Week 8:: DNA Structure A ND Function

Week 8:
DNA Structure a
nd Function
© Cengage Learning 2016

9.1 A Hero Dog’s Golden Clones
• James Symington and his search dog Trakr
located the last living survivor of the 9/11 attack
on the World Trade Center
• Trakr later died of a degenerative neurological
disease, probably due to toxic smoke exposure at
Ground Zero
• Trakr’s DNA lives on in his clones – genetic
copies produced by inserting his DNA into
donor eggs

The Cloning Controversy
• Few cloned mammal embryos result in a live
birth – many of the clones that survive have
serious health problems
– The problem: DNA in adult cells is controlled
differently than the DNA in embryonic cells
• Perfecting methods for cloning animals brings
us closer to the possibility of cloning humans,
both technically and ethically

9.2 The Discovery of DNA’s Function
• 1869: Johannes Miescher found DNA
(deoxyribonucleic acid) in nuclei, though its
function was unknown
• Early 1900s: Griffith transferred hereditary
material from dead cells to live cells
– Mice injected with live R cells lived
– Mice injected with live S cells died
– Mike injected with killed S cells lived
– Mice injected with killed S cells and live R cells
died; live S cells were found in their blood
Griffith’s Experiments
A B C D

Avery and McCarty Find the
Transforming Principle
• 1940: Avery and McCarty separated deadly S
cells (from Griffith’s experiments) into lipid,
protein, and nucleic acid components
• When lipids, proteins, and RNA were destroyed,
the remaining substance, DNA, still transformed
R cells to S cells
• Conclusion: DNA is the “transforming
principle”

Confirmation of DNA’s Function
• 1950s: Hershey and Chase experimented with
bacteriophages (viruses that infect bacteria)
– Protein parts of viruses, labeled with 35S, stayed
outside the bacteria
– DNA of viruses, labeled with 32P, entered the bacteria
• Conclusion: DNA, not protein, is the material
that stores hereditary information

Bacteriophages
DNA
inside
protein
coat
tail hollow
fiber sheath

Virus particle coat S remains
35
proteins labeled outside cells

with 35S
DNA being
injected into
bacterium
Virus DNA
labeled with 32P
32
P remains
inside cells
Labeled DNA
being injected
into bacterium

The Hershey–Chase Experiments
35
S remains
Virus particle coat
outside cells
proteins labeled
with 35S
DNA being
injected into
bacterium
Virus DNA labeled 32

P remains
with 32P inside cells
Labeled DNA
being injected
into bacterium

9.3 The Discovery of DNA’s Structure
• Nucleotide
– A nucleic acid monomer consisting of a five-carbon
sugar (deoxyribose), three phosphate groups, and one
of four nitrogen-containing bases
• DNA consists of four nucleotide building blocks
– Two pyrimidines: thymine and cytosine
– Two purines: adenine and guanine
DISCLAIMER: This document is a draft and the information contained herein is subject to change as this document is currently undergoing review. The
© Cengage Learningfinal
2016version of this teacher’s resource manual will be published as soon as the review has been completed.
Four Kinds of Nucleotides in DNA
ADENINE (A) THYMINE (T)
deoxyadenosine triphosphate deoxythymidine triphosphate
BASE
SUGA
R
GUANINE (G)
deoxyguanosine triphosphate CYTOSINE (C)
HC deoxycytidine triphosphate
Chargaff’s Rules
• The amounts of thymine and adenine in DNA
are the same, and the amounts of cytosine and
guanine are the same
– A=T
–G=C
• The proportion of adenine and guanine differs
among species
Franklin, Watson, and Crick
• Rosalind Franklin’s research in x-ray
crystallography revealed the dimensions and
shape of the DNA molecule: an alpha helix
• This was the final piece of information James
Watson and Francis Crick needed to build their
model of DNA
Watson and Crick’s DNA Model
• A DNA molecule consists of two nucleotide
chains (strands), running in opposite directions
and coiled into a double helix
• Base pairs form on the inside of the helix, held
together by hydrogen bonds (A-T and G-C)
0.34 nanometer
between each
base pair
2-nanometer
diameter
3.4-nanometer
length of each full
twist of the double
helix
9.4 Eukaryotic Chromosomes
• The DNA in a eukaryotic cell nucleus is
organized as one or more chromosomes that
differ in length and shape
• Chromosome
– A structure that consists of DNA and associated
proteins
– Carries part or all of a cell’s genetic information
Chromosome Organization
• During most of the cell’s life, each chromosome
consists of one DNA strand
• When the cell prepares to divide, it duplicates all
of its chromosomes, so that both offspring
receive a full set
• Each duplicated chromosome
– Has two DNA strands (sister chromatids) attached to
one another at the centromere
– Consists of two long filaments bunched into a
characteristic X shape
Chromosomes and Chromatids
DNA
inside
centromere
protein
coat
one chromatid
its sister chromatid
tail hollow
a chromosome
fiber asheath
chromosome
(unduplicated) (duplicated)
Chromosome Structure
• Each filament consists of a coil of DNA
wrapped around “spools” of proteins called
histones
• Each DNA-histone spools is a nucleosome, the
smallest unit of chromosomal organization in
eukaryotes
• The DNA molecule consists of two strands
twisted into a double helix
Chromosome Structure – Illustrated
DNA
inside
protein
coat
Two strands of DNA twist into a double helix.

At regular intervals, the DNA (blue) wraps
around a core of histone proteins (purple).
The DNA and proteins associated with it
twist tightly into a fiber.
The fiber coils and then coils again to
form a hollow cylinder.
At its most condensed, a duplicated
chromosome has an X shape.
The DNA in the nucleus of a eukaryotic cell
is typically divided into a number of chromosomes.

Chromosome Packing
DNA
inside
protein
coat
Andrew Syred/Science Source.

Chromosome Number
• The total number of chromosomes in a
eukaryotic cell (chromosome number) is
characteristic of the species
• Human body cells have:
– Forty-six chromosomes
– Two of each type of chromosome – so their
chromosome number is diploid (2n)
• A karyotype shows how many chromosomes are
in an individual cell, and reveals major structural
abnormalities
Karyotypes
IT IS TIME TO
MOVE
ITTTTTTTT!!!
TURN ON
YOUR
Autosomes and Sex Chromosomes
• In a diploid organism, one chromosome in a pair
is inherited from the mother and one from the
father
– All except one pair of chromosomes are autosomes –
chromosomes with the same length, shape, and
centromere location
– Pairs of sex chromosomes differ between females
and males – human females have two X
chromosomes (XX); human males have one X and
one Y chromosome (XY)
9.5 DNA Replication
• DNA replication is the energy-intensive process
by which a cell copies its DNA
• A cell copies its DNA before it reproduces
• Each of the two DNA strands in the double helix
is replicated
• DNA replication requires many enzymes,
including DNA polymerase, and other molecules
Replication of the DNA Sequence
• A cell’s genetic information consists of the order
of nucleotide bases (the DNA sequence) of its
chromosomes
• Descendant cells must get an exact copy of that
information
• Each chromosome is copied entirely – the two
chromosomes that result are duplicates of the
parent molecule
Enzymes of DNA Replication
• DNA helicase breaks hydrogen bonds between
DNA strands
• Topoisomerase untwists the double helix
• DNA polymerase joins free nucleotides into a
new strand of DNA
• DNA ligase joins DNA segments on the
discontinuous strand
Primers for DNA Polymerase
• Several types of DNA polymerases exist
• Each requires a primer to initiate DNA synthesis
• A primer is a short, single strand of DNA or RNA
that is complementary to a targeted DNA sequence

Semiconservative DNA Replication
• Each strand of a DNA double helix is a template
for synthesis of a complementary strand of DNA
• One template builds DNA continuously; the
other builds DNA discontinuously, in segments
• Each new DNA molecule consist of one old
strand and one new strand (semiconservative
replication)

1 As replication begins, many initiator proteins attach to the DNA at certain
sites in the chromosome. Eukaryotic chromosomes have many of these initiator proteins
origins of replication; DNA replication proceeds more or less simultaneously
at all of them.
Topoisomerase
2 Enzymes recruited by the initiator proteins begin to unwind the two strands
of DNA from one another.
(untwists the double helix)
Helicase
(breaks hydro gen bonds
3 Primers base-paired with the exposed single DNA strands serve as initiation
sites for DNA synthesis. between bases)
4 Starting at primers, DNA polymerases (green boxes) assemble new strands

of DNA from nucleotides, using the parent strands as templates.
primer
DNA ligase seals any gaps that remain between bases of the “new” DNA, so DNA polymerase
5 a continuous strand forms.

nucleotide
Each parental DNA strand (blue) serves as a template for assembly of a new
strand of DNA (magenta). Both strands of the double helix serve as
6 templates, so two double- stranded DNA molecules result. One strand of
DNA ligase
each is parental (old), and the other is new, so DNA replication is said to be
semiconservative.
Discontinuous Replication
• DNA polymerases attach a free nucleotide only to
the 3′ end of a DNA strand
• Only one of the two new strands of DNA can be
synthesized continuously during DNA replication
• Synthesis of the other strand occurs in segments, in
the direction opposite that of unwinding
• DNA ligase joins segments into a continuous strand
of DNA
Discontinuous Replication
unwinding
A During DNA
synthesis, only one
of the two new
strands can be
assembled in a
single piece. The
other strand forms
in short segments,
DNA which are called
Okazaki fragments
inside after the two
scientists who
protein discovered them.
DNA ligase joins
coat Okazaki fragments
where they meet.
B DNA synthesis proceeds

only in the 5′ to 3′
direction because DNA
polymerase catalyzes only
one reaction: the formation
of a bond between the 3′
carbon on the end of a
DNA strand and the
phosphate on a
nucleotide’s 5′ carbon.

9.6 Mutations: Cause and Effect
• DNA polymerases proofread DNA sequences
during DNA replication and repair damaged
DNA
• When proofreading and repair mechanisms fail,
an error becomes a mutation – a permanent
change in the DNA sequence
Electromagnetic Agents of DNA Damage
• Ionizing radiation (gamma rays, X-rays, most

UV light)
– Knocks electrons out of atoms
– Breaks chromosomes into pieces that may get lost
– Creates free radicals in tissues
• UV light (320-400 nm)
– Forms pyrimidine dimers that kink DNA strands
– Causes skin cancer
Chemical Agents of DNA Damage
• At least fifty-five carcinogenic (cancer-causing)
chemicals in tobacco smoke transfer small
hydrocarbon groups to the nucleotide bases in
DNA
• Many environmental pollutants are converted by
the body to other compounds that bind
irreversibly to DNA, causing replication errors
that lead to mutation
Rosalind Franklin, X-Rays, and Cancer
• In science, as in other professions, public
recognition does not always include everyone
who contributed to a discovery
– Rosalind Franklin was first to discover the molecular
structure of DNA, but did not share in the Nobel
prize which was given to Watson, Crick, and Wilkins
– Franklin died of cancer at age 37, probably caused
by extensive exposure to x-rays during her work
9.7 Cloning Adult Animals
• Clones
– Exact copies of a molecule, cell, or individual
– Occur in nature by asexual reproduction or embryo
splitting (identical twins)
• As cells develop, they become differentiated
– Different in form and function
– Usually a one-way process in animal cells
• Reproductive cloning technologies produce an
exact copy (clone) of an individual
Cloning in the Laboratory
• Somatic cell nuclear transfer (SCNT)
– Nuclear DNA of an adult is transferred to an
enucleated egg
– Egg cytoplasm reprograms differentiated (adult)
DNA to act like undifferentiated (egg) DNA
– The hybrid cell develops into an embryo that is
genetically identical to the donor individual
Somatic Cell Nuclear Transfer (SCNT)
A A cow’s egg is held in D The micropipette

place by suction through a enters the egg and delivers
hollow glass tube called a the skin cell to a region
micropipette. DNA is between the cytoplasm and
identified by a purple stain. the plasma membrane.
E After the pipette is

withdrawn, the donor’s skin
B Another micropipette
cell is visible next to the
punctures the egg and sucks
cytoplasm of the egg. The
out the DNA. All that remains
transfer is now complete.
inside the egg’s plasma
membrane is cytoplasm.
F An electric current causes the

C A new micropipette pre- foreign cell to fuse with and
pares to enter the egg at the deposit its nucleus into the
puncture site. The pipette cytoplasm of the egg. The egg
contains a cell grown from the begins to divide, and an embryo
skin of a donor animal. forms.
Therapeutic Cloning
• Therapeutic cloning uses SCNT to produce
human embryos for research purposes
• Researchers harvest undifferentiated (stem) cells
from the cloned human embryos
• Such research may ultimately lead to treatments
for people who suffer from fatal diseases
9.8 Cloning DNA
• Restriction enzymes
– Bacterial enzymes that cut DNA wherever a specific
nucleotide sequence occurs
• Single-stranded DNA tails produced by the same
restriction enzyme base-pair together
– DNA ligase bonds “sticky ends” together
• Recombinant DNA
– Composed of DNA from two or more organisms
Making Recombinant DNA
1 The restriction enzyme EcoRI (named after the E. coli bacteria from 3 When the DNA fragments from the two sources are mixed
which it was isolated) recognizes a specific base sequence (GAATTC) in together, matching sticky ends base-pair with each other.
DNA from two different sources.
4 DNA ligase joins the base-paired DNA fragments to produce

molecules of recombinant DNA.
2 The enzyme cuts the DNA into fragments. EcoRI leaves single- stranded tails (“sticky ends”) where it cuts DNA.
Making Recombinant DNA
restriction mix DNA ligase

enzyme (cut) (paste)
1 A restriction enzyme 2 The enzyme cuts 3 When the DNA 4 DNA ligase joins
recognizes a specific DNA from two sources fragments from the the base-paired DNA
base sequence (orange into fragments. This two sources are mixed fragments. Molecules
boxes) in DNA from any enzyme leaves sticky together, matching of recombinant DNA
source. ends. sticky ends base-pair are the result.
with each other.
DNA Cloning
• Making recombinant DNA is the first step in
DNA cloning, a set of laboratory methods that
uses living cells to mass-produce specific DNA
fragments
– DNA cut into fragments by restriction enzymes is
inserted into cloning vectors (plasmids) cut with the
same enzyme
– Cloning vectors with foreign DNA are placed in host
cells, which divide and produce many clones, each
with a copy of the foreign DNA
Plasmid Cloning Vectors
Kpnl
Sphl
Pstl
BamHl
EcoRI
Sall
Accl
Xhol
Xbal
BstXI
Sacl
A B Notl
DNA Cloning
chromosomal DNA fragments of chromosomal DNA
recombinant
plasmid
cut plasmid
cloning
plasmid
vector
A A restriction enzyme (gold B A fragment of chromosomal DNA and C The recombinant plasmid is inserted into a
triangles) cuts a specific nucleotide the cut plasmid base-pair at their sticky host bacterial cell. When the cell reproduces, it
sequence in chromosomal DNA ends. DNA ligase joins the two pieces of copies the plasmid along with its chromosome.
and in a plasmid cloning vector. DNA, so a recombinant plasmid forms. Each descendant cell receives a plasmid.
DNA Cloning
A A restriction enzyme cuts
a specific base sequence in
chromosomal DNA and in
a plasmid cloning vector.
chromosomal
chromosomal DNA fragments
DNA
B A fragment of chromosomal
DNA and the plasmid base-pair recombinant
at their sticky ends. DNA ligase
+
plasmid
joins the two pieces of DNA.
plasmid cut C The recombinant plasmid is

cloning plasmi
vector inserted into a host cell. When the
d
cell multiplies, it makes multiple
copies of the plasmids.

cDNA Cloning
• Complementary DNA (cDNA)
– DNA made from an mRNA template
• Reverse transcriptase transcribes mRNA to
DNA, forming a hybrid molecule
– DNA polymerase builds a double-stranded DNA
molecule that can be cloned
cDNA Cloning
mRN
A
mRN
A
cDN
A
DN
A
cDN
A
EcoRI recognition
site
© Cengage Learning 2016final version of this teacher’s resource manual will be published as soon as the review has been completed.
9.9 Isolating Genes
• Genome
– The entire set of genetic material of an organism
• DNA libraries are sets of cells containing
various cloned DNA fragments
– Genomic libraries (all DNA in a genome)
– cDNA libraries (all active genes in a cell)
Probes
• Probe
– A fragment of DNA labeled with a tracer
– Used to find a specific clone carrying DNA of
interest in a library of many clones
• Nucleic acid hybridization
– Base pairing between DNA from different sources
– A probe hybridizes with the targeted gene
DNA libraries and the polymerase chain reaction (PCR) help
researchers find and isolate targeted DNA fragments.
A Individual bacterial cells from a DNA library are

spread over the surface of a solid growth medium. The
cells divide repeatedly and form colonies—clusters of
millions of genetically identical descendant cells.
B Special paper is pressed onto the surface of the growth

medium. Some cells from each colony stick to the paper.
C The paper is soaked in a solution that ruptures the

cells and makes the released DNA single-stranded.
The DNA clings to the paper in spots mirroring the
distribution of colonies.
D A radioactive probe is added to the liquid bathing

the paper. The probe hybridizes with any spot of DNA
that contains a complementary sequence.
E The paper is pressed against x-ray film. The radioactive probe darkens the film in a spot where it has hybridized. The
spot’s position is compared to the positions of the original bacterial colonies. Cells from the colony that corresponds to the
spot are cultured, and their DNA is harvested.
PCR
• Polymerase chain reaction (PCR)
– A cycled reaction that uses a heat-tolerant form of
DNA polymerase (Taq polymerase) to produce
billions of copies of a DNA fragment
– DNA to be copied is mixed with DNA polymerase,
nucleotides and primers that base-pair with certain
DNA sequences
– Cycles of high and low temperatures break and
reform hydrogen bonds between DNA strands,
doubling the amount of DNA in each cycle
PCR
targeted section
1 DNA template (blue) is mixed with primers (pink), nucleotides, and heat-tolerant Taq DNA
polymerase.
2 When the mixture is heated, the double-stranded DNA separates into single strands.
When the mixture is cooled, some of the primers base-pair with the DNA at opposite ends of
the targeted sequence.
3 Taq polymerase begins DNA synthesis at the primers, so it produces complementary

strands of the targeted DNA sequence.
4 The mixture is heated again, so all double-stranded DNA separates into single
strands. When it is cooled, primers base-pair with the targeted sequence in the original
template DNA and in the new DNA strands.
5 Each cycle of heating and cooling can double the number of copies of the targeted
DNA section.
9.10 DNA Sequencing
• DNA is synthesized with normal nucleotides and
dideoxynucleotides tagged with different colors
– When a tagged base is added, DNA synthesis stops;
fragments of all lengths are made
• Electrophoresis separates the fragments of DNA,
each ending with a tagged base, by length
– The order of colored bases is the sequence of DNA
DNA template strand
pigment: green blue black red

base:
adenine cytosine guanine thymine
1 This sequencing method depends on dideoxynucleotides, which

are nucleotides that have a hydrogen atom instead of a hydroxyl
group on their 3' carbon. Each base (G, A, T, or C) is labeled with a
different colored pigment.
2 DNA polymerase uses a section of DNA as a template to synthesize

new strands of DNA. Synthesis of each new strand stops when a
dideoxynucleotide is added.
3 At the end of the reaction, there are many incomplete copies of

the template DNA in the mixture. 4
5
4 Electrophoresis separates the copied DNA fragments into bands according to their length. All of the DNA strands in each band
end with the same base, so each band is the color of the base’s tracer pigment.
5 A computer detects and records the color of successive bands on the gel (see FIGURE 9.21 for an example). The order of colors of
the bands represents the sequence of the template DNA.
The Human Genome Project
• Automated DNA sequencing and PCR allowed
human genome projects to sequence the 3 billion
bases in the human genome
– 28,976 genes have been identified, but not all of their
products or functions are known
A Human DNA Sequence
9.11 Genomics
• The study of genomes (genomics) is a broad
field that encompasses whole-genome
comparisons, structural analysis of gene
products, and surveys of small-scale variations
in sequence
• All genomes are related to some extent –
comparing genomes provides evidence of
genetic relationships
Comparing Genomes
• Comparing genomes among species also shows
that changes in chromosome structure do not
occur randomly
• Comparing the coding regions of genomes also
offers medical benefits
– Example: APOA5 mutations and triglycerides
Genomic DNA Alignment
DNA Chips
• DNA chips
– Microarrays of many different DNA samples
arranged on a glass plate
– Used to compare patterns of gene expression among
cells of different types or under different conditions
– May be used to screen for genetic abnormalities,
pathogens, or cancer
DNA Profiling: SNPs
• Identifying an individual by his or her unique array
of DNA sequences is called DNA profiling
– One type of DNA profiling involves SNP-chips with
microscopic spots of DNA stamped on them
– An individual’s genomic DNA hybridizes only with
DNA spots that have a matching SNP sequence
– Probes reveal where the genomic DNA has
hybridized
DNA Profiling: STRs
• Another method of DNA profiling involves short
tandem repeats, sections of DNA in which a
series of 4 or 5 nucleotides is repeated several
times in a row
– Types and numbers of STRs vary greatly among
individuals
– Unless two people are identical twins, the chance
that they have identical short tandem repeats in even
three regions of DNA is 1 in a quintillion (1018)
Analyzing STRs
• PCR is used to amplify DNA from regions of
several chromosomes that have STRs
• Electrophoresis is used to separate the fragments
and create a unique DNA fingerprint
• DNA fingerprints have many applications,
including legal cases, forensics, and population
studies
An STR Profile
A Gray boxes indicate which regions of the

individual’s DNA were tested.
D5S818 D13S317 D7S820 D16S539 CSF1PO Penta D
11.0 14.0 11. 13.0 7.0

0 13.0 1 13.0 12.0 3.0 12.0 14.0
B The number of repeats is shown in a box below each peak. A peak’s location on
the x-axis corresponds to the length of the DNA fragment amplified (a measure of
the number of repeats). Peak size reflects the amount of DNA.

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Week 8:

© Cengage Learning 2016

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© Cengage Learning 2016

© Cengage Learning 2016

© Cengage Learning 2016

© Cengage Learning 2016

© Cengage Learning 2016

proteins labeled outside cells

© Cengage Learning 2016

Virus DNA labeled 32

© Cengage Learning 2016

Two strands of DNA twist into a double helix.

© Cengage Learning 2016

Andrew Syred/Science Source.

© Cengage Learning 2016

© Cengage Learning 2016

© Cengage Learning 2016

4 Starting at primers, DNA polymerases (green boxes) assemble new strands

5 a continuous strand forms.

B DNA synthesis proceeds

© Cengage Learning 2016

• Ionizing radiation (gamma rays, X-rays, most

A A cow’s egg is held in D The micropipette

E After the pipette is

F An electric current causes the

4 DNA ligase joins the base-paired DNA fragments to produce

restriction mix DNA ligase

chromosomal DNA fragments of chromosomal DNA

plasmid cut C The recombinant plasmid is

© Cengage Learning 2016

A Individual bacterial cells from a DNA library are

B Special paper is pressed onto the surface of the growth

C The paper is soaked in a solution that ruptures the

D A radioactive probe is added to the liquid bathing

3 Taq polymerase begins DNA synthesis at the primers, so it produces complementary

pigment: green blue black red

1 This sequencing method depends on dideoxynucleotides, which

2 DNA polymerase uses a section of DNA as a template to synthesize

3 At the end of the reaction, there are many incomplete copies of

A Gray boxes indicate which regions of the

D5S818 D13S317 D7S820 D16S539 CSF1PO Penta D

11.0 14.0 11. 13.0 7.0

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