CONCEPTS OF LIFE AND THE SCIENTIFIC METHOD
or measured. It cannot be used to answer all questions.
Scientific Method
- Simply a method of scientific inquiry, a search for
information and explanations of natural phenomena.
(1) Observation:
careful
observation of a
process or
phenomenon
(2) Hypothesis:
guess concering
the observation
(may generate
multiple
hypotheses); an
explanation,
based on observations and assumptions, that leads to
a testable prediction.
(3) Prediction: expected consequences of a correct
hypothesis
(4) Experiment: Test of a hypothesis
Theory and Certainty
A theory is a set of hypotheses that have been thoroughly tested
over and gone through verification. Its acceptance is provisional.
A theory is broader in scope and general enough to spin off
many new, testable hypotheses. Compared to any one
hypothesis, a theory is generally supported by a much greater
body of evidence.
Deductive Reasoning: Examining individual cases by applying
accepted general principles.
- Flows from general to specific; from general premises
a scientist would extrapolate to specific results
- In the scientific process, deductions usually take the
form of predictions of results that will be found if a
particular hypothesis (premise) is correct.
Ex.: If all leaves have chlorophyll, then gumamela leaves
have chlorophyll.
Inductive Reasoning: discovering general principles through
examination of specific cases
- Goes from a set of specific observations to general
conclusions.
- Collecting and analyzing observations can lead to
important conclusions based on a type of logic called
inductive reasoning. Through induction, we derive
generalizations from a large number of specific
observations.
Science, Technology, and Society
Technology applies scientific knowledge for some specific
purpose. For example, forensic technicians use DNA from a
blood sample in a crime scene to obtain a genetic code. Patterns
of bands vary from person to person.
Scientific study is limited to the area that can be observed
Practical limits include spatial and temporal considerations.
The Concept of Life
- A particular set of processes that result from the
organization of matter
Manifestations of the Concept of Life:
(1) High degree of complexity and order: Biological
organization is based on hierarchy of structural level with each
level building on the levels below it.
(2) Reproduction: Organisms reproduce their own kind; life
comes only from life (biogenesis)
(3) Growth and Development: Heritable progress is stored in
DNA and directs the species-specific pattern of growth and
development.
(4) Energy Processing/Utilization: Organisms take in and
transform energy to do work.
(5) Response to Environment: Organisms respond to stimuli
from the environment
(6) Homeostasis/Balance: Regulate their internal environment
to maintain a steady-state, even in the face of fluctuating
external environment
(7) Evolutionary adaptation: Life evolves in response to
interactions
Unifying themes:
(1) Biological hierarchy
(2) Emergent properties
(3) Cell
(4) Heritable information
(5) Structure and function
(6) Interaction with the environment
(7) Feedback mechanism
1. Highly ordered structure
Theme: In exploring levels of biological organization, hierarchy
unfolds (New Properties Emerge at Successive Levels of
Biological Organization)
Reductionism: This method is so named because it reduces
complex systems to simpler components that are more
manageable to study.
Levels of Biological Organization:
(1) Biosphere: the “layer” of the Earth which consists of all
life on Earth and all the places where life exists
(2) Biome: large-scale ecosystems classified by
predominant vegetation type and distinctive
combinations of plants and animals (e.g. aquatic and
terrestrial biomes)
(3) Ecosystems: consists of all the living things in a
particular area, along with all the nonliving components
of the environment with which life interacts, such as
soil, water, atmospheric gases, and light, or an energy-
processing system of community interactions that
include abiotic environment factors
 (4) Communities: The array of organisms inhabiting a
particular ecosystem is called a biological community.
A community is therefore the set of populations that
inhabit a particular area, or a populations of different
species
(5) Population: A population consists of all the individuals
of a species living within the bounds of a specified
area/a localized group of organisms belonging to the
same species
(6) Organisms: Individual living things are called
organisms.
(7) Organs: a body part that is made up of multiple tissues
and has specific functions in the body.
(8) Tissues: is a group of cells that work together,
performing a specialized function
(9) Cells: The cell is life’s fundamental unit of structure and
function.
(10) Organelles: the various functional components present
in cells.
(11) Molecules: a chemical structure consisting of two or
more units called atoms
The biosphere is based on a hierarchy of structural levels. Each
level of biological organization has emergent properties.
Theme: Emergent Properties
With each level upward in the hierarchy of biological
organization, novel properties emerge.
Reflect a hierarchy of structural organization. Life is associated
with numerous emergent properties. Structurally, the biosphere
is the most complex.
Emergent properties, novel properties that emerge at each level
that are absent from the preceding (simpler) one, are due to the
arrangement and interactions of parts as complexity increases.
Isolated components of living systems—the objects of study in
a reductionist approach—lack a number of significant properties
that emerge at higher levels of organization.
Reproduction
Organisms produce their own kind.
Microorganisms: through binary fission
Plants: asexual or sexual (colors and scents)
 Asexual
o Rhizomes like grasses
o Onion stem (reproductive organ)
o Stolons of strawberries
o Tubers of potatoes
o Reproductive leaves
Growth and Development
Heritable programs (DNA) direct species-specific pattern of
growth and development
Ex.: Development of zygote comes from genetic material
inherited. Cells need to differentiate (defining function) and to
undergo morphogenesis (taking form).
Development: an organism undergoes changes to acquire new
structures and abilities.
Levels of control:
1) Genetic instructions
How a plant grows from a seed: Only one genetic
material but different genetic expressions
2) Intercellular interaction
3) Environment factors
Theme: Heritable Information
James Watson and Francis Crick
Rosalind Franklin: X-ray crystallographer made the photo used
in deducing the double helical structure of DNA
Nucleotide: basic chemical unit that consists of 4 nitrogenous
bases linked to a sugar which is in turn linked to phosphate
Flow of Genetic Information
The Central Dogma
The central dogma of biology states that information encoded in
the DNA is transferred to messenger RNA (mRNA) through
transcription, which then directs the synthesis of protein through
translation. The set of instructions that enable the mRNA
nucleotide sequence to be decoded into amino acids is called
the genetic code.
Energy Utilization (including maintenance of ordered state)
Sunlight powers the synthesis of organic substances during
photosynthesis.
Response to Environmental Stimulus
Ex.: Poinsettia leaves. Anthocyanin in the cells is activated by
change in ambient temperature
Tropism: plant movement determined by direction of stimulus
Phototropism: light is the stimulus (positive phototropism)
Light causes diffusion or migration of auxin from the bright side
to the shaded side of the stem.
Auxins stimulate the cells on the shaded side of the plant stem
to elongate
Gravitropism: coordinated process of differential growth by a
plant or fungus in response to gravity pulling on it (mainly roots).
Homeostasis
- Regulation of internal environment
- Ex. Panting Is the dog’s evaporative cooling system
Theme: Regulation
Many biological processes are self-regulating, in which an
output/product of a process regulates that process
1) Negative feedback/feedback inhibition slows/stops
process
2) Positive feedback speeds up the process
Evolutionary Adaptation
Ex.: Giraffes
Natural selection can “edit” a population’s heritable variations
Ex.: Effect of birds preying on a beetle population
Theme: Structure and Function Correlation
Examples: Stomatal crypts restrict water loss; The roots of water
hyacinths are totally submerged and have some adaptations
associated with growth in a Hydric environment. Such traits are
called Hydromorphic (Aerenchyma cells)
Theme: The cell is the basic unit of structure and function
Theme: Unity and diversity
Diversity is the hallmark of life
1.8 M species identified and named
5,200 known species of prokaryotes
100K of fungi
290K of plants
57K vertebrates
1M insects
Estimates of the total species count range from 10M to over
100M
Overview of Protein Functions
1) Enzymatic: selective acceleration of chemical reactions
Example: Digestive enzymes catalyze the hydrolysis of bonds in
food molecules.
2) Structural: support
Examples: Keratin is the protein of hair, horns, feathers, and
other skin appendages. Insects and spiders use silk fibers to
make their cocoons and webs, respectively. Collagen and
elastin proteins provide a fibrous framework in animal
connective tissues.
3) Storage: storage of amino acids
Examples: Casein, the protein of milk, is the major source of
amino acids for baby mammals. Plants have storage proteins in
their seeds. Ovalbumin is the protein of egg white, used as an
amino acid source for the developing embryo
4) Transport: Transport of substances
Examples: Hemoglobin, the iron-containing protein of vertebrate
blood, transports oxygen from the lungs to other parts of the
body. Other proteins transport molecules across membranes.
5) Hormonal: Coordination of an organism’s activities
Example: Insulin, a hormone secreted by the pancreas, causes
other tissues to take up glucose, thus regulating blood sugar
concentration.
6) Receptor: Response of cell to chemical stimuli
Example: Receptors built into the membrane of a nerve cell
detect signaling molecules released by other nerve cells
7) Contractile and motor: Movement
Examples: Motor proteins are responsible for the undulations of
cilia and flagella. Actin and myosin proteins are responsible for
the contraction of muscles.
8) Defense: Protection against certain microorganisms,
antibodies combat bacteria
Example: Antibodies inactivate and help destroy viruses and
bacteria
Unity: Genetic Code
1) All independently living creatures have hereditary
material, DNA.
2) Similar ways of forming proteins
3) Same genetic code
Structure and Function
Because such correlations of structure and function are
common in all forms of life, analyzing a biological structure gives
us clues about what it does and how it works. Conversely,
knowing the function of something provides insight into its
structure and organization.
The Cell
The so-called Cell Theory was first developed in the 1800s,
based on the observations of many scientists. The theory states
that all living organisms are made of cells, which are the basic
unit of life. In fact, the actions of organisms are all based on the
functioning of cells.
Theme: Life’s Processes Involve the Expression and
Transmission of Genetic Information
Heritable Information
Transmitted from parents to offspring, genes are the units of
inheritance. They encode the information necessary to build all
of the molecules synthesized within a cell, which in turn
establish that cell’s identity and function.
The molecular structure of DNA accounts for its ability to store
information. A DNA molecule is made up of two long chains,
called strands, arranged in a double helix.
In carrying out gene expression, all forms of life employ
essentially the same genetic code: A particular sequence of
nucleotides says the same thing in one organism as it does in
another. Differences between organisms reflect differences
between their nucleotide sequences rather than between their
genetic codes.
Theme: Life Requires the Transfer and Transformation of
Energy and Matter
Molecules: Interactions Within Organisms
In feedback regulation, the output or product of a process
regulates that very process. The most common form of
regulation in living systems is negative feedback, a loop in which
the response reduces the initial stimulus. As seen in the
example of insulin signaling (Figure 1.10), after a meal the level
of the sugar glucose in your blood rises, which stimulates cells
of the pancreas to secrete insulin. Insulin, in turn, causes body
cells to take up glucose and liver cells to store it, thus decreasing
blood glucose levels. This eliminates the stimulus for insulin
secretion, shutting off the pathway. Thus, the output of the
process negatively regulates that process.
Positive feedback, in which an end product speeds up its own
production: Positive feedback occurs as chemicals released by
the platelets attract more platelets. The platelet pileup then
initiates a complex process that seals the wound with a clot.
Unity and Diversity
Monera Protista Plantae Fungi Animalia
Earliest organisms
Phylogeny: the evolutionary history of a species or group of
species.
Phylogenies show evolutionary relationships
Taxonomy: the scientific discipline of naming and classifying
organisms
Binomial Nomenclature:
To avoid ambiguity when communicating about their research,
biologists refer to organisms by Latin scientific names. Instituted
in the 18th century by Carolus Linnaeus. First part: genus,
second part: species.
Hierarchical Classification:
Related species into genus, related genera into family, families
into orders, orders into classes, classes into phyla, phyla into
kingdoms, and, more recently, kingdoms into domains.
Linking Classification and Phylogeny
Phylogenetic tree: the branching pattern often matches how
taxonomists have classified groups of organisms nested within
more inclusive groups.
Evolution accounts for the unity and diversity of life
The scientific explanation for the unity and diversity of
organisms—as well as for the adaptation of organisms to their
particular environments—is evolution: the concept that the
organisms living on Earth today are the modified
descendants of common ancestors.
Unity: Two species share certain traits because they have
descended from a common ancestor (descent with modification)
Diversity: Certain heritable changes occurred after the two
species diverged from their common ancestor.
Three Domains of Life
New methods of assessing species relationships, such as
comparisons of DNA sequences, have led to a reevaluation of
the classification of life. Sequencing of rRNA suggests that all
organisms evolved from a common ancestor along three
lineages.
Bacteria, Archaea, and Eukarya
 Bacteria and archaea are prokaryotic.
 Bacteria are the most diverse and widespread
prokaryotes and are now classified into multiple
kingdoms.
 Domain Archaea includes multiple kingdoms. Some of
the prokaryotes known as archaea live in Earth’s
extreme environments, such as salty lakes and boiling
hot springs.
o Archaea were considered bacteria because
they appeared prokaryotic.
o Based on biochemical characteristics and
DNA sequence analysis & rRNA, they were
differences between the two.
 Archaea and Eukarya are more closely related.
 All organisms with eukaryotic cells are in domain
Eukarya
o includes four subgroups: kingdom Plantae,
kingdom Fungi, kingdom Animalia, and the protists.
o Distinguished partly by their modes of nutrition:
Plants produce their own sugars and other food
molecules by photosynthesis, fungi absorb
nutrients in dissolved form from their surroundings,
and animals obtain food by eating and digesting
other organisms.
o Kingdom Plantae (land plants) consists of terrestrial
multicellular eukaryotes that carry out
photosynthesis, the conversion of light energy to
the chemical energy in food.
o Kingdom Fungi is defined in part by the nutritional
mode of its members, which absorb nutrients from
outside their bodies.
o Kingdom Animalia consists of multicellular
eukaryotes that ingest other organisms.
o Protists are mostly unicellular eukaryotes and some
relatively simple multicellular relatives. Scientists
are currently debating how to classify protists in a
way that accurately reflects their evolutionary
relationships. The most numerous and diverse
eukaryotes are the protists, which are mostly
single-celled organisms. Although protists were
once placed in a single kingdom, they are now
classified into several groups. One major reason for
this change is the recent DNA evidence showing
that some protists are less closely related to other
protists than they are to plants, animals, or fungi.
Charles Darwin and the Theory of Natural Selection
 1859 – Charles Darwin published On the Origin of
Species.
 As populations become separated by a geographical
barrier and adapt to their local environments, they
become separate species.
 RNA sequencing proves this theory.
1) Descent w/ modification: contemporary species arose
from a succession of ancestors
2) Natural selection: a proposed mechanism of descent
with modification
Ex. Unity and diversity in the rose family with different
scents and features
 Darwin’s Observations:
1) Individuals in a population vary in their traits, many of
which seem to be heritable (passed on from parents to
offspring).
2) A population can produce far more offspring than can
survive to produce offspring of their own.
 3) Species generally are suited to their environments—in
other words, they are adapted to their circumstances.
 He reasoned that individuals with inherited traits that
are better suited to the local environment are more
likely to survive and reproduce than less well-suited
individuals.
 Natural selection: the natural environment consistently
“selects” for the propagation of certain traits among
naturally occurring variant traits in the population.
 Galapagos finches (example of radiation of new
species from a common ancestor)
o Large ground – wide, strong beaks for
cracking big hard seeds
o Cactus – tough beak for eating cactus parts
and insects (act as pair of pliers)
o Warbler – small, narrow beak for eating small
insects
 Darwin also saw that when man chooses organisms
with specific characteristics as breeding stock, they are
performing the role of the environment in a process
called artificial selection.
CELL STRUCTURES
Cell Theory
 The discovery of the cell was facilitated by the
improvement of the microscope in the 17th century by
Anton van Leeuwenhoek. He observed the movements
of Protista and sperm (which he called “animalcules”)
 In a 1665 publication called Micrographia,
experimental scientist Robert Hooke coined the term
“cell” for the box-like structures he observed when
viewing cork tissue through a lens.
 In the 1670s, van Leeuwenhoek discovered bacteria
and protozoa. Later advances in lenses, microscope
construction, and staining techniques enabled other
scientists to see some components inside cells.
 By the late 1830s, botanist Matthias Schleiden and
zoologist Theodor Schwann were studying tissues and
proposed the unified cell theory. The unified cell theory
states that: all living things are composed of one or
more cells; the cell is the basic unit of life; and new cells
arise from existing cells. Rudolf Virchow later made
important contributions to this theory.
The Cell Theory (Modern Tenets)
1. The cell is the fundamental unit of structure and
function in living things.
2. All organisms are made up of one or more cells.
3. Cells arise from other cells through cellular division.
The expanded version of the cell theory can also include:
4. Cells carry genetic material passed to daughter cells
during cellular division.
5. All cells are essentially the same in chemical
composition.
6. Energy flow (metabolism and biochemistry) occurs
within cells.
The Cell Theory predates the Theory of Evolution (1859), the
Laws of Inheritance (1865), and the Theory of Comparative
Biochemistry
General Attributes
All cells share certain basic features: They are all bounded by a
selective barrier, called the plasma membrane (also referred to
as the cell membrane). Inside all cells is a semifluid, jellylike
substance called cytosol, in which subcellular components are
suspended. All cells contain chromosomes, which carry genes
in the form of DNA. And all cells have ribosomes, tiny
complexes that make proteins according to instructions from the
genes.
A major difference between prokaryotic and eukaryotic cells is
the location of their DNA. In a eukaryotic cell, most of the DNA
is in an organelle called the nucleus, which is bounded by a
double membrane (chromosomes are contained within a
membranous nuclear envelope. In a prokaryotic cell, the DNA is
concentrated in a region that is not membrane-enclosed, called
the nucleoid.
Plasma membrane is a selective barrier that allows passage of
oxygen, nutrients, and waste.
The interior of either type of cell is called the cytoplasm; in
eukaryotic cells, this term refers only to the region between the
nucleus and the plasma membrane. Within the cytoplasm of a
eukaryotic cell, suspended in cytosol, are a variety of organelles
of specialized form and function. These membrane-bounded
structures are absent in almost all prokaryotic cells, another
distinction between prokaryotic and eukaryotic cells. In spite of
the absence of organelles, though, the prokaryotic cytoplasm is
not a formless soup. For example, some prokaryotes contain
regions surrounded by proteins (not membranes), within which
specific reactions take place.
Internal membranes compartmentalize the functions of
eukaryotic cells
- Extensive and elaborate internal membranes which
partition the cell compartments
Ex. Mitochondria and chloroplast
The cell’s compartments provide different local environments
that support specific metabolic functions, so incompatible
processes can occur simultaneously in a single cell.
The plasma membrane and organelle membranes also
participate directly in the cell’s metabolism because many
enzymes are built right into the membranes.
 The basic fabric of most biological membranes is a
double layer of phospholipids and other lipids.
Embedded in this lipid bilayer or attached to its
surfaces are diverse proteins.
The eukaryotic cell’s genetic instructions are housed in the
nucleus and carried out by the ribosomes
The Endomembrane System
 Carries out a variety of tasks in the cell, including synthesis
of proteins, transport of proteins into membranes and
organelles or out of the cell, metabolism and movement of
lipids, and detoxification of poisons.
o Plays a key role in synthesis and hydrolysis of
macromolecules
o Modify macromolecules for various functions
 The membranes of this system are related either through
direct physical continuity (direct contact) or by the
transfer of membrane segments as tiny vesicles (sacs
made of membrane).
 The thickness, molecular composition, and types of
chemical reactions carried out in a given membrane are not
fixed, but may be modified several times during the
membrane’s life.
 Composed of the: nuclear envelope, endoplasmic reticulum,
Golgi apparatus, lysosomes, vacuoles/vesicles, and the
plasma membrane
Endoplasmic Reticulum
 Manufactures membranes and performs biosynthetic
functions
 Accounts for more than half the total membrane in
many eukaryotic cells.
 Consists of a network of membranous tubules and
fluid-filled spaces called cisternae
 The ER membrane separates the internal
compartment of the ER, called the ER lumen (cavity)
or cisternal space, from the cytosol.
 ER membrane is continuous with the nuclear envelope;
mRNA either exits the nucleus through a nuclear pore
or through the ER
 Has two regions: rough ER (protein synthesis) and
smooth ER (synthesis of lipids, oils, and steroids;
metabolism of carbohydrates)
Smooth ER
 synthesis of lipids, metabolism of carbohydrates,
detoxification of drugs and poisons, and storage of
calcium ions.
 Enzymes of the smooth ER are important in the
synthesis of lipids, including oils, steroids (sex
hormones of vertebrates and steroid hormones
secreted by the adrenal glands), and new membrane
phospholipids.
 Other enzymes of the smooth ER help detoxify drugs
and poisons, especially in liver cells. Detoxification
usually involves adding hydroxyl groups to drug
molecules, making them more soluble and easier to
flush from the body. The sedative phenobarbital and
other barbiturates are examples of drugs metabolized
in this manner by smooth ER in liver cells (alcohol
dehydrogenase).
 Enzymes of the smooth ER catalyze key steps in the
mobilization of glucose from stored glycogen in the
liver.
 The smooth ER also stores calcium ions. In muscle
cells, for example, the smooth ER membrane pumps
calcium ions from the cytosol into the ER lumen.
Rough ER
 Rough ER is abundant in cells that secrete proteins.
For example, certain pancreatic cells synthesize the
protein insulin in the ER and secrete this hormone into
the bloodstream. As a polypeptide chain grows from a
bound ribosome, the chain is threaded into the ER
lumen through a pore formed by a protein complex in
the ER membrane. The new polypeptide folds into its
functional shape as it enters the ER lumen. Most
secretory proteins are glycoproteins, proteins with
carbohydrates covalently bonded to them. The
carbohydrates are attached to the proteins in the ER
lumen by enzymes built into the ER membrane. After
secretory proteins are formed, the ER membrane
keeps them separate from proteins in the cytosol,
which are produced by free ribosomes. Secretory
proteins depart from the ER wrapped in the
membranes of vesicles that bud like bubbles from a
specialized region called transitional ER. Vesicles in
transit from one part of the cell to another are called
transport vesicles.
 Many of these polypeptides are glycoproteins, a
polypeptide to which an oligosaccharide is attached
 These secretory proteins are packaged in transport
vesicles. The glycoproteins attached to the membrane.
 The rough ER is also a membrane factory
o Membrane bound proteins are synthesized
directly into the ER membrane. They are
essential in movement, receiving/releasing
macromolecules.
o As polypeptides destined to be membrane
proteins grow from the ribosomes, they are
inserted into the ER membrane itself and
anchored there by their hydrophobic portions.
 Enzymes built into the ER membrane assemble
phospholipids from precursors in the cytosol.
  As ER membrane expands, parts can be transformed
as transport vesicles of other components of the EMS.
Golgi apparatus: Shipping and receiving center
After leaving the ER, many transport vesicles travel to the Golgi
apparatus.
 The organelle where products of the ER are modified
and stored and then sent to other destinations.
Vesicles carry modified, functional proteins.
 Finishes, stores, and ships cell products
 Transport vesicles from the ER travel to the Golgi for
modification.
 Usually extensive in cells specialized for the secretion
of glycoproteins
 It consists of a group of associated, flattened
membranous sacs—cisternae
 The membrane of each cisterna in a stack separates
its internal space from the cytosol.
 A Golgi stack has a distinct structural directionality,
with the membranes of cisternae on opposite sides of
the stack differing in thickness and molecular
composition. The two sides of a Golgi stack are
referred to as the cis face and the trans face; these act,
respectively, as the receiving and shipping
departments of the Golgi apparatus.
 Transport vesicles move material from the ER to the
Golgi apparatus. A vesicle that buds from the ER can
add its membrane and the contents of its lumen to the
cis face by fusing with a Golgi membrane on that side.
The trans face (“on the opposite side”) gives rise to
vesicles that pinch off and travel to other sites.
 Glycoproteins formed in the ER have their
carbohydrates modified, first in the ER itself, and then
as they pass through the Golgi. The Golgi removes
some sugar monomers and substitutes others,
producing a large variety of carbohydrates. Membrane
phospholipids may also be altered in the Golgi. In
addition to its finishing work, the Golgi apparatus also
manufactures some macromolecules. Many
polysaccharides secreted by cells are Golgi products.
 Before a Golgi stack dispatches its products by
budding vesicles from the trans face, it sorts these
products and targets them for various parts of the cell.
Molecular identification tags, such as phosphate
groups added to the Golgi products.
Lysosomes: Digestive Compartments
A lysosome is a membranous sac of hydrolytic enzymes that
many eukaryotic cells use to digest (hydrolyze)
macromolecules. Lysosomal enzymes work best in the acidic
environment found in lysosomes.
 While ruptured one or a few lysosomes, massive
leakage from lysosomes can destroy an entire cell by
autodigestion.
 Hydrolytic enzymes and lysosomal membrane are
made by rough ER and then transferred to the Golgi
apparatus for further processing. Lysosomes probably
arise by budding from the trans face of the Golgi
apparatus
 Food vacuoles fuse with lysosomes (food items
brought into the cell by phagocytosis)
 Lysosomes carry out intracellular digestion in a variety
of circumstances. Amoebas and many other unicellular
eukaryotes eat by engulfing smaller organisms or food
particles, a process called phagocytosis
 The food vacuole formed in this way then fuses with a
lysosome, whose enzymes digest the food. Digestion
products, including simple sugars, amino acids, and
other monomers, pass into the cytosol and become
nutrients for the cell. Some human cells also carry out
phagocytosis. Among them are macrophages, a type
of white blood cell that helps defend the body by
engulfing and destroying bacteria and other invaders.
 Lysosomes can also fuse with other organelles or parts
of the cytosol.
o Lysosomes also use their hydrolytic enzymes
to recycle the cell’s own organic material, a
process called autophagy. During autophagy,
a damaged organelle or small amount of
cytosol becomes surrounded by a double
membrane (of unknown origin), and a
lysosome fuses with the outer membrane of
this vesicle.
o The lysosomal enzymes dismantle the inner
membrane with the enclosed material, and
the resulting small organic compounds are
released to the cytosol for reuse. With the
help of lysosomes, the cell continually renews
itself.
Vacuoles: Diverse Maintenance Compartments
Vesicles and vacuoles (large version of vesicles are membrane-
bound sacs with varied functions:
(1) Food vacuole: formed by phagocytosis, fuses with
lysosomes
(2) Contractile vacuole: found in freshwater protists, pump
excess water out of the cell, thereby maintaining a
suitable concentration of ions and molecules inside the
cell.
(3) Central vacuole: found in many mature plant cells
(4) In plants and fungi, certain vacuoles carry out
enzymatic hydrolysis, a function shared by lysosomes
in animal cells.
(5) In plants, small vacuoles can hold reserves of
important organic compounds, such as the proteins
stockpiled in the storage cells in seeds. Vacuoles may
also help protect the plant against herbivores by storing
compounds that are poisonous or unpalatable to
animals. Some plant vacuoles contain pigments, such
as the red and blue pigments of petals that help attract
pollinating insects to flowers.
Central Vacuole
The membrane surrounding the central vacuole (tonoplast) is
selective in its transport of solutes. It contains glycolipids.
Functions:
(1) Stockpiling proteins and inorganic ions
(2) Depositing metabolic byproducts
(3) Storing pigments
(4) Storing defensive compounds against herbivory
It plays a major role in the growth of the plasma membrane.
Cells enlarge as the vacuole absorbs H2O, with minimal
investment in new cytoplasm.
Other membranous organelles
 Mitochondria
 Chloroplast
 Peroxisomes
Proteins synthesized in bound ribosomes are transferred to
ER. Membranes formed by incorporation of proteins from
free ribosomes.
Peroxisomes: Oxidation
The peroxisome is a specialized metabolic compartment
bounded by a single membrane.
(1) Regulates movement of H+: Peroxisomes contain
enzymes that remove hydrogen atoms from various
substrates and transfer them to oxygen (O2). An
intermediate product of this is H2O2, a poison, but the
peroxisome has another enzyme that converts H2O2
to water.
(2) Some peroxisomes use oxygen to break fatty acids
down into smaller molecules that are transported to
mitochondria and used as fuel for cellular respiration.
(3) Peroxisomes in the liver detoxify alcohol and other
harmful compounds by transferring hydrogen from the
poisonous compounds to oxygen.
(4) In plants, they detoxify cells with foreign substances
(e.g. bacteria, viruses)
(5) Specialized peroxisomes called glyoxysomes are
found in the fat-storing tissues of plant seeds. They
contain enzymes that initiate the conversion of fatty
acids to sugar, which the emerging seedling uses as a
source of energy and carbon until it can produce its
own sugar by photosynthesis.
(6) Grow by incorporating proteins made in the cytosol and
ER, as well as lipids made in the ER and within the
peroxisome itself.
(7) Split in two when they reach a certain size
Mitochondria and chloroplasts are the organelles that
convert energy to forms that cells can use for work.
Some algae have chloroplasts.
Mitochondria are sites of cellular respiration, generating ATP
from the catabolism of sugars, fats, and others (phospholipids)
in the presence of oxygen.
Chloroplasts convert solar energy to chemical energy by
absorbing sunlight and using it to drive the synthesis of organic
compounds such as sugars from carbon dioxide and water.
They grow and reproduce as semiautonomous organelles.
Mitochondria
Each of the two membranes enclosing the mitochondrion is a
phospholipid bilayer with a unique collection of embedded
proteins.
(1) They have a smooth outer membrane and have a
highly folded/convoluted inner membrane with
infoldings called cristae.
(2) The first is the intermembrane space, the narrow
region between the inner and outer membranes. The
second compartment, the mitochondrial matrix, is
enclosed by the inner membrane.
(3) The matrix contains many different enzymes as well as
the mitochondrial DNA and ribosomes. Enzymes in the
matrix catalyze some of the steps of cellular
respiration. Other proteins that function in respiration,
including the enzyme that makes ATP, are built into the
inner membrane. As highly folded surfaces, the cristae
give the inner mitochondrial membrane a large surface
area, thus enhancing the productivity of cellular
respiration.
Chloroplast
- One of the members of a generalized class of plant
structures called plastids
(1) Amyloplasts store starch in roots and tubers.
(2) Choromplasts store pigments for fruits and flowers
The chloroplast produces sugar via photosynthesis (chlorophyll
along with enzymes and other molecules)
(1) Measures about 2 micrometers by 3 micrometers and
is found primarily in leaves (although some can exist in
stems and roots)
(2) Processes in the chloroplast are separated from the
cytosol by two membranes which in turn are separated
by a very narrow intermembrane space.
(3) The inner cytosol is called the stroma, the fluid outside
the thylakoids which contains the chloroplast DNA and
ribosomes as well as many enzymes.
(4) Thylakoids: Inside the chloroplast, membranous
system in the form of flattened, interconnected sacs
that capture light. A stack of thylakoids is called a
granum.
(5) Three compartments: the intermembrane space, the
stroma, and the thylakoid space
(6) Their shape is changeable, and they grow and
occasionally pinch in two, reproducing themselves.
As with mitochondria, their shape is changeable, and they grow
and occasionally pinch in two, reproducing themselves. They
move around the cell along tracks of the cytoskeleton.
The Cytoskeleton
 - A network of fibers extending throughout the cytoplasm
organize the structures and activities of the cell
(1) Functions in cell motility
(2) Provides mechanical support, which is important for
animal cells which lack cell walls (stabilized by a
balance between opposing forces exerted by its
elements)
(3) Provides anchorage for nucleus and cystolic enzyme
molecules
(4) Dynamic, dismantled in one part of the cell and
reassembled in a new location, changing the shape of
the cell.
Support and Motility:
Some types of cell motility (movement) also involve the
cytoskeleton. The term cell motility includes both changes in cell
location and movements of cell parts. Cell motility generally
requires interaction of the cytoskeleton with motor proteins.
(1) Cytoskeletal elements and motor proteins work
together with plasma membrane molecules to allow
whole cells to move along fibers outside the cell. Inside
the cell, vesicles and other organelles often use motor
protein “feet” to “walk” to their destinations along a
track provided by the cytoskeleton. This is how vesicles
containing neurotransmitter molecules migrate to the
tips of axons, the long extensions of nerve cells that
release these molecules as chemical signals to
adjacent nerve cells.
(2) The cytoskeleton also manipulates the plasma
membrane, bending it inward to form food vacuoles or
other phagocytic vesicles.
Components of the Cytoskeleton
Microtubules: hollow rods constructed from globular proteins
called tubulins
(1) Maintenance of cell shape (compression-resisting
“girders”); cell motility (as in cilia or flagella);
chromosome movements in cell division; organelle
movements
(2) Shape and support the cell and also serve as tracks
along which organelles equipped with motor proteins
can move.
(3) Guide vesicles from the ER to the Golgi apparatus and
from the Golgi to the plasma membrane
(4) Involved in the separation of chromosomes during cell
division
Centrosomes and Centrioles: In animal cells, microtubules
grow out from a centrosome, a region that is often located
near the nucleus. These microtubules function as
compression-resisting girders of the cytoskeleton. Within
the centrosome is a pair of centrioles, each composed of
nine sets of triplet microtubules arranged in a ring.
Cilia and Flagella: In eukaryotes, a specialized
arrangement of microtubules is responsible for the beating
of flagella (singular, flagellum) and cilia (singular, cilium),
microtubule-containing extensions that project from some
cells.
Motile cilia usually occur in large numbers on the cell
surface. Flagella are usually limited to just one or a few per
cell, and they are longer than cilia. Flagella and cilia differ
in their beating patterns. A flagellum has an undulating
motion like the tail of a fish. In contrast, cilia have alternating
power and recovery strokes.
A cilium may also act as a signal-receiving “antenna” for the cell. Cilia
that have this function are generally nonmotile, and there is only one
per cell. (In fact, in vertebrate animals, it appears that almost all cells
have such a cilium, which is called a primary cilium.) Membrane
proteins on this kind of cilium transmit molecular signals from the cell’s
environment to its interior, triggering signaling pathways that may lead
to changes in the cell’s activities. Cilium-based signaling appears to be
crucial to brain function and to embryonic development.
Microfilaments: thin solid rods also called actin filaments
because they are built from molecules of actin, a globular protein
twisted in a double chain of actin subunits.
(1) Can form structural networks when certain proteins
bind along the side of such a filament and allow a new
filament to extend as a branch.
(2) The structural role of microfilaments in the cytoskeleton
is to bear tension (pulling forces). A three-dimensional
network formed by microfilaments just inside the
plasma membrane (cortical microfilaments) helps
support the cell’s shape.
(3) Maintenance of cell shape (tension-bearing elements);
changes in cell shape made of a protein called myosin
interact to cause contraction of muscle cells
(4) Muscle contraction: Thousands of actin filaments and
thicker filaments
(5) Cytoplasmic streaming in plant cells: a circular flow of
cytoplasm within cells. This movement, which is
especially common in large plant cells, speeds the
movement of organelles and the distribution of
materials within the cell.
(6) Cell motility (as in amoeboid movement): Localized
contractions brought about by actin and myosin are
involved in the amoeboid (crawling) movement of the
cells.
(7) Division of animal cells
Intermediate filaments: larger than the diameter of
microfilaments but smaller than that of microtubules, only found
in some animals, including vertebrates. Each type is constructed
from a particular molecular subunit belonging to a family of
proteins whose members include the keratins.
(1) More permanent fixtures of cells than are
microfilaments and microtubules, which are often
disassembled and reassembled in various parts of a
cell
(2) Maintenance of cell shape (tension-bearing elements):
(3) Anchorage of nucleus and certain other organelles: the
nucleus typically sits within a cage made of
intermediate filaments, fixed in location by branches of
the filaments that extend into the cytoplasm.
(4) Formation of nuclear lamina
Microfilaments: cytoplasmic streaming, change in shape,
tension-bearing (muscles & tendons)
Microtubules: functions with mobile proteins, transport proteins
from cytoplasm to surface of the plasma membrane
Intermediate: responsible for nuclear lamina in animals
Cytoskeleton
(1) Plays a major role in cell motility
(2) Microtubules transport ATP from mitochondria,
allowing proteins to move
(3) Interacts with motor proteins
(4) In cilia and flagella, motor proteins pull components
past each other (also true for muscles)
(5) Motor molecules also carry vesicles/organelles to
various destinations along monorails provided by the
cytoskeleton
(6) Interactions of motor proteins and the cytoskeleton
circulate material within the cell via streaming
(7) May transmit signals that rearrange the nucleoli and
other structures
Microtubules
(1) Move chromosomes during cell division
(2) In many cells, they grow out from a centrosome near
the nucleus
(3) These microtubules function as compression-resisting
girders
(4) Though different in length, number per cell, and
beating pattern, motile cilia and flagella share a
common structure. Each motile cilium or flagellum has
a group of microtubules sheathed in an extension of
the plasma membrane. Nine doublets of
microtubules are arranged in a ring with two single
microtubules in its cente. This arrangement, referred to
as the “9 + 2” pattern, is found in nearly all eukaryotic
flagella and motile cilia. (Nonmotile primary cilia have
a “9 + 0” pattern, lacking the central pair of
microtubules.)
(5) The microtubule assembly of a cilium or flagellum is
anchored in the cell by a basal body, which is
structurally very similar to a centriole, with microtubule
triplets in a “9 + 0” pattern. In fact, in many animals
(including humans), the basal body of the fertilizing
sperm’s flagellum enters the egg and becomes a
centriole
(6) Bending involves large motor proteins called dyneins
that are attached along each outer microtubule
doublet. A typical dynein protein has two “feet” that
“walk” along the microtubule of the adjacent doublet,
using ATP for energy. One foot maintains contact,
while the other releases and reattaches one step
farther along the microtubule. The outer doublets and
two central microtubules are held together by flexible
cross-linking proteins, and the walking movement is
coordinated so that it happens on one side of the circle
at a time. If the doublets were not held in place, the
walking action would make them slide past each other.
Instead, the movements of the dynein feet cause the
microtubules—and the organelle as a whole—to bend.
Microfilaments
(1) Found in the microvilli (small intestine)
(2) In muscle cells, thousands of actin filaments are
arranged parallel to each other
(3) Actin filaments in between myosin allow for contraction
in rotary motion. Myosin resists total contract of actin
filaments.
(4) Too much ATP, lactic acid
(5) Thicker filaments called myosin interdigitate with the
actin
(6) Myosin molecules walk along actin filaments, pulling
stacks of actin fibers together and shortening the cell
(7) Without water, there is no breakdown of sugars
a. Lactic acid forms within actin filaments.
Electrolytes replenish loss
(8) A contracting belt of microfilaments divides the
cytoplasm of animal cells during cell division (cell
furrow)
(9) Localized contraction also drives amoeboid movement
a. Pseudopoadia extend and contract through
the reversible assembly and contraction of
actin subunits
b. Microfilament network acts as if floating. The
cell itself changes its shape
c. Amoeba – euglena
(10) In plants, actin-myosin interactions and sol gel
transformations during cytoplasmic streaming –
structure of the cytoplasm in undividing cell shows the
circular flow of the cytoplasm.
Intermediate filaments
(1) Reinforcement of other cytoskeletal elements
Cell Surface
Cell Wall (plants, prokaryotes, fungi, and some protists)
 Protects the cell, maintains its shape, prevents
excessive uptake of water (opening and closing of the
wall)
 Thickness and chemical composition of cell walls difer
from species to species
 Its basic design consists of microfibrils of cellulose
embedded in a matrix of polysaccharide and proteins.
 Microfibrils: A mature cell wall consists of a primary cell
made of cellulose. A middle lamella with sticky
polysaccharides (calcium pectate) that holds cell
together, and layers of secondary cell wall
Extracellular Matrix
 Support adhesive, movement, regulation
 Consists of a matrix of several components external to
the cell
o Collagen: extension and flexibility (hair for
larger cells, microvilli for smaller)
 o Proteoglycans: Polysaccharide molecules to
absorb and attach to surface which are then
transferred to integrins
o Integrins: proteins
 In many cells, fibronectin in the ECM connects to
integrins (exposed to both sides), which are intrinsic
membrane proteins
 This fibronectin-integrin network accepts and ships
proteins and other substances to connect the ECM to
cytoskeleton
 Interconnections from ECM to cytoskeleton via
fibronectin-integrin permit interactions of cells
Intercellular junctions help integrate cells into a higher level of
structure. Neighboring cells often adhere, interact, and
communicate, through direct physical contact.
Plant cells are perforated with plasmodesmata, cytoplasmic
channels that connect cells.
In animals:
 Tight junctions: open if there is an excessive uptake of
a substance; not present all throughout the cell, no
cilia/filaments. Membranes of adjacent cells are fused,
forming continuous belts around cells. This prevents
leakage of extracellular fluid.
 Desmosomes (with filaments for anchoring function):
found in the stomach and intestine, for nutrient
exchange. Fastens cells into strong sheets much like
nets. Intermediate filaments of keratin reinforce
desmosomes
 Gap junctions (communicating function): regularly
allows movement and provides cytoplasmic channels
o Salt ions, sugars, and other small molecules
can pass.
o In embryos, gap junctions facilitate chemical
communication during development
Plant Crystals
 Waste and excretory products of protoplasts
 Either CaC2O4 or CaCO3
 H2O and O2 are essentially waste
 Prismatic, druse, raphides, and styloids
 Club-like cystolith and worm-like cystolith contained in
a cell called a lithocyst
Membrane Structure and Function
The plasma membrane separates the living cell from its
surroundings. It exhibits selective permeability.
** insert structure **
Fluidity
 Lateral movement (~107 times per second)
 Flip-flop (~once a month)
 Most lipids and some proteins drift laterally/
 Rarely does a molecule flip-flop transversely
 Difference between unsaturated and saturated
hydrocarbon tails (with and without kinks)
A membrane is a collage of different proteins
 Integral: embedded to surface
 Peripheral: loosely bound
Transmembrane proteins are integral proteins that span the
membrane. The hydrophobic region consists of one or more
stretches of nonpolar amino acids, often coiled into alpha
helices.
** insert functions **
Passive transport
** insert the one from the other handout **
Facilitated Diffusion: Passive Transport Aided by Proteins
Many polar molecules and ions impeded by the lipid bilayer of
the membrane diffuse passively with the help of transport
proteins that span the membrane. This phenomenon is called
facilitated diffusion.
(1) Most transport proteins are very specific: They
transport some substances but not others. Channel
proteins simply provide corridors that allow specific
molecules or ions to cross the membrane. The
hydrophilic passageways provided by these proteins
can allow water molecules or small ions to diffuse very
quickly from one side of the membrane to the other.
Aquaporins, the water channel proteins, facilitate the
massive levels of diffusion of water (osmosis) that
occur in plant cells and in animal cells such as red
blood cells. Certain kidney cells also have a high
number of aquaporins, allowing them to reclaim water
from urine before it is excreted.
(2) Channel proteins that transport ions are called ion
channels. Many ion channels function as gated
channels, which open or close in response to a
stimulus. For some gated channels, the stimulus is
electrical. In a nerve cell, for example, an ion channel
opens in response to an electrical stimulus, allowing a
stream of potassium ions to leave the cell. Other gated
channels open or close when a specific substance
other than the one to be transported binds to the
channel.
(3) Carrier proteins, such as the glucose transporter
mentioned earlier, seem to undergo a subtle change in
shape that somehow translocates the solute-binding
site across the membrane. Such a change in shape
may be triggered by the binding and release of the
transported molecule. Like ion channels, carrier
proteins involved in facilitated diffusion result in the net
movement of a substance down its concentration
gradient.
Active transport uses energy to move solutes against their
gradients
To pump a solute across a membrane against its gradient
requires work; the cell must expend energy. Therefore, this type
of membrane traffic is called active transport. The transport
proteins that move solutes against their concentration gradients
are all carrier proteins rather than channel proteins. This makes
sense because when channel proteins are open, they merely
allow solutes to diffuse down their concentration gradients rather
than picking them up and transporting them against their
gradients. Active transport enables a cell to maintain internal
concentrations of small solutes that differ from concentrations in
its environment.
For example, compared with its surroundings, an animal cell has
a much higher concentration of potassium ions (K+ ) and a much
lower concentration of sodium ions (Na+ ). The plasma
membrane helps maintain these steep gradients by pumping
Na+ out of the cell and K+ into the cell. As in other types of
cellular work, ATP hydrolysis supplies the energy for most active
transport. One way ATP can power active transport is when its
terminal phosphate group is transferred directly to the transport
protein. This can induce the protein to change its shape in a
manner that translocates a solute bound to the protein across
the membrane. One transport system that works this way is the
sodium-potassium pump, which exchanges Na+ for K+ across
the plasma membrane of animal cells.
(1) Cytoplasmic Na+ binds to the sodium-potassium
pump. The affinity for Na+ is high when the protein has
this shape.
(2) Na+ binding stimulates phosphorylation by ATP.
(3) Phosphorylation leads to a change in protein shape,
reducing its affinity for Na+, which is released outside.
(4) The new shape has a high affinity for K+, which binds
on the extracellular side and triggers release of the
phosphate group
(5) Loss of the phosphate group restores the protein’s
original shape, which has a lower affinity for K+.
(6) K+ is released; affinity for Na+ is high again, and the
cycle repeats.
How Ion Pumps Maintain Membrane Potential
All cells have voltages across their plasma membranes. Voltage
is electrical potential energy—a separation of opposite charges.
The cytoplasmic side of the membrane is negative in charge
relative to the extracellular side because of an unequal
distribution of anions and cations on the two sides. The voltage
across a membrane, called a membrane potential, ranges from
about -50 to -200 millivolts (mV). (The minus sign indicates that
the inside of the cell is negative relative to the outside.)
The membrane potential acts like a battery, an energy source
that affects the traffic of all charged substances across the
membrane. Because the inside of the cell is negative compared
with the outside, the membrane potential favors the passive
transport of cations into the cell and anions out of the cell. Thus,
two forces drive the diffusion of ions across a membrane: a
chemical force (the ion’s concentration gradient, which has been
our sole consideration thus far in the chapter) and an electrical
force (the effect of the membrane potential on the ion’s
movement).
This combination of forces acting on an ion is called the
electrochemical gradient. In the case of ions, then, we must
refine our concept of passive transport: An ion diffuses not
simply down its concentration gradient but, more exactly, down
its electrochemical gradient. For example, the concentration of
Na+ inside a resting nerve cell is much lower than outside it.
When the cell is stimulated, gated channels open that facilitate
Na+ diffusion. Sodium ions then “fall” down their electrochemical
gradient, driven by the concentration gradient of Na+ and by the
attraction of these cations to the negative side (inside) of the
membrane. In this example, both electrical and chemical
contributions to the electrochemical gradient act in the same
direction across the membrane, but this is not always so. In
cases where electrical forces due to the membrane potential
oppose the simple diffusion of an ion down its concentration
gradient, active transport may be necessary.
Some membrane proteins that actively transport ions contribute
to the membrane potential. An example is the sodium-potassium
pump. The pump does not translocate Na+ and K+ one for one,
but pumps three sodium ions out of the cell for every two
potassium ions it pumps into the cell. With each “crank” of the
pump, there is a net transfer of one positive charge from the
cytoplasm to the extracellular fluid, a process that stores energy
as voltage. A transport protein that generates voltage across a
membrane is called an electrogenic pump. The sodium-
potassium pump appears to be the majorelectrogenic pump of
animal cells. The main electrogenic pump of plants, fungi, and
bacteria is a proton pump, which actively transports protons
(hydrogen ions, H+) out of the cell. The pumping of H+ transfers
positive charge from the cytoplasm to the extracellular solution.
By generating voltage across membranes, electrogenic pumps
help store energy that can be tapped for cellular work. One
important use of proton gradients in the cell is for ATP synthesis
during cellular respiration.
Cotransport: Coupled Transport by a Membrane Protein
A solute that exists in different concentrations across a
membrane can do work as it moves across that membrane by
diffusion down its concentration gradient. In a mechanism called
cotransport, a transport protein (a cotransporter) can couple the
“downhill” diffusion of the solute to the “uphill” transport of a
second substance against its own concentration gradient.
For instance, a plant cell uses the gradient of H+ generated by
its ATP-powered proton pumps to drive the active transport of
amino acids, sugars, and several other nutrients into the cell. A
cotransporter couples the return of H+ to the transport of
sucrose into the cell. This protein can translocate sucrose into
the cell against its concentration gradient, but only if the sucrose
molecule travels in the company of an H+. The H+ uses the
transport protein as an avenue to diffuse down its own
electrochemical gradient, which is maintained by the proton
pump. Plants use H+/sucrose cotransport to load sucrose
produced by photosynthesis into cells in the veins of leaves. The
vascular tissue of the plant can then distribute the sugar to roots
and other non-photosynthetic organs that do not make their own
food.

What we know about cotransport proteins in animal cells has

helped us find more effective treatments for diarrhea, a serious
problem in developing countries. Normally, sodium in waste is
reabsorbed in the colon, maintaining constant levels in the body,
but diarrhea expels waste so rapidly that reabsorption is not
possible, and sodium levels fall precipitously. To treat this life-
threatening condition, patients are given a solution to drink
containing high concentrations of salt (NaCl) and glucose. The
solutes are taken up by sodium-glucose cotransporters on the
surface of intestinal cells and passed through the cells into the
blood. This simple treatment has lowered infant mortality
worldwide.
How Ion Pumps Maintain Membrane Potential
 Voltage is created by differences in the distribution of
positive and negative ions
 Membrane potential is the voltage difference across a
membrane
 Two combined forces, collectively called the
electrochemical gradient, drive the diffusion of ions
o Chemical: ion concentration
o Electrical: the effect of the membrane
potential (voltage difference) on the ion’s
movement
 An ion diffuses not simply down its concentration
gradient but, more exactly, down its electrochemical
gradient. For example, the concentration of Na+ inside
a resting nerve cell is much lower than outside it. When
the cell is stimulated, gated channels open that
facilitate Na+ diffusion. Sodium ions then “fall” down
their electrochemical gradient, driven by the
concentration gradient of Na+ and by the attraction of
these cations to the negative side (inside) of the
membrane.
 Electrogenic pumps: A transport protein that
generates voltage across a membrane
o Sodium-potassium pump - animals
o Proton pump – plants, fungi, and bacteria;
actively transports protons (hydrogen ions,
H+) out of the cell. The pumping of H+
transfers positive charge from the cytoplasm
to the extracellular solution.
o By generating voltage across membranes,
electrogenic pumps help store energy that
can be tapped for cellular work. One
important use of proton gradients in the cell is
for ATP synthesis during cellular respiration.
 Proton pumps are electrogenic pumps that store
energy by generating voltage (charge separation)
across membranes. A proton pump translocates
positive charge in the form of hydrogen ions. The
voltage and H+ concentration gradient represent a dual
energy source that can drive other processes, such as
the uptake of nutrients. Most proton pumps are
powered by ATP hydrolysis.
Cotransport occurs when the active transport of a solute
indirectly drives the transport of another solute. A solute that
exists in different concentrations across a membrane can do
work as it moves across that membrane by diffusion down its
concentration gradient.
 A plant cell uses the gradient of H+ generated by its
ATP-powered proton pumps to drive the active
transport of amino acids, sugars, and several other
nutrients into the cell.
 A carrier protein, such as this H+ /sucrose
cotransporter in a plant cell, is able to use the diffusion
of H+ down its electrochemical gradient into the cell to
drive the uptake of sucrose. Although not technically
part of the cotransport process, an ATP-driven proton
concentrates H+ outside the cell. The resulting H+
gradient represents potential energy that can be used
for active transport—of sucrose, in this case. Thus,
ATP hydrolysis indirectly provides the energy
necessary for cotransport.
 Plants use H+ /sucrose cotransport to load sucrose
produced by photosynthesis into cells in the veins of
leaves. The vascular tissue of the plant can then
distribute the sugar to roots and other
nonphotosynthetic organs that do not make their own
food.
Bulk Transport
Large molecules like polysaccharides and proteins cross the
membrane in bulk via vesicles and this requires energy.
(1) Exoocytosis: A transport vesicle that has budded from the
Golgi apparatus moves along microtubules of the
cytoskeleton to the plasma membrane. When the vesicle
membrane and plasma membrane come into contact,
specific proteins rearrange the lipid molecules of the two
bilayers so that the two membranes fuse. The contents of
the vesicle spill out of the cell, and the vesicle membrane
becomes part of the plasma membrane. This is used by
many secretory cells (oils, crystals, proteins)
(2) Endocytosis: The cell takes in macromolecules by forming
vesicles from the plasma membrane.
 Phagocytosis: In phagocytosis, a cell engulfs a particle
by extending pseudopodia (singular, pseudopodium)
around it and packaging it within a membranous sac
called a food vacuole. The particle will be digested after
the food vacuole fuses with a lysosome containing
hydrolytic enzymes. Example: Amoeba, bacteria
 Pinocytosis: In pinocytosis, a cell continually “gulps”
droplets of extracellular fluid into tiny vesicles, formed
by infoldings of the plasma membrane. In this way, the
cell obtains molecules dissolved in the droplets
 Receptor-mediated endocytosis: is a specialized type
of pinocytosis that enables the cell to acquire bulk
quantities of specific substances, even though those
substances may not be very concentrated in the
extracellular fluid
o Binding of ligands to receptors triggers vesicle
formation
o A ligand is any molecule that binds
specifically to a receptor site of another
molecule
o Embedded in the plasma membrane are
proteins with receptor sites exposed to the
extracellular fluid. Specific solutes bind to the
receptors. The receptor proteins then cluster
in coated pits, and each coated pit forms a
vesicle containing the bound molecules. After
the ingested material is liberated from the
vesicle, the emptied receptors are recycled to
the plasma membrane by the same vesicle.
 o Example: In plant cells, when a foreign
substance like viruses surround the cell, the
plasma membrane produces special receptor
proteins and ligands in order to digest the
coated vesicle
o In humans, receptor-mediated endocytosis
occurs to take in cholesterol for membrane
synthesis and the synthesis of other steroids.
CELL CYCLE
Cell division plays several important roles in life. When a
prokaryotic cell divides, it is actually reproducing, since the
process gives rise to a new organism (another cell). The same
is true of any unicellular eukaryote, such as the amoeba shown.
As for multicellular eukaryotes, cell division enables each of
these organisms to develop from a single cell—the fertilized
egg. And cell division continues to function in renewal and repair
in fully grown multicellular eukaryotes, replacing cells that die
from accidents or normal wear and tear. For example, dividing
cells in your bone marrow continuously make new blood cells
(1) Asexual reproduction: An amoeba, a single-celled
eukaryote, is dividing into two cells. Each new cell will
be an individual organism (LM).
(2) Growth and development: An embryo shortly after
the fertilized egg divided, forming two cells (LM).
(3) Tissue renewal: These dividing bone marrow cells will
give rise to new blood cells (LM).
Most cell division results in genetically identical daughter
cells
A dividing cell replicates its DNA, distributes the two copies to
opposite ends of the cell, and then splits into daughter cells.
Cellular Organization of the Genetic Material
A cell’s DNA, its genetic information, is called its genome.
Although a prokaryotic genome is often a single DNA molecule,
eukaryotic genomes usually consist of a number of DNA
molecules. Each eukaryotic chromosome consists of one very
long, linear DNA molecule associated with many proteins. The
associated proteins maintain the structure of the chromosome
and help control the activity of the genes. Together, the entire
complex of DNA and proteins that is the building material of
chromosomes is referred to as chromatin.
Every eukaryotic species has a characteristic number of
chromosomes in each cell’s nucleus. For example, the nuclei of
human somatic cells (all body cells except the reproductive
cells) each contain 46 chromosomes, made up of two sets of 23,
one set inherited from each parent. Reproductive cells, or
gametes—such as sperm and eggs—have half as many
chromosomes as somatic cells.
Distribution of Chromosomes During Eukaryotic Cell
Division
When a cell is not dividing, and even as it replicates its DNA in
preparation for cell division, each chromosome is in the form of
a long, thin chromatin fiber. After DNA replication, however, the
chromosomes condense as a part of cell division: Each
chromatin fiber becomes densely coiled and folded, making the
chromosomes much shorter and so thick that we can see them
with a light microscope. Each duplicated chromosome consists
of two sister chromatids, which are joined copies of the
original chromosome. The two chromatids, each containing an
identical DNA molecule, are typically attached all along their
lengths by protein complexes called cohesins; this attachment
is known as sister chromatid cohesion. Each sister chromatid
has a centromere, a region made up of repetitive sequences in
the chromosomal DNA where the chromatid is attached most
closely to its sister chromatid. The portion of a chromatid to
either side of the centromere is referred to as an arm of the
chromatid. (An unduplicated chromosome has a single
centromere, distinguished by the proteins that bind there, and
two arms.)
(1) One of the multiple chromosomes in a eukaryotic cell
is represented here, not yet duplicated. Normally it
would be a long, thin chromatin fiber containing one
DNA molecule and associated protein.
(2) Once duplicated, a chromosome consists of two sister
chromatids connected along their entire lengths by
sister chromatid cohesion. Each chromatid contains a
copy of the DNA molecule.
(3) Molecular and mechanical processes separate the
sister chromatids into two chromosomes and distribute
them to two daughter cells.
Mitosis, the division of the genetic material in the nucleus, is
usually followed immediately by cytokinesis, the division of the
cytoplasm. One cell has become two, each the genetic
equivalent of the parent cell. In contrast, you produce
gametes—eggs or sperm—by a variation of cell division called
meiosis, which yields daughter cells with only one set of
chromosomes.
Phases of the Cell Cycle
The mitotic (M) phase alternates with a much longer stage
called interphase, which often accounts for about 90% of the
cycle. Interphase can be divided into three phases: The G1
phase (“first gap”), the S phase (“synthesis”), and the G2
phase (“second gap”).
 During all three phases of interphase, in fact, a cell
grows by producing proteins and cytoplasmic
organelles such as mitochondria and endoplasmic
reticulum. Duplication of the chromosomes, crucial for
eventual division of the cell, occurs entirely during the
S phase.
 Thus, a cell grows (G1), continues to grow as it copies
its chromosomes (S), grows more as it completes
preparations for cell division (G2), and divides (M).
 Some cells in a multicellular organism divide very
infrequently or not at all. These cells spend their time
in G1 (or a related phase called G0, to be discussed
later in the chapter) doing their job in the organism—a
 cell of the pancreas secretes digestive enzymes, for
example.
Mitosis in an Animal Cell:
G2 of Interphase
 A nuclear envelope encloses the nucleus.
 The nucleus contains one or more nucleoli (singular,
nucleolus).
 Two centrosomes have formed by duplication of a
single centrosome. Centrosomes are regions in animal
cells that organize the microtubules of the spindle.
Each centrosome contains two centrioles.
 Chromosomes, duplicated during S phase, cannot be
seen individually because they have not yet
condensed.
Prophase
 The chromatin fibers become more tightly coiled,
condensing into discrete chromosomes observable
with a light microscope.
 The nucleoli disappear.
 Each duplicated chromosome appears as two identical
sister chromatids joined at their cen- tromeres and, in
some species, all along their arms by cohesins (sister
chromatid cohesion).
 The mitotic spindle (named for its shape) begins to
form. It is composed of the centro- somes and the
microtubules that extend from them. The radial arrays
of shorter microtubules that extend from the
centrosomes are called asters (“stars”).
 The centrosomes move away from each other,
propelled partly by the lengthening micro- tubules
between them.
Prometaphase
 The nuclear envelope fragments.
 The microtubules extending from each centrosome
can now invade the nuclear area.
 The chromosomes have become even more
condensed.
 A kinetochore, a specialized protein structure, has now
formed at the centromere of each chromatid (thus, two
per chromosome).
 Some of the microtubules attach to the kinetochores,
becoming “kinetochore microtubules,” which jerk the
chromosomes back and forth.
 Nonkinetochore microtubules interact with those from
the opposite pole of the spindle, lengthening the cell.
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, often lasting
only a few minutes.
 Anaphase begins when the cohesin proteins are
cleaved. This allows the two sister chromatids of each
pair to part suddenly. Each chromatid thus becomes an
independent chromosome.
 The two new daughter chromosomes begin moving
toward opposite ends of the cell as their kinetochore
microtubules shorten. Because these microtubules are
attached at the centromere region, the centromeres
are pulled ahead of the arms, moving at a rate of about
1 µm/min.
 The cell elongates as the nonkinetochore microtubules
lengthen.
 By the end of anaphase, the two ends of the cell have
equivalent—and complete— collections of
chromosomes.
Telophase:
 Two daughter nuclei form in the cell. Nuclear
envelopes arise from the fragments of the parent cell’s
nuclear envelope and other portions of the
endomembrane system.
 Nucleoli reappear.
 The chromosomes become less condensed.
 Any remaining spindle microtubules are
depolymerized.
 Mitosis, the division of one nucleus into two genetically
identical nuclei, is now complete.
Cytokinesis
 The division of the cytoplasm is usually 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
 The first sign of cleavage is the appearance of a
cleavage furrow, a shallow groove in the cell surface
near the old metaphase plate. On the cytoplasmic side
of the furrow is a contractile ring of actin microfilaments
associated with molecules of the protein myosin. The
actin microfilaments interact with the myosin
molecules, causing the ring to contract.
 Cytokinesis in plant cells has no cleavage furrow.
Instead, during telophase, vesicles derived from the
Golgi apparatus move along microtubules to the middle
of the cell, where they coalesce, producing a cell plate.
Mitotic spindles: This structure consists of fibers made of
microtubules and associated proteins. While the mitotic spindle
assembles, the other microtubules of the cytoskeleton partially
disassemble, providing the material used to construct the
spindle. The spindle microtubules elongate (polymerize) by
incorporating more subunits of the protein tubulin and shorten
(depolymerize) by losing subunits.
Mitosis in a Plant Cell
 (1) Prophase. The chromosomes are condensing and the
nucleolus is beginning to disappear. Although not yet
visible in the micrograph, the mitotic spindle is starting
to form.
(2) Prometaphase. Discrete chromosomes are now
visible; each consists of two aligned, identical sister
chromatids. Later in prometaphase, the nuclear
envelope will fragment.
(3) Metaphase. The spindle is complete, and the
chromosomes, attached to microtubules at their
kinetochores, are all at the metaphase plate.
(4) Anaphase. The chromatids of each chromosome have
separated, and the daughter chromosomes are moving
to the ends of the cell as their kinetochore microtubules
shorten.
(5) Telophase. Daughter nuclei are forming. Meanwhile,
cytokinesis has started: The cell plate, which will divide
the cytoplasm in two, is growing toward the perimeter
of the parent cell.
Bacterial cell division by binary fission
(1) Chromosome replication begins. Soon after, one copy
of the origin moves rapidly toward the other end of the
cell by a mechanism involving an actin-like protein.
(2) Replication continues. One copy of the origin is now at
each end of the cell. Meanwhile, the cell elongates.
(3) Replication finishes. The plasma membrane is pinched
inward by a tubulin-like protein, and a new cell wall is
deposited.
(4) Two daughter cells result.
Meiosis Aye
Any cell with two chromosome sets is called a diploid cell and
has a diploid number of chromosomes, abbreviated 2n.
Unlike somatic cells, gametes contain a single set of
chromosomes. Such cells are called haploid cells, and each has
a haploid number of chromosomes (n).
Meiosis I: Separates Homologous Chromosomes
Prophase I: Duplicated homologous chromosomes pair up and
exchange segments; 2n = 6 in this example.
 Centrosome movement, spindle formation, and
nuclear envelope breakdown occur as in mitosis.
Chromosomes condense progressively throughout
prophase I.
 During early prophase I, before the stage shown
above, each chromosome pairs with its homolog,
aligned gene by gene, and crossing over occurs: The
DNA molecules of nonsister chromatids are broken (by
proteins) and are rejoined to each other.
 Each homologous pair has one or more X-shaped
regions called chiasmata (singular, chiasma), where
crossovers have occurred.
 Later in prophase I, microtubules from one pole or the
other attach to the kinetochores, one at the centromere
of each homolog. (The two kinetochores on the sister
chromatids of a homolog are linked together by
proteins and act as a single kinetochore.) Microtubules
move the homologous pairs toward the metaphase
plate.
Metaphase I: Chromosomes line up by homologous pairs
 Pairs of homologous chromosomes are now arranged
at the metaphase plate, with one chromosome of each
pair facing each pole.
 Both chromatids of one homolog are attached to
kinetochore microtubules from one pole; the
chromatids of the other homolog are attached to
microtubules from the opposite pole.
Anaphase I: The two homologous chromosomes of each pair
separate
 Breakdown of proteins that are responsible for sister
chromatid cohesion along chromatid arms allows
homologs to separate.
 The 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.
Telophase I and Cytokinesis: Two haploid cells form; each
chromosome still consists of two sister chromatids.
 • 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 include regions of
nonsister chromatid DNA.
 Cytokinesis (division of the cytoplasm) usually occurs
simultaneously with telophase I, forming two haploid
daughter cells.
 In animal cells like these, a cleavage furrow forms. (In
plant cells, a cell plate forms.)
 In some species, chromosomes decondense and
nuclear envelopes form.
 No chromosome duplication occurs between meiosis I
and meiosis II.
Meiosis II: Separates sister chromatids
Prophase II:
 A spindle apparatus forms.
 In late prophase II (not shown here), chromosomes,
each still composed of two chromatids associated at
the centromere, are moved by microtubules toward the
metaphase II plate.
Metaphase II:
 The chromosomes are positioned at the metaphase
plate as in mitosis.
 Because of crossing over in meiosis I, the two sister
chromatids of each chromosome are not genetically
identical.
 The kinetochores of sister chromatids are attached to
microtubules extending from opposite poles.
Anaphase II:
 Breakdown of proteins holding the sister chromatids
together at the centromere allows the chromatids to
 separate. The chromatids move toward opposite poles
as individual chromosomes.
Telophase II and Prophase II Cytokinesis:
 Nuclei form, the chromosomes begin decondensing,
and cytokinesis occurs.
 The meiotic division of one parent cell produces four
daughter cells, each with a haploid set of
(unduplicated) chromosomes.
 The four daughter cells are genetically distinct from
one another and from the parent cell.
Crossing Over and Synapsis During Prophase I
(1) Early in prophase I, the two members of a homologous
pair associate loosely along their length. Each gene on
one homolog is aligned precisely with the
corresponding allele of that gene on the other homolog.
The DNA of two nonsister chromatids—one maternal
and one paternal—is broken by specific proteins at
precisely matching points.
(2) Next, the formation of a zipper-like structure called the
synaptonemal complex holds one homolog tightly to
the other.
(3) During this association, called synapsis, the DNA
breaks are closed up so that each broken end is joined
to the corresponding segment of the nonsister
chromatid. Thus, a paternal chromatid is joined to a
piece of maternal chromatid beyond the crossover
point, and vice versa.
(4) These points of crossing over become visible as THE REPRODUCTIVE ADAPTIATIONS OF ANGIOSPERMS
chiasmata (singular, chiasma) after the synaptonemal Commonly known as flowering plants, angiosperms are seed
complex disassembles and the homologs move slightly plants with the reproductive structures called flowers and fruits.
apart from each other. The homologs remain attached The flower is a unique angiosperm structure that is specialized
because sister chromatids are still held together by for sexual reproduction. In many angiosperm species, insects or
sister chromatid cohesion, even though some of the other animals transfer pollen from one flower to the sex organs
DNA may no longer be attached to its original on another flower, which makes pollination more directed than
chromosome. At least one crossover per chromosome the wind-dependent pollination of most species of
must occur in order for the homologous pair to stay gymnosperms.
together as it moves to the metaphase I plate. Starting at the base of the flower are the sepals, which are
usually green and enclose the flower before it opens (think of a
A Comparison of Mitosis and Meiosis rosebud). Interior to the sepals are the petals, which are brightly
(1) Synapsis and crossing over. During prophase I, colored in most flowers and can aid in attracting pollinators.
duplicated homologs pair up and crossing over occurs. Within the petals are two types of fertile floral organs that
Synapsis and crossing over do not occur during produce spores, the stamens and carpels. Stamens and carpels
prophase of mitosis. modified leaves that are specialized for reproduction.
(2) Alignment of homologous pairs at the metaphase plate. Stamens are microsporophylls: They produce microspores
At metaphase I of meiosis, pairs of homologs are that develop into pollen grains containing male gametophytes.
positioned at the metaphase plate, rather than A stamen consists of a stalk called the filament and a terminal
individual chromosomes, as in metaphase of mitosis. sac, the anther, where pollen is produced.
(3) Separation of homologs. At anaphase I of meiosis, the Carpels are megasporophylls: They produce megaspores
duplicated chromosomes of each homologous pair that give rise to female gametophytes. At the tip of the carpel is
move toward opposite poles, but the sister chromatids a sticky stigma that receives pollen. A style leads from the
of each duplicated chromosome remain attached. In stigma to a structure at the base of the carpel, the ovary; the
anaphase of mitosis, by contrast, sister chromatids ovary contains one or more ovules. As in gymnosperms, each
separate. angiosperm ovule contains a female gametophyte. If fertilized,
an ovule develops into a seed. A flower may have one or more
carpels. In many species, multiple carpels are fused into one
structure. The term pistil is sometimes used to refer to a single
carpel (a simple pistil) or two or more fused carpels (a
compound pistil).
Plants and some species of algae exhibit a second type of life
cycle called alternation of generations. This type includes both
diploid and haploid stages that are multicellular. The
multicellular diploid stage is called the sporophyte. Meiosis in
the sporophyte produces haploid cells called spores. Unlike a
gamete, a haploid spore doesn’t fuse with another cell but
divides mitotically, generating a multicellular haploid stage
called the gametophyte. Cells of the gametophyte give rise to
gametes by mitosis. Fusion of two haploid gametes at
fertilization results in a diploid zygote, which develops into the
next sporophyte generation. Therefore, in this type of life cycle,
the sporophyte generation produces a gametophyte as its
offspring, and the gametophyte generation produces the next
sporophyte generation.
The Angiosperm Life Cycle
(1) In the megasporangium of each ovule, the
megasporocyte divides by meiosis, producing four
megaspores. One survives and gives rise to a female
gametophyte.
(2) In the anther of a stamen, each microsporangium
contains microsporocytes that divide by meiosis,
producing microspores.
(3) A microspore develops into a pollen grain. The
generative cell of the gametophyte will divide, forming
two sperm. The tube cell will produce the pollen tube.
(4) After pollination, eventually two sperm cells are
discharged in each ovule.
(5) Double fertilization occurs. One sperm fertilizes the
egg, forming a zygote. The other sperm fertilizes the
central cell, forming the endosperm (a food supply, 3n
in this example).
(6) The zygote develops into an embryo that is packaged
along with food into a seed. (The fruit tissues
surrounding the seed are not shown.)
(7) When a seed germinates, the embryo develops into a
mature sporophyte.
CELLULAR RESPIRATION
Theme 1: Glycolysis harvests chemical energy by oxidizing
glucose to pyruvate
Energy Investment Phase:
(1) Hexokinase transfers a phosphate group from ATP to
glucose, forming glucose-6-phosphate and making it
more chemically reactive. The charge on the
phosphate also traps the sugar in the cell.
(2) Glucose 6-phosphate is converted to fructose 6-
phosphate by phosphogluco-isomerase.
(3) Phosphofructokinase transfers a phosphate group
from ATP to the opposite end of fructose 6-phosphate,
forming fructose 1,6-bisphosphate and investing a
second molecule of ATP. This is a key step for
regulation of glycolysis.
(4) Aldolase cleaves the sugar molecule into two different
three-carbon sugars: Glyceraldehyde 3-phosphate
(G3P) and dihydroxyacetone phosphate (DHAP)
(5) Conversion between DHAP and G3P by isomerase
This reaction never reaches equilibrium; G3P is used
in the next step as fast as it forms.
Energy Payoff Phase
(6) Two sequential reactions: (1) G3P is oxidized by the
transfer of electrons to NAD+, forming NADH by triose
phosphate dehydrogenase (2) Using energy from this
exergonic redox reaction, a phosphate group is
attached to the oxidized substrate, making a high-
energy product called 1,3-bisphosphoglycerate
(7) The phosphate group is transferred to ADP (substrate-
level phosphorylation) in an exergonic reaction
catalyzed by phospho-glycerokinase. The carbonyl
group of G3P has been oxidized to the carboxyl group
(—COO–) of an organic acid (3-phosphoglycerate).
(8) Phospho-glyceromutase relocates the remaining
phosphate group of 3-phosphoglycerate (to 2-
phosphoglycerate)
(9) Enolase causes a double bond to form in the substrate
by extracting a water molecule, yielding
phosphoenolpyruvate (PEP), a compound with a
very high potential energy.
(10) Pyruvate kinase transfers the phosphate group from
PEP to ADP (a second example of substrate-level
phosphorylation), forming pyruvate.
Products: 2 pyruvate, net of 2 ATP, and 2NADH
After pyruvate is oxidized, the citric acid cycle completes
the energy-yielding oxidation of organic molecules.
When O2 is present, the pyruvate in eukaryotic cells enters a
mitochondrion, where the oxidation of glucose is completed.
Oxidation of Pyruvate to Acetyl CoA
Upon entering the mitochondrion via active transport, pyruvate
is first converted to a compound called acetyl coenzyme A, or
acetyl CoA
(1) Pyruvate’s carboxyl group (—COO-), already
somewhat oxidized and thus carrying little chemical
energy, is now fully oxidized and given off as a
molecule of CO2. This is the first step in which CO2 is
released during respiration.
(2) Next, the remaining two-carbon fragment is oxidized
and the electrons transferred to NAD+, storing energy
in the form of NADH.
(3) Finally, coenzyme A (CoA), a sulfur-containing
compound derived from a B vitamin, is attached via its
sulfur atom to the two-carbon intermediate, forming
acetyl CoA. Acetyl CoA has a high potential energy,
which is used to transfer the acetyl group to a molecule
in the citric acid cycle, a reaction that is therefore highly
exergonic.
The Krebs Fucking Cycle (in the mitochondrial matrix)
(1) Acetyl CoA (from oxidation of pyruvate) adds its two-
carbon acetyl group to oxaloacetate (oxaloacetic
acid), producing citrate (citric acid).
(2) Citrate is converted to its isomer, isocitrate, by
removal of one water molecule and addition of another.
(3) Isocitrate is oxidized, reducing NAD+ to NADH and
forming alpha-ketoglutarate. Then the resulting
compound loses a CO2 molecule.This is catalyzed by
isocitrate dehydrogenase.
(4) Another CO2 is lost, and the resulting compound is
oxidized, reducing NAD+ to NADH. The remaining
molecule is then attached to coenzyme A by an
unstable bond, forming succinyl CoA.
(5) CoA is displaced by a phosphate group, which is
transferred to GDP, forming GTP (guanosine
triphosphate), a molecule with functions similar to
ATP. GTP can also be used, to generate ATP.
(6) Two hydrogens are transferred to FAD, forming
FADH2 and oxidizing succinate (forming fumarate).
(7) Addition of a water molecule rearranges bonds in the
substrate, forming malate.
(8) The substrate is oxidized, reducing NAD+ to NADH
and regenerating oxaloacetate.
Products (for 2 pyruvate molecules): 6 NADH, 2 FADH2, 2
ATP, 4 CO2 released
During oxidative phosphorylation, chemiosmosis couples
electron transport to ATP synthesis
At this point, molecules of NADH (and FADH2) account for most
of the energy extracted from each glucose molecule. These
electron escorts link glycolysis and the citric acid cycle to the
machinery of oxidative phosphorylation, which uses energy
released by the electron transport chain to power ATP
synthesis.
The electron transport chain is a collection of molecules
embedded in the inner membrane of the mitochondrion in
eukaryotic cells. (In prokaryotes, these molecules reside in the
plasma membrane.) The folding of the inner membrane to form
cristae increases its surface area, providing space for thousands
of copies of each component of the electron transport chain in a
mitochondrion. The infolded membrane with its concentration of
electron carrier molecules is well-suited for the series of
sequential redox reactions that take place along the electron
transport chain. Most components of the chain are proteins,
which exist in multiprotein complexes numbered I through IV.
Tightly bound to these proteins are prosthetic groups,
nonprotein components such as cofactors and coenzymes
essential for the catalytic functions of certain enzymes.
Protein Complex I
Electrons acquired from glucose by NAD+ during glycolysis and
the citric acid cycle are transferred from NADH to the first
molecule of the electron transport chain in complex I. This
molecule is a flavoprotein, so named because it has a
prosthetic group called flavin mononucleotide (FMN). In the
next redox reaction, the flavoprotein returns to its oxidized form
as it passes electrons to an iron-sulfur protein (FeS in complex
I), one of a family of proteins with both iron and sulfur tightly
bound. The iron-sulfur protein then passes the electrons to a
compound called ubiquinone. This electron carrier is a small
hydrophobic molecule, the only member of the electron
transport chain that is not a protein. Ubiquinone is individually
mobile within the membrane rather than residing in a particular
complex. (Another name for ubiquinone is coenzyme Q, or
CoQ; you may have seen it sold as a nutritional supplement.)
Most of the remaining electron carriers between ubiquinone and
oxygen are proteins called cytochromes. Their prosthetic group,
called a heme group, has an iron atom that accepts and donates
electrons. (The heme group in a cytochrome is similar to the
heme group in hemoglobin, the protein of red blood cells, except
that the iron in hemoglobin carries oxygen, not electrons.)
Another source of electrons for the electron transport chain is
FADH2, the other reduced product of the citric acid cycle.
FADH2 adds its electrons from within complex II, at a lower
energy level than NADH does.
Populating the inner membrane of the mitochondrion or the
prokaryotic plasma membrane are many copies of a protein
complex called ATP synthase, the enzyme that makes ATP
from ADP and inorganic phosphate. ATP synthase works like an
ion pump running in reverse. Ion pumps usually use ATP as an
energy source to transport ions against their gradients.
Enzymes can catalyze a reaction in either direction, depending
on the ∆G for the reaction, which is affected by the local
concentrations of reactants and products. Rather than
hydrolyzing ATP to pump protons against their concentration
gradient, under the conditions of cellular respiration ATP
synthase uses the energy of an existing ion gradient to power
ATP synthesis. The power source for ATP synthase is a
difference in the concentration of H+ on opposite sides of the
inner mitochondrial membrane. This process, in which energy
stored in the form of a hydrogen ion gradient across a
membrane is used to drive cellular work such as the synthesis
of ATP, is called chemiosmosis.
(1) H+ ions flowing down their gradient enter a channel in
a stator, which is anchored in the membrane.
(2) H+ ions enter binding sites within a rotor, changing the
shape of each subunit so that the rotor spins within the
membrane.
(3) Each H+ ion makes one complete turn before leaving
the rotor and passing through a second channel in the
stator into the mitochondrial matrix
(4) Spinning of the rotor causes an internal rod to spin as
well. This rod extends like a stalk into the knob below
it, which is held stationary by part of the stator.
(5) Turning of the rod activates catalytic sites in the knob
that produce ATP from ADP and P.
Chemiosmosis is an energy-coupling mechanism that uses
energy stored in the form of an H+ gradient across a membrane
to drive cellular work
The electron transport chain is a series of proteins and
organic molecules found in the inner membrane of the
mitochondria. Electrons are passed from one member of the
transport chain to another in a series of redox reactions. Energy
released in these reactions is captured as a proton gradient,
which is then used to make ATP in a process
called chemiosmosis. Together, the electron transport chain
and chemiosmosis make up oxidative phosphorylation.
Delivery of electrons by NADH and FADH2. Reduced
electron carriers (NADH and FADH2 from other steps of cellular
respiration transfer their electrons to molecules near the
beginning of the transport chain. In the process, they turn back
into NAD+ and FAD, which can be reused in other steps of
cellular respiration.
Electron transfer and proton pumping. As electrons are
passed down the chain, they move from a higher to a lower
energy level, releasing energy. Some of the energy is used to
pump H+, moving them out of the matrix and into the
intermembrane space. This pumping establishes an
electrochemical gradient.
Splitting of oxygen to form water. At the end of the electron
transport chain, electrons are transferred to molecular oxygen,
which splits in half and takes up H+ to form water.
Gradient-driven synthesis of ATP. As H+ ions flow down their
gradient and back into the matrix, they pass through an enzyme
called ATP synthase, which harnesses the flow of protons to
synthesize ATP.
NADH is very good at donating electrons in redox reactions (that
is, its electrons are at a high energy level), so it can transfer its
electrons directly to complex I, turning back into NAD+. As
electrons move through complex I in a series of redox reactions,
energy is released, and the complex uses this energy to pump
protons from the matrix into the intermembrane space.
FADH2 is not as good at donating electrons as NADH (that is,
its electrons are at a lower energy level), so it cannot transfer its
electrons to complex I. Instead, it feeds them into the transport
chain through complex II, which does not pump protons across
the membrane.
Beyond the first two complexes, electrons from NADH and
FADH2 travel exactly the same route. Both complex I and
complex II pass their electrons to a small, mobile electron carrier
called ubiquinone (Q), which is reduced to form QH2 and
travels through the membrane, delivering the electrons to
complex III. As electrons move through complex III, more H+
ions are pumped across the membrane, and the electrons are
ultimately delivered to another mobile carrier
called cytochrome C (cyt C). Cyt C carries the electrons to
complex IV, where a final batch of H+ ions is pumped across the
membrane. Complex IV passes the electrons to O2, which splits
into two oxygen atoms and accepts protons from the matrix to
form water. Four electrons are required to reduce each molecule
of O2 and two water molecules are formed in the process.
Complexes I, III, and IV of the electron transport chain are
proton pumps. As electrons move energetically downhill, the
complexes capture the released energy and use it to pump
H^++start superscript, plus, end superscript ions from the matrix
to the intermembrane space. This pumping forms an
electrochemical gradient across the inner mitochondrial
membrane. The gradient is sometimes called the proton-
motive force. This process, in which energy from a proton
gradient is used to make ATP, is called chemiosmosis. More
broadly, chemiosmosis can refer to any process in which energy
stored in a proton gradient is used to do work.
Based on a lot of experimental work, it appears that four H+ ions
must flow back into the matrix through ATP synthase to power
the synthesis of one ATP molecule. When electrons from NADH
move through the transport chain, about 10 H+ ions are pumped
from the matrix to the intermembrane space, so each NADH
yields about 2.5 ATP. Electrons from FADH2, which enter the
chain at a later stage, drive pumping of only 6 H+ leading to
production of about 1.5 ATP.
Direct products Ultimate ATP yield
Stage (net) (net)
Glycolysis 2 ATP 2 ATP
2 NADH 3-5 ATP
Pyruvate
oxidation 2 NADH 5 ATP
Citric acid cycle 2 ATP/GTP 2 ATP
6 NADH 15 ATP
2 FADH2 3 ATP
Total 30-32 ATP