Chapter 16

Nucleic Acids and Inheritance

陳逸凌 I-Ling Chen, PhD
呼吸治療學系 助理教授
[email protected]
Ext. 2325#76
DNA is the Genetic Material
• Early in the 20th century, the identification of the molecules of inheritance loomed as a
major challenge to biologists.
• 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 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 studied two strains of the
Streptococcus Pneumoniae.
• He called this phenomenon
transformation, now defined as a
change in genotype and phenotype
due to assimilation of foreign 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.
• A virus is DNA (or sometimes RNA) enclosed by a protective coat, often simply protein.
Evidence That Viral DNA Can Program Cells
Hershey-Chase experiment
Additional Evidence That DNA Is the Genetic
Material
• DNA is a polymer of nucleotides, each consisting of
a nitrogenous base, a sugar, and a phosphate
group.
• The nitrogenous bases can be adenine (A),
thymine (T), guanine (G), or cytosine (C)
• 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.
Additional Evidence That DNA Is the Genetic
Material
• Two findings became known as Chargaff’s rules:

✓ The base composition of DNA varies between species.

✓ For each species, the percentages of A and T bases are roughly, as are those of G
and C bases.
• The basis for these rules was not understood until the discovery of the double helix.
Building a Structural Model of DNA
• 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.
Building a Structural Model of DNA
• Franklin’s X-ray crystallographic images of DNA enabled Watson to deduce that DNA was
helical.
• The pattern in the photo suggested that the DNA molecule was made up of two strands,
forming a double helix.
• The X-ray images also enabled Watson to deduce the width of the helix and the spacing
of the nitrogenous bases.

1962
Nobel Prize Physiology or Medicine
Building a Structural Model of DNA
• Franklin had concluded that there were two outer sugar-phosphate backbones, with the
nitrogenous bases paired in the molecule’s interior.
• Watson and Crick built models of a double helix to conform to the X-rays and chemistry of
DNA.
• Watson built a model in which the backbones were antiparallel (their subunits run in
opposite directions.
Building a Structural Model of DNA
Building a Structural Model of DNA
• 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 (A or G) with a pyrimidine (C or T) resulted in a uniform width
consistent with the X-ray data.
Building a Structural Model of DNA
• 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.
Many Proteins Work Together in DNA
Replication and Repair
• 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 two new daughter strands are built
based on base-pairing rules.
The Basic Principle: Base Pairing to a Template
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).
The Basic Principle: Base Pairing to a Template
Strand
• Experiments by Matthew Meselson and Franklin
Stahl supported the semiconservative model.
DNA Replication - Getting Started
• Replication begins at particular sites called origins of replication, where the two DNA
strands are separated, opening up a replication “bubble”.
• 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.
Origins of Replication
DNA Replication - Getting Started
• 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 relieves the strain of twisting of the double helix by breaking, swiveling,
and rejoining DNA strands.
DNA Replication - Synthesizing a New DNA
Strand
• DNA polymerases require a primer to which they can add nucleotides.
• The initial nucleotide strand is a short RNA primer.
• This is synthesized by the enzyme primase.
• 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.
DNA Replication - Synthesizing a New DNA
Strand
• Enzymes called DNA polymerases catalyze the synthesis 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 (proofreading).
DNA Replication - Synthesizing a New DNA
Strand
• 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 joins the DNA strand, via a H+

dehydration reaction, it loses two phosphate

groups as a molecule of pyrophosphate.
+ H2O
DNA Replication - 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.
DNA Replication - Antiparallel Elongation

5’ 3’
3’ 5’
DNA Replication - Antiparallel Elongation
• 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.

5’ 3’
3’ 5’
DNA Replication - Antiparallel Elongation
A Summary of DNA Replication
A Summary of DNA Replication
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.
• The exact mechanism is not yet resolved.
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.
• In nucleotide excision repair, a nuclease cuts out and
replaces damaged stretches of DNA.
• 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.
Evolutionary Significance of Altered DNA
Nucleotides
• The error rate after proofreading and 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 and are ultimately responsible for the appearance of new species.
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.
Replicating the Ends of DNA 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.
Replicating the Ends of DNA Molecules
• 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.
A chromosome consists of a DNA molecule
packed together with proteins
• 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.
• In a bacterium, the DNA is “supercoiled” and found in a region of the cell called the nucleoid.
A chromosome consists of a DNA molecule
packed together with proteins
• In the eukaryotic cell, DNA is precisely
combined with proteins in a complex
called chromatin.
• Proteins called histones are responsible for
the first level of packing in chromatin.
• Chromosomes fit into the nucleus through an
elaborate, multilevel system of packing.
A chromosome consists of a DNA molecule
packed together with proteins
• Unfolded chromatin resembles beads on a string, with each “bead” being a nucleosome,
the basic unit of DNA packaging.
• They are composed of two each of the four basic histone types, with DNA wrapped twice
around the core of the eight histones.
A chromosome consists of a DNA molecule
packed together with proteins
• Chromatin undergoes changes in packing during the cell cycle.
• At interphase, some chromatin seems to be organized into a 10-nm fiber, but much is
compacted into a 30-nm fiber, through folding and looping.
• Interphase chromosomes occupy specific restricted regions in the nucleus, and the fibers of
different chromosomes do not become entangled.
The degree of DNA packing affects gene
expression of cells
• 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
condensation (Me-, Ac-…).
• These changes can also have multiple effects on gene expression.
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