Documente Academic
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International Univeristy
BIOLOGY
(Guidelines for the preparation of the
entrance exam to MSc program in Biotechnology )
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Contents
Chapter
Chapter
Chapter
Chapter
1. Bio-Chemistry of life
2. Cell biology
3. Genetics
4: Evolution
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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.
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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
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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
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1.1.1 Monosaccharides
Molecular formulas are some multiple of CH2O (glucose
has the formula C6H12O6 )
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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.
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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.
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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
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Glycogen.
The storage form of polysaccharide of
glucose in animal
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Cellulose
a major component of the tough wall of plant
cells
Cellulose is also a polymer of glucose
monomers, but using beta rings
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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
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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?
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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.
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Amino acids
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
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R group is hydrophobic
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Primary structure
unique sequence of amino acids.
slight change in primary structure can
affect a proteins conformation and
ability to function.
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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).
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Tertiary structure
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.
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Quarternary structure
Hemoglobin is a
globular protein
with two copies
of two kinds
of polypeptides
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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?
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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.
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Adenine (A) always pairs with thymine (T) and guanine (G) with
cytosine (C).
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?
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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.
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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.
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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)
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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
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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?
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Guidelines
Focus on the mechanism of processes
Refer to the structure of organelles
that lead to these processes.
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selective permeability
passive transport
active transport
bulk transport
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Proteins can assist and regulate the transport of ions and polar
molecules
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Specific ions and polar molecules can cross the lipid bilayer
by passing through transport proteins that span the
membrane.
For example, the glucose transport protein in the liver will carry
glucose from the blood to the cytoplasm, but not fructose, its
structural isomer
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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?
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2.2 Metabolism
ATP
Enzymes speed reactions by lowering
energy barrier
Regulation of enzyme reaction
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2.2.1 ATP
ATP powers cellular work by coupling
exergonic reactions to endergonic
reactions
A cell does three main kinds of work:
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Structure of ATP
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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
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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.
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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.
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Concept check
How can an activator and an inhibitor
have different effects in an
allosterically regulated enzyme?
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2.3 Respiration
Glycolysis
Citric cycle
Oxydative phosphorylation
Fermentation
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2.3.1 Glycolysis
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Concept check
During the redox reaction in
glycolysis, which molecule acts as
oxidizing agent? The reducing agent?
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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?
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Free-energy change
during electron
transport
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Concept check
What effect would an absence of O2
have on the process shown in figure
9.15?
In the presence of O2
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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.
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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
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Light reaction
An overview of photosynthesis
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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
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Phase 2: Reduction
Net
3 CO2 + 1 RuBP + 9 ATP + 6 NADH 1 G3P
The light reactions regenerate the ATP and NADPH
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Receptors
Three major types: G-proteinlinked receptors, tyrosine-kinase
receptors, and ion-channel
receptors
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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.
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Tyrosine-kinase receptors
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Intracellular receptors
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Steroid hormone
interacting with
an intracellular
receptor
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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
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Nuclear response to
a signal
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Chapter 3. Genetics
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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.
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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.
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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
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Cytokinesis separates
the cytoplasm.
At the end of meiosis,
there are four haploid
daughter cells.
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Three events, unique to meiosis, occur during the first division cycle.
1. During prophase I, homologous chromosomes pair up in a process
called synapsis.
The processes during the second meiotic division are virtually identical
to those of mitosis.
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Concept check
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A Punnett square
predicts the results
of a genetic cross
between individuals
of known genotype
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Mendel laws
1.
2.
3.
4.
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5.
6.
7.
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Concept check
1.
2.
3.
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Sex-linked genes
These sex-linked genes follow the
same pattern of inheritance as the
white-eye locus in Drosophila.
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Hemophilia
Hemophilia is a sex-linked recessive
trait defined by the absence of one or
more clotting factors.
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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.
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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?
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Meiosis
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Mendel laws
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Concept check
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DNA replication
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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
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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.
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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?
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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
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Transcription
can be separated
into three stages:
initiation,
elongation, and
termination.
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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.
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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
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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?
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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.
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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?
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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.
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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
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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.
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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?
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Concept check
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DNA cloning
Restriction fragment analysis
Genome mapping
Genome sequence
Application of DNA technology
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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.
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The process of
cloning a human
gene in a bacterial
plasmid can be
divided into five
steps.
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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?
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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
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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.
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Genome mapping
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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.
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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?
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Genome sequence
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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.
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Spots where
any of the cDNA
hybridizes
fluoresce with
an intensity
indicating the
relative amount
of the mRNA
that was in the
tissue.
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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?
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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
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Chapter 4: evolution
1. Darwinian evolution
2. The origin of species
3. The population evolution
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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
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Homology
- Analyzing the similarities among different organisms by
anatomical and molecular homology
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Reproductive
barriers
can occur before
mating, between
mating and
fertilization, or
after fertilization.
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3.
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- 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.
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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.
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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 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%.
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Example
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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.
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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.
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The end
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