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Chapter 16
The Molecular Basis of
Inheritance
Overview: Life s Operating Instructions
•  In 1953, Watson and Crick introduced an
elegant double-helical model for the structure of
deoxyribonucleic acid, or DNA
•  Hereditary information is encoded in DNA and
reproduced in all cells of the body
•  This DNA program
directs the development
of biochemical, anatomical,
physiological, and
(to some extent)
behavioral traits
Nucleic acid
1869:
Friedrich Miescher
isolated DNA from pus!
DNA and RNA are nucleic acids.
Each nucleotide
consists of a:
1. pentose sugar
2. nitrogenous base
3. phosphate group
1
Sugar–phosphate
backbone
Nitrogenous bases
5ʹ′ end
Thymine (T)
Adenine (A)
Cytosine (C)
Phosphate
Guanine (G)
Sugar
(deoxyribose)
DNA
nucleotide
3ʹ′ end
Nitrogenous base
What is the genetic material?
•  When genes were shown to be located on chromosomes,
the 2 components of chromosomes- DNA and proteinbecame candidates for the genetic material
–  Protein seemed more complex than DNA
•  The key factor in determining the genetic material was
choosing appropriate experimental organisms
–  The role of DNA in heredity was first discovered by studying
bacteria and the viruses that infect them
Evidence That DNA Can Transform Bacteria
Discovery of genetic role of DNA began w/ research by Frederick Griffith in 1928,
who worked with two strains of a bacterium, Streptococcus pneumoniae
1.  pathogenic S (smooth) strain
2.  harmless R (rough) strain
When he mixed heat-killed
remains of the pathogenic
strain with living cells of the
harmless strain, some living
cells became pathogenic
He called this phenomenon
transformation,
now defined as a change in
genotype and phenotype
due to assimilation of
foreign DNA
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Evidence That Viral DNA Can Program Cells
• 
In 1944, Oswald Avery, Maclyn McCarty, and Colin MacLeod announced
that the transforming substance was DNA
• 
More evidence for DNA as the genetic material came from studies of a
virus that infects bacteria
• 
Such viruses, called bacteriophages (or phages),
are widely used in molecular genetics research
In 1952, Hershey and Chase performed experiments showing that only
one of the two components (DNA/ protein) of a phage T2
enters an E. coli cell during infection
Phage
Empty
Radioactive protein
shell
protein
Radioactivity
(phage
protein)
in liquid
Bacterial cell
DNA
Batch 1:
radioactive
sulfur (35S)
Phage
DNA
radioactive
sulfur
labels protein
Centrifuge
shake loose
Pellet (bacterial
cells and contents)
Radioactive phages that
DNA
remained
outside the
bacteria
Batch 2:
radioactive
phosphorus (32P)
radioactive
phosphorus
labels DNA
Centrifuge
Pellet
Radioactivity
(phage DNA)
in pellet
They concluded that the injected DNA of the phage provides the genetic information
Building a Structural Model of DNA
Clue #1
Erwin Chargaff
A T
Chargaff s rules state that in any species
there is an equal number of A and T bases,
and an equal number of G and C bases
G C
In 1950, reported that DNA
composition varies from one
species to the next
• 
This evidence of diversity made
DNA a more credible candidate
for the genetic material
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Building a Structural Model of DNA
Clue #2
• 
Wilkins and Franklin were using a technique called
X-ray crystallography to study molecular structure
•  Franklin produced a
picture of the DNA
molecule using this
technique
Rosalind Franklin (1920-1958)
The X-ray crystallographic images of DNA enabled Watson to deduce that:
1. DNA was helical
2. the width of the helix and the spacing of the nitrogenous bases
–  suggested that the DNA molecule was made up of two strands,
forming a double helix
4
•  At first, Watson and Crick thought the bases paired
like with like (A with A, and so on), but such pairings
did not result in a uniform width
•  Instead, pairing a purine with a pyrimidine resulted
in a uniform width consistent with the X-ray
They determined:
adenine (A) paired
only with thymine (T)
guanine (G) paired
only with cytosine (C)
2 hydrogen bonds
Sugar
Adenine (A)
Sugar
Thymine (T)
3 hydrogen bonds
Sugar
Sugar
Guanine (G)
Cytosine (C)
DNA Replication
•  Watson and Crick noted that the specific base pairing
suggested a possible copying mechanism for genetic material
•  Since the two strands of DNA are complementary,
each strand acts as a template for building a new strand in replication
•  In DNA replication, the parent molecule unwinds,
and 2 new daughter strands are built based on base-pairing rules
A
T
A
T
A
C
G
C
G
C
T
A
T
A
T
T
G
A
A
T
A
T
A
T
G
C
G
C
G
C
A
T
A
T
A
T
C
G
C
G
C
G
T
A
T
A
T
A
A
T
A
T
A
T
C
G
C
G
C
G
The parent molecule has
two complementary
strands of DNA. Each base
is paired by hydrogen
bonding with its specific
partner, A with T and G
with C.
The first step in replication
is separation of the two
DNA strands.
Each parental strand now
serves as a template that
determines the order of
nucleotides along a new,
complementary strand.
The nucleotides are
connected to form the
sugar-phosphate backbones of the new strands.
Each daughter DNA
molecule consists of one
parental strand of one
new strand.
5
• 
Watson and Crick s
Conservative
model. The two
parental strands
reassociate after
acting as
templates for
new strands,
thus restoring
the parental
double helix.
model
of replication predicts that
when a double helix replicates,
each daughter molecule
will have one old strand
(derived or conserved
from the parent molecule)
and one newly made strand
• 
Competing models were
conservative model &
dispersive model
Second
replication
First
replication
Parent cell
semiconservative
Semiconservative
model. The two
strands of the
parental
molecule
separate, and
each functions as
a template for
synthesis of a
new, complementary strand.
the
the
Dispersive model.
Each strand of
both daughter
molecules
contains
a mixture of
old and newly
synthesized
DNA.
Bacteria
cultured in
medium
containing
15N
heavy (15N)
Meselson & StahlTo test the 3 models they
labeled the nucleotides of the
old strands with a
heavy isotope of nitrogen,
while any new nucleotides
were labeled with a
lighter isotope
Bacteria
transferred to
medium
containing
14N light (14N)
light (14N)
DNA sample
centrifuged
after 20 min
(after first
replication)
DNA sample
centrifuged hybrid
after 40 min
(after second
replication)
hybrid
Conservative
model light (14N)
DNA Replication begins at
special sites called
origins of replication,
§ 
A eukaryotic chromosome
may have 100-1,000 s
The two DNA strands
are separated,
opening up a
replication bubble
light (14N)
heavy (15N)
A second replication produced
both light and hybrid DNA,
eliminating the dispersive
model and supporting the
semiconservative model
heavy (15N)
Semiconservative
model
hybrid
light (14N)
Dispersive
model
mostly
light (14N)
hybrid
hybrid
Origin of
replication
More
dense
Second replication
First replication
The first replication produced a
band of hybrid DNA,
eliminating the
conservative model
Less
dense
Parental (template) strand
Daughter (new) strand
Doublestranded
DNA molecule
Replication fork
Replication
bubble
0.5 µm
Two
daughter
DNA
molecules
(a) Origins of replication in E. coli
Origin of replication
Double-stranded DNA molecule
replication
fork
Parental (template) strand
Daughter (new) strand
consisting of a
0.25 µm
replication fork,
a Y-shaped region where
new DNA strands are
elongating at each end
Bubble
Replication fork
Two daughter DNA molecules
(b) Origins of replication in eukaryotes
6
• 
Helicaseuntwists the double helix and separates the template DNA strands at the replication fork
• 
Single-strand binding proteinbinds to and stabilizes single-stranded DNA until it can be used as a template
• 
Topoisomerasecorrects overwinding ahead of replication forks by breaking, swiveling, & rejoining DNA strands
Single-strand
binding proteins
RNA primer
(5-10 nucleotides)
3ʹ′
Topoisomerase
5ʹ′
3ʹ′
Primase5ʹ′
5ʹ′
3ʹ′
synthesizes the initial
nucleotide strand,
a short RNA primer
Helicase
Elongating a New DNA Strand
The rate of elongation is ~ 500 nucleotides/ sec in bacteria & 50 nucleotides/ sec in human cells
New strand
5ʹ′ end
Template strand
3ʹ′ end
Each nucleotide
that is added to a
growing DNA
strand is a
nucleoside
triphosphate
3ʹ′ end
enzymes that
catalyze the
elongation of
new DNA at a
replication fork
Sugar
Base
Phosphate
5ʹ′ end
DNA polymerase
3ʹ′ end
Pyrophosphate 3ʹ′ end
Nucleoside
triphosphate
5ʹ′ end
5ʹ′ end
Antiparallel Elongation
•  The antiparallel structure of the double helix
(two strands oriented in opposite directions)
affects replication
•  DNA polymerases add nucleotides only to the
free 3ʹ′ end of a growing strand;
therefore, a new DNA strand
can elongate only in the 5ʹ′ to 3ʹ′ direction
7
Overview
Along one template
strand of DNA, called the
leading strand,
Origin of replication
Leading strand
Lagging strand
5ʹ′
3ʹ′
Primer
3ʹ′
5ʹ′
Lagging strand
Leading strand
Overall directions
of replication
Origin of replication
DNA polymerase
can synthesize a
complementary
strand continuously,
moving toward the
replication fork
3ʹ′
5ʹ′
RNA primer
5ʹ′
Sliding clamp
3ʹ′
5ʹ′
Parental DNA
DNA poll III
3ʹ′
5ʹ′
5ʹ′
3ʹ′
5ʹ′
To elongate the other
new strand, called the
lagging strand,
DNA polymerase must work
in the direction away from
the replication fork
The lagging strand is
synthesized as a
series of segments called
Okazaki fragments,
which are joined together by
DNA ligase
Synthesis of the lagging strand
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Primasejoins
joinsRNA
RNAnucleotides
nucleotides
Primase
intoaaprimer.
primer.
into
3ʹ′3ʹ′
Template
Template
Template
strand
strand
strand
3ʹ′3ʹ′
5ʹ′5ʹ′
5ʹ′5ʹ′
3ʹ′3ʹ′
22
RNA
primer
RNAprimer
primer
RNA
DNApol
polIII
IIIadds
addsDNA
DNAnucleotides
nucleotidesto
tothe
the
DNA
primer,forming
formingan
anOkazaki
Okazakifragment.
fragment.
primer,
5ʹ′5ʹ′
3ʹ′3ʹ′
5ʹ′5ʹ′
33
Afterreaching
reachingthe
thenext
next
After
RNAprimer
primer(not
(notshown),
shown),
RNA
DNA pol
polIII
IIIfalls
fallsoff.
off.
DNA
Okazaki
Okazaki
Okazaki
fragment
fragment
fragment
3ʹ′3ʹ′
3ʹ′3ʹ′
5ʹ′5ʹ′
5ʹ′5ʹ′
44
Afterthe
thesecond
secondfragment
fragmentis
is
After
primed,DNA
DNApol
polIII
IIIadds
addsDNA
DNA
primed,
nucleotidesuntil
untilititreaches
reachesthe
the
nucleotides
firstprimer
primerand
andfalls
fallsoff.
off.
first
55
DNA pol
pol11replaces
replacesthe
the
DNA
RNAwith
withDNA,
DNA,adding
addingto
to
RNA
the3ʹ′3ʹ′end
endof
offragment
fragment2.
2.
the
6
DNA ligase forms a bond
between the newest DNA
and the adjacent DNA of
fragment 1.
5ʹ′5ʹ′
3ʹ′3ʹ′
3ʹ′3ʹ′
5ʹ′5ʹ′
5ʹ′5ʹ′
3ʹ′3ʹ′
3ʹ′3ʹ′
5ʹ′5ʹ′
7
5ʹ′
The lagging strand
in this region is now
complete.
3ʹ′
5ʹ′
3ʹ′
Overall
Overalldirection
direction
directionof
of
ofreplication
replication
replication
Overall
8
Overview
Origin of replication
Lagging strand
Leading strand
Leading strand
Lagging strand
Overall directions
of replication
Single-strand
binding protein
Helicase
Leading strand
5ʹ′
3ʹ′
3ʹ′
Parental DNA
DNA pol III
Primer
5ʹ′
Primase
3ʹ′
5ʹ′
DNA pol III
4
3ʹ′ 5ʹ′
Lagging strand
DNA pol I
3
DNA ligase
2
1
3ʹ′
5ʹ′
R
E
V
I
E
W
The DNA Replication Machine
•  The proteins that participate in DNA replication form a large complex,
a DNA replication machine
–  is probably stationary during the replication process
•  Recent studies support
a model in which
molecules reel in
parental DNA and
extrude newly made
daughter DNA molecules
DNA polymerase
9
Proofreading &
Repairing DNA
nucleotide excision repair
A thymine dimer
distorts the DNA molecule.
often caused by UV
DNA polymerases proofread
newly made DNA, replacing any
incorrect nucleotides
A nuclease enzyme cuts
the damaged DNA strand
at two points and the
damaged section is
removed.
DNA can be damaged by:
§ 
§ 
§ 
§ 
chemicals
X-rays
UV light
toxic chemicals- cigarettes
mismatch repair of DNA-
Nuclease
Repair synthesis by
a DNA polymerase
fills in the missing
nucleotides.
DNA
polymerase
repair enzymes correct errors
in base pairing
DNA
ligase
nucleotide excision repair-
DNA ligase seals the
free end of the new DNA
to the old DNA, making the
strand complete.
enzymes cut out and replace
damaged stretches of DNA
Replicating the
Ends of
DNA Molecules
End of parental
DNA strands
5ʹ′
Leading strand
Lagging strand
3ʹ′
Last fragment
Previous fragment
RNA primer
• 
• 
Limitations of DNA
polymerase create problems
for the linear DNA of
eukaryotic chromosomes
The usual replication
machinery provides no way
to complete the 5ʹ′ ends,
so repeated rounds of
replication produce
shorter DNA molecules with
uneven ends
Lagging strand 5ʹ′
3ʹ′
Primer removed but
cannot be replaced
with DNA because
no 3ʹ′ end available
for DNA polymerase
Removal of primers and
replacement with DNA
where a 3ʹ′ end is available
5ʹ′
3ʹ′
Second round
of replication
5ʹ′
New leading strand 3ʹ′
New leading strand 5ʹ′
3ʹ′
Further rounds
of replication
Shorter and shorter
daughter molecules
•  Eukaryotic chromosomal DNA molecules have at
their ends nucleotide sequences called
telomeres
•  Telomeres do not prevent the shortening of DNA
molecules, but they do postpone the erosion of genes
near the ends of DNA molecules
TTAGGG
100 - 1,000 x
telomeres
10
•  If chromosomes of germ cells became shorter in every cell cycle,
essential genes would eventually be missing from gametes they produce
•  An enzyme called telomerase
catalyzes the lengthening of telomeres in germ cells
•  There is evidence of telomerase activity in cancer cells,
which may allow cancer cells to persist
•  It has been proposed that the shortening of telomeres is
connected to aging
–  The shortening of telomeres might protect cells from
cancerous growth by limiting the number of cell divisions
Chromosomes
•  The bacterial chromosome is a double-stranded, circular
DNA molecule associated with a small amount of protein
•  Eukaryotic chromosomes have linear DNA molecules
associated with a large amount of protein
•  Chromatin is a complex of DNA and protein, and is found in
the nucleus of eukaryotic cells
•  Histones are proteins that are responsible for the first
level of DNA packing in chromatin
Nucleosome
(10 nm in diameter)
DNA
double helix
(2 nm in diameter)
H1
Histones
DNA, the double helix
Histones
Histone tail
Nucleosomes,
or beads on a
string (10-nm fiber)
§  DNA winds around
histones to form
nucleosome beads
§  Nucleosomes are
strung together like beads
on a string by linker DNA
11
Chromatid
(700 nm)
30-nm fiber
Loops
Scaffold
300-nm fiber
Interactions between
nucleosomes cause the
thin fiber to coil or fold
into this thicker fiber
30-nm fiber
The 30-nm fiber forms
looped domains that
attach to proteins
Replicated
chromosome
(1,400 nm)
Looped domains
(300-nm fiber)
Metaphase
chromosome
•  Most chromatin is loosely packed in the nucleus during
interphase and condenses prior to mitosis
•  euchromatinloosely packed chromatin
•  heterochromatinhighly condensed chromatin
•  during interphase a few regions of chromatin
(centromeres and telomeres)
•  Dense packing of the heterochromatin makes it
difficult for the cell to express genetic information
coded in these regions
Painted Chromosomes
•  At interphase, some chromatin is organized into a
10-nm fiber, but much is compacted into a 30-nm fiber,
through folding and looping
•  Interphase chromosomes are not highly condensed,
but still occupy specific restricted regions in nucleus
12