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Viruses called bacteriophages can infect and set in motion a

genetic takeover of bacteria, such as Escherichia coli


Bacteria are prokaryotes with cells much smaller and more simply
organized than those of eukaryotes
Viruses are smaller and simpler than bacteria

Tobacco mosaic disease stunts growth of tobacco


plants and gives their leaves a mosaic coloration
In the late 1800s, researchers hypothesized that
a particle smaller than bacteria caused the
disease
In 1935, Wendell Stanley confirmed this
hypothesis by crystallizing the infectious particle,
now known as tobacco mosaic virus (TMV)

Viruses are not cells


Viruses are very small infectious
particles consisting of nucleic acid
enclosed in a protein coat and, in some
cases, a membranous envelope
Viral genomes may consist of
Double- or single-stranded DNA
Double- or single-stranded RNA

Depending on its type of nucleic acid, a


virus is called a DNA virus or an RNA
virus

Capsomere
of capsid

RNA

A capsid is the
protein shell that
encloses the viral
genome and can have
various structures
18 250 mm

20 nm
Tobacco mosaic virus

Capsomere
DNA

Glycoprotein
7090 nm (diameter)

50 nm
Adenoviruses

Some viruses have structures that have


membranous envelopes that help them
infect hosts
These viral envelopes surround the capsids
of influenza viruses and many other viruses
found in animals
Viral envelopes, which are derived from
the host cells membrane, contain a
combination of viral and host cell molecules

Membranous
envelope
Capsid
RNA

Glycoprotein
80200 nm (diameter)

50 nm
Influenza viruses

Bacteriophages, also called phages, are


viruses that infect bacteria
Phages have an elongated capsid head that
encloses their DNA
A protein tailpiece attaches the phage to
the host and injects the phage DNA inside
Viruses use enzymes, ribosomes, and
small host molecules to synthesize
progeny viruses

Head
Tail
sheath
Tail
fiber

DNA

80 225 nm

50 nm
Bacteriophage T4

VIRUS
Entry into cell and
uncoating of DNA DNA
Capsid
Transcription

Replication
HOST CELL
Viral DNA

mRNA
Viral DNA

Capsid
proteins

Self-assembly of
new virus particles
and their exit from cell

The Lytic Cycle


The lytic cycle is a phage
reproductive cycle that culminates in
the death of the host cell
The lytic cycle produces new phages and
digests the hosts cell wall, releasing the
progeny viruses
A phage that reproduces only by the lytic
cycle is called a virulent phage
Bacteria have defenses against phages,
including restriction enzymes that
recognize and cut up certain phage DNA

Attachment

Phage assembly

Release

Entry of phage DNA


and degradation of
host DNA

Head Tails Tail fibers


Assembly

Synthesis of viral
genomes and proteins

The Lysogenic Cycle


The lysogenic cycle replicates the phage
genome without destroying the host
The viral DNA molecule is incorporated by genetic
recombination into the host cells chromosome
This integrated viral DNA is known as a prophage
Every time the host divides, it copies the phage
DNA and passes the copies to daughter cells
Phages that use both the lytic and lysogenic
cycles are called temperate phages

Phage
DNA

The phage attaches to a


host cell and injects its DNA.

Daughter cell
with prophage
Many cell divisions
produce a large
population of
bacteria infected with
the prophage.

Phage DNA
circularizes

Phage
Bacterial
chromosome

Lytic cycle
The cell lyses, releasing phages.

Occasionally, a prophage
exits the bacterial chromosome,
initiating a lytic cycle.

Lysogenic cycle

Certain factors
determine whether
Lytic cycleorLysogenic cycle
is induced
is entered

The bacterium reproduces


normally, copying the prophage
and transmitting it to daughter cell
Prophage

Phage DNA integrates into the


New phage DNA and proteins are
synthesized and assembled into phages.bacterial chromosomes, becoming a
prophage.

Reproductive Cycles of
Animal
Viruses
Two key variables in classifying viruses
that infect animals:
DNA or RNA?
Single-stranded or double-stranded?

Viral Envelopes
Many viruses that infect animals have a
membranous envelope
Viral glycoproteins on the envelope
bind to specific receptor molecules
on the surface of a host cell

Capsid

Capsid and viral genome


enter cell

RNA

HOST CELL
Envelope (with
glycoproteins)
Viral genome (RNA)
Template
mRNA
ER

Glycoproteins

Capsid
proteins Copy of
genome (RNA)

New virus

RNA as Viral Genetic


Material
The broadest variety
of RNA genomes is

found in viruses that infect animals


Retroviruses use reverse transcriptase
to copy their RNA genome into DNA
HIV is the retrovirus that causes AIDS

Glycoprotein

Viral envelope
Capsid

Reverse
transcriptase

RNA
(two identical
strands)

The viral DNA that is integrated into the


host genome is called a provirus
Unlike a prophage, a provirus remains a
permanent resident of the host cell
The hosts RNA polymerase transcribes
the proviral DNA into RNA molecules
The RNA molecules function both as mRNA
for synthesis of viral proteins and as
genomes for new virus particles released
from the cell

HIV

Membrane of
white blood cell

HOST CELL
Reverse
transcription

Viral RNA

0.25 m

HIV entering a cell

RNA-DNA
hybrid
DNA
NUCLEUS
Chromosomal
DNA

RNA genome
for the
next viral
generation

New HIV leaving a cell

mRNA

Provirus

Viroids and Prions: The


Simplest Infectious Agents
Viroids are circular RNA molecules that
infect plants and disrupt their growth
Prions are slow-acting, virtually
indestructible infectious proteins that
cause brain diseases in mammals
Prions propagate by converting normal
proteins into the prion version

Prion

Original
prion

Many prions
Normal
protein

New
prion

The Bacterial Genome


and Its Replication
The bacterial chromosome is usually a circular
DNA molecule with few associated proteins
Many bacteria also have plasmids, smaller
circular DNA molecules that can replicate
independently of the chromosome
Bacterial cells divide by binary fission, which
is preceded by replication of the chromosome

Mutation and Genetic


Recombination as Sources of
Genetic Variation

Since bacteria can reproduce rapidly, new


mutations quickly increase genetic diversity
More genetic diversity arises by
recombination of DNA from two different
bacterial cells
Three processes bring bacterial DNA from
different individuals together:
Transformation
Transduction
Conjugation

Transformation and
Transduction
Transformation is the alteration of a

bacterial cells genotype and phenotype


by the uptake of naked, foreign DNA
from the surrounding environment
For example, harmless Streptococcus
pneumoniae bacteria can be
transformed to pneumonia-causing cells
In the process known as transduction,
phages carry bacterial genes from one
host cell to another

Phage DNA
A+ B+

A+ B+
Donor
cell

A+
Crossing
over
A+
A B
Recipient
cell

A+ B
Recombinant cell

Conjugation and
Plasmids

Conjugation is the direct transfer of


genetic material between bacterial
cells that are temporarily joined
The transfer is one-way: One cell
(male) donates DNA, and its mate
(female) receives the genes

Sex pilus

5 m

Mixture

Mutant
strain
arg+ trp

Mutant
strain
arg trp+

Mixture
Mutant
strain
arg+ trp

Mutant
strain
arg trp+
No
colonies
(control)

Colonies
grew

No
colonies
(control)

The F Plasmid and


Conjugation

Cells containing the F plasmid, designated F+


cells (fertile), function as DNA donors during
conjugation
F+ cells transfer DNA to an F recipient cell
Chromosomal genes can be transferred during
conjugation when the donor cells F factor is
integrated into the chromosome
A cell with a built-in F factor is called an Hfr
cell
The F factor of an Hfr (high frequency of
recombination) cell brings some
chromosomal DNA along when transferred to
an F cell

F plasmid

Bacterial chromosome

F+ cell
Mating
bridge
F cell

F+ cell
F+ cell

Bacterial
chromosome
Conjunction and transfer of an F plasmid from and F+ donor to an F recip

Hfr cell

F+ cell
F factor
Hfr cell
F cell

Temporary
Recombinant F
partial
bacterium
diploid
Conjugation and transfer of part of the bacterial chromosome from an
Hfr donor to an F recipient, resulting in recombination

R plasmids and Antibiotic


Resistance
R plasmids confer
resistance to various

antibiotics
When a bacterial population is exposed to an
antibiotic, individuals with the R plasmid will
survive and increase in the overall population

Transposition of Genetic
The DNA of a Elements
cell can also undergo

recombination due to movement of


transposable elements within the
cells genome
Transposable elements, often called
jumping genes, contribute to genetic

Insertion Sequences
The simplest transposable elements, called
insertion sequences, exist only in
bacteria
An insertion sequence has a single gene for
transposase, an enzyme catalyzing
movement of the insertion sequence from
one site to another within the genome

Insertion sequence

5
3

3
5
Inverted
repeat

Transposase gene

Inverted
repeat

Transposons
Transposable elements called transposons are
longer and more complex than insertion
sequences
In addition to DNA required for
transposition, transposons have extra
genes that go along for the ride, such as
genes for antibiotic resistance

Transposon
Insertion
sequence

Antibiotic
resistance gene

Insertion
sequence

5
3

3
5
Inverted repeat

Transposase gene

Operons: The Basic


Concept
In bacteria, genes are often clustered
into operons, composed of
An operator, an on-off switch
A promoter
Genes for metabolic enzymes

An operon can be switched off by a


protein called a repressor
A corepressor is a small molecule
that cooperates with a repressor to
switch an operon off

trp operon
Promoter

Promoter
DNA

mRNA

trpE

trpR

Regulatory
gene

trpD

trpC

trpB

trpA

Operator
Stop codon
RNA
Start codon
polymerase
mRNA 5

Protein

Genes of operon

E
Inactive
repressor

Polypeptides that make up


enzymes for tryptophan synthesis

Tryptophan absent, repressor inactive, operon on

DNA

mRNA

Active
repressor

Protein

Tryptophan
(corepressor)
Tryptophan present, repressor active, operon off

DNA
No RNA made

mRNA

Active
repressor

Protein

Tryptophan
(corepressor)
Tryptophan present, repressor active, operon off

Repressible and Inducible


Operons: Two Types of
Negative Gene Regulation

A repressible operon is one that is


usually on; binding of a repressor to the
operator shuts off transcription
The trp operon is a repressible operon
An inducible operon is one that is usually
off; a molecule called an inducer
inactivates the repressor and turns on
transcription
The classic example of an inducible
operon is the lac operon, which contains
genes coding for enzymes in hydrolysis
and metabolism of lactose

Promoter

Regulatory
gene

Operator
lacl

DNA

lacZ
No
RNA
made

3
mRNA
5

Protein

RNA
polymerase

Active
repressor

Lactose absent, repressor active, operon off

lac operon
DNA

lacl

mRNA
5

lacY

-Galactosidase

Permease

lacA

RNA
3 polymerase
mRNA 5

Protein
Allolactose
(inducer)

lacZ

Inactive
repressor

Lactose present, repressor inactive, operon on

Transacetylase

Inducible enzymes usually function in


catabolic pathways
Repressible enzymes usually function
in anabolic pathways
Regulation of the trp and lac operons
involves negative control of genes because
operons are switched off by the active form
of the repressor

Positive Gene Regulation


Some operons are also subject to positive
control through a stimulatory activator
protein, such as catabolite activator
protein (CAP)
When glucose (a preferred food source of E.
coli ) is scarce, the lac operon is activated
by the binding of CAP
When glucose levels increase, CAP detaches
from the lac operon, turning it of

Promoter

DNA

lacl

lacZ

CAP-binding site
cAMP

Inactive
CAP

RNA
Operator
polymerase
Active can bind
and transcribe
CAP
Inactive lac
repressor

Lactose present, glucose scarce (cAMP level high): abunda


mRNA synthesized

Promoter
DNA

lacl

lacZ

CAP-binding site

Operator

Inactive
CAP

RNA
polymerase
cant bind

Inactive lac
repressor

Lactose present, glucose present (cAMP level low): littl


mRNA synthesized

Two features of eukaryotic genomes are a


major information-processing challenge:
First, the typical eukaryotic genome is much
larger than that of a prokaryotic cell
Second, cell specialization limits the
expression of many genes to specific cells

The DNA-protein complex, called


chromatin, is ordered into higher
structural levels than the DNA-protein
complex in prokaryotes

Nucleosomes, or Beads on
a String

Proteins called histones are responsible for


the first level of DNA packing in chromatin
The association of DNA and histones seems
to remain intact throughout the cell cycle
In electron micrographs, unfolded chromatin
has the appearance of beads on a string
Each bead is a nucleosome, the basic
unit of DNA packing

2 nm
DNA double helix
Histones

Histone
tails
Histone H1 10 nm

Linker DNA
(string)

Nucleosome
(bead)

Nucleosomes (10-nm fiber)

30 nm

Nucleosome
30-nm
fiber

Protein scaffold
Loops
300 nm
Looped domains (300-nm
fiber)

Scaffold

700 nm

1,400 nm

Metaphase
chromosome

Differential Gene
Expression

Differences between cell types result from


differential gene expression, the
expression of different genes by cells within
the same genome
In each type of differentiated cell, a unique
subset of genes is expressed
Many key stages of gene expression can be
regulated in eukaryotic cells

Signal

NUCLEUS
Chromatin

DNA

Gene available
for transcription
Gene
Transcription

RNA

Exon
Primary transcript
Intro
RNA processing
Tail

Cap

mRNA in nucleus
Transport to cytoplasm

CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA

Translation

Polypeptide
Cleavage
Chemical modification
Transport to cellular
destination
Active protein
Degradation of protein
Degraded protein

Regulation of Chromatin
Structure

Genes within highly packed heterochromatin


are usually not expressed
Chemical modifications to histones and DNA
of chromatin influence both chromatin
structure and gene expression

Histone Modification
In histone acetylation, acetyl groups are attached
to positively charged lysines in histone tails
This process seems to loosen chromatin structure,
thereby promoting the initiation of
transcription

Histone
tails

DNA
double helix

Amino acids
available
for chemical
modification

Histone tails protrude outward from a nucleosome

Unacetylated histones

Acetylated histones

Acetylation of histone tails promotes loose chromatin


structure that permits transcription

DNA Methylation
DNA methylation, the addition of methyl groups
to certain bases in DNA, is associated with reduced
transcription in some species
In some species, DNA methylation causes longterm inactivation of genes in cellular
differentiation
In genomic imprinting, methylation turns of either
the maternal or paternal alleles of certain genes at
the start of development lions, tigers, ligers?

The Roles of
Transcription Factors

To initiate transcription, eukaryotic RNA


polymerase requires the assistance of
proteins called transcription factors
General transcription factors are essential for
the transcription of all protein-coding genes
In eukaryotes, high levels of transcription of
particular genes depend on control elements
interacting with specific transcription factors

Enhancers and Specific


Transcription Factors
Proximal control elements are located close
to the promoter
Distal control elements, groups of which are
called enhancers, may be far away from a
gene or even in an intron
An activator is a protein that binds to an
enhancer and stimulates transcription of a
gene

Enhancer
Proximal
(distal control elements) control elements
Exon

Intron

Exon

Poly-A signal
Termination
sequence
region
Intron Exon

DNA
Upstream

Promoter
Primary RNA
transcript 5
(pre-mRNA)

Exon

Intron

Intron RNA

Downstream
Transcription
Poly-A signal
Exon
IntronExon
Cleaved 3 end
of primary
transcript
RNA processing:
Cap and tail added;
introns excised and
exons spliced together

Coding segment
mRNA

3
5 Cap 5 UTR
(untranslated
region)

Start Stop
codon codon

3 UTR Poly-A
(untranslatedtail
region)

Distal control
element

Activators

Promoter
Gene

DNA
Enhancer

TATA
box
General
transcription
factors
DNA-bending
protein
Group of
mediator proteins

RNA
polymerase II

RNA
polymerase II

Transcription
Initiation complex

RNA synthesis

Some transcription factors


function as repressors, inhibiting
expression of a particular gene
Some activators and repressors act
indirectly by influencing
chromatin structure

Liver cell
nucleus

Available
activators

Lens cell
nucleus

Available
activators

Enhancer Promoter

Control
elements

Albumin
gene

Crystallin
gene

Albumin
gene not
expressed

Albumin
gene
expressed

Crystallin gene
not expressed
Liver cell

Crystallin gene
expressed
Lens cell

In alternative RNA splicing, different


mRNA molecules are produced from the
same primary transcript, depending on
which RNA segments are treated as
exons and which as introns
Exons

DNA

Primary
RNA
transcript
RNA splicing
mRNA

or

mRNA Degradation
The life span of mRNA molecules in the
cytoplasm is a key to determining the protein
synthesis
The mRNA life span is determined in part by
sequences in the leader and trailer regions

RNA interference by single-stranded


microRNAs (miRNAs) can lead to
degradation of an mRNA or block its
translation
The phenomenon of inhibition of gene
expression by RNA molecules is called

Protein
complex

Degradation of mRNA

Dicer
OR
miRNA
Target mRNA

Hydrogen
bond

Blockage of translation

Protein Processing and


Degradation
After translation, various types of protein
processing, including cleavage and the
addition of chemical groups, are subject to
control
Proteasomes are giant protein complexes
that bind protein molecules and degrade them

Ubiquitin
Proteasome

Protein to
be degraded

Proteasome
and ubiquitin
to be recycled

Ubiquitinated
protein
Protein entering a
proteasome

Protein
fragments
(peptides)

Types of Genes Associated


with Cancer

Genes that normally regulate cell growth


and division during the cell cycle include:
Genes for growth factors
Their receptors
Intracellular molecules of signaling
pathways

Mutations altering any of these genes in


somatic cells can lead to cancer

Oncogenes and ProtoOncogenes

Oncogenes are cancer-causing genes


Proto-oncogenes are normal cellular
genes that code for proteins that
stimulate normal cell growth and division
A DNA change that makes a protooncogene excessively active converts it
to an oncogene, which may promote
excessive cell division and cancer

Proto-oncogene
DNA

Translocation or transposition:
gene moved to new locus,
under new controls

Gene amplification:
multiple copies of the gene

New
promoter

Normal growth-stimulating
protein in excess

Point mutation
within a control
element

Oncogene

Normal growth-stimulating
protein in excess

Point mutation
within the gene

Oncogene

Normal growth-stimulating
Hyperactive or
protein in excess
degradationresistant protein

Tumor-Suppressor Genes
Tumor-suppressor genes encode proteins
that inhibit abnormal cell division
Any decrease in the normal activity of a
tumor-suppressor protein may contribute to
cancer

Interference with Normal


Cell-Signaling Pathways
Many proto-oncogenes and tumor
suppressor genes encode
components of growth-stimulating and
growth-inhibiting pathways, respectively

The Ras protein, encoded by the ras


gene, is a G protein that relays a
signal from a growth factor receptor to
a cascade of protein kinases
Many ras oncogenes have a
mutation that leads to a hyperactive
Ras protein that issues signals on its

The p53 gene,guardian angel of the


genome encodes a tumor-suppressor
protein that is a specific transcription
factor that promotes synthesis of cell
cycleinhibiting proteins
Mutations that knock out the p53 gene can
lead to excessive cell growth and cancer

Increased cell division, possibly


leading to cancer, can result if the
cell cycle is over stimulated or not
inhibited when it normally would
be

MUTATION

Growth
factor

Hyperactive
Ras protein
(product of
oncogene)
issues signals
on its own

G protein
Cell cycle-stimulating
pathway

Receptor

Protein kinases
(phosphorylation
cascade)

NUCLEUS

Transcription
factor (activator)
DNA

Gene expression
Protein that
stimulates
the cell cycle

Cell cycle-inhibiting
pathway

Protein kinases

MUTATION
Defective or
missing
transcription
factor, such as
p53, cannot
activate
transcription

Active
form
of p53

UV
light

DNA damage
in genome DNA

Protein that
inhibits
the cell cycle

Effects of
mutations

EFFECTS OF MUTATIONS
Protein overexpressed

Protein absent

Cell cycle overstimulateIncreased cell


division

Cell cycle not


inhibited

Individuals who inherit a mutant oncogene


or tumor-suppressor allele have an
increased risk of developing certain types
of cancer (Inherited Predisposition to
Cancer)
Colon

Activation of
ras oncogene

Loss of
tumorsuppressor
Colon wallgene APC (or
other)

Normal colon
epithelial cells

Small benign
growth (polyp)

Loss of
tumorsuppressor
gene DCC

Loss of
tumorsuppressor
gene p53

Additional
mutations
Larger benign
growth (adenoma)

Malignant tumor
(carcinoma)

Transposable Elements
and Related Sequences
The first evidence for wandering DNA segments
came from geneticist Barbara McClintocks
breeding experiments with Indian corn
McClintock identified changes in the color of corn
kernels that made sense only by postulating that
some genetic elements move from other
genome locations into the genes for kernel color

Movement of Transposons
and Retrotransposons
Eukaryotic transposable elements are
of two types:
Transposons, which move within a
genome by means of a DNA intermediate
Retrotransposons, which move by
means of an RNA intermediate

Transposon
DNA of genome
Transposon
is copied

New copy of
transposon

Insertion

Mobile transposon
Transposon movement (copy-and-paste mechanism)

Retrotransposon

New copy of
retrotransposon

DNA of genome
RNA
Reverse
transcriptase

Retrotransposon movement

Insertion

Genes and Multigene


Families

Most eukaryotic genes are present in


one copy per haploid set of
chromosomes
The rest of the genome occurs in
multigene families, collections of
identical
or very
similar
genes
Globin
gene
family
clusters
also
include pseudogenes, nonfunctional
nucleotide sequences that are similar
to the functional genes

DNA

RNA transcripts

Non-transcribed
spacer

Transcription unit

DNA
18S

5.8S

28S

rRNA
28S

5.8S

18S
Part of the ribosomal RNA gene family

-Globin

Heme

Hemoglobin
-Globin
-Globin gene family

-Globin gene family


Chromosome 11

Chromosome 16

Embryo

1 2 1

Fetus
and adult

Embryo Fetus

Adult

The human -globin and -globin gene families

DNA technology has revolutionized


biotechnology, the manipulation of organisms
or their genetic components to make useful
products
An example of DNA technology is the
microarray, a measurement of gene expression
of thousands of different genes

DNA Cloning and Its


Applications

To work directly with specific genes, scientists


prepare gene-sized pieces of DNA in identical
copies, a process called gene cloning
Most methods for cloning pieces of DNA in the
laboratory share general features, such as the
use of bacteria and their plasmids
Cloned genes are useful for making copies of
a particular gene and producing a gene
product

Bacterium

Cell containing gene


of interest
Gene inserted into
plasmid

Bacterial
Plasmid
chromosome
Recombinant
DNA (plasmid)

Gene of
interest
Plasmid put into
bacterial cell

DNA of
chromosome

Recombinant
bacterium
Host cell grown in culture
to form a clone of cells
containing the cloned
gene of interest
Gene of
interest

Protein expressed
by gene of interest

Copies of gene

Basic
research
on gene

Protein harvested
Basic research and
various applications

Basic
research
on protein

Gene for pest


Gene used to alter Protein dissolves Human growth horresistance inserted
bacteria for cleaning
blood clots in heart
mone treats stunted
into plants
up toxic waste
attack therapy
growth

Using Restriction Enzymes


to Make Recombinant DNA
Bacterial restriction enzymes cut DNA
molecules at DNA sequences called
restriction sites usually makes many cuts,
yielding restriction fragments
The most useful restriction enzymes cut DNA
in a staggered way, producing fragments with
sticky ends that bond with
complementary sticky ends of other
fragments
DNA ligase is an enzyme that seals the
bonds between the sticky ends restriction
fragments

Restriction site
DNA 5
3

3
5

Restriction enzyme cuts


the sugar-phosphate
backbones at each arrow.

Sticky end

DNA fragment from another


source is added. Base pairing Fragment from different
of sticky ends produces
DNA molecule cut by the
various combinations.
same restriction enzyme

One possible combination


DNA ligase
seals the strands.

Recombinant DNA molecule

Bacterial cell
Isolate plasmid DNA
and human DNA.

lacZ gene
Human
(lactose
cell
breakdown)
Restriction
site

ampR gene Bacterial


(ampicillin plasmid
resistance)

Gene of
interest
Sticky
ends

Cut both DNA samples with


the same restriction enzyme.

Human DNA
fragments

Mix the DNAs; they join by base pairing.


The products are recombinant plasmids
and many nonrecombinant plasmids.
Recombinant DNA plasmids
Introduce the DNA into bacterial cells
that have a mutation in their own lacZ
gene.
Recombinant
bacteria
Plate the bacteria on agar
containing ampicillin and X-gal.
Incubate until colonies grow.

Colony carrying nonrecombinant plasmid


with intact lacZ gene

Colony carrying
recombinant
plasmid with
disrupted lacZ gene

Bacterial
clone

Amplifying DNA in Vitro: The


Polymerase Chain Reaction
(PCR)

The polymerase chain reaction, PCR, can


produce many copies of a specific target
segment of DNA
A three-step cycleheating, cooling, and
replicationbrings about a chain reaction
that produces an exponentially growing
population of identical DNA molecules

3
Target
sequence

Genomic DNA

Cycle 1
yields
2
molecules

5
Denaturation:
Heat briefly
to separate DNA
strands

Annealing:
Cool to allow
primers to form
hydrogen bonds
with ends of
target sequence

Primers

Extension:
DNA polymerase
adds nucleotides to
the 3 end of each
New
primer
nucleotides

Cycle 2
yields
4
molecules

Cycle 3
yields 8
molecules;
2 molecules
(in white boxes)
match target
sequence

Gel Electrophoresis
One indirect method of rapidly analyzing and
comparing genomes is gel electrophoresis
This technique uses a gel as a molecular sieve
to separate nuclei acids or proteins by size

In restriction fragment analysis,


DNA fragments produced by restriction
enzyme digestion of a DNA molecule
are sorted by gel electrophoresis
Restriction fragment analysis is useful
for comparing two different DNA
molecules, such as two alleles for a

Cathode

Power
source

Mixture
of DNA
molecules
of different sizes

Shorter
molecules
Gel
Glass
plates

Anode

Longer
molecules

Normal -globin allele

175 bp
Ddel

201 bp

Ddel

Large fragment

Ddel

Ddel

Sickle-cell mutant -globin allele

376 bp
Ddel

Large fragment
Ddel

Ddel

Ddel restriction sites in normal and sickle-cell alleles of


-globin gene
Normal Sickle-cell
allele
allele

Large
fragment

201 bp
175 bp

376 bp

Electrophoresis of restriction fragments from normal


and sickle-cell alleles

Medical Applications
One benefit of DNA technology is
identification of human genes in which
mutation plays a role in genetic diseases
Scientists can diagnose many human
genetic disorders by using PCR and
primers corresponding to cloned disease
genes, then sequencing the amplified
product to look for the disease-causing
mutation
Even when a disease gene has not been
cloned, presence of an abnormal allele
can be diagnosed if a closely linked RFLP

RFLP marker
DNA

Restriction
sites

Disease-causing
allele

Normal allele

Human Gene Therapy


Gene therapy is the alteration of an afflicted
individuals genes
Gene therapy holds great potential for treating
disorders traceable to a single defective gene
Vectors are used for delivery of genes into
cells
Gene therapy raises ethical questions, such as
whether human germ-line cells should be
treated to correct the defect in future
generations

Cloned gene
Insert RNA version of normal allele
into retrovirus.

Viral RNA

Retrovirus
capsid

Let retrovirus infect bone marrow cells


that have been removed from the
patient and cultured.

Viral DNA carrying the normal


allele inserts into chromosome.
Bone
marrow
cell from
patient

Inject engineered
cells into patient.

Bone
marrow

Pharmaceutical Products
Some pharmaceutical applications of
DNA technology:
Large-scale production of human hormones
and other proteins with therapeutic uses
Production of safer vaccines

Forensic Evidence
DNA fingerprints obtained by analysis
of tissue or body fluids can provide
evidence in criminal and paternity cases
A DNA fingerprint is a specific pattern of
bands of RFLP markers on a gel
The probability that two people who are
not identical twins have the same DNA
fingerprint is very small
Exact probability depends on the number
of markers and their frequency in the
population

DefendantsBlood from defendants


blood (D)
clothes

Victims
blood (V)

Animations and Videos


Processing of Gene Information
Control of Gene Expression in Eukaryote
s
RNA Interface
Regulatory Proteins Regulation by
Repression
Tryptophan Repressor
Lac Operon
Bozeman - Lac Operon
The Lac Operon in E. coli
Bozeman - Gene Regulation

Animations and Videos

Bozeman - Restriction Enzyme


DNA Transformation 1
DNA Transformation 2
Conjugation: Transfer of Chromosomal
DNA
Conjugation - Transfer of F Plasmid
Integration and Excision of a Plasmid
Transduction (Generalized)
Bacterial Transformation
Lamda Phage Replication Cycle

Animations and Videos

Early Genetic Engineering Experiment


Genetic Engineering
Cloning
Steps in Cloning a Gene
Tutorial - Human Cloning
Human Cloning - Reproductive Cloning
Human Cloning - Therapeutic Cloning
Genetic Engineering to Produce Insulin
Polymerase Chain Reaction

Animations and Videos

PCR 1
PCR 2
Gel Electrophoresis 1
Gel Electrophoresis 2
DNA Fingerprinting
Construction of a DNA Library
DNA Restriction Enzymes
Restriction Enzyme Digestion of DNA
Restriction Endonucleases

Animations and Videos

Principles of Biotechnology
Applications of Biotechnology
Constructing Vaccines
DNA Probe (DNA Hybridization)
Restriction Length Ploymorphisms
cDNA
Southern Blot
Entry of Virus into Host Cell
Replication Cycle of a Retrovirus

Animations and Videos


HIV Replication
Mechanism for Releasing Enveloped
Viruses
Treatment of HIV
Prions Disease
How Prions Arise
Stem Cells
Embryonic Stem Cells
Human Embryonic Stem Cells
Human Stem Cells

Animations and Videos

Microarray
Sanger Sequencing
DNA Fingerprinting
RNA Interface
miRNA
Dicer
DNA Microarrays
Bozeman - DNA Fingerprinting
Bozeman - Viral Replication

Animations and Videos

Genes into Plants Using the Ti-plasmid


Highput Through Sequencing
Sequencing the Genome
Cycle Sequencing
Bozeman - Effects of Change in Pathways
Chapter Quiz Questions 1
Chapter Quiz Questions 2
Chapter Quiz Questions 3
Chapter Quiz Questions 4

What does the operon


model attempt to explain?

the coordinated control of gene


expression
in bacteria
bacterial resistance to antibiotics
how genes move between homologous
regions of DNA
the mechanism of viral attachment to a
host cell
horizontal transmission of plant viruses

What does the operon


model attempt to explain?

the coordinated control of gene


expression
in bacteria
bacterial resistance to antibiotics
how genes move between homologous
regions of DNA
the mechanism of viral attachment to a
host cell
horizontal transmission of plant viruses

When tryptophan (an amino acid) is present


in the external medium, the bacterium
brings in the tryptophan and does not need
to make this amino acid. Which of the
The repressor
is active
and
to the
following
is true when
there
is binds
no tryptophan
in operator.
the medium?
The repressor is inactive, and RNA
polymerase moves through the operator.
The operator is bound, and mRNA is made.
Genes are inactive.
The corepressor binds to the repressor.

When tryptophan (an amino acid) is present


in the external medium, the bacterium
brings in the tryptophan and does not need
to make this amino acid. Which of the
The repressor
active
andisbinds
to the
following
is true is
when
there
no tryptophan
in operator.
the medium?
The repressor is inactive, and RNA
polymerase moves through the
operator.
The operator is bound, and mRNA is made.
Genes are inactive.
The corepressor binds to the repressor.

Each of a group of bacterial cells has a


mutation in its lac operon. Which of
the following will make it impossible
for
the cell to
lactose?
mutation
in metabolize
lac (-galactosidase
gene)
mutation in lac (cannot bind to
operator)
mutation in operator (cannot bind to
repressor)
mutation in lac (cannot bind to
inducer)

Each of a group of bacterial cells has a


mutation in its lac operon. Which of
the following will make it impossible
for the cell to metabolize lactose?
mutation in lac (-galactosidase
gene)
mutation in lac (cannot bind to
operator)
mutation in operator (cannot bind to
repressor)
mutation in lac (cannot bind to
inducer)

Which element(s) from the


following list constitute(s) a
bacterial operon?

repressor gene
promoter
inducer
repressor protein
all of the above

Which element(s) from the


following list constitute(s) a
bacterial operon?

repressor gene
promoter
inducer
repressor protein
all of the above

Which of the following statements


about specific transcription factors is
false?
The binding of specific transcription factors to the control
elements of enhancers influences the rate of gene
expression.
Specific transcription factors include activators and
repressors.
MyoD is one.
Some act indirectly by affecting chromatin structure.
Interaction of specific transcription factors and RNA
polymerase II with a promoter leads to a low rate of
initiation and production of a few RNA transcripts.

Which of the following statements


about specific transcription factors is
false?
The binding of specific transcription factors to the control
elements of enhancers influences the rate of gene
expression.
Specific transcription factors include activators and
repressors.
MyoD is one.
Some act indirectly by affecting chromatin structure.
Interaction of specific transcription factors and RNA
polymerase II with a promoter leads to a low rate of
initiation and production of a few RNA transcripts.

Approximately what proportion


of the DNA in the human
genome codes for proteins or
functional
83%
RNA?

46%
32%
13%
1.5%

Approximately what proportion


of the DNA in the human
genome codes for proteins or
functional
RNA?
83%

46%
32%
13%
1.5%

A specific gene is known to code


for three different but related
proteins. This could be due to
which
of themRNA
following?
premature
degradation

alternative RNA splicing


use of different enhancers
protein degradation
differential transport

A specific gene is known to code


for three different but related
proteins. This could be due to
premature
degradation
which
of themRNA
following?

alternative RNA splicing


use of different enhancers
protein degradation
differential transport

RNA is cut up into small 22-nucleotide


fragments to regulate another target
mRNA. Which of the following is/are
The target mRNA is degraded, and its protein is
true?
not made.
The RNA fragments enhance protein synthesis by
the mRNA.
The RNA fragments bind the ribosome to enhance
use of the mRNA and protein synthesis.
The target mRNA is blocked from being used in
translation.
The RNA fragments act on the ribosome to shut
down translation of all mRNAs.

RNA is cut up into small 22-nucleotide


fragments to regulate another target
mRNA. Which of the following is/are
The target mRNA is degraded, and its
true?

protein is
not made.
The RNA fragments enhance protein synthesis by
the mRNA.
The RNA fragments bind the ribosome to enhance
use of the mRNA and protein synthesis.
The target mRNA is blocked from being used
in translation.
The RNA fragments act on the ribosome to shut
down translation of all mRNAs.

Even though the two cells have numerous


transcription factors and many are present
in both cells, the lens cell makes the
crystallin protein (not albumin), whereas the
liver cell makes albumin (not crystallin).
Specific
transcription
made
in cell
the cell
Which
of the
followingfactors
explains
this
determine which genes are expressed.
specificity?
At fertilization, specific cells are destined for
certain functions.
The activators needed for expression of the
crystallin gene are present in all cells.
The promoters are different for the different
genes.

Even though the two cells have numerous


transcription factors and many are present
in both cells, the lens cell makes the
crystallin protein (not albumin), whereas the
liver cell makes albumin (not crystallin).
Specific
transcription
factors made
in the cell
Which
of the
following explains
this cell
determine which genes are expressed.
specificity?

At fertilization, specific cells are destined for


certain functions.
The activators needed for expression of the
crystallin gene are present in all cells.
The promoters are different for the different genes.

Differential gene expression


(different genes turned on in
different cells) leads to different
tissues developing in the embryo.
Which of the following is not a
cytoplasmic determinants
cause of differential gene
expression?
induction
the environment around a particular
cell
corepressor proteins

Differential gene expression


(different genes turned on in
different cells) leads to different
tissues developing in the embryo.
Which
cytoplasmic
determinants
of the following
is not a
cause
of differential gene
induction
expression?
the environment around a particular
cell
corepressor proteins

Initially, cytoplasmic determinants


are localized in one part of a
zygote and could be which of the
following? (Choose more than one
gene
answer.)

mRNA
transcription factor
ribosome
myoblast

Initially, cytoplasmic determinants


are localized in one part of a
zygote and could be which of the
following?
(Choose more than one
gene
answer.)
mRNA
transcription factor
ribosome
myoblast

Scientists showed that bicoid mRNA, and


then its Bicoid protein, is normally found in
highest concentrations in the flys anterior.
What would happen if Bicoid were injected
at
the posterior
end? would form at both
Anterior
structures
ends.
Posterior structures would form at both
ends.
The embryo would have no dorsal-ventral
axis.
Bicoid mRNA wouldnt be translated into
protein.

Scientists showed that bicoid mRNA, and


then its Bicoid protein, is normally found in
highest concentrations in the flys anterior.
What would happen if Bicoid were injected
at
the posterior
end?
Anterior
structures
would form at both
ends.
Posterior structures would form at both
ends.
The embryo would have no dorsal-ventral
axis.
Bicoid mRNA wouldnt be translated into
protein.

Mutations in _______ genes caused


the development of legs in the
place of antennae.

homeotic
embryonic lethal
Wild type
myoD
Ras
Eye
wild-type

Mutant

Mutations in _______ genes caused


the development of legs in the
place of antennae.

homeotic
embryonic lethal
Wild type
myoD
Ras
Eye
wild-type

Mutant

The shape of an organ, the


number of brain cells in an
embryonic brain, the removal of
mutated cells, and the webbing
cells
certain
cells becoming
larger
between
the toesmuch
of a human
embryo
are all
regulated by which
certain cells
shrinking
of
the following?
certain
cells dying
formation of embryonic cells
concentration of Bicoid protein

The shape of an organ, the


number of brain cells in an
embryonic brain, the removal of
mutated cells, and the webbing
cells between the toes of a human
certain cells becoming much larger
embryo are all regulated by which
certain cells shrinking
of the following?
certain cells dying
formation of embryonic cells
concentration of Bicoid protein

Which of the following would not


typically cause a proto-oncogene
to become an oncogene?

gene suppression
translocation
amplification
point mutation
retroviral activation

Which of the following would not


typically cause a proto-oncogene
to become an oncogene?

gene suppression
translocation
amplification
point mutation
retroviral activation

Which of the following statements


about the APC gene is false?
It is a tumor-suppressor gene.
It is mutated in 60% of colorectal
cancers.
It regulates cell migration and adhesion.
It may be deleted in colon cancer.
Mutations in one allele are enough to
lose the
genes function.

Which of the following statements


about the APC gene is false?
It is a tumor-suppressor gene.
It is mutated in 60% of colorectal
cancers.
It regulates cell migration and adhesion.
It may be deleted in colon cancer.
Mutations in one allele are enough
to lose the
genes function.

Scientific Skills Exercise

The diagrams on the next slide show an intact


DNA sequence (top) and three experimental
DNA sequences. A red X indicates the possible
control element (1, 2, or 3) that was deleted in
each experimental DNA sequence. The area
between the slashes represents the
approximately 8 kilobases of DNA located
between the promoter and the enhancer
region. The horizontal bar graph shows the

What was the independent


variable in this experiment?
the length of time that the cells were
incubated
the relative level of reporter gene
mRNA
the distance between the promoter
and the enhancer
the possible control element that was
deleted

What was the independent


variable in this experiment?
the length of time that the cells were
incubated
the relative level of reporter gene
mRNA
the distance between the promoter
and the enhancer
the possible control element that
was deleted

What was the dependent


variable in this experiment?
the length of time that the cells were
incubated
how many of the artificial DNA
molecules were taken up by the cells
the relative level of reporter gene
mRNA
the distance between the promoter
and the enhancer

What was the dependent


variable in this experiment?
the length of time that the cells were
incubated
how many of the artificial DNA
molecules were taken up by the cells
the relative level of reporter
gene mRNA
the distance between the promoter
and the enhancer

What was the control


treatment in this
experiment?
the reporter gene

the construct that had no DNA


deleted from the enhancer
the temperature, pH, and salt
concentration of the incubation
medium
the construct that resulted in the
lowest amount of reporter mRNA

What was the control


treatment in this
experiment?
the reporter gene

the construct that had no DNA


deleted from the enhancer
the temperature, pH, and salt
concentration of the incubation
medium
the construct that resulted in the
lowest amount of reporter mRNA

Do the data suggest that any


of these possible control
elements are actual control
elements?
Only control elements 1 and 2 appear

to be control elements.
Only control element 3 appears to be a
control element.
All three appear to be control
elements.
None of the possible control elements
appear to be actual control elements.

Do the data suggest that any


of these possible control
elements
are
actual
control
Only control elements 1 and 2 appear
elements?
to be control elements.
Only control element 3 appears to be a
control element.
All three appear to be control
elements.
None of the possible control elements
appear to be actual control elements.

Did deletion of any of the possible


control elements cause
areductionin reporter gene
Deletion of element 3 caused a reduction in
expression?
How can
tell?
reporter gene expression;
thatyou
construct
resulted
in less than 50% of the control level of mRNA.
Deletion of elements 2 and 3 caused a
reduction in reporter gene expression; those
constructs resulted in less than the highest
level of mRNA.
None of the deletions caused a reduction in
reporter gene expression; all of them still
resulted in reporter mRNA being made.

Did deletion of any of the possible


control elements cause
areductionin reporter gene
Deletion of element
3 caused
reduction
expression?
How can
you atell?

in reporter gene expression; that construct


resulted
in less than 50% of the control level of
mRNA.
Deletion of elements 2 and 3 caused a reduction
in reporter gene expression; those constructs
resulted in less than the highest level of mRNA.
None of the deletions caused a reduction in
reporter gene expression; all of them still

If deletion of a control element causes


a reduction in gene expression, what
must be the normal role of that control
To repress gene expression; without the control element,
element?
repressors are not able to bind to the enhancer, and the
level of gene expression decreases.
To activate gene expression; without the control element,
activators are not able to bind to the enhancer, and the
level of gene expression decreases.
To repress gene expression; without the control element,
repressors are not able to bind to the enhancer, and the
level of gene expression increases.
To activate gene expression; without the control element,
repressors are not able to bind to the enhancer, and the
level of gene expression increases.

If deletion of a control element causes


a reduction in gene expression, what
must be the normal role of that control
element?
To repress gene expression; without the control element,
repressors are not able to bind to the enhancer, and the
level of gene expression decreases.
To activate gene expression; without the control
element, activators are not able to bind to the
enhancer, and the level of gene expression
decreases.
To repress gene expression; without the control element,
repressors are not able to bind to the enhancer, and the
level of gene expression increases.
To activate gene expression; without the control element,
repressors are not able to bind to the enhancer, and the
level of gene expression increases.

Did deletion of any of the possible control


elements cause anincreasein reporter gene
expression? How can you tell?
Deletion of control element 1 or 2 caused an increase
in reporter gene expression; both constructs resulted in
over 100% of the control level of mRNA.
Deletion of control element 1 caused an increase in
reporter gene expression; that construct resulted in the
highest level of mRNA.
Deletion of control element 3 caused an increase in
reporter gene expression; that construct resulted in less
reporter mRNA than the control.
All of the deletions caused an increase in reporter gene
expression; all of them still resulted in reporter mRNA
being made.

Did deletion of any of the possible control


elements cause anincreasein reporter gene
expression? How can you tell?
Deletion of control element 1 or 2 caused an increase
in reporter gene expression; both constructs resulted
in
over 100% of the control level of mRNA.
Deletion of control element 1 caused an increase in
reporter gene expression; that construct resulted in the
highest level of mRNA.
Deletion of control element 3 caused an increase in
reporter gene expression; that construct resulted in less
reporter mRNA than the control.
All of the deletions caused an increase in reporter gene
expression; all of them still resulted in reporter mRNA being
made.

If deletion of a control element causes an


increase in gene expression, what must be
the normal role of that control element?
To activate gene expression; without the control element,
repressors are not able to bind to the enhancer, and the
level of gene expression increases.
To repress gene expression; without the control element,
activators are not able to bind to the enhancer, and the
level of gene expression decreases.
To repress gene expression; without the control element,
repressors are not able to bind to the enhancer, and the
level of gene expression increases.
To activate gene expression; without the control element,
activators are not able to bind to the enhancer, and the
level of gene expression decreases.

If deletion of a control element causes an


increase in gene expression, what must be
the normal role of that control element?
To activate gene expression; without the control element,
repressors are not able to bind to the enhancer, and the
level of gene expression increases.
To repress gene expression; without the control element,
activators are not able to bind to the enhancer, and the
level of gene expression decreases.
To repress gene expression; without the control
element, repressors are not able to bind to the
enhancer, and the level of gene expression increases.
To activate gene expression; without the control element,
activators are not able to bind to the enhancer, and the
level of gene expression decreases.

Which of the following is a property of life


shared by prokaryotic cells and eukaryotic
cells, but not viruses?
nucleic acids used to store hereditary
information
order and complexity in arrangement of
biological molecules
the ability to process energy through
metabolic reactions
the capacity to evolve

Which of the following is a property of life


shared by prokaryotic cells and eukaryotic
cells, but not viruses?
a) nucleic acids used to store hereditary information
b) order and complexity in arrangement of biological
molecules
c) the ability to process energy through metabolic
reactions
d) the capacity to evolve

Which of the following is characteristic of


the lytic cycle?
Viral DNA is incorporated into the host genome.
The virus-host relationship usually lasts for
generations.
A large number of phages are released at a time.
Many bacterial cells containing viral DNA are
produced.
The viral genome replicates without destroying
the host.

Which of the following is characteristic of


the lytic cycle?
Viral DNA is incorporated into the host genome.
The virus-host relationship usually lasts for
generations.
A large number of phages are released at a
time.
Many bacterial cells containing viral DNA are
produced.
The viral genome replicates without destroying
the host.

What is the function of reverse


transcriptase in retroviruses?
It converts host cell RNA into viral DNA.
It hydrolyzes the host cell's DNA.
It uses viral RNA as a template for
making complementary RNA strands.
It translates viral RNA into proteins.
It uses viral RNA as a template for DNA
synthesis.

What is the function of reverse


transcriptase in retroviruses?
It converts host cell RNA into viral DNA.
It hydrolyzes the host cell's DNA.
It uses viral RNA as a template for making
complementary RNA strands.
It translates viral RNA into proteins.
It uses viral RNA as a template for DNA
synthesis.

Why are viruses referred to as


obligate parasites?
They use the host cell to reproduce.
Viral DNA always inserts itself into host
DNA.
They invariably kill any cell they infect.
They can incorporate nucleic acids from
other viruses.
They must use enzymes encoded by the
virus itself.

Why are viruses referred to as


obligate parasites?
They use the host cell to reproduce.
Viral DNA always inserts itself into host
DNA.
They invariably kill any cell they infect.
They can incorporate nucleic acids from
other viruses.
They must use enzymes encoded by the
virus itself.

Which of the following molecules


make up the viral envelope?
viral glycoproteins
capsid
phospholipids from human host cell
membrane
membrane proteins from human host
cell
viral DNA

Which of the following molecules


make up the viral envelope?
viral glycoproteins
capsid
phospholipids from human host cell
membrane
membrane proteins from human host
cell
viral DNA

You have isolated viral particles from a patient, but you


are not sure whether they are adenoviruses or
influenza viruses. The presence of which class of
biological molecules would allow you to distinguish
between the two types of virus?

RNA
phospholipids
proteins
glycoproteins
DNA

You have isolated viral particles from a patient, but you


are not sure whether they are adenoviruses or
influenza viruses. The presence of which class of
biological molecules would allow you to distinguish
between the two types of virus?

RNA
phospholipids
proteins
glycoproteins
DNA

The HIV virus attacks only a certain


type of white blood cells, and not other
cell
types.
Why?
HIV
receptors are not found on the other
cell types.
Reverse transcriptase cannot transcribe
RNA
to DNA.
Viral mRNA cannot be transcribed from
the integrated provirus.
Viruses cannot bud from the host cell.

The HIV virus attacks only a


certain type of white blood cells,
and
not
other cell
types.
HIV
receptors
are not
foundWhy?
on the
other cell types.
Reverse transcriptase cannot transcribe
RNA
to DNA.
Viral mRNA cannot be transcribed from the
integrated provirus.
Viruses cannot bud from the host cell.

Which is not an accepted theory about the evolution


of viruses:
a) Viruses originated from naked bits of cellular nucleic
acids.
b) Genes coding for capsid proteins allowed viruses to
bind cell membranes.
c) Plasmids and transposons may have been the
original sources of viral genomes.
d) Viruses are the descendents of precellular life forms.

Which is not an accepted theory about the evolution


of viruses:
a) Viruses originated from naked bits of cellular nucleic
acids.
b) Genes coding for capsid proteins allowed viruses to
bind cell membranes.
c) Plasmids and transposons may have been the
original sources of viral genomes.
d) Viruses are the descendents of precellular life
forms.

AZT is a nucleoside analog used to treat


HIV infections. It is a modified nucleoside.
Which step does AZT hamper in the
reproductive cycle of the HIV virus?
entry into the cell
synthesis of DNA from RNA catalyzed by
reverse transcription
transcription of RNA from proviral DNA
viral assembly within the cell

AZT is a nucleoside analog used to treat


HIV infections. It is a modified nucleoside.
Which step does AZT hamper in the
reproductive cycle of the HIV virus?
entry into the cell
synthesis of DNA from RNA catalyzed
by reverse transcription
transcription of RNA from proviral DNA
viral assembly within the cell

Which of the following most likely


describes the vertical transmission of
a plant
virus?
The plant
shows symptoms of disease after being

grazed on by herbivores.
Sap from one plant is rubbed on the leaves of a
second plant; both plants eventually show disease
symptoms.
Seeds are planted and reared under protected
conditions, but mature plants show disease
symptoms.
After a gardener prunes several plants with the same
shears, they all show disease symptoms.

Which of the following most likely


describes the vertical transmission of
a plant
virus?
The plant
shows symptoms of disease after being

grazed on by herbivores.
Sap from one plant is rubbed on the leaves of a
second plant; both plants eventually show disease
symptoms.
Seeds are planted and reared under protected
conditions, but mature plants show disease
symptoms.
After a gardener prunes several plants with the same
shears, they all show disease symptoms.

The photograph shows Rainbow and CC


(CC is Rainbows clone). Why is CCs coat
pattern different from Rainbows given that
CC and Rainbow are genetically identical?
random X chromosome
inactivation
heterozygous at coat
color gene locus
environmental effects
on gene expression
all of the above

The photograph shows Rainbow and CC


(CC is Rainbows clone). Why is CCs coat
pattern different from Rainbows given that
CC and Rainbow are genetically identical?
random X chromosome
inactivation
heterozygous at coat
color gene locus
environmental effects
on gene expression
all of the above

Which is an incorrect
statement about STRs (Short
Tandem
They are repeats)?
tandemly repeated units of 5

to 10 nucleotide sequences
The number of repeats is polymorphic
from person to person
Two alleles of an STR may differ in an
individual
They occur in specific regions of the
genome
PCR is used to amplify particular STRs.

Which is an incorrect
statement about STRs (Short
Tandem repeats)?

They are tandemly repeated units of


5- to 10 nucleotide sequences
The number of repeats is polymorphic
from person to person
Two alleles of an STR may differ in an
individual
They occur in specific regions of the
genome
PCR is used to amplify particular STRs.

Which of the following


beneficial traits have not
resulted from DNA technology
and
genetic
engineering
of
Delayed ripening
crop
plants?

Resistance to drought
Resistance to herbicides
Resistance to salinity
Superweeds

Which of the following


beneficial traits have not
resulted from DNA technology
and genetic engineering of
crop
Delayed
ripening
plants?

Resistance to drought
Resistance to herbicides
Resistance to salinity
Superweeds

Which of the following is not a


correct statement about third
sequencing?
generation
A single DNA molecule
is sequenced on
its own
Different bases interrupt an electric
current for a particular length of time a
compound and an isotope; a molecule
DNA moves through a small nanopore a
molecule and a compound; a molecule
DNA must be cut into fragments or
amplified

Which of the following is not a


correct statement about third
generation
sequencing?
A single DNA molecule
is sequenced on
its own
Different bases interrupt an electric
current for a particular length of time a
compound and an isotope; a molecule
DNA moves through a small nanopore a
molecule and a compound; a molecule
DNA must be cut into fragments or
amplified

Place the steps in a cycle of PCR


(Polymerase Chain Reaction) in the
correct order:
1.
2.
3.

AnnealingCool to allow primers to form hydrogen bonds with ends of


target sequence
ExtensionDNA polymerase adds nucleotides to the 3 end of each
primer
DenaturationHeat briefly to separate DNA strands

3-1-2
3-2-1
1-2-3
2-3-1
1-3-2
2-1-3

Place the steps in a cycle of PCR


(Polymerase Chain Reaction) in the
correct
order:
1. AnnealingCool to allow primers to form hydrogen bonds with ends of
2.
3.

target sequence
ExtensionDNA polymerase adds nucleotides to the 3 end of each
primer
DenaturationHeat briefly to separate DNA strands

3-1-2
3-2-1
1-2-3
2-3-1
1-3-2
2-1-3

Which of the following is an


example of recombinant DNA?
combining alternate alleles of a gene in a
single cell
manipulating a meiotic crossing-over event
cloning genes from homologous pairs of
chromosomes
introducing a human gene into a bacterial
plasmid
alternate alleles assorting independently

Which of the following is an


example of recombinant DNA?

combining alternate alleles of a gene in a


single cell
manipulating a meiotic crossing-over event
cloning genes from homologous pairs of
chromosomes
introducing a human gene into a
bacterial plasmid
alternate alleles assorting independently

This segment of DNA is cut at restriction sites 1


and 2, which creates restriction fragments A, B,
and C. Which of the following electrophoretic gels
represents the separation of these fragments?
a)
b)
c)
d)

This segment of DNA is cut at restriction sites 1


and 2, which creates restriction fragments A, B,
and C. Which of the following electrophoretic gels
represents the separation of these fragments?
a)
b)
c)
d)

Scientific Skills Exercise


1) The top diagram depicts the very large regulatory region upstream
of the Hoxd13 gene. The area between the slashes represents the
DNA located between the promoter and the regulatory region.
2) The diagrams to the left of the bar graph show, first, the intact DNA
and, next, the three altered DNA sequences. A red X indicates the
segment (A, B, and/or C) that was deleted in each line of transgenic
mice.
3) The horizontal bar graph shows the amount of Hoxd13 mRNA that
was present in the digit-formation zone of each transgenic 12.5-dayold embryo paw relative to the amount that was in the digit-formation
zone of a wild-type mouse that had the intact regulatory region (top
bar = 100%). The paw images have blue stain visible where
the Hoxd13 mRNA is located.

Which of the four


treatments
was the
control
the wild-type mouse
C
for
experiment?
thethe
transgenic
mouse with all three
segments deleted N
the transgenic mouse with segments
B and C deleted
the transgenic mouse with only
segment C deleted

Which of the four treatments was the


control for the experiment?
the wild-type mouse C
the transgenic mouse with all three
segments deleted N
the transgenic mouse with segments
B and C deleted
the transgenic mouse with only
segment C deleted

The hypothesis was that all three


segments of the regulatory region
are required for highest expression
ofYes;
when any of the segments
theHoxd13gene.
Iswere
thisdeleted, the
expression level dropped to less than 100% of the
hypothesis
supported by the
control.
results?
No; they did not delete the promoter, so the gene
could still be expressed even without the
segments.
Yes; when all three segments were present, the
expression level was at 100%.
No; even when segments were deleted,
theHoxd13gene was still being expressed.

The hypothesis was that all three


segments of the regulatory region
are required for highest expression
of theHoxd13gene. Is this
Yes; when any of the segments were deleted,
hypothesis
supported
bytothe
the expression
level dropped
less than
100% of the control.
results?
No; they did not delete the promoter, so the gene
could still be expressed even without the
segments.
Yes; when all three segments were present, the
expression level was at 100%.
No; even when segments were deleted,

What was the effect on the amount


Only about 60% when
of the segments
control amount
ofHoxd13mRNA
B
of C
Hoxd13
mRNA
was produced.
and
were both
deleted?

The deletion of segments B and C had


no effect on the amount
ofHoxd13mRNA produced.
Only about 35% of the control amount
of Hoxd13 mRNA was produced.
Only about 5% of the control amount of
Hoxd13 mRNA was produced.

What was the effect on the amount


segments
ofHoxd13mRNA
Only about 60% of when
the control
amountBof
and
C were
both
deleted?
Hoxd13
mRNA
was
produced.
The deletion of segments B and C had no
effect on the amount ofHoxd13mRNA
produced.
Only about 35% of the control amount
of Hoxd13 mRNA was produced.
Only about 5% of the control amount of
Hoxd13 mRNA was produced.

Look at the blue stain in thein


There is very light
stain in the mouse
center of
situhybridization
for blue
the transgenic
eachsegments
digit zone B
asand
compared
the control.
lacking
C. Howtowould
you
The blue
is generally
lighter
in the
describe
thestain
spatial
pattern of
genethan
expression
control,
but paw
all four
zones are
stillcontrol?
visible.
in the
embryo
as digit
compared
to the
There is almost no blue stain anywhere in the
paw as compared to the control.
There is no blue stain at the base of the paw
as compared to the control.

Look at the blue stain in the in situ hybridization for the


transgenic mouse lacking segments B and C. How
would you describe the spatial pattern of gene
expression in the embryo paw as compared to the
control?
There is very light blue stain in the center of
each digit zone as compared to the control.
The blue stain is generally lighter than in
the control, but all four digit zones are still
visible.
There is almost no blue stain anywhere in the
paw as compared to the control.
There is no blue stain at the base of the paw as
compared to the control.

What was the effect on the amount of Hoxd13 mRNA


when just segment C was deleted?

The deletion of segment C had no effect


on the amount ofHoxd13mRNA
produced.
Only about 60% of the control amount
of Hoxd13 mRNA was produced.
Only about 35% of the control amount
of Hoxd13 mRNA was produced.
Only about 5% of the control amount of
Hoxd13 mRNA was produced.

What was the effect on the amount of Hoxd13 mRNA


when just segment C was deleted?

The deletion of segment C had no effect


on the amount ofHoxd13mRNA produced.
Only about 60% of the control amount
of Hoxd13 mRNA was produced.
Only about 35% of the control amount of
Hoxd13 mRNA was produced.
Only about 5% of the control amount of
Hoxd13 mRNA was produced.

How would you describe the spatial pattern of gene


expression in the embryo paw lacking segment C as
compared to the control and to the paw lacking
segments B and C?
The digit zones are not visibly stained as they
are in the control and the paw lacking B and C.
The top of the paw is stained darker than both
the control and the paw lacking B and C.
The base of the paw is stained darker than
both the control and the paw lacking B and C.
The digit zones are defined with darker stain
than both the control and the paw lacking B
and C.

How would you describe the spatial pattern of gene


expression in the embryo paw lacking segment C as
compared to the control and to the paw lacking
segments B and C?
The digit zones are not visibly stained as
they are in the control and the paw lacking
B and C.
The top of the paw is stained darker than both the
control and the paw lacking B and C.
The base of the paw is stained darker than both
the control and the paw lacking B and C.
The digit zones are defined with darker stain than
both the control and the paw lacking B and C.

Suppose the researchers had only measured the


amount of Hoxd13 mRNA and not done the in
situ hybridizations. What important information about
the role of the regulatory segments would have been
missed?
The interaction of the regulatory region with the
promoter would have been missed.
The interaction among the different segments of
the regulatory region would have been missed.
The mRNA would not have been blue; therefore it
could not have been measured for the results
shown in the bar graph.
The spatial patterns ofHoxd13gene expression
in the paws would have been missed.

Suppose the researchers had only measured the


amount of Hoxd13 mRNA and not done the in
situ hybridizations. What important information about
the role of the regulatory segments would have been
missed?
The interaction of the regulatory region with the
promoter would have been missed.
The interaction among the different segments of
the regulatory region would have been missed.
The mRNA would not have been blue; therefore it
could not have been measured for the results
shown in the bar graph.
The spatial patterns ofHoxd13gene
expression in the paws would have been
missed.

Suppose the researchers had only done the in


situ hybridizations and not measured the amount
of Hoxd13 mRNA. What important information would
have been missed?
The information about which regulatory
segments were deleted would have been
missed.
The spatial patterns ofHoxd13gene expression
in the paws would have been missed.
Qualitative data aboutHoxd13mRNA levels
would have been missed.
Quantitative data aboutHoxd13mRNA levels
would have been missed.

Suppose the researchers had only done the in


situ hybridizations and not measured the amount
of Hoxd13 mRNA. What important information would
have been missed?
The information about which regulatory
segments were deleted would have been
missed.
The spatial patterns ofHoxd13gene expression
in the paws would have been missed.
Qualitative data aboutHoxd13mRNA levels
would have been missed.
Quantitative data aboutHoxd13mRNA
levels would have been missed.