Biology

Vietnam National University
International Univeristy
BIOLOGY
(Guidelines for the preparation of the
entrance exam to MSc program in Biotechnology )
School of Biotechnology
Contents
Chapter
Chapter
Chapter
Chapter
1. Bio-Chemistry of life
2. Cell biology
3. Genetics
4: Evolution
Reading materials
Campbell N.A. & Reece J.B. (2004) Biology,
any Edition. Benjamin Cumming Publisher.
1312 p.
Ross F.C., Bailey D., Enger E.D. (2008)
Concepts in Biology, 13rd Edition. McGraw
Hill Higher Education.
Chapter 1. Chemistry of Life

Structure and function of macromolecules
Carbohydrate
Protein
Nucleic acid
Lipid
Guidelines
4 groups of macromolecule, three of
them are polymer.
All polymer is synthesized by
polymerization of a number of
monomers dehydration reactions
Structure of monomer
Structure and function of polymer
1.1 Carbohydrate
Carbohydrates include both sugars and
polymers.
The simplest carbohydrates are
monosaccharides or simple sugars.
Disaccharides, double sugars, consist of
two monosaccharides joined by a
condensation reaction.
Polysaccharides are polymers of
monosaccharides
1.1.1 Monosaccharides
Molecular formulas are some multiple of CH2O (glucose
has the formula C6H12O6 )
Consist of carbonyl group and multiple hydroxyl

groups
If the carbonly group is at the end, the sugar is an
aldose, if not, the sugars is a ketose.
Glucose, an aldose, and fructose, a ketose, are
structural isomers.
Monosaccharides are also classified by the number of
carbons in the backbone.
Glucose and other six carbon sugars are hexoses.
Five carbon backbones are pentoses and three
carbon sugars are trioses.
Monosaccharides, particularly glucose, are

a major fuel for cellular work.
They also function as the raw material for
the synthesis of other monomers, including
those of amino acids and fatty acids
While often drawn as a linear skeleton, in
aqueous solutions monosaccharides form
rings
Two ring forms of glucose differ in whether the

hydroxyl group attached to the number 1
carbon fixed above (beta glucose) or below
(alpha glucose) the ring plane
1.1.2 Disaccharides
Two monosaccharides can join with a
glycosidic linkage to form a
dissaccharide via dehydration.
Maltose, malt sugar, is formed by joining
two glucose molecules.
Sucrose, table sugar, is formed by
joining glucose and fructose and is the
major transport form of sugars in plants.
1.1.3 Polysaccharides
Polysaccharides are polymers of hundreds
to thousands of monosaccharides joined by
glycosidic linkages.
One function of polysaccharides is as an
energy storage macromolecule that is
hydrolyzed as needed.
Other polysaccharides serve as building
materials for the cell or whole organism.
Starch
storage polysaccharide composed
entirely of glucose monomers.
Most monomers are joined by 1-4
linkages between the glucose molecules.
One unbranched form of starch,
amylose, forms a helix.
Branched forms, like amylopectin, are
more complex.
Starch is a polysaccharide of alpha
glucose monomers
Glycogen.
The storage form of polysaccharide of
glucose in animal
Cellulose
a major component of the tough wall of plant
cells
Cellulose is also a polymer of glucose
monomers, but using beta rings
While polymers built with alpha

glucose form helical structures,
polymers built with beta glucose form
straight structures.
This allows H atoms on one strand to
form hydrogen bonds with OH groups
on other strands.
Groups of polymers form strong strands,
microfibrils, that are basic building
material for plants (and humans).
Chitin
A structural polysaccharide used in the
exoskeletons of arthropods (including
insects, spiders, and crustaceans).
also forms the structural support for the
cell walls of many fungi.
Chitin is similar to cellulose, except that it
contains a nitrogen-containing appendage on
each glucose.
Pure chitin is leathery, but the addition of
calcium carbonate hardens the chitin
Concept check
Write the formula for a
monosaccharide that has three, six
carbons?
A dehydration reaction joins two
glucose molecules to form maltose.
The formula of glucose is C6H12O6,
what is the formula of maltose?
Compare and contract starch and
cellulose?
1.2 Protein
All protein polymers are constructed
from the same set of 20 monomers,
called amino acids.
Polymers of proteins are called
polypeptides.
A protein consists of one or more
polypeptides folded and coiled into a
specific conformation.
Amino acids
consist of four components attached to a central carbon,

the alpha carbon.
These components include a
hydrogen atom, a carboxyl
group, an amino group, and
a variable R group
(or side chain).
Differences in R groups
produce the 20 different
amino acids.
The physical and chemical
characteristics of the R group
determine the unique
characteristics of a particular amino acid
R group is hydrophobic
R groups are polar hydrophilic.
R groups are charged (ionized) at

cellular pH (some groups are basic,
some are acidic)
Peptide bond formation

Amino acids are joined together when a dehydration
reaction removes a hydroxyl group from the carboxyl
end of one amino acid and a hydrogen from the amino
group of another.
Protein structure and function

A proteins function depends on its specific
conformation
The folding of a protein from a chain of
amino acids occurs spontaneously.
The function of a protein is an emergent
property resulting from its specific
molecular order.
Three levels of structure: primary,
secondary, and tertiary structure, are used
to organize the folding within a single
polypeptide.
Primary structure
unique sequence of amino acids.
slight change in primary structure can
affect a proteins conformation and
ability to function.
Secondary structure
Results from hydrogen bonds at regular
intervals along
the polypeptide
backbone
Typical shapes
that develop from
secondary structure
are coils (an alpha
helix) or folds
(beta pleated
sheets).
Tertiary structure
is determined by a variety of interactions among R groups

and between R groups and the polypeptide backbone
These interactions
include hydrogen
bonds among polar
and/or charged
areas, ionic bonds
between charged
R groups, and
hydrophobic
interactions and
van der Waals
interactions among
hydrophobic R
groups.
Quarternary structure
Results from the aggregation of two or more polypeptide

subunits.
Collagen is a fibrous protein of three polypeptides that are

supercoiled like a rope.
This provides the structural strength for their role in connective

tissue.
Hemoglobin is a
globular protein
with two copies
of two kinds
of polypeptides
A proteins conformation can change in response to

the physical and chemical conditions.
Alterations in pH, salt concentration, temperature, or
other factors can unravel or denature a protein.
These forces disrupt the hydrogen bonds, ionic
bonds, and disulfide bridges that maintain the
proteins shape.
Some proteins can return to their functional shape
after denaturation, but others cannot, especially in
the crowded environment of the cell.
Concept check
Differentiate between secondary and
tertiary structure by describing the parts of
the polypeptide chain that participate in the
bonds that hold together each level of
structure?
A genetic mutation can change a primary
structure, how can this destroy the protein
function?
Why does a denatured protein no longer
function normally?
1.3 Nucleic acid

The amino acid sequence of a polypeptide is
programmed by a gene.
A gene consists of regions of DNA, a polymer of
nucleic acids.
DNA (and their genes) is passed by the mechanisms
of inheritance
There are two types of nucleic acids: ribonucleic
acid (RNA) and deoxyribonucleic acid (DNA).
DNA provides direction for its own replication.
DNA also directs RNA synthesis and, through RNA,
controls protein synthesis.
Nucleotides
Nucleic acids are polymers of
monomers called nucleotides.
Each nucleotide consists of three
parts: a nitrogen base, a pentose
sugar, and a phosphate group.
The nitrogen bases, rings of carbon and

nitrogen, come in two types: purines and
pyrimidines.
Pyrimidines have a single six-membered ring.
The three different pyrimidines, cytosine (C),
thymine (T), and uracil (U) differ in atoms
attached to the ring.
Purine have a six-membered ring joined to a
five-membered ring.
The two purines are adenine (A) and guanine
(G).
The pentose joined to the nitrogen base is

ribose in nucleotides of RNA and
deoxyribose in DNA.
The only difference between the sugars is the
lack of an oxygen atom on carbon two in
deoxyribose.
The combination of a pentose and nucleic acid is
a nucleoside.
The addition of a phosphate group creates

a nucleoside monophosphate or nucleotide
Polynucleotides are synthesized by

connecting the sugars of one
nucleotide to the phosphate of the
next with a phosphodiester link.
This creates a repeating backbone of
sugar-phosphate units with the
nitrogen bases as appendages
Functions of nucleic acids

Nucleic acids store and transmit hereditary information
-There are two types of nucleic acids: ribonucleic acid (RNA)
and deoxyribonucleic acid (DNA).
- DNA provides direction for its own replication.
- DNA also directs RNA synthesis and, through RNA, controls
protein synthesis
Inheritance is based on replication of the DNA double

helix
Because of the shapes of nucleic acids, only some bases are
compatible with each other.
Adenine (A) always pairs with thymine (T) and guanine (G) with
cytosine (C).
With these base-pairing rules, if we know the sequence of bases

on one strand, we know the sequence on the opposite strand.
The two strands are complementary
DNA and proteins as tape measures of evolution
Because DNA molecules are passed from parents to offspring,

siblings have greater similarity than do unrelated individuals of the
same species.
Concept check
In a DNA double helix, a region along
one DNA strand had this sequence of
nitrogen bases: 5-TAGGCCT-3. List
the bases sequence along the other
strand of the molecule, clearly
indicating the 5 and 3 ends of this
strand?
Explain the role of nucleic acid?
1.4 Lipid
Lipids are an exception among
macromolecules because they do not have
polymers.
The unifying feature of lipids is that they all
have little or no affinity for water.
This is because their structures are dominated
by nonpolar covalent bonds.
Lipids are highly diverse in form and

function.
A fat is constructed from two kinds of
smaller molecules, glycerol and fatty acids.
Glycerol consists of a three carbon skeleton with a

hydroxyl group attached to each.
A fatty acid consists of a carboxyl group attached
to a long carbon skeleton, often 16 to 18 carbons
long.
In a fat, three fatty acids are joined to glycerol by an

ester linkage, creating a triacylglycerol
The three fatty acids in a fat can be the same or
different.
Fatty acids may vary in length (number of carbons)
and in the number and locations of double bonds
- saturated fatty acid - no carbon-carbon double
bonds the molecule is a hydrogen at every possible
position.
- unsaturated fatty acid one or more carbon-carbon
double bonds
Saturated fatty acids are straight chains, but
unsaturated fatty acids have a kink wherever there is
a double bond
Functions of fat
The major function of fats is energy storage.
A gram of fat stores more than twice as much energy
as a gram of a polysaccharide.
Plants use starch for energy storage when mobility is
not a concern but use oils when dispersal and
packing is important, as in seeds.
Humans and other mammals store fats as long-term
energy reserves in adipose cells.
Fat also functions to cushion vital organs.
A layer of fats can also function as insulation.
This subcutaneous layer is especially thick in whales,
seals, and most other marine mammals.
Phospholipids
Phospholipids have two fatty acids attached to
glycerol and a phosphate group at the third position.
When phospholipids are added to water, they selfassemble into aggregates with the hydrophobic tails
pointing toward the center and the hydrophilic heads
on the outside (micelle).
At the surface of a cell phospholipids are arranged as
a bilayer (component of cell membrane)
Steroids
Include cholesterol and certain hormones
Steroids are lipids with a carbon skeleton consisting of four
fused carbon rings.
Different steroids are created by varying functional groups
attached to the rings.
Cholesterol: (1)component in animal cell membranes, and
(2) precursor from which all other steroids are synthesized
in which many of them are hormones
Concept check
Compare the structure of a fat
(triglyceride) with that of
phospholipid?
How do saturated fat differ from
unsaturated fat both in structure and
behavior?
Chapter 2. Cell biology
Transport through cellular membrane

Metabolism
Respiration
Photosynthesis
Cell communication
Guidelines
Focus on the mechanism of processes
Refer to the structure of organelles
that lead to these processes.
2.1 Transport through cellular

membrane
selective permeability
passive transport
active transport
bulk transport
2.1.1 Selective permeability
Permeability of a molecule through a membrane depends

on the interaction of that molecule with the hydrophobic
core of the membrane.
Hydrophobic molecules, like hydrocarbons, CO2, and O2, can

dissolve in the lipid bilayer and cross easily.
Ions and polar molecules pass through with difficulty.
This includes small molecules, like water, and larger critical

molecules, like glucose and other sugars.
Ions, whether atoms or molecules, and their surrounding shell
of water also have difficulties penetrating the hydrophobic
core.
Proteins can assist and regulate the transport of ions and polar
molecules
Membranes are selectively permeable
Specific ions and polar molecules can cross the lipid bilayer
by passing through transport proteins that span the
membrane.
Some transport proteins have a hydrophilic channel that certain

molecules or ions can use as a tunnel through the membrane.
Others bind to these molecules and carry their passengers across
the membrane physically.
Each transport protein is specific as to the substances that

it will translocate (move).
For example, the glucose transport protein in the liver will carry
glucose from the blood to the cytoplasm, but not fructose, its
structural isomer
2.1.2 Passive transport
Diffusion across a membrane

Requires no energy from the cell to make it happen
The concentration gradient represents potential energy and drives
diffusion
Diffusion is the tendency of molecules of any substance to

spread out in the available space
Diffusion is driven by the intrinsic kinetic energy (thermal motion
or heat) of molecules.
Movements of individual molecules are random.

However, movement of a population of molecules may be
directional.
However, because membranes are selectively permeable,
the interactions of the molecules with the membrane play a
role in the diffusion rate.
Diffusion of molecules with limited permeability through the
lipid bilayer may be assisted by transport proteins.
2.1.3 Active transport

The pumping of solutes against their gradients
Some facilitated transport proteins can move solutes
against their concentration gradient, from the side
where they are less concentrated to the side where
they are more concentrated.
This active transport requires the cell to expend its
own metabolic energy.
Active transport is critical for a cell to maintain its
internal concentrations of small molecules that would
otherwise diffuse across the membrane
The sodium-potassium pump

actively maintains the gradient of
sodium (Na+) and potassium ions
(K+) across the membrane.
Typically, an animal cell has higher
concentrations of K+ and lower
concentrations of Na+ inside the cell.
The sodium-potassium pump uses the
energy of one ATP to pump three Na+
ions out and two K+ ions in.
2.1.4 Bulk transport

Exocytosis and endocytosis transport large
molecules
Small molecules and water enter or leave
the cell through the lipid bilayer or by
transport proteins.
Large molecules, such as polysaccharides
and proteins, cross the membrane via
vesicles.
When the two membranes come in contact,
the bilayers fuse and spill the contents to
the outside
During exocytosis, a transport vesicle

budded from the Golgi apparatus is moved
by the cytoskeleton to the plasma
membrane.
During endocytosis, a cell brings in
macromolecules and particulate matter by
forming new vesicles from the plasma
membrane.
Endocytosis is a reversal of exocytosis.
A small area of the palsma membrane sinks inward to

form a pocket
As the pocket into the plasma membrane deepens, it
pinches in, forming a vesicle containing the material
that had been outside the cell
Concept check
What are properties of O2 and CO2
that allow them the cross a lipid
bilayer without help from the
membrane protein?
Why would water molecules need a
transport protein (aquaporin) to
move rapidly in large quantities
across a membrane?
2.2 Metabolism
ATP
Enzymes speed reactions by lowering
energy barrier
Regulation of enzyme reaction
2.2.1 ATP
ATP powers cellular work by coupling
exergonic reactions to endergonic
reactions
A cell does three main kinds of work:
Mechanical work, beating of cilia, contraction of muscle

cells, and movement of chromosomes
Transport work, pumping substances across membranes
against the direction of spontaneous movement
Chemical work, driving endergonic reactions such as the
synthesis of polymers from monomers.
In most cases, the immediate source of

energy that powers cellular work is ATP.
Structure of ATP
ATP (adenosine triphosphate) is a type of nucleotide

consisting of
- the nitrogenous base adenine
- the sugar ribose
- a chain of three phosphate groups.
The bonds between phosphate groups can be broken by

hydrolysis.
Hydrolysis of the end phosphate group forms adenosine

diphosphate [ATP -> ADP + Pi] and releases 7.3 kcal of energy
per mole of ATP under standard conditions.
In the cell delta G is about -13 kcal/mol.
While the phosphate bonds of ATP are sometimes referred

to as high-energy phosphate bonds, these are actually fairly
weak covalent bonds.
They are unstable however and their hydrolysis yields
energy as the products are more stable.
The phosphate bonds are weak because each of the three
phosphate groups has a negative charge
Their repulsion contributes to the instability of this region of
the ATP molecule
ATP is a renewable resource that is continually regenerated
by adding a phosphate group to ADP.
In the cell the energy from the hydrolysis of ATP is coupled
directly to endergonic processes by transferring the
phosphate group to another molecule.
This molecule is now phosphorylated.

This molecule is now more reactive.
2.2.2 Enzyme
Enzymes speed up metabolic reactions
by lowering energy barriers enzyme is
protein catalyst
Enzymes regulate the movement of
molecules through metabolic pathways
Activation energy is the amount of energy

necessary to push the reactants over an
energy barrier.
At the summit the
molecules are at
an unstable point,
the transition state.
The difference between
free energy of the
products and the free
energy of the reactants
is the delta G.
For some processes, the barrier is not high

and the thermal energy provided by room
temperature is sufficient to reach the
transition state.
In most cases, EA is higher and a significant
input of energy is required.
A spark plug provides the energy to energize
gasoline.
Without activation energy, the hydrocarbons of
gasoline are too stable to react with oxygen.
Enzyme speed reactions by lowering EA.

The transition state can then be reached even at
moderate temperatures.
Enzymes do not change delta G.

It hastens reactions that would occur eventually.
Because enzymes
are so selective,
they determine
which chemical
processes will
occur at any time
Enzyme are substrate specific

The active site is enzymes catalytic
center
The cells physical and chemical
environment affects enzyme activity
(temperature, pH, cofactors )
Concept check
Describe why enzymes act on very
specific substrate.
Malonate is a competitive inhibitor of
the enzyme succinate
dehydrogenase. Describe how
malonate would prevent the enzyme
from acting on its normal substrate
succinate.
2.2.3 Regulation of enzyme reaction

Allosteric regulation
The molecules that naturally regulate
enzyme activity behave like reversible
noncompetitive inhibitors.
Allosteric site (the binding site of
inhibitors): specific receptor on the
enzyme that is not the active site
Binding by these molecules can either
inhibit or stimulate enzyme activity
Feedback inhibition,
metabolic pathway is
turned off by its end
product.
The end product acts as
an inhibitor of an enzyme
in the pathway.
When the product is
abundant the pathway is
turned off, when rare the
pathway is active.
Concept check
How can an activator and an inhibitor
have different effects in an
allosterically regulated enzyme?
2.3 Respiration
Glycolysis
Citric cycle
Oxydative phosphorylation
Fermentation
Glycolysis occurs in the cytoplasm.

It begins catabolism by breaking glucose into two
molecules of pyruvate.
The Krebs cycle occurs in the mitochondrial matrix.
It degrades pyruvate to carbon dioxide.
Several steps in glycolysis and the Krebs cycle transfer
electrons from substrates to NAD+, forming NADH.
NADH passes these electrons to the electron transport
chain.
As they are passed along the chain, the energy carried by
these electrons is stored in the mitochondrion in a form
that can be used to synthesize ATP via oxidative
phosphorylation.
Oxidative phosphorylation produces almost 90% of the
ATP generated by respiration
2.3.1 Glycolysis
During glycolysis, glucose, a six carbon-sugar, is split into

two, three-carbon sugars.
These smaller sugars are oxidized and rearranged to form
two molecules of pyruvate.
Each of the ten steps in glycolysis is catalyzed by a specific
enzyme.
These steps can be divided into two phases: an energy
investment phase and an energy payoff phase.
The net yield from glycolysis is 2 ATP and 2 NADH per
glucose.
No CO2 is produced during glycolysis.
If O2 is present, pyruvate moves to the Krebs cycle and the

energy stored in NADH can be converted to ATP by the
electron transport system and oxidative phosphorylation.
Glycolysis occurs whether O2 is present or not.
Concept check
During the redox reaction in
glycolysis, which molecule acts as
oxidizing agent? The reducing agent?
2.3.2 Kreb cycle (citric cycle)
If oxygen is present, pyruvate enters the

mitochondrion where enzymes of the Krebs
cycle complete the oxidation of the organic
fuel to carbon dioxide.
As pyruvate enters the mitochondrion, a
multienzyme complex modifies pyruvate to
acetyl CoA which enters the Krebs cycle in
the matrix.
The Kreb cycle has 8 steps, each

catalyzed by a specific enzyme .
- 2 C enter in the relatively reduced form
of acetate (step 1), and
- 2 C leave in the completely oxidized
form of CO2 (steps 3 and 4).
- Subsequent steps decompose the citrate
back to oxaloacetate, giving off CO2 as
"exhaust." It is this regeneration of
oxaloacetate that accounts for the "cycle"
in the Krebs cycle.
Most of the energy harvested by the oxidative steps

of the cycle is conserved in NADH
- For each acetate that enters the cycle, 3 NAD+ are
reduced to NADH (steps 3, 4, and 8).
- In one oxidative reaction (step 6) electrons are
transferred to FAD (flavin adenine dinucleotide,
derived from riboflavin, a B vitamin). The reduced
form, FADH2, donates its electrons to the electron
transport chain, as does NADH.
- Step 5, that forms 1 ATP directly by substrate-level
phosphorylation,
- But most of the ATP output of respiration results
from oxidative phosphorylation, when the NADH and
FADH2 produced by the Krebs cycle relay the
electrons extracted from food to the electron
transport chain
Concept check
In which molecules is most of the
energy from the citric acid cycles
redox reactions conserved? How will
these molecules convert their energy
to a form that can be used to make
ATP?
What cellular processes produce the
carbon dioxide that you inhale?
2.3.3 Electron Transport Chain
Electrons removed from food (during glycolysis and the Krebs

cycle) are transferred by NADH to flavoprotein, the first
molecule of the electron transport chain. This molecule is a
prosthetic group called flavin mononucleotide
- In the next redox reaction, the flavoprotein returns to its
oxidized form as it passes electrons to an iron-sulfur protein
(FeS ), one of a family of proteins with both iron-sulfur tightly
bound.
- The iron-sulfur protein then passes the electrons to
ubiquinone (Q ). This electron carrier is a lipid, the only
member of the electron transport chain that is not a protein.
- Most of the remaining electron carriers between Q and O2 are
proteins called cytochromes (cyt).
- Another source of electrons for the transport chain is FADH2
(the other reduced product of the Krebs cycle) adds its electrons
to the electron transport chain at a lower energy level than
NADH does.
Free-energy change
during electron
transport
Chemiosmosis couples the electron transport

chain to ATP synthesis
Concept check
What effect would an absence of O2
have on the process shown in figure
9.15?
In the presence of O2
2.3.4 Fermentation
Fermentation consists of glycolysis plus
reactions that regenerate NAD+ by
transferring electrons from NADH to pyruvate
or derivatives of pyruvate.
The NAD+ can then be reused to oxidize
sugar by glycolysis, which nets 2 ATP by
substrate-level phosphorylation
There are many types of fermentation,
differing in the waste products formed from
pyruvate. Two common types are alcohol
fermentation and lactic acid fermentation.
Fermentation. In the absence of oxygen, many cells use

fermentation to produce ATP by substrate-level
phosphorylation
Fermentation. In the absence of oxygen, many cells use

fermentation to produce ATP by substrate-level
phosphorylation
2.4 Photosynthesis
The light reactions and the Calvin cycle
cooperate in converting light energy to the
chemical energy of food
The light reactions convert solar energy to
the chemical energy of ATP and NADPH
The Calvin cycle uses ATP and NADPH to

convert CO2 to sugar
Light reaction
The light reactions are processed in chlorophyll
The light reactions are the steps of photosynthesis that

convert solar energy to chemical energy
Light absorbed by chlorophyll drives a transfer of

electrons and H2 from H2O to an acceptor called NADP+
(nicotinamide adenine dinucleotide phosphate), which
temporarily stores the energized electrons
The light reactions also generate ATP by powering the

addition of a phosphate group to ADP, a process called
photophosphorylation
Thus, light energy is initially converted to chemical

energy in the form of 2 compounds: NADPH and ATP
An overview of photosynthesis
During the light reactions of

photosynthesis, there are 2 possible
routes for electron flow: cyclic and
noncyclic.
How noncyclic electron flow during the light reactions

generates ATP and NADPH
Cyclic electron flow
Calvin cycle
The Calvin cycle is processed in stroma
- The cycle begins by incorporating CO2 from the air
into organic molecules already present in the
chloroplast known as carbon fixation.
- The Calvin cycle reduces the fixed carbon to
carbohydrate by the addition of electrons
- The reducing power is provided by NADPH, which
acquired energized electrons in the light reactions
- To convert CO2 to carbohydrate, the Calvin cycle also

requires chemical energy in the form of ATP, which is also
generated by the light reactions.
- Thus, it is the Calvin cycle that makes sugar, with the

help of the NADPH and ATP produced by the light
reactions
- The metabolic steps of the Calvin cycle are sometimes

referred to as the dark reactions because none of the
steps requires light directly.
- The Calvin cycle in most plants occurs during daylight,

for only then can the light reactions regenerate the
NADPH and ATP spent in the reduction of CO2 to sugar.
Phase 1: Carbon fixation

RuBP carboxylase
3 CO2 + 1 RuBP -------------------- 6 (3-phosphate glycerate )
Phase 2: Reduction
6 (3-phospho glycerate) + 6ATP 6 (1,3-biphosphate glycerate) + 6

NADPH 6 G3P (glycealdehyde-3-phosphate) + 6NAD+ + 6Pi
1 G3P is out put
Phase 3: Regeneration of CO2 acceptor (RuBP)
5 G3P + 3ATP 3 RuBP (ribulose biphosphate) + 3ADP
Net
3 CO2 + 1 RuBP + 9 ATP + 6 NADH 1 G3P
The light reactions regenerate the ATP and NADPH
The Calvin cycle

2.5 Cell communication

The three stages of cell signaling
are reception, transduction, and
response
(1) Reception. Reception is the target cells detection of a

signal coming from outside the cell. A chemical signal is
"detected" when it binds to a cellular protein (receptor
protein), usually at the cells surface
(2) Transduction. The binding of the signal molecule changes

the receptor protein in some way, initiating the process of
transduction. Transduction sometimes occurs in a single step
but more often requires a sequence of changes in a signaltransduction pathway. The molecules in the pathway are
often called relay molecules
(3) Response. In the third stage of cell signaling, the transduced

signal finally triggers a specific cellular response. The
response may be almost any imaginable cellular activity: such as
catalysis by an enzyme (for example, glycogen phosphorylase),
rearrangement of the cytoskeleton, or activation of specific
genes in the nucleus.
Overview of cell signaling
Receptors
Three major types: G-proteinlinked receptors, tyrosine-kinase
receptors, and ion-channel
receptors
G-protein-linked receptors
A G-protein-linked receptor = plasma membrane
receptor + G protein works .
- Many different signal molecules use G-proteinlinked receptors, including yeast mating factors,
epinephrine and many other hormones, and
neurotransmitters.
- These receptors vary in their binding sites for
recognizing signal molecules and for recognizing
different G proteins inside the cell.
The structure of a G-protein-linked receptor
Tyrosine-kinase receptors
The receptor for a growth factor is often a tyrosine-kinase

receptor, one of a major class of plasma membrane receptors
characterized by having enzymatic activity.
Part of the receptor protein on the cytoplasmic side of the
membrane functions as an enzyme, called tyrosine kinase, that
catalyzes the transfer of P groups from ATP to the amino acid
tyrosine on a substrate protein.
Thus tyrosine-kinase receptors = membrane receptors + attach
P to tyrosines.
Many tyrosine-kinase receptors have the structure roughly
Before the signal molecule binds, the receptors exist as individual
polypeptides.
Each has an extracellular signal-binding site, a single a helix
spanning the membrane, and an intracellular tail containing a
number of tyrosines. The binding of a signal molecule to such a
receptor does not cause enough of a conformational change to
activate the cytoplasmic side of the protein directly
The structure and function of a tyrosine-kinase receptor

Ion channel receptors

Some membrane receptors of chemical
signals are ligand-gated ion channels.
- These channels are protein pores in the
plasma membrane that open or close in
response to a chemical signal, allowing
or blocking the flow of specific ions, such
as Na+ or Ca2+.
- These channel proteins bind a signal

molecule as a ligand at a specific site on
their extracellular side
A ligand-gated ionchannel receptor
Intracellular receptors
Not all signal receptors are membrane proteins
Some are proteins dissolved in the cytosol or nucleus of target

cells.
To reach such a receptor, a chemical messenger (chemical

signaling) must be able to pass through the target cells plasma
membrane
Hydrophobic chemical messengers include the steroid

hormones and thyroid hormones of animals.
Another chemical signal with an intracellular receptor is NO

(nitric oxide), a gas; its very small molecules readily pass
between the membrane phospholipids.
Steroid hormone
interacting with
an intracellular
receptor
Transduction
In a phosphorylation cascade, a
series of different molecules in a
pathway are phosphorylated in turn,
each molecule adding a phosphate
group to the next one in line
The extracellular signal molecule that

binds to the membrane receptor is a
pathways "first messenger."
- Not all components of signaltransduction pathways are proteins.
- Many signaling pathways also involve
small, nonprotein, water-soluble
molecules or ions, called second
messengers.
- Because second messengers are both
small and water-soluble, they can readily
spread throughout the cell by diffusion
cAMP as a second messenger
Cellular responses to signals

In response to a signal, a cell may regulate
activities in the cytoplasm or transcription in
the nucleus
Elaborate pathways amplify and specify the
cells response to signals
Nuclear response to
a signal
Chapter 3. Genetics
Meiosis ant the process of meiosis

Mendelian laws of inheritance, Mendelian genetics
The chromosomal basis of inheritance (linked gene
inheritance, X-inactivation, human genetic defect)
DNA replication and repair
From gene to protein (transcription, translation, point
mutation)
Eukaryotic genome (DNA organization, gene
expression regulation)
DNA technology and genomics (DNA cloning,
restriction fragment analysis, genome mapping,
genome sequence, application of DNA technology
3.1 Meiosis and the process of

meiosis.
In the sexual life cycle
Sperm cells or ova (gametes) have
only one set of chromosomes
A cell with a single chromosome set is
haploid.
For humans, the haploid number of
chromosomes is 23 (n = 23).
By means of sexual
intercourse, a haploid sperm
reaches and fuses with a
haploid ovum.
These cells fuse (syngamy)
resulting in fertilization.
The fertilized egg (zygote)
now has two haploid sets of
chromosomes bearing genes
from the maternal and
paternal family lines.
The zygote and all cells with
two sets of chromosomes are
diploid cells.
For humans, the diploid

number of chromosomes is
46 (2n = 46).
gametes undergo the process of

meiosis in which the chromosome
number is halved.
Fertilization restores the diploid
condition by combining two haploid
sets of chromosomes.
Fertilization and meiosis alternate in
sexual life cycles.
In meiosis, there are two consecutive

cell divisions, meiosis I and meiosis
II, which results in four daughter cells.
Each final daughter cell has only half as
many chromosomes as the parent cell
Meiosis reduces
chromosome number
by copying the
chromosomes once,
but dividing twice.
The first division,
meiosis I, separates
homologous
chromosomes.
The second, meiosis II,
separates sister
chromatids.
Division in meiosis I occurs

in four phases: prophase,
metaphase, anaphase, and
telophase.
During the preceding
interphase the chromosomes
are replicated to form sister
chromatids.
These are genetically identical
and joined at the centromere.
Also, the single centrosome

is replicated
In prophase I, the chromosomes

condense and homologous
chromosomes pair up to form tetrads.
In a process called synapsis, special
proteins attach homologous
chromosomes tightly together.
At several sites the chromatids of
homologous chromosomes are
crossed (chiasmata) and segments
of the chromosomes are traded.
A spindle forms from each
centrosome and spindle fibers
attached to kinetochores on
the chromosomes begin to
move the tetrads around
At metaphase I, the tetrads

are all arranged at the
metaphase plate.
Microtubules from one
pole are attached to the
kinetochore of one
chromosome of each
tetrad, while those from
the other pole are
attached to the other.
In anaphase I,
the homologous
chromosomes
separate and
are pulled toward
opposite poles
In telophase I, movement of
homologous chromosomes continues
until there is a haploid set at each
pole.
Each chromosome consists of linked
sister chromatids.
Cytokinesis by the same
mechanisms as mitosis
usually occurs simultaneously.
In some species, nuclei
may reform, but there is
no further replication
of chromosomes
Meiosis II is very similar to

mitosis.
During prophase II a spindle
apparatus forms, attaches to
kinetochores of each sister
chromatids, and moves them
around.
Spindle fibers from one pole
attach to the kinetochore of
one sister chromatid and
those of the other pole to
the other sister chromatid.
At metaphase II, the

sister chromatids are
arranged at the
metaphase plate.
The kinetochores of sister

chromatids face opposite
poles.
At anaphase II, the

centomeres of sister
chromatids separate
and the now separate
sisters travel toward
opposite poles.
In telophase II, separated sister

chromatids arrive at opposite
poles.
Nuclei form around
the chromatids.
Cytokinesis separates
the cytoplasm.
At the end of meiosis,
there are four haploid
daughter cells.
Three events, unique to meiosis, occur during the first division cycle.
1. During prophase I, homologous chromosomes pair up in a process
called synapsis.
A protein zipper, the synaptonemal complex, holds homologous

chromosomes together tightly.
Later in prophase I, the joined homologous chromosomes are visible as a
tetrad.
At X-shaped regions called chiasmata, sections of nonsister chromatids
are exchanged.
Chiasmata is the physical manifestation of crossing over, a form of genetic
rearrangement
2. At metaphase I homologous pairs of chromosomes, not individual

chromosomes are aligned along the metaphase plate.
In humans, you would see 23 tetrads.
3. At anaphase I, it is homologous chromosomes, not sister

chromatids, that separate and are carried to opposite poles of the
cell.
Sister chromatids remain attached at the centromere until anaphase II.
The processes during the second meiotic division are virtually identical
to those of mitosis.
Concept check
How are trait of parents (such as hair color) transmitted to

their offspring?
Int eh absense of mutation, asexually reproducing organism
produce offspring that are genetically identical to each and to
their parents. Explain.
In organism that reproduce sexually, how similar are the
offspring to their parent. Explain.
Dog sperm contain 39 chromosomes. What are the haploid
number and diploid number for dog.
What process (meiosis or mitosis) is more directly involved in
the production of gametes in animal? In plant and most fungi?
Using the concept of chromosome sets, explain briefly how
mitosis conserve chromosome number, whereas meiosis
reduce the number of chromosome by half
How are the chromosome in metaphase of mitosis similar to
and different from the chromosomes in a cell at metaphase of
meiosis II
3.2 Mendelian laws of inheritance

the law of segregation the two alleles for
a characters are packaged into separate
gametes
the law of independent assortment, each
pair of alleles segregates into gametes
independently
3.2.1 The law of segragation

Mendel developed a hypothesis
to explain these results that
consisted of four related ideas.
1. Alternative version of genes
(different alleles) account for
variations in inherited
characters.
Different alleles vary somewhat
in the sequence of nucleotides
at the specific locus of a gene.
The purple-flower
allele and white-flower
allele are two DNA
variations at the
flower-color locus
2. For each character, an organism inherits two

alleles, one from each parent.
A diploid organism inherits one set of chromosomes
from each parent.
Each diploid organism has a pair of homologous
chromosomes and therefore two copies of each locus.
These homologous loci may be identical, as in the
true-breeding plants of the P generation.
Alternatively, the two alleles may differ
In the flower-color example, the F1 plants inherited a
purple-flower allele from one parent and a whiteflower allele from the other.
3. If two alleles differ, then one, the

dominant allele, is fully expressed
in the the organisms appearance.
The other, the recessive allele, has
no noticeable effect on the organisms
appearance.
Mendels F1 plants had purple flowers
because the purple-flower allele is
dominant and the white-flower allele is
recessive.
4. The two alleles for each character segregate

(separate) during gamete production.
This segregation of alleles corresponds to the
distribution of homologous chromosomes to different
gametes in meiosis.
If an organism has identical allele for a particular
character, then that allele exists as a single copy in
all gametes.
If different alleles are present, then 50% of the
gametes will receive one allele and 50% will receive
the other.
The separation of alleles into separate gametes is
summarized as Mendels law of segregation
Mendels law of segregation accounts for

the 3:1 ratio that he observed in the F2
generation.
The F1 hybrids will produce two classes of
gametes, half with the purple-flower allele
and half with the white-flower allele.
During self-pollination, the gametes of
these two classes unite randomly.
This can produce four equally likely
combinations of sperm and ovum.
A Punnett square
predicts the results
of a genetic cross
between individuals
of known genotype
3.2.2 The law of independent

assortment
In one dihybrid cross experiment, Mendel
studied the inheritance of seed color and
seed shape.
The allele for yellow seeds (Y) is dominant to the
allele for green seeds (y).
The allele for round seeds (R) is dominant to the
allele for wrinkled seeds (r).
Mendel crossed true-breeding plants that

had yellow, round seeds (YYRR) with truebreeding plants that has green, wrinkled
seeds (yyrr).
One possibility is that the two

characters are transmitted from
parents to offspring as a
package.
The Y and R alleles and y and r
alleles stay together.
If this were the case, the F1
offspring would produce
yellow, round seeds. The F2
offspring would produce two
phenotypes in a 3:1 ratio, just
like a monohybrid cross. This
was not consistent with Mendels
results
An alternative hypothesis is that the two

pairs of alleles segregate independently of
each other.
The presence of one specific allele for one trait
has no impact on the presence of a specific
allele for the second trait.
In our example, the F1 offspring would still

produce yellow, round seeds.
However, when the F1s produced gametes,
genes would be packaged into gametes
with all possible allelic combinations.
Four classes of gametes (YR, Yr, yR, and yr)
would be produced in equal amounts.
When sperm with four

classes of alleles and ova
with four classes of
alleles combined, there
would be 16 equally
probable ways in which
the alleles can combine
in the F2 generation.
These combinations
produce four distinct
phenotypes in a
9:3:3:1 ratio.
This was consistent with
Mendels results.
Mendel repeated the dihybrid cross experiment for

other pairs of characters and always observed a
9:3:3:1 phenotypic ration in the F2 generation.
Each character appeared to be inherited
independently.
The independent assortment of each pair of alleles
during gamete formation is now called Mendels law
of independent assortment.
One other aspect that you can notice in the dihybrid
cross experiment is that if you follow just one
character, you will observe a 3:1 F2 ratio for each,
just as if this were a monohybrid cross.
Mendel laws
1.
2.
3.
4.
Pea plants heterozygous for flower position and stem

length (AaTt) are allowed to self-pollinate, and 400 of the
resulting seeds are planted. How many offspring would be
predicted to be dwarf with terminal flowers?
For any gene with dominant allele C and recessive allele c,
what propotions of the offspring from a CCxCc cross are
expected to be homozygous dominant, homozygous
recessive and heterozygous?
An organism with the genotype BbDD is mated to oen with
the genotype BBDd. Assuming independent assortment of
these two genes, write the genotypes of all possible
offspring fromt his cross and calculate the chance of each
genotype occuring using the rules of probability
What is the probability that an offspring fromteh cross in
question 2 above will exhibit either of the two recessive
traits coded by the b and d alelle? Explain
5.
6.
7.
A rooster with gray feather is mated with a hen of the same

phenotype. Among their offspring, 15 chicks are gray, 6 are black,
and 8 are white. What is the simplest explanation for the inheritance
of these colors in chickens? What phenotypes would you expect in
the offspring resulting from a cross between a gray rooter and a
black hen?
In human, tall parents tend to have tall children, and short parents
tend to have short children. Adult heights, however, vary in a
population over a wide range, following a normal bell-shaped curve.
Explain these observations Beth and Tom each have a sibling with
cystic fibrosis, but neither Beth nor Tom nor any other parents have
this disease. Calculate the probability that if this couple has a child,
the child will have cystic fibrosis. What would be the probability if
the test reveal that Tom is the carrier but Beth is not.
Joan was born with 6 toes on each foot, a dominant trait called
polydactyly. Two of her 5 siblings and her mother, but not her
father, also have extra digits. What is Joans genotype for thenumber-of-digits character? Explain your answer. Use D and d to
symbolize the alleles for this character.
3.3 The chromosomal basics of

inheritance
Around 1902, Walter
Sutton, Theodor Boveri,
and others noted these
parallels and a
chromosome theory
of inheritance began
to take form.
3.3.1 Linked genes inheritance

Linked genes tend to be inherited
together because they are located on
the same chromosome
Results of crosses with linked genes
deviate from those expected
according to independent assortment.
Morgan observed this linkage and its

deviations when he followed the inheritance
of characters for body color and wing size.
The wild-type body color is gray (b+) and the
mutant black (b).
The wild-type wing size is normal (vg+) and the
mutant has vestigial wings (vg).
Morgan crossed F1 heterozygous females

(b+bvg+vg) with homozygous recessive
males (bbvgvg).
Surprisingly, Morgan observed a large

number of wild-type (gray-normal) and
double-mutant (black-vestigial) flies among
the offspring.
These phenotypes correspond to those of the
parents.
Morgan reasoned that body color and wing

shape are usually inherited together
because their genes are on the same
chromosome.
These new phenotypic variations must be
the result of crossing over.
Concept check
1.
2.
3.
When 2 genes are located on the same chromosome,

what is the physical basis for the production of
recombinant offspring in a testcross between a
hybrid parent and a double-mutant parent?
For each type of offspring in figure 15.5, explain the
relation ship between its phenotype and the alleles
contributed by the female parent
Gene A, B and C are located on the same
chromosome. Testcrosses show that the recombinant
frequency between A and B is 28% and between A
and C is 12%. Can you determine the linear order of
these genes?
Sex-linked genes
These sex-linked genes follow the
same pattern of inheritance as the
white-eye locus in Drosophila.
Because males have only one X

chromosome (hemizygous), any male
receiving the recessive allele from his
mother will express the trait.
The chance of a female inheriting a double
dose of the mutant allele is much less than
the chance of a male inheriting a single
dose.
Therefore, males are far more likely to
inherit sex-linked recessive disorders than
are females.
Hemophilia
Hemophilia is a sex-linked recessive
trait defined by the absence of one or
more clotting factors.
Although female mammals inherit two X chromosomes, only

one X chromosome is active.
Therefore, males and females have the same effective dose
(one copy ) of genes on the X chromosome.
During female development, one X chromosome per cell

condenses into a compact object, a Barr body.
This inactivates most of its genes.
The condensed Barr body chromosome is reactivated in

ovarian cells that produce ova
females consist of a mosaic of cells, some with an active
paternal X, others with an active maternal X.
After Barr body formation, all descendent cells have the same
inactive X.
If a female is heterozygous for a sex-linked trait,
approximately half her cells will express one allele and the
other half will express the other allele.
X inactivation involves the attachment of methyl

(CH3) groups to cytosine nucleotides on the X
chromosome that will become the Barr body.
One of the two X chromosomes has an active XIST
gene (X-inactive specific transcript).
This gene produces multiple copies of an RNA
molecule that almost cover the X chromosome where
they are made.
This initiates X inactivation, but the mechanism that
connects XIST RNA and DNA methylation is unknown.
What determines which of the two X chromosomes
will have an active XIST gene is also unknown.
Concept check
A white eyed female Drosophila is mated
with a red-eyed (white type) male, the
reciprocal cross of that shown in figure
15.4. What phenotype and genotypes do
you predict for the offspring?
Neither Tim nor Rhoda has Duchenne
muscular dystrophy, but their firstborn son
does have it. What is the probability that a
second child of this couple will have this
disease?
Human genetic defect

Nondisjunction occurs when problems
with the meiotic spindle cause errors in
daughter cells.
This may occur if
tetrad chromosomes
do not separate
properly during
meiosis I.
Alternatively, sister
chromatids may fail
to separate during
meiosis II
Several serious human disorders are due to alterations of

chromosome number and structure.
Although the frequency of aneuploid zygotes may be quite high in
humans, most of these alterations are so disastrous that the
embryos are spontaneously aborted long before birth.
Certain aneuploid conditions upset the balance less, leading to

survival to birth and beyond.
These developmental problems results from an imbalance among gene

products.
These individuals have a set of symptoms - a syndrome - characteristic
of the type of aneuploidy. One aneuploid condition, Down syndrome,
is due to three copies of chromosome 21.
It affects one in 700 children born in the United States.
Although chromosome 21 is the smallest human chromosome, it

severely alters an individuals phenotype in specific ways
Most cases of Down syndrome result from nondisjunction during
gamete production in one parent
Organisms with more than two complete

sets of chromosomes, have undergone
polypoidy.
This may occur when a normal gamete
fertilizes another gamete in which there has
been nondisjunction of all its chromosomes.
The resulting zygote would be triploid (3n).
Alternatively, if a 2n zygote failed to divide

after replicating its chromosomes, a
tetraploid (4n) embryo would result from
subsequent successful cycles of mitosis.
Meiosis
How are trait of parents (such as hair color) transmitted to their

offspring?
Int eh absense of mutation, asexually reproducing organism
produce offspring that are genetically identical to each and to their
parents. Explain.
In organism that reproduce sexually, how similar are the offspring
to their parent. Explain.
Dog sperm contain 39 chromosomes. What are the haploid number
and diploid number for dog.
What process (meiosis or mitosis) is more directly involved in the
production of gametes in animal? In plant and most fungi?
Using the concept of chromosome sets, explain briefly how mitosis
conserve chromosome number, whereas meiosis reduce the
number of chromosome by half
How are the chromosome in metaphase of mitosis similar to and
different from the chromosomes in a cell at metaphase of meiosis
II
Fruit fly have a diploid number of 8, and

honey bees have 32. assuming that no
crossing over, is the genetic variation
among offspring from the same two parents
likely to be greater in fruit flies or honey
bees. Explain
Under what circumstances would crossing
over during meiosis not contribute to
genetic variation among daughter cells
Mendel laws
Pea plants heterozygous for flower position and stem length

(AaTt) are allowed to self-pollinate, and 400 of the resulting
seeds are planted. How many offspring would be predicted
to be dwarf with terminal flowers?
For any gene with dominant allele C and recessive allele c,
what propotions of the offspring from a CCxCc cross are
expected to be homozygous dominant, homozygous
recessive and heterozygous?
An organism with the genotype BbDD is mated to oen with
the genotype BBDd. Assuming independent assortment of
these two genes, write the genotypes of all possible
offspring fromt his cross and calculate the chance of each
genotype occuring using the rules of probability
What is the probability that an offspring fromteh cross in
question 2 above will exhibit either of the two recessive
traits coded by the b and d alelle? Explain
Concept check
More common than completely polyploidy animals

are mosaic polyploidy, animal that are diploid except
for patches of polyploidy cells. How might a mosaic
tetraploid-an animal with some cells containing some
sets of chromosomes- arise?
About 5% of individual with Down syndrome have a
chromosomal translocation in which one copy of
chromosome 21 is attached to chromosomal 14. how
could this translocation in a parent gonad lead to
Down syndrome in a child?
Explain how a male cat could have the tortoiseshell
phenotype?
DNA replication and repair

During DNA replication, base pairing
enables existing DNA strands to serve as
templates for new complimentary strands
A large team of enzymes and other proteins
carries out DNA replication
Enzymes proofread DNA during its
replication and repair damage to existing
DNA
The ends of DNA molecules are replicated
by a special mechanism
DNA replication
At the replication fork, the leading stand is

copied continuously into the fork from a
single primer.
The lagging strand is copied away from the
fork in short segments, each requiring a
new primer.
Enzymes involved in DNA

replication
A helicase untwists and separates the template DNA
strands at the replication fork.
Single-strand binding proteins keep the unpaired
template strands apart during replication
Primase, an RNA polymerase, links ribonucleotides
that are complementary to the DNA template into the
primer.
RNA polymerases can start an RNA chain from a
single template strand.
DNA polymerases catalyze the elongation of new
DNA at a replication fork.
DNA ligase join nucleotides to form the sugarphosphate backbone of a single DNA strand.
DNA repair
DNA polymerase proofreads each new nucleotide
against the template nucleotide as soon as it is added.
If there is an incorrect pairing, the enzyme removes
the wrong nucleotide and then resumes synthesis.
The final error rate is only one per billion nucleotides.
Mismatched nucleotides that are missed by DNA
polymerase or mutations that occur after DNA
synthesis is completed can often be repaired.
Each cell continually monitors and repairs its genetic
material, with over 130 repair enzymes identified in
humans
In mismatch repair,
special enzymes fix
incorrectly paired
nucleotides.
A hereditary defect in one
of these enzymes
is associated with a form
of colon cancer.
In nucleotide excision
repair, anuclease cuts out
a segment of a damaged
strand.
The gap is filled in by
DNA polymerase and
ligase.
Concept check
What role does complementary base
pairing play in the replication of DNA?
Identify 2 major functions of DNA pol III in
DNA replication.
Why is DNA pol I necessary to complete
synthesis of a leading strand? Point out in
the overview box in figure 16.16 where
DAN pol I would function on the top
leading strand
How are the telomeres important for
preserveing eukaryotic genes?
3.5 From gene to protein

Transcription
Translation
Transcription
Messenger RNA is transcribed from the template
strand of a gene.
RNA polymerase separates the DNA strands at the
appropriate point and bonds the RNA nucleotides as
they base-pair along the DNA template.
Like DNA polymerases, RNA polymerases can add
nucleotides only to the 3 end of the growing polymer.
Genes are read 3->5, creating a 5->3 RNA
molecule.
RNA polymerase attaches and initiates transcription
at the promotor, upstream of the information
contained in the gene, the transcription unit.
The terminator signals the end of transcription
Transcription
can be separated
into three stages:
initiation,
elongation, and
termination.
In eukaryotes, proteins
called transcription
factors recognize the
promotor region, especially
a TATA box, and bind to
the promotor.
After they have bound
to the promotor, RNA
polymerase binds to
transcription factors to
create a transcription
initiation complex.
RNA polymerase then
starts transcription.
As RNA polymerase
moves along the
DNA, it untwists the
double helix, 10 to 20
bases at time.
The enzyme adds
nucleotides to the 3
end of the growing
strand.
Behind the point of
RNA synthesis, the
double helix re-forms
and the
RNA molecule peels
away
Concept check
Compare and contract the functioning of
DNA polymerase and RNA polymerase.
Is the promoter at the upstream of
downstream end of a transcription unit?
In a prokaryote, how does RNA polymerase
know where to start transcribing a gene?
In a eukaryote?
How is the primary transcript produced by
a prokaryotic cell different from that
produced by a eukaryotic cell?
Translation
In the process of
translation, a cell interprets
a series of codons along a
mRNA molecule.
Transfer RNA (tRNA)
transfers amino acids from
the cytoplasms pool to a
ribosome.
The ribosome adds each
amino acid carried by tRNA
to the growing end of the
polypeptide chain.
During translation, each type of tRNA links a mRNA

codon with the appropriate amino acid.
Each tRNA arriving at the ribosome carries a specific
amino acid at one end and has a specific nucleotide
triplet, an anticodon, at the other.
The anticodon base-pairs with a complementary
codon on mRNA.
If the codon on mRNA is UUU, a tRNA with an AAA
anticodon and carrying phenyalanine will bind to it.
Codon by codon, tRNAs deposit amino acids in the
prescribed order and the ribosome joins them into a
polypeptide chain.
Each amino acid is joined

to the correct tRNA by
aminoacyl-tRNA
synthetase.
The 20 different
synthetases match the 20
different amino acids.
Each has active sites for

only a specific tRNA and
amino acid combination.
The synthetase catalyzes
a covalent bond between
them, forming aminoacyltRNA
or activated amino acid.
Each ribosome has a binding site for mRNA and three

binding sites for tRNA molecules.
The P site holds the tRNA carrying the growing
polypeptide chain.
The A site carries the tRNA with the next amino acid.
Discharged tRNAs leave the ribosome at the E site
Ribosomes facilitate the specific coupling of the tRNA

anticodons with mRNA codons.
Each ribosome has a large and a small subunit.

These are composed of proteins and ribosomal RNA (rRNA),
the most abundant RNA in the cell.
Translation can be divided into three

stages:
initiation
elongation
termination
All three phase require protein factors
that aid in the translation process.
Both initiation and chain elongation require

energy provided by the hydrolysis of GTP
Initiation brings together mRNA, a tRNA with the

first amino acid, and the two ribosomal subunits.
First, a small ribosomal subunit binds with mRNA and
a special initiator tRNA, which carries methionine and
attaches to the start codon.
Initiation factors bring in the large subunit such that
the initiator tRNA occupies the P site.
Elongation consists of a series of three step

cycles as each amino acid is added to the
proceeding one.
During codon recognition, an elongation
factor assists hydrogen bonding between the
mRNA codon under the A site with the
corresonding anticodon of tRNA carrying the
appropriate
amino acid.
This step requires the hydrolysis of two GTP.
During peptide bond formation, an

rRNA molecule catalyzes the formation
of a peptide bond between the
polypeptide in the P site with the new
amino acid in the A site.
This step separates the tRNA at the P
site from the growing polypeptide chain
and transfers the chain, now one amino
acid longer, to the tRNA at the A site.
During translocation, the ribosome moves

the tRNA with the attached polypeptide from
the A site to the P site.
Because the anticodon remains bonded to the mRNA
codon, the mRNA moves along with it.
The next codon is now available at the A site.
The tRNA that had been in the P site is moved to the
E site and then leaves the ribosome.
Translocation is fueled by the hydrolysis of GTP.
Effectively, translocation ensures that the mRNA is
read 5 -> 3 codon by codon.
The three steps

of elongation
continue codon
by codon to add
amino acids until
the polypeptide
chain is
completed.
Termination occurs when one of the three stop codons

reaches the A site.
A release factor binds to the stop codon and hydrolyzes the
bond between the polypeptide and its tRNA in the P site.
This frees the polypeptide and the translation complex
disassembles.
Concept check
Which 2 processes ensure that the
correct amino acid is added to
growing polypeptide chain?
Describe how the formation of
polyribosomes can benefit the cell
Describe how a polypeptide to be
secreted transported to the
endomembrane system?
Point mutation
Mutations are changes in the genetic
material of a cell (or virus).
These include large-scale mutations in
which long segments of DNA are affected
(for example, translocations, duplications,
and inversions).
A chemical change in just one base pair of
a gene causes a point mutation.
If these occur in gametes or cells producing
gametes, they may be transmitted to future
generations.
A point mutation that results in replacement of a pair of

complimentary nucleotides with another nucleotide pair is
called a base-pair substitution.
Some base-pair substitutions have little or no impact on
protein function
In silent mutations, alterations of nucleotides still indicate the

same amino acids because of redundancy in the genetic code.
Other changes lead to switches from one amino acid to
another with similar properties.
Still other mutations may occur in a region where the exact
amino acid sequence is not essential for function.
Other base-pair substitutions cause a readily detectable

change in a protein.
These are usually detrimental but can occasionally lead to an

improved protein or one with novel capabilities.
Changes in amino acids at crucial sites, especially active sites,
are likely to impact function.
Insertions and deletions are additions or

losses of nucleotide pairs in a gene.
These have a disastrous effect on the resulting
protein more often than substitutions do.
Unless these mutations occur in multiples

of three, they cause a frameshift
mutation.
All the nucleotides downstream of the deletion

or insertion will be improperly grouped into
codons.
The result will be extensive missense, ending
sooner or later in nonsense - premature
termination.
Mutations can occur in a number of ways.

Errors can occur during DNA replication, DNA repair,
or DNA recombination.
These can lead to base-pair substitutions, insertions,
or deletions, as well as mutations affecting longer
stretches of DNA.
These are called spontaneous mutations.
Researchers have developed various methods to test
the mutagenic activity of different chemicals.
These tests are often used as a preliminary screen of
chemicals to identify those that may cause cancer.
This make sense because most carcinogens are
mutagenic and most mutagens are carcinogenic.
Concept check
What happens when one nucleotide pair is
lost from the middle of the coding
sequence of a gene?
The template strand of a gene contains the
sequence 3-TACTTGTCCGATATC-5. Draw
the double strand of DNA and the resulting
mRNA, labeling all 5 and 3 ends.
Determine the amino acid sequence? Then
show the same after the mutation changes
the template DNA sequence to 3TACTTGTCCAATAATC-5. What is the effect
on the amino acid sequence
3.6 Eukaryotic genome

DNA organization
Gene expression regulation
DNA organization
1. Repetitive DNA and other noncoding
sequences account for much of eukaryotic
genome
In eukaryotes, most of the DNA (about
97% in humans) does not code for protein
or RNA.
Some noncoding regions are regulatory

sequences.
Other are introns.
Finally, even more of it consists of repetitive
DNA, present in many copies in the genome
2. Gene families have evolved by duplication of ancestral

genes
While most genes are present as a single copy per
haploid set of chromosomes, multigene families
exist as a collection of identical or very similar genes.
These likely evolved from a single ancestral gene.
The members of multigene families may be clustered
or dispersed in the genome
The classic example traces the duplication and
diversification of the two related families of globin
genes, (alpha) and (beta), of hemoglobin.
The subunit family is on human chromosome 16
and the subunit family is on chromosome 11.
3. Gene amplification, loss, or rearrangement can alter a cells

genome during an organisms lifetime
In gene amplification, certain genes are replicated as a
way to increase expression of these genes.
Rearrangement of the loci of genes in somatic cells may
have a powerful effect on gene expression.
Transposon are genes that can move from one location to
another within the genome.
Up to 50% of the corn genome and 10% of the human

genome are transposons.
If one jumps into a coding sequence of another gene, it can
prevent normal gene function as seen in the pigment of this
morning glory leaf.
If the transposon is inserted in a regulatory area, it may
increase or decrease transcription
Concept check
Describe the structure of a
nucleosome, the basic unit of DNA
packaging in eukaryotic cells.
What chemical properties of histones
and DNA enable these molecules to
bind tightly together?
In general, how does dense packing
of DNA in chromosomes prevent
gene expression?
Gene expression regulation

1. Each cell of a multicellular eukaryote expresses only a
small fraction of its genes
2. The control of gene expression can occur at any step
in the pathway from gene to functional protein: an
overview
3. Chromatin modifications affect the availability of
genes for transcription
4. Transcription initiation is controlled by proteins that
interact with DNA and each other
5. Post-transcriptional mechanisms play supporting roles
in the control of gene expression
These levels of control

include chromatin
packing, transcription,
RNA processing,
translation, and
various alterations to
the protein product.
DNA methylation is the attachment by specific

enzymes of methyl groups (-CH3) to DNA bases after
DNA synthesis.
Inactive DNA is generally highly methylated compared
to DNA that is actively transcribed.
For example, the inactivated mammalian X
chromosome in females is heavily methylated.
Genes are usually more heavily methylated in cells
where they are not expressed.
Histone acetylation (addition of an acetyl group COCH3) and deacetylation appear to play a direct role
in the regulation of gene transcription.
Acetylated histones grip DNA less tightly, providing
easier access for transcription proteins in this region.
A eukaryotic gene and the DNA segments

that control transcription include introns
and exons, a promoter sequence upstream
of the gene, and a large number of other
control elements.
Control elements are noncoding DNA
segments that regulate transcription by binding
transcription factors.
The transcription initiation complex assembles
on the promotor sequence and one component,
RNA polymerase, then transcribes the gene.
Concept check
In general, what is the effect of histone acetylation

and DNA methylation on gene expression?
Compare the roles of general and specific
transcription factors in regulating gene expression?
If you compared the nucleotide sequence of the distal
control elements in the enhancers of three
coordinately regulated genes, what would you expect
to find? Why?
Once mRNA encoding a particular protein reaches the
cytoplasm, what are four mechanisms that can
regulate the amount of the active protein in the cell?
3.7 DNA technology and genomics
DNA cloning
Restriction fragment analysis
Genome mapping
Genome sequence
Application of DNA technology
DNA cloning
The potential uses of cloned genes fall into two
general categories.
First, the goal may be to produce a protein product.
For example, bacteria carrying the gene for human
growth hormone can produce large quantities of the
hormone for treating stunted growth.
Alternatively, the goal may be to prepare many copies
of the gene itself.
This may enable scientists to determine the genes
nucleotide sequence or provide an organism with a
new metabolic capability by transferring a gene from
another organism.
The process of
cloning a human
gene in a bacterial
plasmid can be
divided into five
steps.
1. Isolation of vector and gene-source DNA.

The source DNA comes from human tissue cells.
The source of the plasmid is typically E. coli.
This plasmid carries two useful genes, ampR,
conferring resistance to the antibiotic ampicillin and
lacZ, encoding the enzyme beta-galactosidase which
catalyzes the hydrolysis of sugar.
The plasmid has a single recognition sequence, within
the lacZ gene, for the restriction enzyme used.
2. Insertion of DNA into the vector.

By digesting both the plasmid and human
DNA with the same restriction enzyme we
can create thousands of human DNA
fragments, one fragment with the gene that
we want, and with compatible sticky ends
on bacterial plasmids.
After mixing, the human fragments and cut
plasmids form complementary pairs that
are then joined by DNA ligase.
This creates a mixture of recombinant DNA
molecules.
3. Introduction of the cloning vector into

cells.
Bacterial cells take up the recombinant
plasmids by transformation.
These bacteria are lacZ-, unable to hydrolyze
lactose.
This creates a diverse pool of bacteria,

some bacteria that have taken up the
desired recombinant plasmid DNA, other
bacteria that have taken up other DNA,
both recombinant and nonrecombinant
4. Cloning of cells (and foreign genes).

We can plate out the transformed bacteria
on solid nutrient medium containing
ampicillin and a sugar called X-gal.
Only bacteria that have the ampicillin-resistance
plasmid will grow.
The X-gal in the medium is used to identify
plasmids that carry foreign DNA.
Bacteria with plasmids lacking foreign DNA stain
blue when beta-galactosidase hydrolyzes X-gal.
Bacteria with plasmids containing foreign DNA
are white because they lack beta-galactosidase
5. Identifying cell clones with the right gene.

In the final step, we will sort through the thousands of
bacterial colonies with foreign DNA to find those
containing our gene of interest.
One technique, nucleic acid hybridization, depends
on base pairing between our gene and a
complementary sequence, a nucleic acid probe, on
another nucleic acid molecule.
The sequence of our RNA or DNA probe depends on
knowledge of at least part of the sequence of our
gene.
A radioactive or fluorescent tag labels the probe
Cloned genes are stored in DNA

libraries
In the shotgun cloning approach, a
mixture of fragments from the entire
genome is included in thousands of
different recombinant plasmids.
A complete set of recombinant plasmid
clones, each carrying copies of a particular
segment from the initial genome, forms a
genomic library.
The library can be saved and used as a source of
other genes or for gene mapping
Concept check
Imagine that you want to study human
beta-globin, a protein present in red blood
cell. To obtain sufficient amounts of the
protein, you decide to clone the betaglobin gene. Wouldyou construct a
genomic library or cDNA library? What
material would you use as a source of DNA
or RNA?
What are two potential difficulties in using
plasmid vectors and bacterial host cells for
production of large quatity of human
proteins from clone genes?
Restriction fragment analysis
Restriction fragment analysis indirectly detects certain differences

in DNA nucleotide sequences.
We can use restriction fragment analysis to compare two different

DNA molecules representing, for example, different alleles.
After treating long DNA molecules with a restriction enzyme, the

fragments can be separated by size via gel electrophoresis.
This produces a series of bands that are characteristic of the starting
molecule and that restriction enzyme.
The separated fragments can be recovered undamaged from gels,
providing pure samples of individual fragments.
Because the two alleles must differ slightly in DNA sequence, they may
differ in one or more restriction sites.
If they do differ in restriction sites, each will produce different-sized
fragments when digested by the same restriction enzyme.
In gel electrophoresis, the restriction fragments from the two alleles
will produce different band patterns, allowing us to distinguish the two
alleles
Restriction fragment analysis is sensitive enough to distinguish

between two alleles of a gene that differ by only base pair in a
restriction site.
Gel electrophoresis combined with nucleic acid

hybridization allows analyses to be conducted on the
whole genome, not just cloned and purified genes.
Southern blotting (Southern hybridization) allows us
to transfer the DNA fragments from the gel to a sheet of
nitrocellulose paper, still separated by size.
Differences in DNA sequence on homologous
chromosomes that produce different restriction fragment
patterns are scattered abundantly throughout genomes,
including the human genome.
These restriction fragment length polymorphisms
(RFLPs) can serve as a genetic marker for a particular
location (locus) in the genome.
A given RFLP marker frequently occurs in numerous
variants in a population
RFLPs are detected and analyzed by

Southern blotting, frequently using the
entire genome as the DNA starting
material.
These techniques will detect RFLPs in noncoding

or coding DNA.
Because RFLP markers are inherited in a

Mendelian fashion, they can serve as
genetic markers for making linkage maps.
The frequency with which two RFPL markers - or

a RFLP marker and a certain allele for a gene are inherited together is a measure of the
closeness of the two loci on a chromosome.
Concept check
Suppose that you carry out electrophoresis
on a sample of genomic DNA isolated from
an individual and treated with restriction
enzyme. After staining the gel with DNAbinding dye, what would you see? Explain.
Explain why restriction fragment length
polymorphisms (RFLPs) can serve as
genetic marker even though they produce
no visible phenotype differences.
Genome mapping
In mapping a large genome, the first stage is to construct a

linkage map of several thousand markers spaced
throughout the chromosomes.
The order of the markers and the relative distances between

them on such a map are based on recombination frequencies.
The markers can be genes or any other identifiable sequences
in DNA, such as RFLPs or microsatellites.
The next step was converting the relative distances to some

physical measure, usually the number of nucleotides along
the DNA.
For whole-genome mapping, a physical map is made by
cutting the DNA of each chromosome into identifiable
restriction fragments and then determining the original
order of the fragments.
The key is to make fragments that overlap and then use

probes or automated nucleotide sequencing of the ends to find
the overlaps.
In chromosome
walking, the
researcher starts
with a known DNA
segment (cloned,
mapped, and
sequenced) and
walks along the
DNA from that
locus, producing a
map of overlapping
fragments.
When working with large genomes, researchers carry out several

rounds of DNA cutting, cloning, and physical mapping.
The first cloning vector is often a yeast artificial chromosome (YAC),

which can carry inserted fragments up to a million base pairs long, or a
bacterial artificial chromosome (BAC), which can carry inserts of
100,000 to 500,000 base pairs.
After the order of these long fragments has been determined (perhaps
by chromosome walking), each fragment is cut into pieces, which are
cloned and ordered in turn.
The final sets of fragments, about 1,000 base pairs long, are cloned in
plasmids or phage and then sequenced.
The complete nucleotide sequence of a genome is the ultimate

map.
Starting with a pure preparation of many copies of a relatively short

DNA fragment, the nucleotide sequence of the fragment can be
determined by a sequencing machine.
The usual sequencing technique combines DNA labeling, DNA synthesis
with special chain-terminating nucleotides, and high resolution gel
electrophoresis.
Concept check
What is the major different between
genetic linkage map and a physical
map of a chromosome?
In general, how does the approach to
genome mapping used in human
genome project differ from short gun
approach?
Genome sequence
Genomics, the study of genomes based on their DNA

sequences, is yielding new insights into fundamental
questions about genome organization, the control of gene
expression, growth and development, and evolution.
Rather than inferring genotype from phenotype like
classical geneticists, molecular geneticists try to determine
the impact on the phenotype of details of the genotype.
DNA sequences, long lists of As, Ts, Gs,and Cs, are being
collected in computer data banks that are available to
researchers everywhere via the Internet.
Special software can scan the sequences for the telltale
signs of protein-coding genes, such as start and stop
signals for transcription and translation, and those for RNAsplicing sites.
From these expressed sequence tags (ESTs), researchers
can collect a list of gene candidates
Comparisons of genome sequences confirm very strongly the evolutionary

connections between even distantly related organisms and the relevance of
research on simpler organisms to our understanding of human biology.
For example, yeast has a number of genes close enough to the human versions
that they can substitute for them in a human cell.
Researchers may determine what a human disease gene does by studying its
normal counterpart in yeast.
Bacterial sequences reveal unsuspected metabolic pathways that may have
industrial or medical uses
Studies of genomes have also revealed how genes act together to produce
a functioning organism through an unusually complex network of
interactions among genes and their products.
To determine which genes are transcribed under different situations,
researchers isolate mRNA from particular cells and use the mRNA as
templates to build a cDNA library.
This cDNA can be compared to other collections of DNA by hybridization.
This will reveal which genes are active at different developmental stages, in
different tissues, or in tissues in different states of health.
Automation has allowed scientists to detect

and measure the expression of thousands
of genes at one time using DNA
microarray assays.
Tiny amounts of a large number of singlestranded DNA fragments representing different
genes are fixed on a glass slide in a tightly
spaced array (grid).
The fragments are tested for hybridization with
various samples of fluorescently-labeled cDNA
molecules.
Spots where
any of the cDNA
hybridizes
fluoresce with
an intensity
indicating the
relative amount
of the mRNA
that was in the
tissue.
Concept check
Current estimates are that the human
genome contains about 25,000 genes, but
there is evidence for many more different
human polypeptides. What processes
might explain this discrepancy?
What is the major value of DNA microarray
analysis for studying gene expression?
Why is the genetic variation among people
so much less than it is among individuals
of many other species?
Applications
DNA technology is reshaping medicine
and the pharmaceutical industry
DNA technology offers forensic,
environmental, and agricultural
applications
DNA technology raises important
safety and ethical questions
Chapter 4: evolution
1. Darwinian evolution
2. The origin of species
3. The population evolution
4.1. The Darwinian evolution

The Origin of Species developed two
main points: the occurrence of evolution
and natural selection as its mechanism
Darwinism as a dual meaning.

It refers to evolution as the
explanation for lifes unity and
diversity.
It also refers to the Darwinian
concept of natural selection as the
cause of adaptive evolution.
Central to Darwins view of the

evolution of life is descent with
modification.
In descent with modification, all present
day organisms are related through descent
from unknown ancestors in the past.
Descendents of these ancestors
accumulated diverse modifications or
adaptations that fit them to specific ways of
life and habitats.
Observation from Darwins view of

evolution
Observation #1: All species have such great potential

fertility that their population size would increase
exponentially if all individuals that are born reproduced
successfully.
Observation #2: Populations tend to remain stable in size,
except for seasonal fluctuations.
Observation #3: Environmental resources are limited.

Inference #1: Production of more individuals
than the
environment can support leads to a
struggle for existance
among the individuals of a population, with only a fraction of
the
offspring surviving each generation.
Observation #4: Individuals of a

population vary extensively in their
characteristics; no two individuals are
exactly alike.
Observation #5: Much of this variation

is heritable
Inference #2: Survival in the struggle for existence is not random,

but depends in part on the hereditary constitution of the individuals.
Those individuals whose inherited characteristics best fit

them to their environment are likely to leave more
offspring than less fit individuals.
Inference #3: This unequal ability of individuals to survive and

reproduce will lead to a gradual change in a population, with favorable
characteristics accumulating over the generations
Darwins main ideas can be summarized

in three points.
Natural selection is differential success in
reproduction (unequal ability of individuals to
survive and reproduce).
Natural selection occurs through an interaction
between the environment and the variability
inherent among the individual organisms making
up a population.
The product of natural selection is the adaptation
of populations of organisms to their environment.
Evidences for evolution

The evolutionary changes that
artificially observed
The fossil record
Homology
Biogeography
Example 1. Insecticide resistance
Example 2. Drug resistance of HIV
Patients treated with

drug 3TC 3TC
resistant strain
increase in few
weeks
Fossil record
-The fossil record shows that past organisms differed from presentday organisms
- Many have become extinct
- Fossils also show the evolutionary changes that have occurred
over time in various groups of organisms
- Over longer time scales, fossils document the origins of major
new groups of organisms
- use the radioactive dating techniques to test the age of fossil
The fossil evidences of

evolution in the group of
the trilobites
The transition to life in the sea

Homology
- Analyzing the similarities among different organisms by
anatomical and molecular homology
The mammal forelimb: homologous structure

4.2. origin of species

In 1942 Ernst Mayr enunciated the biological
species concept to divide biological diversity.
A species is a population or group of
populations whose members have the
potential to interbreed with each other in
nature to produce viable, fertile offspring, but
who cannot produce viable, fertile offspring
with members of other species.
A biological species is the largest set of
populations in which genetic exchange is
possible and is genetically isolated from other
populations.
Species are based on interfertility, not physical similarity.

For example, the eastern and western meadowlarks may have
similar shapes and coloration, but differences in song help prevent
interbreeding between the two species.
In contrast, humans have
considerable diversity,
but we all belong to the
same species because of
our capacity to interbreed.
2. Prezygotic and postzygotic barriers

isolate the gene pools of biological
species
Prezygotic barriers impede mating

between species or hinder fertilization of
ova if members of different species
attempt to mate.
These barriers include habitat isolation, behavioral isolation,
temporal isolation, mechanical isolation, and gametic isolation.
Habitat isolation. Two organisms that use different habitats

even in the same geographic area are unlikely to encounter each
other to even attempt mating.
This is exemplified by the two species of garter snakes, in the
genus Thamnophis, that occur in the same areas but because
one lives mainly in water and the other is primarily terrestrial,
they rarely encounter each other.
Behavioral isolation. Many species use elaborate behaviors
unique to a species to attract mates.
Temporal isolation. Two species that breed during different
times of day, different seasons, or different years cannot mix
gametes
Mechanical isolation. Closely related species may attempt to
mate but fail because they are anatomically incompatible and
transfer of sperm is not possible.
Gametic isolation occurs when gametes of two species do not
form a zygote because of incompatibilities preventing fusion or
other mechanisms
If a sperm from one species does fertilize the ovum

of another, postzygotic barriers prevent the
hybrid zygote from developing into a viable, fertile
adult.
These barriers include reduced hybrid viability,
reduced hybrid fertility, and hybrid breakdown.
1. Reduced hybrid viability. Genetic incompatibility between
the two species may abort the development of the hybrid at
some embryonic stage or produce frail offspring.
This is true for the occasional hybrids between frogs in the
genus Rana, which do not complete development and those
that do are frail.
2. Reduced hybrid fertility. Even if the hybrid offspring are
vigorous, the hybrids may be infertile and the hybrid cannot
backbreed with either parental species.
3. Hybrid breakdown. In some cases, first generation
hybrids are viable and fertile.
Reproductive
barriers
can occur before
mating, between
mating and
fertilization, or
after fertilization.
3.
Evolutionary biologists have

proposed several alternative
concepts of species
The ecological species concept defines a species in terms of
its ecological niche, the set of environmental resources that a
species uses and its role in a biological community
The pluralistic species concept may invoke reproductive
isolation or adaptation to an ecological niche, or use both in
maintaining distinctive, cohesive groups of individuals
The morphological species concept, the oldest and still most
practical, defines a species by a unique set of structural
features.
A more recent proposal, the genealogical species concept,
defines a species as a set of organisms with a unique genetic
history - one tip of the branching tree of life.
2. The modes of speciation

Two general modes of speciation are
distinguished by the mechanism by which
gene flow among populations is initially
interrupted.
In allopatric speciation,
geographic separation
of populations restricts
gene flow.
In sympatric speciation, speciation occurs in

geographically overlapping populations when
biological factors, such as chromosomal changes
and nonrandom mating, reduce gene flow.
1. Allopatric speciation: geographic barriers can

lead to the origin of species:
Several geological processes can fragment a population into two or

more isolated populations.
Mountain ranges, glaciers, land bridges, or splintering of

lakes may divide one population into isolated groups.
Alternatively, some individuals may colonize a new,
geographically remote area and become isolated from the
parent population.
For example, mainland organisms that colonized the
Galapagos Islands were isolated from mainland
populations.
How significant a barrier must be to limit gene exchange depends

on the ability of organisms to move about.
A geological feature that is only a minor hindrance to

one species may be an impassible barrier to another.
The valley of the Grand Canyon is a significant barrier
for ground
squirrels which have
speciated on opposite
sides, but birds which
can move freely have
no barrier.
Ring species provide examples of what seem to be various stages in

the gradual divergence of new species from common ancestors.
- In ring species,
populations are
distributed around
some geographic
barrier, with
populations that have
diverged the most in
their evolution
meeting where the
ring closes.
- Some populations
are capable of
interbreeding, others
cannot.
One example of a ring species is the salamander, Ensatina

escholtzii, in Oregon
2. Sympatric speciation: a new species can

originate in the geographic midst of the
parent species
In sympatric speciation, new species arise within the range of the

parent populations.
Here reproductive barriers must evolve between

sympatric populations
In plants, sympatric speciation can result from accidents
during cell division that result in extra sets of
chromosomes, a mutant condition known as
polyploidy.
In animals, it may result from gene-based shifts in
habitat or mate preference.
An individual can have more that two sets of chromosomes from a

single species if a failure in meiosis results in a tetraploid (4n)
individual.
This autopolyploid mutant can reproduce with itself (selfpollination) or with other tetraploids.
It cannot mate
with diploids
from the original population,
because of abnormal meiosis
by the triploid
hybrids.
3. The punctuated equilibrium model has

stimulated research on the tempo of
speciation
Traditional evolutionary trees diagram

the diversification of species as a
gradual divergence over long spans of
time.
These trees assume that big

changes occur as the
accumulation of many small
one, the gradualism model.
In the punctuated equilibrium model, the tempo of speciation

is not constant.
Species undergo most

morphological modifications
when they first bud from
their parent population.
After establishing themselves
as separate species, they
remain static for the vast
majority of their existence.
4.3 the evolution of population
4.3.1. The population genetics

1. The modern evolutionary synthesis integrated
Darwinian selection and Mendelian inheritance
The modern synthesis emphasizes:
(1) the importance of populations as the units of evolution,

(2) the central role of natural selection as the most important
mechanism of evolution, and
(3) the idea of gradualism to explain how large changes can
evolve as an accumulation of small changes over long periods
of time.
While many evolutionary biologists are now challenging some of the

assumptions of the modern synthesis, it shaped most of our ideas
about how populations evolve.
2. A populations gene pool is defined by

its allele frequencies
The total aggregate of genes in a population at any one time is
called the populations gene pool.
It consists of all alleles at all gene loci in all individuals of a

population.
Each locus is represented twice in the genome of a diploid
individual.
Individuals can be homozygous or heterozygous for
these homologous loci.
If all members of a population are homozygous for the
same allele, that allele is said to be fixed.
Often, there are two or more alleles for a gene, each
contributing a relative frequency in the gene pool.
For example, imagine a wildflower population with two flower colors.
The allele for red flower color (R) is completely dominant to the
allele for white flowers (r).
Suppose that in an imaginary population of 500 plants, 20 have white
flowers (homozygous recessive - rr).
The other 480 plants have red flowers.

Some are heterozygotes (Rr), others are homozygous (RR).
Suppose that 320 are RR and 160 are Rr.
Because these plants are diploid, in our population of 500 plants there
are 1,000 copies of the gene for flower color.
The dominant allele (R) accounts for 800 copies (320 x 2 for
RR + 160 x 1 for Rr).
The frequency of the R allele in the gene pool of this population
is 800/1000 = 0.8, or 80%.
The r allele must have a frequency of 1 - 0.8 = 0.2, or 20%.
3. The Hardy-Weinberg Theorem

describes a nonevolving population
The Hardy-Weinberg theorem describes the gene pool of a
nonevolving population.
This theorem states that the frequencies of alleles and genotypes in
a populations gene pool will remain constant over generations
unless acted upon by agents other than Mendelian segregation and
recombination of alleles.
The shuffling of alleles after meiosis and random

fertilization should have no effect on the overall gene pool
of a population.
Example
In our imaginary wildflower population of 500 plants, 80% (0.8) of

the flower color alleles are R and 20% (0.2) are r.
How will meiosis and sexual reproduction affect the frequencies of
the two alleles in the next generation?
We assume that fertilization is completely random and all

male-female mating combinations are equally likely.
Because each gamete has only one allele for flower color, we expect
that a gamete drawn from the gene pool at random has a 0.8 chance
of bearing an R allele and a 0.2 chance of bearing an r allele.
Using the rule of multiplication, we can determine the frequencies of

the three possible genotypes in the next generation.
For the RR genotype, the probability of picking two R

alleles is 0.64 (0.8 x 0.8 = 0.64 or 64%).
For the rr genotype, the probability of picking two r alleles
is 0.04 (0.2 x 0.2 = 0.04 or 4%).
Heterozygous individuals are either Rr or rR, depending on
whether the R allele arrived via sperm or egg.
The probability of ending up with both alleles is 0.32
(0.8 x 0.2 = 0.16 for Rr, 0.2 x 0.8 = 0.16 for rR, and
0.16 + 0.16 = 0.32 or 32% for Rr + rR).
In the wildflower example p is the frequency of red alleles (R) and q of

white alleles (r).
The probability of generating an RR offspring is p2 (an

application of the rule of multiplication).
In our example, p = 0.8 and p2 = 0.64.
The probability of generating an rr offspring is q2.
In our example, q = 0.2 and q2 = 0.04.
The probability of generating Rr offspring is 2pq.
In our example, 2 x 0.8 x 0.2 = 0.32.
The genotype frequencies should add to 1:
p2 + 2pq + q2 = 1
For the wildflowers, 0.64 + 0.32 + 0.04 = 1.

This general formula is the Hardy-Weinberg equation.
Using this formula, we can calculate frequencies of alleles in a gene
pool if we know the frequency of genotypes or the frequency of
genotypes if we know the frequencies of alleles
We can use the Hardy-Weinberg theorem to estimate the percentage

of the human population that carries the allele for a particular
inherited disease, phenyketonuria (PKU) in this case.
About 1 in 10,000 babies born in the United States is born

with PKU, which results in mental retardation and other
problems if left untreated.
The disease is caused by a recessive allele.
Populations at Hardy-Weinberg equilibrium must

satisfy five conditions.
(1) Very large population size. In small populations,
chance fluctuations in the gene pool, genetic drift, can
cause genotype frequencies to change over time.
(2) No migrations. Gene flow, the transfer of alleles due to
the movement of individuals or gametes into or out of our
target population can change the proportions of alleles.
(3) No net mutations. If one allele can mutate into another,
the gene pool will be altered.
(4) Random mating. If individuals pick mates with certain
genotypes, then the mixing of gametes will not be random
and the Hardy-Weinberg equilibrium does not occur.
(5) No natural selection. If there is differential survival or
mating success among genotypes, then the frequencies of
alleles in the next variation will deviate from the frequencies
predicted by the Hardy-Weinberg equation.
4.3.2. Microevolution
1. Microevolution is a generation-togeneration change in a populations
allele frequencies
The Hardy-Weinberg theory provides a baseline against which we
can compare the allele and genotype frequencies of an evolving
population.
We can define microevolution as generation-to-generation change
in a populations frequencies of alleles.
Microevolution occurs even if the frequencies of alleles are

changing for only a single genetic locus in a population
while the others are at equilibrium.
2. The two main causes of microevolution

are drift and natural selection
Four factors can alter the allele frequencies in a population:
genetic drift
natural selection
gene flow
mutation
All represent departures from the conditions required for the HardyWeinberg equilibrium.
Natural selection is the only factor that generally adapts a population to
its environment.
Selection always favors the disporportionate propagation of

favorable traits.
The other three may effect populations in positive, negative, or neutral
ways.
Genetic drift occurs when changes in gene frequencies from one

generation to another occur because of chance events (sampling
errors) that occur when populations are finite in size.
For example, one would not be too surprised if a coin produced
seven heads and three tails in ten tosses, but you would be
surprised if you saw 700 heads and 300 tails in 1000 tosses you expect 500 of each.
The smaller the sample, the greater the chance of deviation
from an idealized result.
Genetic drift at small population sizes often occurs as a result of
two situations: the bottleneck effect or the founder effect.
For example, in a small wildflower population with a stable size of

only ten plants, genetic drift can completely eliminate some alleles.
Natural selection is clearly a violation of the conditions necessary

for the Hardy-Weinberg equilibrium.
The later expects that all individuals in a population have equal
ability to survive and produce viable, fertile offspring.
However, in a population with variable individuals, natural
selection will lead some individuals to leave more offspring than
others.
Selection results in some alleles being passed along to the next
generation in numbers disproportionate to their frequencies in
the present generation.
4.3.3. Genetic Variation, the Substrate

for Natural Selection
1. Genetic variation occurs within and

between populations
Both quantitative and discrete characters contribute to variation
within a population.
Quantitative characters are those that vary along a continuum within
a population.
For example, plant height in our wildflower population

includes short and tall plants and everything in between.
Quantitative variation is usually due to polygenic
inheritance in which the additive effects of two or more
genes influence a single phenotypic character.
Discrete characters, such as flower color, are usually determined by
a single locus with different alleles with distinct impacts on the
phenotype.
Population geneticists measure genetic variation both at the level of whole

genes and at the molecular level of DNA.
Gene diversity measures the average percent of gene loci that are
heterozygous.
In the fruit fly (Drosophila), about 86% of their 13,000 gene

loci are homozygous (fixed).
About 14% (1,800 genes) are heterozygous.
Nucleotide diversity measures the level of difference in nucleotide
sequences (base pair differences) among individuals in a population.
In fruit flies, about 1% of the bases are different between two

individuals.
Two individuals would differ at 1.8 million of the 180 million
nucleotides in the fruit fly genome.
Humans have relatively little genetic variation.
Gene diversity is about 14% in humans.

Nucleotide diversity is only 0.1%.
You and your neighbor have the same nucleotide at 999 out
of every 1,000 nucleotide sites in your DNA.
Geographic variation results from differences in genetic structure either

between populations or between subgroups of a single population that
inhabit different areas.
Often geographic variation results from natural selection that

modifies gene frequencies in response to differences in local
environmental factors.
Alternatively, genetic drift can lead to chance variations among
populations.
Geographic variation can occur on a local scale, within a
population, if the environment is patchy or if dispersal of
individuals is limited, producing subpopulations.
2. Mutation and sexual recombination

generate genetic variation
New alleles originate only by mutation.
Mutations are changes in the nucleotide sequence of DNA.

Mutations of individual genes are rare and random.
Mutations in somatic cells are lost when the individual dies.
Only mutations in cell lines that produce gametes can be
passed along to offspring.
Most point mutations, those affecting a single base of DNA, are

probably harmless.
Mutations that alter the structure of a protein enough to impact its
function are more likely to be harmful than beneficial
Chromosomal mutations, including rearrangements of chromosomes,
affect many genes and are likely to disrupt proper development of
an organism.
Duplications of chromosome segments, whole chromosomes, or sets
of chromosomes are nearly always harmful.
3. Diploidy and balanced polymorphism

preserve variation
The tendency for natural selection to reduce variation is countered
by mechanisms that preserve or restore variation, including diploidy
and balanced polymorphisms.
Diploidy in eukaryotes prevents the elimination of recessive alleles
via selection because they do not impact the phenotype in
heterozygotes.
Even recessive alleles that are unfavorable can persist in a
population through their propagation by heterozygous
individuals.
Balanced polymorphism maintains genetic diversity in a

population via natural selection.
One mechanism in balance polymorphism is heterozygote
advantage.
In some situations individuals that are heterozygous at a
particular locus have greater survivorship and reproductive
success than homozygotes.
In these cases, multiple alleles will be maintained at that locus by
natural selection.
The end

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Biology

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Vietnam National University

Chapter 1. Chemistry of Life

Consist of carbonyl group and multiple hydroxyl

Monosaccharides, particularly glucose, are

Two ring forms of glucose differ in whether the

While polymers built with alpha

consist of four components attached to a central carbon,

R groups are polar hydrophilic.

R groups are charged (ionized) at

Peptide bond formation

Protein structure and function

is determined by a variety of interactions among R groups

Results from the aggregation of two or more polypeptide

Collagen is a fibrous protein of three polypeptides that are

This provides the structural strength for their role in connective

A proteins conformation can change in response to

1.3 Nucleic acid

The nitrogen bases, rings of carbon and

The pentose joined to the nitrogen base is

The addition of a phosphate group creates

Polynucleotides are synthesized by

Functions of nucleic acids

Inheritance is based on replication of the DNA double

With these base-pairing rules, if we know the sequence of bases

DNA and proteins as tape measures of evolution

Because DNA molecules are passed from parents to offspring,

Lipids are highly diverse in form and

Glycerol consists of a three carbon skeleton with a

In a fat, three fatty acids are joined to glycerol by an

Chapter 2. Cell biology

Transport through cellular membrane

2.1 Transport through cellular

2.1.1 Selective permeability

Permeability of a molecule through a membrane depends

Hydrophobic molecules, like hydrocarbons, CO2, and O2, can

This includes small molecules, like water, and larger critical

Membranes are selectively permeable

Some transport proteins have a hydrophilic channel that certain

Each transport protein is specific as to the substances that

2.1.2 Passive transport

Diffusion across a membrane

Diffusion is the tendency of molecules of any substance to

Movements of individual molecules are random.

2.1.3 Active transport

The sodium-potassium pump

2.1.4 Bulk transport

During exocytosis, a transport vesicle

A small area of the palsma membrane sinks inward to

Mechanical work, beating of cilia, contraction of muscle

In most cases, the immediate source of

ATP (adenosine triphosphate) is a type of nucleotide

The bonds between phosphate groups can be broken by

Hydrolysis of the end phosphate group forms adenosine

While the phosphate bonds of ATP are sometimes referred

This molecule is now phosphorylated.

Activation energy is the amount of energy

For some processes, the barrier is not high

Enzyme speed reactions by lowering EA.

Enzymes do not change delta G.

Enzyme are substrate specific

2.2.3 Regulation of enzyme reaction

Glycolysis occurs in the cytoplasm.

During glycolysis, glucose, a six carbon-sugar, is split into

No CO2 is produced during glycolysis.