Carolyn Yao

Biology Research Manwell Study Sheet

[Have fun!]
I. Classification and Organization of Living Things
Taxonomy: the classification and organization of living organisms.
Rank: Kingdom, Phylum, Class, Order, Family, Genus, Species
Organisms are in the same species when they can breed and mate to produce
fertile offspring. In some cases where similar species do, only a substantial amount
of offspring counts.
Classification of Cells: Cell type prokaryotes/eukaryotes, Cell numberunicellular/multi-cellular, and Energy Absorption:
autotrophic/heterotrophic
Five Kingdoms
Animalia: multi-cellular, eukaryotic heterotrophs. Most produce sexually, with adult
members containing two copies of the genetic material.
Plantae: multi-cellular, eukaryotic, and photosynthetic autotrophs. They are able to
adapt on land because they have internal structures for transporting water and
nutrients and providing erect support.
Monera: Prokaryotes.
Fungi: Multi-cellular eukaryotes that absorb their nutrients.
Protista: Unicellular, multi-cellular, or colonial eukaryotes that all thrive in waterbased environments. Perform cellular respiration, some with the ability to go
through photosynthesis with chloroplasts.
(In the case of the Six Kingdom System, Monera splits into Eubacteria and Archaebacteria.)

The Three Domain System more accurately reflects lifes history

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Binomial Nomenclature: conceived by

Carolus Linnaeus - Genus species.
Other methods of Classification:
Cladistics: nested sets constructed using
a timeline and list of characteristics.
Phenetics: given points for similar traits,
where each characteristic is equal in
significance.
Homologies are structural resemblances that are the results of shared ancestry.
Living things respond to stimuli.
Living things are both complex and organized.

Living things acquire and use materials and energy.

Living things grow and develop.

Living things reproduce.

Living things get rid of waste.

Living things need to maintain homeostasis.

II. Biochemistry
Atom Proton (positive), Electron (negative), Neutron (no charge)
Element - pure chemical substance consisting of one type of atom distinguished by
its atomic number, which is the number of protons in its nucleus. It cannot be
broken down into simpler substances.
Molecule a neutral group made of at least 2 different atoms in a definite
arrangement held together by strong covalent bonds.
Mixture two or more different substances that are not chemically combined.
Compound pure chemical substance consisting of two or more different elements
that cannot be separated physically, but may separate by means of chemical
reactions.
Chemical bonds ionic bonds, covalent bonds,
and hydrogen bonds.
Ionic bonds: caused by the attraction between
oppositely charged ions.
Covalent bonds: two atoms share one or more
pairs of electrons. They may be categorized into
polar and non-polar bonds.

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Hydrogen bonds: the attraction between a slightly negative hydrogen atom in a
molecule and a slightly positive hydrogen atom in a molecule. (i.e. water)

To the right are the principle functional groups found in biomacromolecules. They
contain covalent bonds, which may either be polar or non-polar.
All shown besides carbon-hydrogen are made up of polar bonds.

Dehydration Synthesis: the joining of two monomers through the loss of

hydrogen to form a polymer.
Hydrolysis: the breaking apart of a polymer through the gaining of hydrogen.

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Biomacro
molecule
Functions

Carbohydrates

Lipids

Nucleic Acids

Proteins

Important energy
source for cells,
energy storage in
plants/animals,
provides
structure, and
material in
plants.

Energy storage in
animals/some
plants, component
of cell membranes,
steroids, waterproof
covering on
leaves/stems.

Genetic material
of cells/viruses,
transfer of
genetic info from
DNA -> protein
(intracellular
messenger,
principle shortterm energy
carrier (ATP).

Glycerol
(Hydrophilic) + Fatty
Acids (Hydrophobic)
= Triglyceride
(Nonpolar)

http://www.uq.edu
.au/vdu/DNA
%20nucleotide.gif

Compone
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hair,
transport
ation of
oxygen,
enzymes,
importan
t factor
for
growth.
http://bio
tech.mat
cmadison
.edu/reso
urces/pro
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Manual/i
mages/2
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C, O, H

C, O, H, P

C, O, H, N, P

Glucose
(monosaccharide
), sucrose
(dissacharide),
glycogen, starch,
cellulose
(polaysaccharide
s).

Oil, fat, waves,

cholesterol,
phophatidycholine.

DNA
[deoxyribonucleic
acid], RNA
[ribonucleic acid]

Structure

Chemical
Makeup
Examples

nitrogenous base,
phosphate group,
and sugar
(ribose).

pH: the measure of the acidity of basicity of a solution.

III. Cell theory and Structures

1. Cells are the basic structural and functional units of life.
2. If it is a living thing, then it must contain one or more cells.
3. All cells come from pre-existing cells.
Structures of a Cell:
Prokaryotic

C, O, H
N, S
Keratin,
silk,
hemoglo
bin.

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Eukaryotic: Animal

Eukaryotic: Plant

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Eukaryotes
- membrane-enclosed organelles
- multiple linear chromosomes (often in
pairs)
- streaming in cytoplasm
- cell division by mitosis
- complex flagella
- larger ribosomes
- cytoskeleton
- cellulose in cell walls
- DNA wrapped around proteins

Prokaryotes
- no membrane enclosed organelles
- single circular chromosome
- no streaming in cytoplasm
-cell division without mitosis
-simple flagella
-small ribosomes
- no known cytoskeleton
- no cellulose in cell walls
- proteins bound to DNA

Division of Labor:
Elementary Particle Quark
Subatomic Particles Proton, Electron, Neutron
Atom
Molecule Water
Macromolecule Hemoglobin
Organelle Mitochondrion
Cell Blood Cell
Tissue Groups of cells with similar functions Muscle
Organ Eyes, Heart
Organ System Circulatory, Skeletal
Organism Striped Bass
Population All Striped Bass in Chesapeake Bay
Community All organisms in Chesapeake Bay
Ecosystem Chesapeake Bay
Biosphere Part of Earth that contains life

Organelles:
Central Vacuoles A large, fluid-filled vacuole occupying most of the volume in
plant cells ; performs several functions, including maintaining turgor pressure.

Carolyn Yao
Centriole in animal cells: a short, barrel-shaped ring consisting of nine
microtubule triplets.
Chloroplast organelle in plant/some protist cells that is the site of
photosynthesis. It consists of a double membrane and an extensive internal
membrane that bears chlorophyll.
Cytoplasm the material contained within the plasma membrane of a cell,
exclusive of the nucleus.
Cytoskeleton a network of protein fibers in the cytoplasm that gives shape to a
cell, holds and moves organelles, and is typically involved in cell movement.
Endoplasmic Reticulum a system of membranous tubes and channels within
eukaryotic cells; the site of most protein and lipid synthesis.
Golgi Complex - stack of membranous sacs found in most eukaryotic cells that is
the site of processing/separation of membrane components and secretory materials.
Lysosome membrane-bound organelle containing intracellular digestive enzymes.
Microfilament part of the cytoskeleton of eukaryotic cells that is composed of
proteins actin and myosin; function in the movement of cell organelles and in
locomotion by extension of the plasma membrane.
Microtubule hollow, cylindrical strand found in eukaryotic cells. In the
cytoskeleton, it is involved in movement of organelles, cell growth, and construction
of cilia and flagella.
Mitochondrion an organelle bounded by two membranes; site of aerobic
metabolism (cellular respiration).
Nucleoid location of genetic material in prokaryotic cells; not membraneenclosed.
Nucleolus region of eukaryotic nucleus that is engaged in ribosome synthesis,
consists of genes encoding ribosomal RNA, newly synthesized mRna, and ribosomal
proteins.
Rough Endoplasmic Reticulum ER lined with ribosomes.
Smooth Endoplasmic Reticulum ER without ribosomes, also the location of
detoxification.
Vesicle small, membrane-bound sac with the cytoplasm.
Cell Membrane:
The plasma membrane isolates the cell while allowing communication with its
surroundings.
Membranes are "fluid mosaics" in which proteins move within layers of
lipids.

The phospholipid bilayer is the fluid portion of the membrane.

A mosaic of proteins is embedded in the membrane.

Molecules in fluids move in response to gradients pressure, concentration,

electrical.

Movement across membranes occurs by both passive and active

Transport.

Passive transport includes simple diffusion, facilitated diffusion, and osmosis.

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o

Plasma Membranes are selectively permeable to diffusion of molecules.

Some move across membrane by simple diffusion.

Others cross the membrane by facilitated diffusion, with the help of

membrane transport proteins.

Osmosis Is the Diffusion of Water Across Membranes

Active transport uses energy to move molecules against their concentration

gradients.

Cells engulf particles or fluids by endocytosis.

Pinocytosis moves liquids into the cell.

Receptor-mediated endocytosis moves specific molecules into the cell.

Phagocytosis Moves Large Particles into the Cell

Exocytosis Moves Material Out of the Cell

Membrane Traffic
1. mRNA leaves nucleus. mRNA
leaves nucleus.
2. Proteins synthesized on
ribosomes.
3. Protein-filled vesicles travel to
Golgi Complex.
4. Proteins are sorted and
repackaged.
5. Digestive proteins are
packaged in lysosomes.
6. Others are packages to be
released from the cell.

IV.

Energy - Enzymes

Energy: potential and kinetic

Potential: stored energy
Kinetic: energy of movement
First Law of Thermodynamics: As long as no energy enters or exits a system, the
total amount of energy in a system remains constant, though the energy form may
change.
Second Law of Thermodynamics: As long as no energy enters or exits a system,
the amount of useful energy decreases as energy is converted from one form to

Carolyn Yao
another. AND/OR processes that proceed spontaneously result in an increase in
randomness/disorder of the system over time.
-In an exergonic reaction, the products have less energy than the reactants do; the
reactants release energy to surroundings.
-In an endergonic reaction, the products have more energy than the reactants do;
the reaction removes the energy from the surroundings.
-All reactions require an initial input of energy called activation energy.
-When an endergonic reaction is coupled with an exergonic one, the energy released
by the exergonic reaction drives the endergonic reaction.
Enzymes are catalysts that decrease the amount of activation energy required for a
certain reaction, therefore adding speed to the reaction.
The enzyme binds to the molecules or molecules it is going to affect, forming an
enzyme-substrate complex. The bond is usually by means of relatively weak
chemical bonds. They are substrate/reaction-specific and are reusable.
The enzymes function is determined by its tertiary structure.
Two factors that may affect enzymes are pH and temperature.

V.

Cellular Respiration

Eukaryotic cells derive their energy, or ATP,

through cellular respiration, either aerobically
or not.
The three steps are: glycolysis, the Krebs
Cycle, and the Electron Transport System.

-Glycolysis occurs in the cytoplasm.

-The enzymes for the Krebs Cycle are located
in the mitochondrial matrix.
-Those for the Electron Transport System
are located in the inner mitochondrial
membrane.

Carolyn Yao
The overall equation for glucose metabolism is C6H12O6+6O2 => 6O2+
6H2O+ATP.
The synthesis of ATP by the cell using both the Krebs Cycle and an electron
transport chain is called respiration.
Cellular respiration also involves 2 electron carriers, NAD+ and FAD that lend
electrons to the electron transport chain during the final stage.
Glycolysis: the breaking down of glucose from a 6-carbon sugar to 2 molecules of a
3-molecule pyruvate.
What follows glycolysis is determined by the presence of oxygen. If yes, then it will
proceed to the Krebs Cycle. If not, then it will go to fermentation to regenerate
electron carriers in order for glycolysis to work again. Glycolysis makes a net 2ATP.

If lacking in oxygen, the pyruvate with

become either 2 molecules of lactate or 2
molecules of ethanol + CO2.
This is so NAD+ is able to regenerate so that
glycolysis is able to occur again. Muscle
soreness is a result of the body not making
lactate fast enough when the muscles have
used up oxygen.

Pyruvate becomes
acetyl CoA with the
help of coenzyme A
and the release of
CO2 because only
2-carbon molecules
can enter the Krebs
Cycle. Once in the
Krebs Cycle, several

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reduction processes occur 3NAD+ -> 3NADH and FAD -> FADH2. ADP -> ATP and 2
CO2 are released.
This process repeats twice for both pyruvate molecules. Thus, all the 6 original
carbons are used up and the result is a total of 2ATP, 8NADH, and 2FADH2.
After this comes the Electron
Transport System. The electron carriers,
NADH and FADH2 lend electrons to the
electron transport chain. As they pass
through the inner mitochondrial
membrane, they lose some energy.
Here, the electrons attract a proton in your
body, hydrogen. The energy from electrons
is used to pump protons across the
membrane, and the gradient of protons
then becomes potential energy.
The final electron acceptor is oxygen. 2 hydrogens + oxygen + electron = H2O,
or water, which is a waste product.
The proton gradient is used by
a membrane protein, ATP
synthase, that synthesizes ATP.
It allows protons to diffuse
across the gradient because of
their concentration gradient,
and uses the energy to create
ATP from ADP.
This creates 32 to 34 ATP.
The overall energy accounting
because 2 ATP + 2 ATP + 32 or
34 ATP =

36 to 38 ATP
VI. Digestive System
Food enters the oral cavity, where it
begins physical digestion. Food is bit
into smaller pieces to increase the
surface area of chemical digestion.
Salivary glands release saliva,
which contains amylase, an enzyme

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that breaks down polysaccharides. Carbohydrates are broken down for example,
starch is broken down into glucose.
All this travels down the esophagus, where it is propelled into the stomach when
the epiglottis covers the air pathway.
At the stomach, food goes through physical digestion as muscle contractions churn
the food. It stores ingested food to release slowly into the small intestine. The lining
produces:
Hydrochloric acid: activates pepsin.
Pepsin: protease enzyme, breaking down proteins to peptides.
Mucus: protection, prevents the stomach from self-digestion.
The liver produces bile, which is stored in the gallbladder. It also stores fats and
carbohydrates, regulates blood glucose levels, synthesizes blood proteins, stores
vitamins, and detoxifies the body.
The pancreas creates pancreatic juice, which provides an abundance of enzymes
that digest food later on in the small intestine.
In the small intestine, chemical breakdown and absorption of food molecules
occur with the help from pancreatic juice and bile.
Bile is a fat emulsifier, which breaks fat globules to increase surface area for
chemical digestion. Lipase from the pancreatic juice then takes over the chemical
digestion they are broken down to glycerol and fatty acids.
Peptidases break down small peptides into amino acids through hydrolysis.

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Hormone
Gastrin

Target/Response
Stimulus
Stimulates gastric acid
Presence of
secretion and proliferation polypeptides/amino acids
of gastric epithelium.
in gastric lumen.
Cholecystokinin
Stimulates secretion of
Presence of fatty acids
pancreatic enzymes, and
and amino acids in small
contraction and employing intestine.
of the gallbladder.
Secretin
Stimulates secretion of
Acidic pH in the lumen of
water and bicarbonate
the small intestine (from
from the pancreas and bile food immediately from the
ducts.
stomach)
Ghrelin
Appears to be a strong
Not clear, but secretion
stimulant for appetite and peaks prior to feeding and
feeding also a potent
diminishes with gastric
stimulator of growth
filling.
hormone secretion.
Gastric Inhibitory
Inhibits gastric secretion
Presence of fat and
Polypeptide
and motility and
glucose in the small
potentiates release of
intestine.
insulin from beta cells in
response to elevated
blood glucose
concentration.
Dissacharidases/carbohydrases breaks down dissaccharides into monosaccharides
through hydrolysis.
Amino acids, glycerol, fatty acids, and
monosaccharides pass through the wall
into the bloodstream as they are absorbed
through villi.
Fiber, usually in the form of cellulose, is
indigestible and stimulates the release of
H2O. It bulks up the waste and keeps the
intestines healthy.
At the large intestine, the bacteria
created there produce vitamins that are
absorbed along with water and salts.
Elimination of undigested material occurs here, where it is led through the rectum
out the anus.
Nutrients:
Water carries nutrients in your body and regulates body temperature by
dissipating heat.
Proteins provide the structures for tissues in the body and transport essential
elements in the blood stream.
Vitamins regulates many functions of the body, some offering a boost in immune
defenses.

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Minerals regulates many functions of the body, combining to maintain structures
in your body.
Fats storage of energy and energy production.
Carbohydrates primary source of energy for the body.

VII. Circulatory System

Different types of organisms have different types of circulatory systems. For
example, humans have closed circulatory systems, meaning blood stays within the
vessels. Some organisms have open circulatory systems, a way of transporting
blood that does not separate it from other intracellular fluid. Blood infiltrated
through sinuses, or space around the organs to exchange chemically with the fluids.
Blood flows faster in a closed circulatory, but the tiny size of some organisms allows
them to harbor open circulatory systems.

Closed Circulatory Systems Humans

and Earthworms (examples)

Open Circulatory Systems Fish/Crayfish

(examples)
Human Heart

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Blood enters through the
superior vena cava (above
the heart) and the inferior
vena cava (below the heart).
These structures that bring
deoxygenated blood to the
heart from the muscles are
called veins.
The blood enters the right
atrium, and as the ventricles
contract, the blood passively
goes through the tricuspid
valve to the right ventricle,
where it is pushed up the
pulmonary valve to the
pulmonary arteries. They
lead to the left and right
lungs.
When the blood circles back,
they come through the
pulmonary veins to the left
atrium. There, it goes through
the mitral valves to the left ventricle, where it is pushed up the aortic valve to
the aorta. The newly oxygenated blood goes to the rest of the body through
arteries.
Plants
Land-dwelling plants evolved from green algae 430 million years ago. They evolved
into two types vascular and non-vascular. Those with vascular tissue could
transport water and nutrients through a series of tubes and are able to grow large.
Those without vascular tissue are limited in size.
Vascular tissue is consisted of
xylem, which transports water,
and phloem, which transports
organic materials. They have
cuticles and structures to protect
their gametes and embryos and
have also developed lignin, a rigid
material embedded in the
cellulose matrix of the cell walls
that support trees and other large
vascular plants. Vascular land
plants have differentiated into an

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underground root system that absorbs water and minerals and an aerial system for
carbon dioxide and sunlight.
Mycorrhizae are modifications of a plants roots through interaction with fungi. The
fungi wrap themselves along the roots of the plants or penetrate the roots to
increase surface area for water and mineral absorption. Fungi also absorb more
minerals and convert them into a substance more readily usable by the plant. Along
with helping in absorption, mycorrhizae also protect the plant from disease-causing
organisms in the soil.
Transportation by xylem is explained by the cohesion-adhesion hypothesis.
Water molecules are cohesive to each other because they have slight charges on
each end, and are attracted to each other. Water molecules are also adhesive to
other charged substances for the same reason. Therefore, capillary action, or the
rising of water, occurs because charged groups on the walls of the tube pull the
water molecules up (adhesion) and the other water molecules are also dragged up
by cohesion.
Transportation by phloem is explained by the pressure-flow hypothesis. Water
and dissolved sugars move from the source (areas of high pressure) to the sink
(area of low pressure).

VIII. Immunity
Kochs Postulates
1. The microorganism must be found in abundance in all organisms suffering from
the disease, but should not be found in healthy animals.
2. The microorganism must be isolated from a diseased organism and grown in pure
culture.
3. The cultured microorganism should cause disease when introduced into a healthy
organism.
4. The microorganism must be re-isolated from the inoculated, diseased
experimental host and identified as being identical to the original specific causative
agent.

The body offers multiple lines of

defense.
1. Non-specific external barriers.
The skin and mucus membranes. If
the pathogen penetrates and enters
the body

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2. Non-specific internal defenses. These include phagocytes and natural killer
cells, fever, and inflammation.
2. Specific internal defenses. These include T and B lymphocytes that engage in
cell-mediated and humoral immunity.

Inflammation
1. Tissue is wounded and bacteria enter.
2. Wounded tissues send signals to
increase white-blood cell production and
stimulate local mast cells to release
histamine.
3. Histamine causes the capillaries to
become leaky and increase blood flow.
4. White blood cells and fluids seep out of
capillaries. White blood cells engulf the
pathogen while the fluids cause swelling
the wound.
5. Local capillary clotting occurs to
prevent future invasions.

the
at

1. Each B-cell contains only one type of

antibody receptor on its surface, and
has a matching antigen. The antigen is
identified by one of the B-cells.
2. B-cells produce memory cells, which
are kept for the future so that immune
responses to a certain antigen will be
faster and plasma cells, which release
antibodies that kill the bacteria.

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1. In order to be activated, T-cells

must have viruses, or viral antigens,
presented to them by other cells
such as macrophages.
2. When activated, T-cells produce
memory cells to speed up future
invasions by the same virus,
cytotoxic cells to search for the
viruses and kill them, and helper Tcells to amplify the immune response
of both B and T cells.

B-cells are produced and matured in the bone marrow, and then sent out to lymph
nodes and the circulatory system.
T-cells are produced in the bone marrow, and mature in the thymus.
HIV/AIDS
Human Immunodeficiency Virus -> Acquired Immune Deficiency Syndrome
HIV is a retrovirus, using reverse transcriptase to go from messenger RNA to DNA.
It fuses with the host cell, causing the immune system to attack the hosts body.

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IX.
Respiratory System

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The human
respiratory
system.

The respiratory system must have

1. A large surface area compared to the volume of the organism
2. A moist surface
3. Thin cell linings on respiratory surfaces.
The function of
countercurrent
exchange in the gills
of fish.

X. Excretory System
XI. Photosynthesis
Sorry guys, I havent finished these topics in class yet!
Hope you guys enjoyed the study sheet. xD