16 the molecular basis of inheritance

LECTURE PRESENTATIONS
For CAMPBELL BIOLOGY, NINTH EDITION
Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson

Chapter 16

The Molecular Basis of
Inheritance

Lectures by
Erin Barley
Kathleen Fitzpatrick

© 2011 Pearson Education, Inc.

Overview: Life’s Operating Instructions
• In 1953, James Watson and Francis Crick
introduced an elegant double-helical model for the
structure of deoxyribonucleic acid, or DNA
• DNA, the substance of inheritance, is the most
celebrated molecule of our time
• 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


DNA is the genetic material
• Early in the 20th century, the identification of the
molecules of inheritance loomed as a major
challenge to biologists


The Search for the Genetic Material:
Scientific Inquiry
• When T. H. Morgan’s group showed that genes
are located on chromosomes, the two components
of chromosomes—DNA and protein—became
candidates for the genetic material
• 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
• The discovery of the genetic role of DNA began
with research by Frederick Griffith in 1928
• Griffith worked with two strains of a bacterium, one
pathogenic and one harmless
• 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


Figure 16.2
EXPERIMENT Mixture of
Heat-killed heat-killed
Living S cells Living R cells S cells S cells and
(control) (control) (control) living R cells

RESULTS

Mouse dies Mouse healthy Mouse healthy Mouse dies

Living S cells

• In 1944, Oswald Avery, Maclyn McCarty, and
Colin MacLeod announced that the transforming
substance was DNA
• Their conclusion was based on experimental
evidence that only DNA worked in transforming
harmless bacteria into pathogenic bacteria
• Many biologists remained skeptical, mainly
because little was known about DNA


Evidence That Viral DNA Can Program Cells
• More evidence for DNA as the genetic material
came from studies of viruses that infect bacteria
• Such viruses, called bacteriophages (or phages),
are widely used in molecular genetics research


Figure 16.3

Phage
head

Tail
sheath

Tail fiber

DNA

100 nm
Bacterial
cell

• In 1952, Alfred Hershey and Martha Chase
performed experiments showing that DNA is the
genetic material of a phage known as T2
• To determine this, they designed an experiment
showing that only one of the two components of
T2 (DNA or protein) enters an E. coli cell during
infection
• They concluded that the injected DNA of the
phage provides the genetic information


Figure 16.4-3

EXPERIMENT
Radioactive Empty
protein protein
shell Radioactivity
Phage (phage protein)
in liquid
Bacterial cell

Batch 1:
Radioactive DNA
sulfur Phage
(35S) DNA

Centrifuge

Radioactive Pellet (bacterial
DNA cells and contents)

Batch 2:
Radioactive
phosphorus
(32P)

Centrifuge
Radioactivity
Pellet (phage DNA)
in pellet

Additional Evidence That DNA Is the
Genetic Material
• It was known that DNA is a polymer of
nucleotides, each consisting of a nitrogenous
base, a sugar, and a phosphate group
• In 1950, Erwin Chargaff 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


• Two findings became known as Chargaff’s rules
– The base composition of DNA varies between
species
– But, in any species the number of A and T bases
are equal and the number of G and C bases are
equal
• The basis for these rules was not understood until
the discovery of the double helix


Figure 16.5
Sugar–phosphate Nitrogenous bases
backbone
5′ end

Thymine (T)

Adenine (A)

Cytosine (C)

Phosphate
Guanine (G)

Sugar
(deoxyribose)
DNA Nitrogenous base
nucleotide 3′ end

Building a Structural Model of DNA:
Scientific Inquiry
• After DNA was accepted as the genetic material,
the challenge was to determine how its structure
accounts for its role in heredity
• Maurice Wilkins and Rosalind Franklin were using
a technique called X-ray crystallography to study
molecular structure
• Franklin produced a picture of the DNA molecule
using this technique


Figure 16.6

(a) Rosalind Franklin (b) Franklin’s X-ray diffraction
photograph of DNA

• Franklin’s X-ray crystallographic images of DNA
enabled Watson to deduce that DNA was helical
• The X-ray images also enabled Watson to deduce
the width of the helix and the spacing of the
nitrogenous bases
• The pattern in the photo suggested that the DNA
molecule was made up of two strands, forming a
double helix


Figure 16.7

G
5′ end
C
C G Hydrogen bond
3′ end
G C
G C T A

3.4 nm
T A

G C G C
C G

A T

1 nm C G
T A
C G
G C
C G A T

A T 3′ end
A T
0.34 nm
T A 5′ end

(a) Key features of (b) Partial chemical structure (c) Space-filling
DNA structure model

• Watson and Crick built models of a double helix to
conform to the X-rays and chemistry of DNA
• Franklin had concluded that there were two outer
sugar-phosphate backbones, with the nitrogenous
bases paired in the molecule’s interior
• Watson built a model in which the backbones were
antiparallel (their subunits run in opposite
directions)


• 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 data


Figure 16.UN01

Purine + purine: too wide

Pyrimidine + pyrimidine: too narrow

Purine + pyrimidine: width
consistent with X-ray data

• Watson and Crick reasoned that the pairing was
more specific, dictated by the base structures
• They determined that adenine (A) paired only with
thymine (T), and guanine (G) paired only with
cytosine (C)
• The Watson-Crick model explains Chargaff’s
rules: in any organism the amount of A = T, and
the amount of G = C


Figure 16.8

Sugar
Sugar
Adenine (A) Thymine (T)

Sugar
Sugar

Guanine (G) Cytosine (C)

Many proteins work together in DNA
replication and repair
• The relationship between structure and function is
manifest in the double helix
• Watson and Crick noted that the specific base
pairing suggested a possible copying mechanism
for genetic material


The Basic Principle: Base Pairing to a
Template Strand
• 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 two new daughter strands are built based on
base-pairing rules


Figure 16.9-3

A T A T A T A T
C G C G C G C G
T A T A T A T A
A T A T A T A T
G C G C G C G C

(a) Parent molecule (b) Separation of (c) “Daughter” DNA molecules,
strands each consisting of one
parental strand and one
new strand

• Watson and Crick’s semiconservative 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 the conservative model
(the two parent strands rejoin) and the dispersive
model (each strand is a mix of old and new)


Figure 16.10
Parent First Second
cell replication replication

(a) Conservative
model

(b) Semiconservative
model

(c) Dispersive model

• Experiments by Matthew Meselson and Franklin
Stahl supported the semiconservative model
• They labeled the nucleotides of the old strands
with a heavy isotope of nitrogen, while any new
nucleotides were labeled with a lighter isotope
• The first replication produced a band of hybrid
DNA, eliminating the conservative model
• A second replication produced both light and
hybrid DNA, eliminating the dispersive model and
supporting the semiconservative model


Figure 16.11 EXPERIMENT
1 Bacteria 2 Bacteria
cultured in transferred to
medium with medium with
15
N (heavy 14
N (lighter
isotope) isotope)

RESULTS
3 DNA sample 4 DNA sample Less
centrifuged centrifuged dense
after first after second
replication replication More
dense
CONCLUSION
Predictions: First replication Second replication

Conservative
model

Semiconservative
model

Dispersive
model

Getting Started
• Replication begins at particular sites called
origins of replication, where the two DNA
strands are separated, opening up a replication
“bubble”
• A bacterial chromosome has 1 origin of
replication
• A eukaryotic chromosome may have hundreds or
even thousands of origins of replication
• Replication proceeds in both directions from each
origin, until the entire molecule is copied


Figure 16.12
(a) Origin of replication in an E. coli cell (b) Origins of replication in a eukaryotic cell
Origin of Double-stranded
Parental (template) strand Origin of replication DNA molecule
replication
Daughter (new)
strand Parental (template) Daughter (new)
strand strand
Replication
Double- fork
stranded
DNA molecule Replication
bubble
Bubble Replication fork

Two daughter
DNA molecules

Two daughter DNA molecules

0.25 µm
0.5 µm

• At the end of each replication bubble is a
replication fork, a Y-shaped region where new
DNA strands are elongating
• Helicases are enzymes that untwist the double
helix at the replication forks
• Single-strand binding proteins bind to and
stabilize single-stranded DNA
• Topoisomerase corrects “overwinding” ahead of
replication forks by breaking, swiveling, and
rejoining DNA strands


• DNA polymerases cannot initiate synthesis of a
polynucleotide; they can only add nucleotides to
the 3′ end
• The initial nucleotide strand is a short RNA
primer
• An enzyme called primase can start an RNA
chain from scratch and adds RNA nucleotides
one at a time using the parental DNA as a
template
• The primer is short (5–10 nucleotides long), and
the 3′ end serves as the starting point for the new
DNA strand

Figure 16.13

Primase

3′
Topoisomerase
5′ RNA
3′ primer
5′
3′

Helicase

5′
Single-strand binding
proteins

Synthesizing a New DNA Strand
• Enzymes called DNA polymerases catalyze the
elongation of new DNA at a replication fork
• Most DNA polymerases require a primer and a
DNA template strand
• The rate of elongation is about 500 nucleotides
per second in bacteria and 50 per second in
human cells


• Each nucleotide that is added to a growing DNA
strand is a nucleoside triphosphate
• dATP supplies adenine to DNA and is similar to
the ATP of energy metabolism
• The difference is in their sugars: dATP has
deoxyribose while ATP has ribose
• As each monomer of dATP, dGTP, dCTP, or dTTP
joins the DNA strand, it loses two phosphate
groups as a molecule of pyrophosphate


Figure 16.14

New strand Template strand
5′ 3′ 5′ 3′

Sugar A T A T
Phosphate Base

C G C G

G C G C
DNA
OH
polymerase
3′ A T A
T
P P Pi OH
P
P C Pyrophosphate 3′ C
OH
Nucleoside 2Pi
triphosphate 5′ 5′

Antiparallel Elongation
• The antiparallel structure of the double helix
affects replication
• DNA polymerases add nucleotides only to the free
3′ end of a growing strand; therefore, a new DNA
strand can elongate only in the 5′ to 3′ direction
• Along one template strand of DNA, the DNA
polymerase synthesizes a leading strand
continuously, moving toward the replication fork


Figure 16.15
Overview
Leading
Origin of replication Lagging
strand
strand

Primer

Lagging Leading
strand strand Origin of
Overall directions replication
of replication

3′
5′

5′ RNA primer
3′
3′ Sliding clamp

DNA pol III
Parental DNA 5′
3′
5′

5′
3′
3′

5′

• 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


Figure 16.16a

Overview
Leading Origin of replication Lagging
strand strand

Lagging strand
2
1
Leading
strand
Overall directions
of replication

LE 16-15_6
Primase joins RNA
nucleotides into a primer.
3′ 5′

5′ 3′
Template
strand DNA pol III adds
DNA nucleotides to
the primer, forming
an Okazaki fragment.

3′ 5′
RNA primer 3′

5′

After reaching the
next RNA primer (not
shown), DNA pol III Okazaki
falls off. fragment 3′
3′
5′

5′

After the second fragment is
primed, DNA pol III adds DNA
nucleotides until it reaches the
first primer and falls off.

5′ 3′
3′
5′

DNA pol I replaces
the RNA with DNA,
adding to the 3′ end
5′ of fragment 2. 3′
3′
5′

DNA ligase forms a
bond between the newest The lagging
DNA and the adjacent DNA strand in the region
of fragment 1. is now complete.
5′ 3′
3′ 5′

Overall direction of replication

Figure 16.17

Overview
Leading Origin of
replication Lagging
strand strand

Leading
Lagging strand
strand Overall directions
Leading strand of replication

5′ DNA pol III
3′ Primer
Primase
3′ 5′
3′
Parental DNA pol III Lagging strand
DNA 5′
4 DNA pol I DNA ligase
3′5′
3 2 1 3′

5′

The DNA Replication Complex
• The proteins that participate in DNA replication
form a large complex, a “DNA replication machine”
• The DNA replication machine may be stationary
during the replication process
• Recent studies support a model in which DNA
polymerase molecules “reel in” parental DNA and
“extrude” newly made daughter DNA molecules
• Primase may act as a molecular brake,
coordinating primer placement and the rates of
replication on the leading and lagging strands


Figure 16.18

DNA pol III
Parental DNA Leading strand
5′
5′ 3′ 3′

3′
3′ 5′ 5′

Connecting Helicase
protein

3′ 5′ Lagging
DNA strand
3′ Lagging strand template
pol III 5′

Proofreading and Repairing DNA
• DNA polymerases proofread newly made DNA,
replacing any incorrect nucleotides
• In mismatch repair of DNA, repair enzymes
correct errors in base pairing
• DNA can be damaged by exposure to harmful
chemical or physical agents such as cigarette
smoke and X-rays; it can also undergo
spontaneous changes
• In nucleotide excision repair, a nuclease cuts
out and replaces damaged stretches of DNA


Figure 16.19
5′ 3′ A thymine dimer
distorts the DNA molecule.
3′ 5′
Nuclease

A nuclease enzyme cuts
the damaged DNA strand
5′ at two points and the
3′ damaged section is
removed.
3′ 5′

DNA
polymerase
Repair synthesis by
a DNA polymerase
5′ 3′ fills in the missing
nucleotides.

3′ 5′
DNA
ligase
DNA ligase seals the
5′ 3′ free end of the new DNA
to the old DNA, making the
strand complete.
3′ 5′

Evolutionary Significance of Altered DNA
Nucleotides
• Error rate after proofreading repair is low but not
zero
• Sequence changes may become permanent and
can be passed on to the next generation
• These changes (mutations) are the source of the
genetic variation upon which natural selection
operates


Replicating the Ends of DNA Molecules
• Limitations of DNA polymerase create problems
for the linear DNA of eukaryotic chromosomes
• The usual replication machinery provides no way
to complete the 5′ ends, so repeated rounds of
replication produce shorter DNA molecules with
uneven ends
• This is not a problem for prokaryotes, most of
which have circular chromosomes


LE 16-18
5′
End of parental Leading strand
DNA strands Lagging strand
3′

Last fragment Previous fragment

RNA primer
Lagging strand 5′
3′

Primer removed but Removal of primers and
cannot be replaced replacement with DNA
with DNA because where a 3′ end is available
no 3′ end available
for DNA polymerase
5′
3′
Second round
of replication

5′
New leading strand 3′
New leading strand 5′
3′
Further rounds
of replication

Shorter and shorter
daughter molecules

• Eukaryotic chromosomal DNA molecules have
special nucleotide sequences at their ends 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
• It has been proposed that the shortening of
telomeres is connected to aging


• If chromosomes of germ cells became shorter in
every cell cycle, essential genes would eventually
be missing from the gametes they produce
• An enzyme called telomerase catalyzes the
lengthening of telomeres in germ cells
• The shortening of telomeres might protect cells
from cancerous growth by limiting the number of
cell divisions
• There is evidence of telomerase activity in cancer
cells, which may allow cancer cells to persist


• Chromatin, a complex of DNA and protein,
is found in the nucleus of eukaryotic cells
• Chromosomes fit into the nucleus through
an elaborate, multilevel system of packing


• Chromatin undergoes changes in packing during
the cell cycle
• At interphase, some chromatin is organized into a
10-nm fiber, but much is compacted into a 30-nm
fiber, through folding and looping
• Though interphase chromosomes are not highly
condensed, they still occupy specific restricted
regions in the nucleus


Figure 16.22a

Nucleosome
(10 nm in diameter)
DNA double helix
(2 nm in diameter)

H1
Histone
Histones tail
Nucleosomes, or “beads on
DNA, the double helix Histones a string” (10-nm fiber)

Figure 16.22b

Chromatid
(700 nm)

30-nm fiber

Loops Scaffold

300-nm fiber

30-nm fiber

Replicated
chromosome
(1,400 nm)
Looped domains
(300-nm fiber) Metaphase
chromosome

Figure 16.22f

Loops Scaffold

Figure 16.22g

Chromatid
(700 nm)

• Most chromatin is loosely packed in the nucleus
during interphase and condenses prior to mitosis
• Loosely packed chromatin is called euchromatin
• During interphase a few regions of chromatin
(centromeres and telomeres) are highly
condensed into heterochromatin
• Dense packing of the heterochromatin makes it
difficult for the cell to express genetic information
coded in these regions
• Histones can undergo chemical modifications that
result in changes in chromatin organization


16 the molecular basis of inheritance

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