail extends beyond the digestive tract. In many chordates, such as
humans, the tail is lost during embryonic development.
Two groups of chordates:
Invertebrate chordates which include the lancelets and trunicates
Vertebrate chordates, which include sharks, fish, amphibians, repitles, burds, and
mammals. Characterized by a series of bones, the vertebrae, that enclose the spinal
cord.
Triploblastic, eumetazoa
bilateral symmetry
ceolomate
circulatory system heart
nervous system complete, brain
respiratory system gills or lungs
digestive system alimentary canal
Major time periods
Precambrian
First invertebrates
Cambrian
First vertebrates, fishes, land plants, reptiles, amphibians
Mesozoic
First mammals, birds
First flowering plants
First dinosaurs: appeared in Triassic period and died at the end of the Cretaceous period.
Cenozoic
Asteroids contain high levels of iridium. Iridium separates the mesozoic from cenozoic
sediments.
Classes
Class gastropoda: snails

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class crustacea: crabs

class arachnida: scorpions
class cephalopoda: squid
class chondrichthys: sharks and skates

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Seed plants
Seed plants include gymnosperms and angiosperms.
Angiosperms are further divided into two groups: dicotyledons (dicots) and
monocotyledons (monocots)
Characteristics that differentiate monocots and dicots
Cotyledons storage tissue that provides nutrition to the developing seeding
Dicots have 2 cotyledons whereas monocots have 1 cotyledon
Leaf venation the pattern of veins in leaves
Dicots have a netted, branching, venation pattern whereas monocots have a parallel
venation pattern.
Flower parts numbers of petals, sepals, stamens, and other flower parts
Dicots are in 4s, 5s, or multiples thereof whereas monocots are in 3s or multiples thereof
Vascular bundles arrangement of bundles of vascular tissue (xylem and phloem) in stems
Dicots are organized in a circle whereas monocots are scattered
Root form of root
Dicots have traproots (a large, single root), whereas monocots have a fibrous system (A
cluster of many fine roots)

Plant tissues
Ground tissues includes all tissues that are neither dermal nor vascular. three basic kinds
of cells that differ mostly by the nature of their cell walls
Parenchyma cells, the most basic component of ground tissue, have thin cell walls and

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serve various functions including storage, photosynthesis, and secretion.

Collencyma cells have thick but flexible cell walls, serve mechanical support functions.
Selerenchyma cells, with thick walls than collenchyma, also provide mechanical
support functions.
Dermal tissue consists of epidermis cells that cover the outside of plant parts, guard cells
that surround stromata, and various specialized surface cells such as hair cells, stinging
cells, and glandular cells. In the aerial portions of the plant, the epidermal cells secrete a
waxy proctive substance, the cuticle to prevent desiccation.
Note that roots do NOT have cuticles or else they would not be able to absorb water!
Vascular tissue consists of two major kinds of tissues: xylem and phloem. The two usually
occur together to form vascular bundles.
Xylem functions in the conduction of water and minerals and also provides mechanical
support.
In addition to the primary cell wall that all plant cells have, xylem cells have a
secondary cell wall made up of lignin that gives them additional strength.
Sometimes, the walls of the xylem cells have pits, or places where the secondary
cell wall is absent.
Most xylem cells are dead at maturity; that is, they are essentially cell wall,
completely lacking cellular components, and contain only the material being
transported.
Two kinds of xylem cells: tracheids and vessel elements/members
Tracheids, which are long and tapered, passes water from one tracheid to
another through pits on the overlapping tapered ends of the cells.
Vessel elements/members are shorter and wider than tracheids, and have less or
no taper at their ends. A column of vessel members is called a vessel. Water
passes from one vessel member to another through areas devoid of both primary
and secondary cell walls. These areas are called perforations and are literally
holes between cells.
Vessel elements/members are more efficient at moving water than tracheids;
therefore, vessel elements are considered a more evolutionarily advanced
feature. They are found most predominantly among the flowering plants.

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Phloem functions in the conduction of sugars.

Made up of cells called sieve-tube members/elements that form fluid-conducting
columns called sieve tubes.
Pores on the end walls of sieve-tube members form sieve plates, areas of the
cytoplasm of one cell makes contact with that of another cell.
Sieve tubes are associated with companion cells, living parenchyma cells that lie
adjacent to each sieve-tube member. Companion cells are connected to sieve-tube
members via plasmodermata.
Phloem cells are living at maturity, although they lack nuclei and ribosomes.

The seed
The seed consists of an embryo, a seed coat, and some kind of storage material.
The major storage material may be endosperm or cotyledon.
Cotyledons are formed by digesting the storage material in the endosperm.
In many monocots, the endosperm is the primary storage tissue. Cotyledons functions to
transfer nutrients from the endosperm to the embryo.
The embryo consists of the following parts:
The top portion of the embryo, the epicotyl, becomes the shoot tip.
Often attached to the epicotyl are young leaves usually called the plumule. (sometimes
the plumule refers to the epicotyl and the leaves)
Below the epicotyl and attached to the cotyledons is the hypocotyl. It becomes the
young shoot.

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In some embryos, a radicle develops below the hypocotyl. The radicle develops into the
root.
In many monocots, a sheath called the coleopitle surrounds and protects the epicotyl. In
a developing young plant, the coleopitle emerges first, appearing as a leaf. The first true
leaves, however, emerge from the plumule within the coleopitle.

Germination and development

After a seed reaches maturity, it remains dormant until specific environmental cues are
encountered. The most important cue is water. Others may include temperature, light, or
seed coat damage.
In some cases, there will be a required dormancy period, during which germination will
not occur, regardless of the presence of external environmental cues.
1) Germination begins with the absorption of water. Water activates enzymes, which
activates biochemical processes including respiration.
2) The growing tips of the radicle produce roots that anchor the seedling.
The growth of the root can be divided into areas based on the activity of the cells.
The root tip, or root cap, protects the apical meristem behind it.
The dividing cells of the apical meristem form the zone of elongation.

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Behind this zone is the zone of differentiation or zone of maturation. Here, cells
mature into xylem, phloem, parenchyma, or epidermal cells.
3) Elongation of the hypocotyl follows, producing a young shoot.
In the young seedling, growth occurs at the tips of the roots and shots, called apical
meristems. These are areas of actively diving, or meristematic cells. This kind of
growth is called primary growth.
Primary growth versus secondary growth
Primary growth increases the length of the plant. Tissues that develop from primary growth
are called primary tissues. Primary xylem and primary phloem refer to vascular tissues
cells originating from apical meristem growth.
Other plants undergo secondary growth, which increases the plant's girth, or lateral
dimension (to the side) and is the origin of woody plant tissues.
Secondary growth occurs at two lateral meristems: the vascular cambrium and the
cork cambrium. These cells are meristematic, capable of diving and producing new
cells thoroughout the lifetime of the plant.
The tissues that arise from the vascluar cambrium are the secondary xylem and the
secondary phloem.
The cork cambrium gives rise to the periderm, the protective material that lines the
outside of woody plants.

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Primary structure of roots

Epidermis lines the outside surface of the root. Epidermal cells produce root hairs, which
increase the absorptive surface of the roots. As the plant gets older, root hairs die. New
epidermal cells form, which will form new root hairs. Therefore, roots must constantly grow
to provide new root hairs for the absorption of water. The older epidermal cells protect the
root.
The cortex makes up the bulk of the root. Main function is to store starch. Also contains
numerous intercellular spaces, providing aeration of cells for respiration.
The endodermis is a ring of tightly packed cells at the intermost portion of the cortex.
A band of fatty material, called suberin, coats the endodermal cell walls where they

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make contact with adjacent endoderm cell walls. The encircling bands around each cell
wall, called a Casparian strip, creates a water-impermable barrier between the cells.
All water passing through the endodermis must pass between the cells and not through
the intercellular spaces. This way, the endodermal cells control the movement of water
to the center of the root (where the vasucalr tissue resides).
The vascular cylinder, or stele, makes up the tissues inside the endodermis.
The outer part of the vascular cylinder consists of one to several layers of cells called the
pericycle, from which lateral roots arise.
Inside the pericycle is the xylem and phloem.
In a typical dicot, xylem cells fill the center of the vascular cylinder. The phloem
cells occupy the regions between the lobes of the xylem core.
In monocots, groups of xylem cells alternate with groups of phloem cells in a ring
that encircles a central tissue area called the pith.

Primary structure of stems

Primary tissue in the stem contain many of the same characteristics as that in the root.
However, the endodermis and the casparian strips are lacking.
The epidermis contains epidermal cells covered with a waxy substance called cutin. The
cutin forms a protective layer called the cuticle.
The cortex consists of the various ground tissue types that lie between the epidermis and the
vascular cylinder. Many of these contain chloroplasts.
The vascular cylinder consists of xylem, phloem, and pith. In dicots, the vascular bundles
appear in a ring whereas in monocots, they appear scattered.
In addition, a single layer of cells between the xylem and the phloem may remain
undifferentiated and later become the vascular cambrium.
Secondary structure of stems and roots
The vascular cambrium originates between the xylem and phloem and becomes a cylinder
of tissue that extends the length of the stem and root.
Cells on the inside differentiate to secondary xylem cells and cells on the outside
differentiate into secondary phloem cells.
Secondary xylem and secondary phloem increase the plant's girth. The outside tissues,
which include primary tissues, break apart as they expand and eventually shed as they
separate from the stem or root.
In order to replace the shed epidermis with a new protective covering, new cells are

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produced by the cork cambrium. The cork cambrium produces new cells on the outside
and sometimes on the inside.
On the inside, the phelloderm may be produced.
Together, the cork cambrium and the phelloderm is called the periderm.
Each year, new layers of secondary xylem are produced by the vasuclar cambrium. Only
xylem produced in recent years remain active in the transport of water.
Active xylem is referred to as sapwood.
Older xylem, located toward the center of the stem, is called heartwood and functions
as support.
In many environments, conditions vary during the year, creating seasons during which
plants alternate growth with dormancy. During periods of growth, the vascular cambrium is
actively dividing, and when the season draws to an end, divisions and growth gradually
come to a halt. When the next season begins, the vascular cambrium begins dividing again.
The alternation of growth and secondary dormancy produces annual rings in the secondary
xylem tissue.
Structure of the leaf
The epidermis is the protective covering of one or more layers of cells. The epidermis is
covered by the cuticle, a protective layer of the waxy material cutin. The cuticle reduces
transpiration, or the loss of water through evaporation.
The palisade mesophyll consists of parenchyma cells equipped with numerous chloroplasts
and large surface areas, specializations for photosynthesis. Photosynthesis in leaves occurs
primarily in this tissue.
The spongy mesophyll consists of parenchyma loosely arranged below the palisade
mesophyll. The numerous intercellular spaces provide air chambers that provide carbon
dioxide to photosynthesizing cells and oxygen to respiring cells.
Guard cells are specialized epidermal cells that control the opening and closing of
stromata. Stromata are openings in the epidermis that allow gas exchange between the
inside of the leaf and the external environment.
Vascular bundles consist of xylem and phloem tissues.
There are unusually specialized mesophyll cells called bundle sheath cells that
surround the vascular bundles in such a way that no vascular tissue is exposed to intercellular space. In this way, air bubbles cannot enter vessels where they could impede the
movement of water.

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Transport of water
Two major pathways by which water moves toward the center of the root:
Water moves through cell walls and inter-cellular spaces from one cell to another
without entering the cells. This pathway is called the apoplast and consists of the
nonliving portion of cells.
Water moves from one cell to another through the symplast, or living portion of cells.
In this pathway, it moves from the cytoplasm of one cell to the cytoplasm of the next
through plasmodesmata, small tubes that connect the cytoplasm of adjacent cells.
When water reaches the endodermis, it can continue through the vascular cylinder through
the symplast pathway. The apoplast pathway is blocked by the casparian strips.
The endodermal cells allow water to enter the stele, but is selective to which ions can
enter the stele.
Potassium is allowed to pass while sodium is not allowed to pass.
Once through the endodermis, the water and dissolved minerals travel through the xylem
through the apoplast pathway.
Three major mechanisms involved in the movement of water and dissolved minerals in
plants:
Osmosis: water moves from the soil through the root and into xylem cells through
osmosis. Concentration gradient is maintained in two ways: (1) continuous movement of
water out of the root by the xylem and (2) the higher mineral concentration inside the
stele maintained by the selective passage of ions through the endodermis.
The osmotic force is called root pressure. This can be seen as guttation, the
formation of small droplets of sap (water and minerals) on the ends of leaves of
grasses and small herbs in the early morning.

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Forces generated by root pressure are too small to have a major effect on the
movement of water in larger plants.
Capillary action is the rise of liquids in narrow tubes against the force of gravity.
Contributes to the movement of water up the xylem.
Capillary action results from the forces of adhesion. Generally creates a menisucs.
However, there is no meniscus in plants.
The effect of capillary action is minimal in plants.
Cohesion-tension theory (main way of movement:
Transpiration, the evaporation of water from plants, removes water from leaves,
creating a negative pressure, or tension, to develop within the leaves and xylem
tissue.
Cohesion between water molecules produce a single, polymerlike column of
water from roots to leaves. The water molecules within a series of xylem cells
behave as a single, polymerlike molecule.
Bulk flow of water through xylem cells occurs as water molecules evaporate from
the leaf surface. When a water molecule is lost from a leaf by transpiration, it pulls
up behind it an entire column of water molecules. In this way, water moves by bulk
flow through the xylem by a pulling action generated by transpiration. Since
transpiration is caused by the heating action of the sun; the sun, then, is the driving
force for the ascent of sap through plants.

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Transport of Sugars
Translocation is the movement of carbs through phloem from a source, such a leaves, to a
sink, a site of carb utilization. Described by the pressure-flow hypothesis:
Creation of concentration gradient. Carbs move from the site of production (pallisade
mesophyll cells in a leaf) to phloem sieve-tube membranes by active transport. This
develops a concentration of solutes in the sieve-tube members at the source that is
higher than that of a sink.
Water enters sieve-tube members. As a result of movement of solutes into the sievetube members, the osmolarity of the sieve-tube members becomes higher than that of the
areas outside the cell. As a result, water diffuses into the high osmolarity region, the
sieve-tube members.
Pressure gradient generates movement. When water enters the sieve-tube members in
the leaves or other source, pressure builds up because the rigid cell wall does not
expand. As a result, water and sugars move by bulk flow through sieve tubes (through
sieve plates between sieve-tube members).
Maintenance of pressure gradient at the sink. As water and sugars move by bulk flow
from source to sink, pressure begins to build at the sink. However, the cells in the area
of sink are using carbohydrates, so they are removing carbs from the sieve-tubes. This
keeps the overall pressure in the sink area low and will maintain the adequate pressure
gradient needed for translocation.
Starch is an important player, since it is essentially insoluble in water.
Any cell that converts extracellular soluble sugars into starch acts as a sink.
Oppositely, any cell can act as a source if it breaks down starch into soluble sugars.

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Control of stomata
The opening and closing of the stomata influence gas exchange and water loss.
Plants need carbon dioxide to create biomolecules via the calvin cycle. When the
stomata opens, the plant is able to uptake atmospheric CO2.
However, the tradeoff from opening the stomata is that the plant risks desiccation from
excessive transpiration.
As a result, the opening and closing of stomata must be regulated.
Each stroma is surrounded by 2 guard cells.
Potassium ions enter the guard cells. This increases the osmolarity of the internal
surroundings of the guard cell compared to the extracellular space. As a result, water
moves into the guard cells. When water flows into the guard cells, the stomata opens.
Because ions are flowing into the cell, a charge gradient is created.
To relieve this gradient, chloride ions are pumped into the cell along with potassium
ions in some plants.
In other plants, hydronium ions are pumped out.

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When water flows out of the guard cells, the stomata closes.
Factors that affect the opening and closing of stomata:
Stomata close when temperatures are high. This reduces loss of water but shuts down
photosynthesis.
Stomata opens when carbon dioxide concentrations are low inside the leaf. Allows
photosynthesis but risks water loss.
Stomata close during the night and opens during the day. May be due to carbon dioxide
levels: CO2 levels are low during the day because the plant is actively doing
photosynthesis but at night, CO2 levels are high because the plant is only respiring.

Plant hormones
Hormones are substances that are produced by specialized cells in one part of an organism
that influence the physiology of cells located elsewhere.

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Very small quantities of hormones are required to alter cell physiology.

Auxin, or IAA, promotes plant growth by facilitating the elongation of developing cells.
Auxin is a modified tryptophan amino acid. Auxin is actively transported (using ATP)
from cell to cell in a specific direction (polar transport).
Increases the concentration of hydronium ions in cell walls, which, in turn, activates
enzymes that loosen cellulose fibers. The result is an increase in cell wall plasticity.
Turgor pressure causes the cell wall to expand, thus generating growth.
Auxin influences plant responses to light (phototropism) and gravity (geotropism).
Auxin is produced at the tips of shoots and roots.
Auxin is active in leaves, fruits, and germinating seeds.
Gibberellins are a group of hormones that promote cell growth.
More than 60 various types of related gibberellins.
Can act together with auxin to stimulate growth.
Produced in young leaves, roots, and seeds but are often transported to other parts of the
plant.
Involved in the promotion of fruit development and seed germination, and inhibition of
aging in leaves.
High concentrations of gibberellins cause the rapid elongation of stems called bolting.
Cytokinins are a group of hormones that stimulate cytokinesis (cell division).
Structurally, they are variations of the nitrogen base adenine.
Two types: naturally occuring zeatin and artificially produced kinetin.
Produced in roots and are transported throughout the plant.
In addition to stimulating cell division, cytokinins influence the direction of organ
development (organogensis).
Also stimulates the growth of lateral buds, thus weakening apical dominance, the
dominant growth of the apical meristem compared to lateral meristems.
Been found to delay senescence (aging) of leaves.
Ethylene is a gas the promotes the ripening of fruit.
During the later stage of fruit development, ethylene gas fills the intercellular spaces
within the fruit and stimulates its ripening by enzymatic breakdown of cell walls.
Also involved in stimulating the production of flowers.
Ethylene, in combination with auxin, inhibits the elongation of fruits, stems, and leaves
and influences leaf abscission, the aging and dropping of leaves.
Absicic acid (ABA) is a growth inhibitor.
In buds, it delays growth and causes the formation of scales in preparation for
overwintering.
In many species of plants, ABA maintains dormancy in seeds.
Dormancy in the seeds is broken by by an increase in giberellins or other
mechanisms that respond to environmental cues such as temperature and light.
Plant responses to stimuli
Phototropism is the response to light. It is achieved by the action of the hormone auxin.
Mechanism of action:
Auxin is produced in the apical meristem, moves downward by active transport into the
zone of elongation, and generates growth by stimulating elongation.

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When all sides of the apical meristem are equally illuminated, growth of the stem is
uniform and the stem grows strength.
When the stem is unequally illuminated, auxin moves downward into the zone of
elongation but concentrates on the shady side of the stem.
The higher concentration of auxin in the shady side of the stem causes
differential growth; that is, the shady side grows more than the sunny side.
When this happens, the stem bends toward the light.
Gravitropism is the response to gravity by stems and roots. Both auxins and gibberellins
are involved but their action depends on their relative concentrations and the target organ.
Mechanism of action for auxin:
If a stem is horizontal, auxin produced at the apical meristem moves down the stem
and concentrates on its lower side. Since auxin stimulates cell elongation, growth of
the lower side is greater than that of the upper side, and the stem bends upward as it
grows.
If a root is horizontal, auxin is produced at the apical meristem (root tip), and, as in
stems, concentrates on the lower side of the root. However, in roots, auxin inhibits
growth.
Thigmotropism is a response to touch.
When vines and other climbing plants contact some object, they respond by wrapping
around it.
Mechanism is not well understood.
Dissolved ions, auxins, gibberellins, and other hormones do not respond directly to gravity
or light. All responses are instead indirect.
It is believed that statholiths, specialized starch-stroning plastids, which settle at the
lower end of the cells, somehow influence the direction of auxin movement.
Photoperiodism
Photoperiodism is the response of plants to changes in the photoperiod, or the relative
length of daylight and night.
To respond to changes in the photoperiod, plants maintain a circadian rhythm, a clock
that measures the length of daylight and night.
The mechanism is endogenous; that is, an internal clock that continues to keep time
even if external cues are absent.
Phytochrome, a protein modified with a light-absorbing chromophore, seems to be
involved.
Two forms are Pr (P660) or Pfr (P730): depending on which wavelengths of light the
phytochrome absorbs red (wavelength 660 nm) or far-red (wavelength 730 nm).
The forms are reversible: when exposed to red light, Pr Pfr and vice versa.
Observations of the phtytochromes:
Pfr seems to reset the circadian-rhythm clock.
Pr is the form of phytochrome synthesized in plant cells. Pr is synthesized in the leaves.
Pr and Pfr are in equilibrium during daylight because the 660 nm and the 730 nm
wavelengths are present during the day.
Pr accumulates at night. Pfr breaks down faster than Pr, and in some plants, Pfr is
metabolically converted back into Pr. The cell also continues to make Pr at night.
At day break, light rapidly converts the accumulated Pr to Pfr. An equilibrium between Pr

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and Pfr is again attained.

Night length is responsible for resetting the circadian-rhythm clock.
Flash of red light during night causes conversion of Pr to Pfr. The plant will read a
shorter night period and the circadian-rhythm is reset.
Flash of far-red after red flash reverses the effect of red light and causes night length
to be restored as before.
In a series of alternating flashes, only the last one affects perception of night length:
red shortens, far-red restores.
Phytochromes may also be involved in more than light-related functions:
Phytochrome can detect if enough light has been exposed to a seed before it germinates
When the critical exposure is exceeded, production of gibberellins or destruction of
ABA occurs and germination follows.
Phytochrome system can evaluate the quality of light reaching the plant. It can
determine shade from the sun as a result.
Many flowering plants initiate flowering in response to changes in the photoperiod. Three
groups:
Long-day plants flower in the spring and early summer when daylight is increasing.
Short-day plants flower in late summer and early fall when daylight is decreasing.
These plants flower when daylight is less than a critical length or when night exceeds a
critical length.
Day-neutral plants do not flower in response to daylight changes.
When flowering is initiated, it is believed that a flowering hormone is produced.
There is evidence that a hormone called florigen does this. It is produced in leaves and
travels to shoot tips.

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Basis of behavior
Behavior can be inherited through genes or learned
Behavioral ecology is the study of behavior that seeks to explain how specific behaviors
increase fitness.
Kinds of animal behavior
Simple and complex reflexes
simple = automatic 2 nerve (afferent/efferent) response to stimulus controled at spinal
cord (lower order animals)
Afferent (sensory) neurons receive infromation from outside environment and
sends them to other neurons so body can produce a response
Efferent (motor) neurons receive information from other neurons and sends that
information to effectors (muscles, glands), which produce a response
complex automatic resposne to significant stimulus (controlled at brainstem or even
cerebrum). Will involve an intermediary interneuron or even the brain for 'processing'
before synapsing with an efferent neuron and target tissue.
Instinct - a behavior that is innate, or inherited
Fixed action patterns (FAP) are instinctive behavioral sequences following a regulary,
unvarying pattern. Are innate and almost inevitably runs to completion.
Initiated by a specific stimulus called a sign stimuli.
Imprinting innate program for acquiring specific behavior only if appropriate stimulus is
experienced during critical period. Once acquired, trait is irreversible.
Ex: Gray goslings accepting any moving object as mother during first day of life
Classical condition standard pavlov conditioning (UCR, UCS, CR, CS)
Operant conditioning reward, punishment, positive reinfrocement, negative
reinfrocement. Extinction (learned behavior stops after not bieng reinforced after a while),
spontaneous recovery
Spatial learning: animal associates attributes of landmark with reward of identifying and
returning to that location.
Habituation: learned behavior that allows animal to disregard meaningless stimuli.
Observational learning: animal copies behavior of another without having experienced any
feedback themselves.
Insight: When animal exposed to new situation without prior experience, performes a
behavior that generates a positive outcome.
Animal movement
Kinesis: An undirected (without direction) change in speed of an animal's movement in
response to a stimulus.
Slows down in favorable environment and speeds up in unfavorable environment
Taxis: Directed movement in response to stimulus. Movement is either toward/away from
stimulus.
Phototaxis is the movement toward light.
Migration: long-distance, seasonal movement of animals.
Usually in response to availability of food/degradation of environmental resources.
Communication in animals
Chemical chemicals used for communication are called pheromones. May be smelled or
eatend.
Chemicals that trigger reversible behavioral changes are called releaser pheromones.
Chemicals that trigger long term physiological and behavior changes are called primer
pheromones
Visual occur during displays of agression or during courtship

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Auditory
Tactile: common in social bonding, infant care, grooming, and mating
Foraging behaviors helpt optimize feeding (minimize energy spent and risk)
Herds, flock, schools have several advantages:
use cooperation carry out behavior more successfully as a group
concealment most individuals in flock are hidden from view
vigalance in a group, individuals can trae off foraging and watching for predators
defense a group of individuals can shield their young or mob their predator
Packs enable members to corner and successfully attack large pray
Social behavior
Agnostic behavioragression and submission
Originates from competition from food, mates, territory
Agnostic behavior is ritualized, so injuries and time spent in contests are minimized
Dominance hierarchies indicate power and status relationships in a group; minimize
fighting for food/mates.
Pecking order linear order of status used to describe dominance hierarchy in chickens
Altruistic behavior seemingly unselfish behavior that appears to reduce the fitness of an
individual but helps the fitness of the receiver.
Altruism increases inclusive fitnessfitness of an individual + relatives
Kin selection natural selection that increases inclusive fitness

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Ecological levels
Population = group of individuals of same species living in same area
Community = group of populations living in same area
Ecosystem = all the organisms in a community plus abiotic factors
Biosphere = composed of all regions of earth that contains living things
Habitat = type of place where organism usually lives
Niche = all biotic and abiotic resources in the environment used by an organism. When an
organism is said to occupy a niche, certain resources are consumed or certain qualities of hte
environment are changed in some way by presence.
Biogeochemical cycles
Flow of essential elements: environment --> living things --> environment
Carbon cycle (we need carbon to build organic molecules)
Abiotic reservoir: CO2 in atmosphere, fossil fuels, peat, cellulose
Enter food chain: Photosynthesis (carbon fixation in calvin cycle) by primary producers,
which will then get eaten up by consumers.
Recycle: no recycling
Return to abiotic: respiration, conbustion, decomposition
Nitrogen cycle (we need nitrogen to make proteins and nucleic acids)
Abiotic reservoir: Atmospheric N2
Nitrogen must be processed, or "fixed" into NH3, to be used by plants. (nitrogen fixation)
Fixation occurs in lightning strikes
Fixation is done by free-living or symbiotic bacteria in the soiil
NH3 is then converted into NO2- (nitrite)and NO3- (nitrate) by nitrifying bacteria
Enter food chain: Plants uptake nitrites and nitrates
Recycling: Detirivores convert organic waste nitrogen back into NH3
Return to abiotic: denitrifying bacteria convert nitrates back into nitrogen gas
Phosphorus cycle (we need phosphorus to make ATP and nucleic acids)
Abiotic reservoir: rocks, minerals soil
Enter food chain: erosion release soluble phosphate. Plants then uptake the soluble
phosphate through the soil
Recycling: decomposing bacteria and fungi
Return to abioitc: plants and animals release phosphorus when they decompose, and animals
excrete waste products
Water cycle (we need water for almost all metabolic processes)
Abiotic reservoir: surface and atmospheric water
Enter food chain: plants absorb water from oil; animals drink and eat other organisms
Recycling: transpiration
Return to abiotic: evaporation and runoff

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Community ecology
Community ecology focuses on interactions between populations living in the same
environment.
Competition
Interspecific competition is competition among members of different species.
Intraspecific competition is competition among members of the same species.
Release from competitive exclusion two species compete for the exactly the same
resource (or occupy the same niche). One is likely to be more successful (no two species
can sustain coexistence if they occupy the same niche).
Niche stuff
Resource partitioning two species occupy the same niche but pursue slightly different
resources or securing their resources in different ways, individuals minimize competition to
maximize success (SLIGHTLY DIFFERENT niches)
Character displacement (niche shift) As a result of resource partitioning, certain traits
allow for more success in obtaining resources in their partitions. This reduces competition
and causes a divergence of features between the two species.
Fundamental niche: The potential area and resources an organism is capable of using. The
presence of limiting facotrs prevent species from occupying the fundamental niche.
Realized niche: niche that an organism occupies in absence of competing species in its
fundamental niche.
Even in the presence of a competing species, both species may be able to occupy their
respective realized niches if there is no overlap between both species' realized niches.
Predation
True predator kills and eats other animals.
Parasites spends most of its life living on host, but the host doesn't usually die unitl the
parasite completes one life cycle.
Parasitoid: an insect that lays its eggs on host. After the eggs hatch, the larvae obtain
nourishment by consuming host tissues. Host eventually dies, but not until larvae complete
development and begin pupation.
Herbivore: animals that eat plants.
Granivores are seed eaters. Grazers are animals that eat grasses. Browsers eat leaves.
Symbiosis
Symbiosis is the permanent association between two organisms. May be obligatory (one or
both organisms cannot survive without the other).
Commensalism (+/o) one species benefits, other is unaffected
Mutualism (+/+) both organisms benefit
Parasitism (+/-) one species benefits at the expense of the other
Coevolution
Secondary compounds: toxic chemicals produced in plants that discourage would-be
herbivores
Camouflage (cryptic coloration): any color, pattern, shape, or behavior that enables an
animal to blend in with its surroundings. Both predator and prey can use camouflage.
Aposematic coloration: conspicuous pattern or coloration of animals that warns predators
that they sting, bite, taste bad, poisonous, or other wise to be avoided.
Mimicry occurs when two or more species resemble one another in appearance.
Mullerian mimicry occurs when several animals, all with some special defense
mechanism, share the same coloration.
Batesian mimicry occurs when an animal without any special defense mechanism
mimics the coloration of an animal that does posses a defense.

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Pollination of many kinds of flowers occur as the result of coevolution of fienly-turned traits
between flower and pollinators.
Ecological succession
Ecological sucession is change in composition of species over time. Describes how one
ocmmunity is gradually replaced by another As it progresses, diversity and total biomass
increase. A final successional stage of constant species composition is called a climax
community (this usually never occurs). A climax community is unchanged until destroyed
by a catastrophic event (blowout). Succession has a factor of randomness that makes it hard
to predict.
Pioneer species: plants and animals that are the first to colonize a newly exposed habitat
(usually opportunistic, r-selected species); can tolerate harsh conditions (lichens and
mosses)
As environment changes, r-selected will be replaced by stable k-selected species (live
longer, slow succession) and reach climax where it remains for hundreds of years
Primary succession: occurs on substrates that never previously supported living things.
Essential and dominant characteristic of primary succession is soil building.
Secondary succession: begins in habitats where communities were entirely/partially
destroyed by damaging event; begins on substrate that already bears soil.
Ecosystems
Ecosystems have trophic levels that categorize plants and animals based on their main
energy source
Primary producers: Autotrophs that convert sun energy into chemical energy: plants,
photosynthetic protists, cyanobacteria, and chemosynthetic bacteria
Primary consumers: herbivores eat primary producers
Herbivores have a long digestive tract with greater surface area and time for more
digestion.
Have symbiotic bacteria in digestive tract to help break down cellulose which the
herbivore itself cannot.
Secondary consumers: primary carnivores (eat primary consumers)
Tertiary consumers: secondary carnivores, eat secondary ocnsumers.
Detritivores: consumers that obtain energy by decomposing dead plants, or animals.
Smallest dentrivores are called decomposers (bacteria).
Larger dentrivores are called scavengers (vulture).
Ecological pyramids (food pyramids) show relationships between trophic levels
Ecological efficiency describes the proportion of energy represented at one trophic level
that is transferred to the next. On average, an efficiency of about 10% is transferred to the
next. 90% is for metaoblism and to detritivores when they die.
Energy/biomass/quantity is greatest at a primary producer level, and lowest at a tertiary
consumer level. Tertiary consumer is least stable and most sensitive to population
fluctuations of lower levels.
Food chain: linear flow chart of who's eaten by whom
food web: an expanded, more complete version of the food chain
Greater number of pathways in a community food web, the more stable the community
is

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Biomes
Biomes are regions with common environmental characteristics
Tropical rain forest (e.g. amazon rain forrest)
High, but stable, temperature and humidity
Heavy rainfall
Tall trees with branch at tops --> little light to enter
Most diverse biome
Epiphytes are plants that grow commensally on other plants (like vines)
Savannas (e.g. south africa)
Grasslands with scattered trees
Have high temperatures, but have very little rainfall
Temperate grasslands (e.g. north american prarie)
Grasslands with scattered trees
Very little rainfall (rainfall occurs in uneven seasonal occurences)
Lower temperatures than savannas
Temperatre deciduous forests (e.g. forests in northeast USA)
Warm summers, cold winters
Moderate precipitation
Deciduous trees shed leaves during winter
Soil is rich due to leaf shed
Vertical stratification: plants and animals live on ground, low branches, and treetops.
Many mammals hibernate through cold winter.
Deserts (e.g. mohave desert)
Hot during the day, cold at night (extreme temperature fluctuations)
Dry (very minimal rainfall)
growth of annual plants is limited to short period following rare rain
plants and animals adapt to conserve as much water as possible
Taiga (e.g. russia)
coniferous forests (and trees with needles for leaves)
very long, cold winters
precipitation in form of heavy snow
largest terrestrial biome
Located below the tundra
Tundras
Cold winters (ground freezes). Top layer thaws during summer --> supports minimal
vegetation (short growing season) but deeper soild remains permanently frozen permafrost.
Very little rainfall that cannot penetrate frozen ground
Polar region
Frozen
No vegetation or terrestrial animals
Chapparral
Terrestrial bime along California coastline characterized by wet winters, dry summers, and
scattered vegetation.
Aquatic biomes
Freshwater biomes are hypotonic to organisms and are affected by climate/weather

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variations.
Marine biomes:
Largest biome (covers 3/4th of surface)
Provides most of earth's food and oxygen
Estuaries are where oceans and rivers meet
Intertidal zones are where ocean meets land
Littoral zones are oceans above contientnal shelfs
Coral reefs have high biodiversity
Benthic zone is the lowest layer of a body of water, including the sediment surface and
sub-surface layers. Most organisms are scavengers and detirivores.
Pelagic zone is open ocean. 2 major areas:
Photic zone is the area to which there is light and you will see autotrophs.
Aphotic zone is beneath the photic zone and does not have light. Heterotrophs only
Rain shadows
Areas of dry land that from on the leeward side (downwind) of a high mountain. The rain
shadow is dry and is like a desert.

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Macro vs micro evolution

Microevolution: changes in allele frequencies that occur over a time within a population
(due to mutation, selection, gene flow & drift).
Macroevolution: patterns of changes in groups of related species over broad periods of
geologic time. Patterns determine phylogeny.
Lamarck's theory
Use and disuse: body parts can develop with increased usage, unused parts are weakened
Inheritance of acquired characteristics: body features acquired during lifetime can be
passed down to offsprings.
Incorrect, since only changes in genetic material of cells can be passed to offspring

Natural transformation of species

organisms produced offspring with changes, transforming each later generation slightly
more complex (no extinction or speciation) incorrect
Evidence for evolution
Paleontology: fossils reveal prehistoric existence of extinct species, often found in sediment
layer (deepest fossils represent old specimens).
Biogeogrpahy: geography to describe distribution of species; unrelated species in different
regions of the world look alike when found in similar environment
Continental drift supercontinent Pangea slowly broke to 7 continents
Embryology: similar stages of development (ontogeny) found among related species. This
allows us to establish evolutionary relationships (phylogeny)
Comparative anatomy: describes two kinds of structures that contribute to identification of

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evolutionary relationships
Homologous structures; body parts that resemble one another in a different species
from a common ancestor.
Analogous structure: body parts that resemble one another in different species because
they evolved independently as adaptations to their environments.
Vestigial structures have no known current function but apparently had some ancestral
function.
Molecular biology: examines nucleotide and amino acid sequences of DNA and proteins
from different species. More than 98% of nucleotide sequences in humans and chimps are
identical. AA's in cytochrome c are often compared because it is highly conserved.
Comparative biochemistry: organisms with a common ancestor have common biochemical
pathways
Natural selection: responsible for producing adaptations (superior inherited traits) that increase
individual's fitness (ability to survive, leave offspring)
Populations possess an enormous reproductive potential if all offspring produced and
survived
Population sizes remain stable: populations generally fluctuate around a constant size
resources are limited: do not increase as population grow larger
Individuals compete for survival: growing pop will exceed available resources and thus
compete
there is variation among individuals in a population
much of the variation is heritable
only the most fit individuals survive
evolution occurs as favorable traits accumulate in the population: best adapted individuals
best adapted offspring leave most offspring
Types of selection
Stabilizing selection: bell curve. Favors an intermediate (heterozygote advantage)
Directional selection: favors traits that are at one extreme of a range of traits. Traits at
opposite extremes are selected against.
Disruptive selection: occurs when environment favors extreme or unusual traits while
selecting against common traits.

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Sexual selection: differential mating of males or females in a population. Females choose

superior males increase fitness of offspring; they invest greater energy so they maximize
quality. Males increase fitness of offspring by maximizing quantity.
Male competition leads to fights. Mating opportunities awarded to strongest male.
Female choice leads to traits/behaviors in males that are favorable to female.
Often leads to sexual dimorphismdifferences in appearance of males and females
becomes form of disruptive selection.
Sources of variation
Mutation: alteration in DNA sequence that leads to a new allele.
Sexual reproduction: genetic recombination (crossing over, independent assortment, random
joining of gametes)
Diploidy: presence of two copies of each chromosome. In heterozygous conditions,
recessive allele is stored for later generations more variations maintained in gene pool
Outbreeding: mating with unrelated partners mixing different allele combinations
Balanced polymorphism: maintenance of different phenotypes in a population. Coexistence
of two or more phenotypes in a population.
Heterozygote advantage: being heterozygous has highest fitness increase
Hybrid vigor: superior quality of offspring resulting from crosses between two different
inbred strains of plants results in reduction of loci with recessive homozygous
conditions and increase in heterozygote advantage
Frequency-dependent selection: least common phenotypes have selective advantage.
Common phenotypes are selected against. Rare will increase in frequency and then
eventually will be selected against and repeat.
Neutral variation: variation without selective value (e.g. fingerprints in humans)
Geographic variation variation of a species dependent on climate or geographic
conditions.
A graded variation of a phenotype due to this is known as a cline.
Causes of changes in allele frequencies
Natural selection: increase/decrease of allele frequencies due to environment
Gene flow: introduction/removal of alleles from population when individuals leave or enter
population
Genetic drift: random increase/decrease of allele by chance. Smaller population = larger
effect
founders effect: allele frequencies in a group of migrating individuals are not the same
as that of their population origin
bottleneck: occurs when population undergoes a dramatic decrease in size (natrual
catastrophe, etc.) vulnerable to genetic drift
Nonrandom mating: individuals choose mates based on their particular traits
Inbreeding: individuals mate with relatives
Sexual selection: females choose males based on superior traits
Mutations
speciation
Speciation is the formation of new species
Species is a group of individuals capable of interbreeding
Before speciation, small, local populations called demes often form within a species.
Members of a deme may resemble one another more closely than they resemble
members of other demes. If the demes become isolated, speciation may occur.
Allopatric speciation: population is divided by geographic barrier. Interbreeding

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between the two resulting populations is prevented. Over time, changes in allele
frequencies can cause both populations to become new species.
Dispersal: group is isolated by being physically removed from
Sympatric speciation: formation of new species without the presence of a geographic
barrier
Balanced polymorphism: two different versions of a gene are maintained in a
population because individuals carrying both versions are better able to survive than
those who have to copies of either version alone.
Polyploidy: possession of more than 2 sets of chromosomes. Leads to reproductive
isolation.
Hybridization: two different forms of species mate and produce along a
geographical boundary called a hybrid zone.
Adaptive radiation: rapid evolution of many species from a single ancestor; occurs
when ancestral species is introduced to an area where diverse geographic/ecological
conditions are available for colonization
Maintaining reproductive isolation
Prezygotic isolating mechanism: prevent fertilization
Habitat isolation: species do not encounter
Behavior isolation: does not perform correct courtship rituals
temporal isolation: species mate at different seasons/time
Mechanical isolation: male/female genitalia are not compatible
Gametic isolation: male gametes do not survive in environment of female gametes
(gametes do not recognize each other)
Postzygotic siolating mechanisms: stuff after fertilization that prevents speication
Hybrid inviability: zygote fails to develop properly and dies before reaching maturity
Hybrid sterility: hybrids become functional adults but cannot produce
Hybrid breakdown: hybrids produce offspring that have reduced viability/fertility
(hybrid's children cannot produce)
Patterns of evolution
Divergent evolution: two+ species that originate from a common ancestor and become
increasingly different over time
convergent evolution: two unrelated species that share similar traits by environment
Parallel evolution: two related species made similar evolutionary changes after their
divergence form common ancestor
Co-evolution: evolution of one species in response to new adaptation that appear in another
species
Macroevolution
Phyletic gradualism: evolution occurs by gradual accumulation of small changes; but
unlikely valid because intermediate stages of evolution are missing
Punctuated equilibrium: evolutionary history consists of geographically long periods of
stasis with little/no evolution followed by geographically short periods of rapid evolutions.

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Population ecology
Population ecology is the study of growth, abundance, and distribution of populations.
Size = N, the total number of individuals in the population
Density: total number of individuals per area or volume occupied.
Dispersion: describes how individuals in a population are distributed; may be clumped,
uniform, or random.
Age structure: description of the abundance of individuals at each age
Survivorship curves: how mortality of individuals in a species varies during their
lifetimes. X axis = percent of maximum lifespan. Y axis = log(number of survivors)
Type I: most individuals survive to middle ages and dies quicker after this age
(human).
Type II: length of survivorship is random (invertebrates-hydra)
Type III: most individuals die young, with few offspring living to reproductive age
and beyond (oysters)

Population growth
Biotic potential: Maximum growth rate under ideal conditions (unlimited resources and
no restrictions).
Carrying capacity (K): maximum number of individuals of a population that can be
sustained by habitat
intrinsic rate of growth is when reproductive rate (r) is maximum (biotic potential)
exponential growth occurs whenever reproductive rate (r) is greater than zero (Jshaped)
Logistic growth occurs when limiting factors restrict size of population due to carrying
capacity of habitat. (S-shaped)

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Growth limiting factors:

density-dependent limiting factors: the effect becomes more intense as population
density increases (spread of disease)
density-independent limiting factors: does not depend on population density
(natural disasters)
Population cycle: predictable fluctuations in population over a period of time.
When population grows over carrying capacity, it may be limited (lower) than the
initial K due to the damage caused to the habitat lower new carrying capacity K
or it may crash to extinction.
Types of populations
K-selected population members have low reproductive rates and are roughly constant
in size (at K). Have a carrying capacity that the population levels out at. Carrying
capacity is a density dependent factor. (like humans)
R-selected population Rapid exponential population growth, numerous offspring, fast
maturation, little postnatal care. Generally found in rapid changing environments
affected by density independent factors. Characterized by opportunistic species. (i.e.
bacteria)
Misc information
Human Population Growth enabled by: increase in food supply, reduction in disease
(medicine), reduction in human wastes, habitat expansion (advancements now allow
inhabitance of previously uninhabitable places)
Ecological footprint: amount of raw land necessary to sustain an individuals lifestyle
habits (consider eating, traveling, housing habits)

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Lecture 1
DNA contains 4 special abilities:
Diversity of structure
Ability to replicate
Mutability
Regulated expression
Central dogma:
DNA gets transcribed into RNA which will get translated into a polypeptide

Genes and organisms

The number of genes varies greatly between organisms
Having more genes doesn't mean the organism is higher order or more complex
Organization of DNA
In viruses: DNA or RNA is surrounded by a protein coat
In prokaryotes: DNA is organized into a circular chromosome or potentially a plasmid
In eukrayotes: Most of the DNA is in the nucleus. Some of the DNA is located in the
mitochondria and the chloroplast.
The nucleus contains multiple linear chromosomes. Each chromosome contains one
double stranded DNA molecule.
Human karyotpe
Diploid = one set of chromosomes from each parent (2 1s, 2 2s, 2 3s....)
22 pairs of autosomes (homologous chromosomes)
Just because you have the same genes doesn't mean you have the same alleles!
1 pair of sex chromosomes (XX homologous, XY not homologous)
All somatic cells in the body have the same DNA
Gene regulation
Determines when and where a given gene is expressed
non-coding DNA also encodes regulatory functions
Most human-chimp differences due to gene regulation-not genes
Genetics and variations
Differences among individuals are called polymorphisms.
They can result from: 1) mutations 2) environment 3) mixture of both
Environmental polymorphisms are usually not heritable
Mutations vs mutants

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Mutations are changes in the DNA sequence that may or may not affect phenotype.
Arise from natural processes as well as environmental factors.
Mutants are individuals that have change sin their DNA that alter the wild-type
phenotype
How can we find mutants
From natural populations:
Spontaneously find them
Survey the population for mutants
Lab populations:
mutagenesis controllable introduction of mutations
selection kill what you don't want
screen look for what you want
Forward vs reverse genetics
Forward genetics: begin with a change in phenotype and then look to see how changes
in genotype cause the observed effects.
Reverse genetics: begin with a change in genotype and then look to see how this causes
a change in phenotype.
Model organisms
Model organisms are
small,
easy to culture,
have short generation times
They also have small genomes
are easy to transport.
Lecture 2
Mendel's law of segregation and independent assortment
Mendel's law of segregation: During gamete formation, the alleles for the same gene
segregate from each other so that each gamete carries only one allele for each gene.

Law of independent assortment: Alleles for different traits segregate independently

during the formation of gametes.

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Mendel's law of segregation allows us to predict outcomes.

Monohybrid cross
Genotypes predicted = 1 homozygous dominant, 2 heterozygous, 1 homozygous
recessive (1:2:1)

Probability stuff
Use multiplication when you see the word AND
Use addition when you see the word or
Common crosses
True-breeding: homozygous for the trait (either dominant or recessive)
Parental cross: parental strains are crossed with one another to form the F1 generation.
P x P = F1

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Parental strains are usually true-breeding

Intercross: crosses between genetically identical individuals (selfing, sibling mating)
F1 x F1 = F2
F2 x F2 = F3
etc
Backcross: F1 progeny mated back to one of the parents
F1 x P = backcross
Testcross: Dominant phenotype x recessive phenotype
A_ x aa
Finding mutants with mutagenesis
Mutagenesis treatment with conditions that cause mutations: chemical mutagens
(carcinogens), radiation, mobile genetic elements.
Screen = look for what you want
selection = kill what you don't want
Lecture 3
X and Y chromosome gene content
X chromosome contains 2000-3000 genes. Nearly all genes are required in both males
and females.
Y chromosome contains ~100 genes. ~5% of gene numbers on X made up the SRY
gene. This is the master control gene for making embryos.
X and Y genes have sequence similarity at the tip of their shorter arms. This is the
region where they pair up in meiosis.
Recombination happens only in regions that pair. Therefore, the Y chromosome has
little recombination.
Y linked traits are very rare
Y-linked traits are neither dominant nor recessive because there is only one copy.
In a pedigree, you'd expect a Y-linked trait to be transmitted from fathers to sons only,
with no affected females observed.
Nondisjunction: meiosis mistakes
Nondisjunction is when homologous chromosomes do not assort correctly during
mitosis. One daughter cell would get too many chromosomes, while the other daughter
cell would be getting too few chromosomes.
Nondisjunction during meiosis I generates a daughter cell with n + 1 chromosomes and
another daughter cell with n 1 chromosomes. After meiosis II, 2 daughter cells will be
n + 1 and 2 daughter cells will be n-1.
Nondisjunction during meiosis II generates 1 daughter cell with n + 1 chromosomes, 1
daughter cell with n 1 chromosomes, and 2 normal daughter cells.
Non-disjunction diseases
XYY = Jacobs syndrome
XXY = Kleinfelter syndrome
XO = Turner Syndrome
XXX = Triple X
Mosaicism in cells that undergo nondisjunction in mitosis during embryonic
development; fraction of body cells have extra or missing chromosome
Polyploidy: all chromosomes undergo meiotic nondisjunction and produce gametes
with twice the number of chromosomes. Common in plants.
Aneuploidy: genome with extra/missing chromosome which is often caused by
nondisjunction.

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Partial monosomy is the partial chromosomal deletion of 1 homologous chromosome.

Inferring the mode of inheritance on pedigrees

Make an educated guess and see whether it is consistent with the available information.
Fill out genotypes. You can't identify all alleles for all individuals usually.
Autosomal recessive diseases tends to skip generations whereas autosomal dominant
diseases tends to be present in every generation.
Lecture 5
Discrete vs continuous traits
Discrete phenotypes fall into distinct classes.
Continuous traits create a bell-shaped normal distribution
Polygenic model for quantitative traits
The polygenic model assumes that phenotype is affected by many gene loci, each with
a similar and additive effect on the trait.
Therefore, genes controlling quantitative traits will fall in a bell-shaped distribution.
Cytoplasmic inheritance
The egg is much larger than the sperm. The egg contains all of the cytoplasm organelles
when fertilized with a sperm. The sperm just carries over DNA.
We know that mitochondria contains its own set of DNA (mtDNA).
We only inherit our mtDNA from our mother. Therefore, any mutation seen in the
mother's mtDNA will affect the progeny.
Cytoplasmic inheritance is uniparental and the genes are NOT located in the nucleus.
Molecular basis of cytoplasmic inheritance
Mitochondria and chloroplasts have their own genomes.
Mitochondria and chloroplasts replicate themselves, and their genomes are circular, like

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bacteria.
Maternal effects
Maternal effect is when genotype of the mother determines phenotype of the child.
Not caused by organelles.
Mediated by RNAs and proteins produced by the mother.
Typically controlled by nuclear genes.
Lecture 6
Recombination
The formation of chiasmata (which determine the location of recombination events) are
necessary for proper chromosome segregation during meiosis.
In each cell, every chromosome is expected to have at least 1 chiasmata.
The location of the crossovers within each germ cell is random and different in each
meiosis.
The production of recombinant phenotypes depends on:
The location of genes on the chromosome
the location of crossing over

Genetic distance
Genetic distance determines the proportions of recombinant gametes produced during
meiosis.
Genetic distance (cM) is proportional to physical distance (bp).
We can estimate the number of parental and recombinant gametes by looking at the
phenotypes produced by particular genetic crosses.
The maximum genetic distance that can be measured between 2 genes in one cross is 50
cM.
If over 50% of your progeny are recombinant, then the two genes are not linked.
Haplotype is a set of DNA variations, or polymorphisms that tend to be inherited

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together. In other words, the two genes are linked.

Lecture 10
Extensions to Mendelism: alleleism (relating genotypes to phenotypes)
Types of alleles: loss of function, gain of function, neofunctional, null allele
Dominance: complete, incomplete, codominant
Lethals: recessive, conditional (e.g. temperature sensitive)
Multiple alleles: codominance, dominance series
Genetics of sickle-cell anemia
example of pleiotropy: where one gene has effects on multiple phenotypes

Sicke-cell anemia has pleiotropic effects:

hemoglobin protein function
cell shape
cell density
malaria resistance
Because of the pleiotropic functions, both the A and S alleles of the beta-globin gene are
found in human populations at high frequency.
The polymorphism is maintained by balancing selection. Heterozygote gives malaria
resistance so it gives higher fitness effects.
Different alleles are favored under different conditions:
A allele is better if no malaria-carrying mosquitoes present
S allele better if malara-carrying mosquitoes present
Multifactorial inheritance
Most traits are controlled by multiple genes. Mutations in two different genes can give
the same phenotype.
Two genes affecting the trait can show:
independence (no interaction)
redundancy
complementarity (mutual epistasis)
epistasis
suppression (another specialized case of epistasis)
Two genes: Additive effects

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Additive effects are when the contribution of each gene adds up to create the
phenotype.
This is basic dihybrid cross (9:3:3:1)

Two genes: Gene interactions

The phenotypic effect of an allelic combination at one gene is influenced by the allelic
combination at another gene.
Complementary gene interaction mutual epistasis
Mutual epistasis results when the protein each individual gene creates is not functional
alone.
When both genes creates the correct proteins, a protein complex will form and each
protein will only be functional then.
Any mutation in either gene will automatically cause a recessive phenotype.
F2 generation would see a 9:7 dominant:recessive frequency. 7 because 3 + 3 + 1.

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Redundancy
Redundancy results when two genes have the same function and only one gene is
necessary for a normal phenotype.
The only way a recessive phenotype can be seen is if the genotypes of both individual
genes are homozygous recessive.
F2 generation would produce a 15:1 dominant:recessive frequency.

Epistasis
Epistasis is when mutation at one gene masks phenotypic effects of mutation at another

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gene
If the epistatic gene is recessive, then the phenotype will be the same, regardless of the
genotype of the other gene. If A is epistatic over B, then aaBB, aaBb, aabb will all
produce the same phenotype.
F2 generation would see a 9:4:3 frequency.

Suppression
suppression results when the mutant phenotype of one gene can be suppressed (or
hidden) by another gene. The gene that does the suppression can do it through the
dominant or recessive genotype.
Produces an F2 generation ratio of 13:3 if the recessive allele was the suppressor. If the
dominant allele was the suppressor the F2 generation would produce a 15:1 ratio.

Incomplete dominance
In incomplete dominance, the heterozygous genotype would produce a phenotype that
is equivalent to mixing the other two phenotypes together. Red, white, pink
codominance
In codominance, the dominant and recessive phenotype are seen equally throughout the

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heterozygous phenotype. Red, white, red + white spots

Lecture 11
Prototrophs vs. auxotrophs
Auxotrophs mutant that requires a specific supplement in the environment in order
for it to grow (cannot synthesize that supplement)
Prototrophs can grow on minimal media. Wild-type. Can synthesize all nutrients
normally.
Gene, protein hypotheses
One-gene-one-enzyme hypothesis: all enzymes are composed of a single gene product
One-gene-one-polypeptide hypothesis: enzymes can be composed of more than one
gene products
This is more accurate because some enzymes require multiple subunits, which are
different polypeptides from different genes
Lecture 12
Hardy-weinberg model
Hardy-weinberg is a null hypothesis for population genetics
By rejecting hardy-weinberg, we can conclude that one or more of the 5 assumptions of
hardy-weinberg have been violated and are present in the population.
Assumptions of hardy-weinberg
No natural selection
No mate preference (random mating)
No mutations
No migrations
Population size is infinite
Hardy-weinberg equilibrium
If populations are in hardy-weinberg equilibrium:
the frequencies of alleles (A and B) do not change over time without an evolutionary
force
loci that are not in equilibrium will be after one generation
with allele frequencies (say A and B), we can predict genotype frequencies,
assuming no evolutionary forces.

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Hardy-weinberg equations
P = dominant allele frequency, q = recessive allele frequency
P^2 + 2PQ + Q^2 = 1
P^2 = homozygous dominant genotype frequency
Q^2 = homozygous recessive genotype frequency
2(PQ) = heterozygous genotype frequency
Lecture 15
Building blocks of DNA
4 nitrogenous bases: Adenine, Guanine, Cytosine, Thymine
Purines = adenine and guanine
Pyrimidines = cytosine, thyamine, uracil

DNA backbone = alternating phosphates and deoxyriboses bonded together by

phosphodiester linkages (5' phosphate group bound to 3'-OH)
Deoxyribonucleotide (structural unit of DNA) = N base + phosphate + deoxyribose
RNA backbone = alternating phosphates and riboses
Ribonculeotide (structural unit of RNA) = N base + phosphate + ribose

Directionality of DNA = 5' to 3'

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5' end is the end with the free 5' phosphate-group

3' end is the end with the free 3' OH group on the sugar

The bases hydrogen bond with one another: one of the most important mode of
interaction between 2 complementary strands of nucleic acid
A bonds to T = 2 hydrogen bonds
C bonds to G = 3 hydrogen bonds
Hydrophilic backbones are on outside of the helix, facing the surrounding water. These
strands are antiparallel to each other one strand goes in 5' to 3' direction whereas the
other strand goes from 3' to 5'.
10.5 base pairs per helical turn when in aqueous solution
Chargaff's rules
A = T, C = G
A + T doesn't always equal C + G

Grooves on DNA
Major groove: big groove created by double helix. Many sequence specific DNA
binding proteins bind here.
Many non-specific DNA binding proteins bind to the backbone.
Minor groove: small grove created by double helix.

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Major forms of DNA

B-form DNA is the most stable structure for DNA molecule under physiological
conditions.
A-form DNA is favored in solutions devoid of water. Right-handed double helix, but the
helix is wider and its 11 base pairs per turn.
Z-form DNA has 12 bps per helical turn and is left handed. Barely a minor groove.
Been found in bacteria and eukaryotes. May play a role in regulating the expression of
genes.
Special DNA sequences
Palindromes are sequences of bases that reads the same forwards and backwards.
Occurs over BOTH strands.
Inverted repeats are sequences of bases that reads the same forwards and backwards.
Occurs over ONE strand in BOTH strands.

RNA information
Single stranded RNA tends to create complex 3D conformations

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Can base-pair with complementary DNA or RNA

Double stranded RNA usually found in the A-form
Uses uracil, not thymine
Uses ribose, not deoxyribose
Lecture 16
Approaches to introducing DNA into organisms
1) take obtained DNA
2) add additional sequences
3) transfer it into the organism
Southern blots
Southern blots are used to analyze the length of restriction fragments of DNA.
Steps:
1) cut DNA with restriction enzyme
2) run on gel
3) Transfer DNA to membrane
4) hybridize with radioactive probe
Northern blots
Northern blots are used to analyze length of RNA fragments.
Steps:
1) Run RNA on gel
2) transfer to membrane
3) hybridize with radioactive probe
Western blot
Western blots are used to analyze lengths of protein fragments.
Steps:
1) run protein on gel
2) transfer to membrane
3) probe blot with antibody
Genes can be isolated by DNA cloning
DNA cloning: The process of cutting the gene out of the larger chromosome, attaching it to
a much smaller piece of carrier DNA, and allow microorganisms to make many copies of it.
The result is selective amplification of a particular gene or DNA segment. There are five
general procedures:
(1) cutting target DNA at precise locations: sequence-specific endonucleases (restriction
endonucleases) provide the necessary molecular scissors.
(2) Selecting a small carrier molecule of DNA capable of self-replication. These DNAs
are called cloning vectors (a vector is a delivery agent). They are typically plasmids or
viral DNAs.
(3) Joining two DNA fragments covalently. The enzyme DNA ligase links the cloning
vector and the DNA to be cloned. Composite DNA molecules comprising covalently
linked segments form two or more sources are called recombinant DNAs.
(4) Moving recombinant DNA from the test tube to a host cell that will provide the
enzymatic machinery for DNA replication.
(5) Selecting or identifying host cells that contain recombinant DNA.
Restriction endonucleases and DNA ligases yield recombinant DNA
Two classes of enzymes that cut DNA are restriction endonucleases and DNA ligases
Restriction endonucleases (also called restriction enzymes) recognize and cleave
DNA at specific sequences (restriction sequences or restriction sites) to generate a

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set of smaller fragments.
They are found in a wide range of bacterial species; they are used originally to
cleave foreign DNA (self = methylated DNA)
There are 3 types of restriction endonulceases: designated I, II, and III.
Types I and III are generally large, multisubunit complexes containing both the
endonuclease and methylase activities. Both require ATP to function. Both types
can cleave DNA at 25bp-1000bp from t he recognition sequence
Type II restriction endonucleases are simpler, require no ATP, and cleaves the
DNA within the recognition sequence itself.
Restriction endonucleases make either sticky ends or blunt ends.
Sticky ends are when there are unpaired nucleotides left on one side of each
strand after cleavage. They can base-pair with each other or with complementary
sticky ends of other DNA fragments. Sticky ends are easier than blunt ends to
paste into a vector because of the overhang.
Blunt ends are when there are no unpaired bases on the ends.
Once the DNA molecule has been cleaved, a particular fragment of known size can be
partially purified by gel electrophoresis. After the target DNA fragment is isolated, DNA
ligase can be used to join it to a similarly digested cloning vectorthat is, a vector
digested by the same restriction endonuclease.
A polylinker is a short DNA sequence containing 2 or more different sites for
cleavage by restriction enzymes. They are introduced into vectors to make cloning
easier by providing sites that allow cloning DNA, cut with any of a number of
different restriction enzymes, into a single plasmid.
Cloning vectors allow amplification of inserted DNA sequences
Plasmids
A plasmid is a circular DNA molecule that replicates separately from the host
chromosome.
If a plasmid becomes incorporated into a chromosome, it is called an episome.
The classic E. Coli plasmid pBR322 is a good example of a plasmid with features
useful in all cloning vectors:
The plasmid pBR322 has an origin of replication, or ori, a sequence where
replication is initiated by cellular enzymes. This sequence is required to
propagate the plasmid.
The plasmid contains genes that confer resistance to the antibiotics tetracycline
and ampicillin, allowing the selection of cells that contain the intact plasmid or a
recombinant version of the plasmid.
Several unique recognition sequences in pBR322 are targets for restriction
endonulceases, providing sites where the plasmid can be cut to insert foreign
DNA.
The small size of the plasmid facilitates its entry into cells and the biochemical
manipulation of the DNA.
In the laboratory, small plasmids can be introduced into bacterial cells by a process
called transformation and plasmid DNA are incubated together at at 0 degrees
Celsius in calcium chloride solution, then subjected to heat shock by rapidly shifting
the temperature between 37-43 degrees Celsius. The calcium ions are bleieved to
neutralize charges on phosphates and membrane. The heat shock causes the cells to
uptake the plasmid DNA.
In an alternative method, cells incubated with the plasmid DNA are subjected ot

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a high voltage pulse; this approach, called electroporation, transiently renders
the bacterial membrane permeable to large molecules.
Only a few cells uptake the plasmid DNA, so a method is needed to identify those
that do.
One strategy is to utilize one of two types of genes in the plasmid, referred to as
selectable and screenable markers.
Selectable markers either permit the growth of a cell (positive selection) or
kill the cell (negative selection) under a defined set of conditions.
A screenable marker is a gene encoding a protein that causes the cell to
produce a colored or fluorescent molecule.
Bacterial artificial chromosomes
Bacterial artificial chromosomes, or BACs, are artificial vectors large enough to
be thought of as chromosomes that can hold much larger DNA segments than
plasmids.
To accommodate very long segments of cloned DNA, BAC vectors have very
stable ori sites that maintain the plasmid.
BAC also include genes that encode proteins that direct reliable distribution of
the recombinant chromosomes to ensure equal division.
The BAC vector includes both selectable and screenable markers.
Yeast Artifical Chromosomes
Yeast is very easy to maintain and grow on a large scale in the laboratory. Plasmid
vectors have been constructed for yeast.
Some of these plasmids have multiple ori sites so it can be used in more than one
speciesthese are called shuttle vectors.
Yeast artificial chromosomes (YACs) contain all the elements needed to maintain a
eukaryotic chromosome in the yeast nucleus needed for stability and proper
segregation of the chromosome ant cell division. YAC vectors can be used to clone
very long segments of DNA.
Pulsed field gel electrophoresis are used to separate the fragments of YAC when
cut up by restriction endonucleases. It is a variation of gel electrophoresis that can
separate very large DNA segments.
Cloned genes can be expressed to amplify protein production
Frequently, the product of a cloned gene, rather than the gene itself, is of interest.
Investigators can manipulate cells to express cloned genes in order to study their protein
products.
The goal is to alter the sequences around a cloned gene to trick the host organism
into producing the protein product of the gene, often at very high levels to make
purification easier.
Cloning vectors with the transcription and translation signals needed for regulated
expression of a cloned gene are called expression vectors. The rate of expression of
the cloned gene is controlled by replacing the gene's normal promoter and regulatory
sequences with more efficient and convenient versions supplied by the vector.
Many different systems are used to express recombinant proteins
Bacteria
Bacteria remains the most common host for protein expression because the
regulatory sequences that govern gene expression in many bacteria are well
understood and can be harnessed to express cloned proteins at high levels.
They are easy to store and grow in the laboratory, on inexpensive growth media.

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Problems: many intrinsically disordered regions, proteins may not fold correctly
Yeast
Yeast is probably the best understood eukaryotic organism and one of the easiest to
grow and manipulate in the laboratory.
Yeast have tough cell walls that are difficult to breach in order to introduce DNA
vectors.
PCR
Polymerase chain reaction amplifies DNA sequences in vitro.
Requires knowledge of the DNA sequence in the region of interest (need primers)
no host cells are involved
requires very little starting material
PCR primers: you need primers (sequences of DNA that are complementary to a
sequence on a DNA strand) that flank both sides of the target region.
Number of DNA strands after n cycles of PCR = 2n * 2
Steps in one cycle (there are usually many):
1) Denaturation (95 C): Two strands of DNA are held together by hydrogen bonds.
With enough heat, the hydrogen bonds can be broken and the two strands will
separate.
2) Annealing (60 C): Once the DNA strands are separated, the solution is cooled to
allow the DNA primer to bind to the original DNA for amplification.
3) Elongation (72 C): The solution is raised in temperature again, so taq polymerase
(a heat resistant DNA polymerase) can replicate the DNA.
RT-PCR
Reverse-transcriptase PCR: amplify mRNA sequence into many DNA sequences with
the help of reverse transcriptase.
Steps:
1) reverse-transcribe the mRNA into a mRNA/cDNA hybrid
2) use RNAse to degrade the RNA. You are now left with a cDNA strand.
3) use cDNA as template in a PCR reaction.
cDNA
Complementary DNA (cDNA) is DNA that consists of only the npart of the gene that
gets translated.
Steps:
1) use intron free mRNA and then reverse transcribe it to create cDNA.
DNA microarray
DNA microarray is a method to determine which genes are expressed and which genes
are not expressed in a given sample. It can provide a snapshot of all the genes in an
organism, informing the researcher about the genes that are expressed at a given stage in
the organisms development or under a particular set of environmental conditions.
Steps:
1) Begin with a glass slide or chip. Attach thousands of copies of DNA for the genes
you want to test for.
2) take all mRNA being transcribe and convert it to cDNA.
3) Use the cDNA as a probe and wash it over your chip. The cDNA will hybridize
(bond) to the complementary strands if they match. When they do, they will light up
with florescence. The brighter the signal, the more you know that gene is being
transcribed.
Karyotyping

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Karyotyping is a method to count the number of chromosomes. Useful in diagnosing

chromsomal disorders such as down's syndrome.
Gel electrophoresis
Gel electrophoresis is a method to separate sequences of DNA, RNA, or proteins by
their size and charge.
Smaller fragments will travel further down the gel towards the positive side than the
larger fragments, which will have a tougher time to move.
The plate is positively charged, so negatively charged molecules will move faster down
the plate.
SDS Page
SDS page is a detergent used to denature proteins into their primary form and to decharge the proteins. When the proteins are ran through gel electrophoresis, then they
will only be separated by size, without having to worry about charge.
Smallest proteins travel the longest; largest proteins travel the shortest.
ELISA
ELISA is a technology to determine if a specific antigen exists. Antibodies are placed
on a microtiter plate, and if they bind to their specific antigen there will be a color
change in the microtiter plate, indicating that a specific antigen exists.
Lecture 18
DNA is organized into chromosomes
A bacterial chromosome is a circular double stranded DNA complexes with nucleoid
proteins.
Replication begins in a specific spot called the origin of replication region (ori) and
ends at the termination region (ter).
Eukaryotic chromosomes are linear and there are more than one chromosome.
Replication begins in multiple different ori spots along the chromosome and extends
to the end of the chromosome, the telomere.
DNA replication basics
DNA replication is semiconservative, meaning that a replicated DNA molecule
contains one old and one new strand.
DNA replication occurs in a 5' to 3' direction. This is because DNA polymerase can
only add new nucleotides to the 3'-OH end.
Eukaryotic DNA synthesis

1) DNA helicase unwinds the DNA helix. DNA gyrase relieves strain while doublestrand DNA is being unwound by helicase. DNA topoisomerase removes the supercoils;
it is ahead of the replication fork. Single-stranded DNA binding proteins (SSBs)
attach to the unwound DNA strands to prevent re-annealing of the DNA strands.
2) In leading strand synthesis, DNA polymerse III synthesizes DNA in a 5' to 3'

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direction. It adds new dNTPs to the 3'-OH end. A sliding clamp tethers the DNA pol II
to the template to allow the enzyme to catalyze consecutive additions without releasing
the DNA strand it is attached to.
3) Lagging strand synthesis occurs discontinuously because the DNA is exposed in the
5' to 3' direction. DNA primase synthesizes a short RNA primer. DNA pol III extends
the RNA with DNA, forming an okazaki fragment. As the fork extends, the process
repeats, forming a continuous leading strand and multiple okazaki fragments. DNA
polymerase I removes it with RNA, replacing it with DNA. DNA ligase joins the DNA
fragments.
4) As the replicating form move son, the leading and lagging strands twist into helical
forms.
In actuality, replication does not take place in discrete steps. The replication machinery
allows all these steps to take place at the same time (concerted).
http://sites.fas.harvard.edu/~biotext/animations/replication1.swf for an excellent
animation of DNA replication!!!!!!
Replication of prokaryotic chromosomes
Replication proceeds bidirectionally from ori to ter.
Replicon is the length of DNA that is replicated following one initiation event at a
single region.
Bacteria have 3 different DNA polymerases:
DNA pol I is used for primer removal and gap filling of okazaki fragments.
DNA pol II is used for DNA repair.
DNA pol III is used for DNA synthesis.

Completing DNA replication: Eukaryotes

At the tips of the chromosome, the lagging strand is getting shorter during each ground
of replication. This is because DNA is synthesized only in a 5' to 3' direction.
Telomeres are long sequences at the tips of the chromosome that are junk sequences.
This is so that when replication occurs, useful sequences aren't chopped off.
Lecture 18
Transcription
Transcription is the creation of RNA molecules from DNA template.

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Proteins are polycistronic, meaning that multiple polypeptides can be synthesized from
the same mRNA.
Eukaryotes are monocistronic, meaning that only one polypeptide can be synthesized
from the same mRNA.

RNA synthesis occurs in the 5' to 3' direction. Transcription is occurring in the 3' to 5'
direction of the DNA-template strand.

Steps of transcription
Initiation: RNA polymerase attaches to the promoter region on DNA and unzip the
DNA into two strands. A promoter region is a sequence, usually found upstream of the
gene region, that RNA polymerase and transcription factors bind to.
For prokaryotes, the pribnow box is the most common sequence of nucleotides at
the promoter. For eukaryotes and archaea, the TATA box is the most common
sequence of nucleotides a the promoter. The most common sequence of nucleotides
at the promoter region is called the consensus sequence; variations from it causes
less tight RNA pol binding lower transcription rate.
Elongation: RNA polymerase unzips the DNA and assembles RNA nucleotides using

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one strand of DNA as a template; only one strand is transcribed. The DNA strand used
for transcription is called the coding strand.
The DNA strand not used for transcription is called the anti-sense DNA strand.
Used for protection against degradation.
Termination: RNA polymerase reaches special sequences that signals for the end of
transcription. RNA polymerase will then release the DNA strand from itself.
Termination in prokaryotes:
Intrinsic (rho-independent): The mRNA contains a sequence that can base pair
with itself to form a stem-loop structure that is rich in GC content. Following the
stem-loop structure is a chain of uracils. When RNA polymerase reaches the
uracil area, it stalls and eventually detaches from the DNA template strand.

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Rho-dependent: When a certain mRNA sequence is transcribed, a rho protein

binds to the forming RNA transcript. When Rho binds, it causes RNA
polymerase to stall and detach from the DNA.

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Termination in Eukaryotes:
The termination sequence is usually AAAAAAAAAAA... (poly-A) signal. When
RNA pol hits this region, it stalls and detaches from the DNA template.

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mRNA processing
In prokaryotes, the primary RNA transcript is the mature mRNA.
In eukaryotes, the primary RNA transcript undergoes modification:
5' cap: A special sequence is added to the 5' end of the mRNA, providing
stability for the mRNA and point of attachment for ribosomes.
Poly-A tail: This sequence is attached to the 3' end of the mRNA. Provides
stability and control movement of mRNA across the nuclear envelope.
Splicing: Removes introns (non-coding sequences) from the RNA transcript.
Done by small nuclear ribonculeoproteins (snRNPs). Different splicing
combinations yield different polypeptides when translated. Therefore, a
combination of genes can yield many different polypeptides.

Lecture 19
Transcription and translation
Prokaryotes: transcription and translation occur simultaneously
Eukaryotes: transcription and translation are spatially and temporally separate.
Transcription occurs first in the nucleus, and translation occurs second in the cytoplasm.
Ribosomes
Ribosomes are sites of protein synthesis. It is a ribozyme: the catalytic function is
performed by rRNA.
50S + 30S = 70S (prokaryotic ribosome)
60S + 40S = 80S (eukaryotic ribosome)
Large subunit is the site of peptidyl transferase activity (tRNA binds here).
Small subunit is the initial binding of mRNA.
Exit site = E site, Peptidyl site = P site, Aminoacyl site = A site.

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TRNA
tRNA is a special RNA molecule that serves as the intermediate between RNA and
amino acids. Contains 2 sites:
One site is attached to a specific amino acid. Another site has a special 3 letter
sequence called an anticodon: this sequence binds to a complementary sequence on
the mRNA.
Aminoacyl-tRNA synthetase binds an amino acid to a specific tRNA. One enzyme for
each amino acid.

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Translation initiation
Eukaryotes:
1) Small subunit binds 5'-cap, scans mRNA for first AUG. There is only one AUG
sequence per mRNA transcript.
2) Once found, the large ribosomal subunit and the charged initiator tRNA (carrying
methionine) binds.
Prokaryotes:
1) Small subunit binds to one of the many shine-dalgarno (AUG + few other
nucleotides) sequences on the mRNA transcript. There are multiple translation
initiation sites.
2) Once found, the large ribosomal subunit and the charged initiator tRNA (carrying
n-formylmethionine) binds.
A polysome is a single mRNA molecule bound by multiple ribosomes.
Translation elongation
Prokaryotes and Eukaryotes
1) Entry of second tRNA into A site.
2) Amino acid bound to tRNA in P site bonds to amino acid bound to tRNA in A site.
A dipeptide is formed.
3) Ribosome moves down 3 more nucleotides. All tRNAs shift down one site. When
the tRNA moves from the P to the E site, the tRNA in the E site gets released. The
growing polypeptide remains in the P site.
4) Repeat steps 1-3 to grow the polypeptide chain.
Translation termination
1) Ribosome hits stop codon (UAG). Release factor binds to the A site instead of
another tRNA.
2) Polypeptide dissociates from the tRNA. tRNA and mRNA separates from the
ribosome. Ribosome dissociates into large and small subunits.

Features of the genetic code

No overlaps, no gaps between codons.
Triplet nature: three nucleotides per amino acid.

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Degenerate: more than one codon per amino acid.

The third nucleotide in the codon is the least important. Usually, this position can vary
yet still produce the same amino acid (wobble effect).
Codon bias: different species prefer different codons that code for the same amino acid.
Lecture 20
Correction mechanisms
DNA polymerase makes mistakes during DNA replication. DNA polymerase has a built
in proofreader.
Removes wrong base by 3'-5' exonuclease activity, replaces it with right one, and
resumes DNA synthesis.
Mismatch repair: enzyme repair things DNA polymerase missed.
Excision repair: enzymes remove nucleotides damaged by mutagens.
Mutagens
A mutagen is an agent/process that catalyzes mutations in the DNA sequence.
Depurination: Purine spontaneously leaves the deoxyribose sugar it was bound to.
Deamination: Amine groups on nucleotide react with water to form a ketone.
Creates wrong base.
Oxidative damage
Base analogs (structures that are similar to bases) are attached by accident.
Intercalating agents insert themselves between nitrogenous bases and causes indel
mutations.
Backbone breaks from UV ray can break DNA molecule in half.
Types of Mutations
Substitution: one nucleotide is switched with another nucleotide.
Silent mutation: A change in a single base of the DNA sequence yields the same
protein. No change in protein function. Due to wobble effect.
Missense mutation: Change in a single base of DNA sequence yields a different
amino acid. Have varying effects depends on how important the amino acid is to
the protein structure and function.
Nonsense mutation: Change in a single base of DNA sequence yields a premature
STOP codon. Have large, negative effects on protein function.
Frameshift: change in length of DNA sequence alters the reading frame of the mRNA,
causing a totally different polypeptide to be produced.
Insertion: Insertion of one or more base pairs.
Deletion: Deletion of one or more base pairs.
Regulatory mutations: Mutations in regulatory sites affecting splicing or expression.
Look on chart for chromosomal mutations!

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DNA organization
Nucleosome: DNA is coiled around bundles of 8/9 histone proteins (beads on a string). This
exists when the cell is not dividing. One of two types:
Euchromatin: loosely bound to nucleosomes, actively being transcribed.
Heterochromatin: areas of tightly packed nucleosomes where DNA is inactive.
Contains a lot of junk DNA.

Transposons: DNA segments that can move to a new location on the same or a different
chromosome. 2 types:
Insertion sequences that consist of only one gene that codes for enzymes that transports
it (transposase)
Insertion sequences that code for transposase and extra genes (antibiotic resistance,
replication, etc.)
Insertions of transposons into another region could cause mutation.
Prokaryotic transcription regulation

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Structure of the Lac operon:

-------lac I----------------------promoter --- operator - lac Z --- lac Y ---- lac A--- lac I gene: encodes for the Lac operon repressor protein.
Promoter: site where RNA polymerase binds.
Operator: site where Lac operon repressor protein binds.
Lac Z, Lac Y, Lac Z = structural genes.
How the lac operon works
1) Lac I gene gets transcribed and translated to create the repressor protein.
2) When there is no lactose present in the cell, the repressor binds to the operator and
prevents RNA polymerase from transcribing the structural genes.
3) When lactose is present in the cell and there are no glucose molecules available,
lactose binds to the allosteric site of the repressor protein. This binding will cause a
conformational change in the protein, and thus a change in activity. The repressor now
cannot bind to the operator and RNA polymerase can proceed to transcribe the structural
genes. With no glucose available, there will be high cAMP levels. cAMP will bind to
the promoter and help RNA polymerase more efficiently transcribe the structural genes.
If there is glucose present in the cell, there won't be transcription of the lac operon
(even if there is lactose present as well). The activator (cAMP) will not bind to the
promoter, and transcription won't occur.
Repressible enzymes
Repressible enzymes are when structural genes stop producing enzymes only in the
presence of an active repressor.
Eukaryotic transcription regulation
Regulatory proteins: repressors and activators influence RNA pol's attachment to the
promoter region.
Nucleosome packing: methylation of histones cause tighter packing and thus preventing
transcription. Acetylation of histones catalyzes uncoiling and promotes transcription.
RNA interference: Short interfering RNAs block mRNA translation by altering the mRNA
conformation or configuration before it gets to the ribosome.
X-inactivation
During embryonic development in female mammals, one of the two X chromosomes does
not uncoil into chromatin.
It remains a dark and coiled chromosome called a Barr body. Barr bodies cannot be
expressed.
Thus, only the genes on the X chromosome will be expressed.
Either X chromosome can be inactivated, meaning genes in the female will not be expressed
similarly, so all calls in a female mammals are not necessarily functional identical.
Human Genome
97% of human DNA is non-coding.
Made up of regulatory sequences, introns, repetitive sequences, etc.
Contains trandem repeats abnormally long stretches of back to back repetitive sequences
within an effected gene.