Chapter 9 Information of Life, DNA and RNA structure, DNA replication.

Chapter 9 – The Information of Life: DNA and RNA
Structure, DNA Replication, and Chromosome Structure
Chapter Outline
1. Properties and identification
of the genetic material
2. Nucleic acid structure
3. Discovery of the double-helix
structure of DNA
4. Overview of DNA replication
5. Molecular mechanisms of
DNA replication
6. Molecular structure of
eukaryotic chromosomes
Remember blue font color marks
important ideas and bold marks
terms to master

9.1 Properties and Identification of the Genetic Material
Section 9.1 Learning
Outcomes
1. List and describe the 4 key
criteria that the genetic
material must fulfill
2. Describe the experiments
that identified DNA as the
genetic material
3. Analyze the results of the
experiments that identified
DNA as the genetic material

9.1 Properties and Identification of the Genetic Material
Four criteria necessary for the genetic material:
1. Information  must contain information
necessary to construct entire organism
2. Replication  must be accurately copied
3. Transmission  must be passed from
parents to offspring and from cell to cell
during cell division
4. Variation  be able to account for
differences between individuals and
between species
• A biochemical basis of heredity was postulated in the late 1800s

9.1 Properties and Identification of the Genetic Material
Griffith’s Bacterial Transformation Experiments
Indicated the Existence of a Genetic Material
• In the late 1920s, Frederick Griffith was working with Streptococcus
pneumoniae bacteria
• Smooth (S) strains
secrete capsules; are
typically deadly
• Rough (R) strains do
not secrete capsules;
are typically survivable
• Griffith injected live
and/or heat-killed bacteria
into mice and observed
the outcome

9.1 Properties and Identification of the Genetic Material
Griffith’s Bacterial Transformation Experiments
Indicated the Existence of a Genetic Material
• A surprising result occurred when a mix of live type R and heat-
killed type S bacteria was injected
• The mouse died and living type S bacteria were isolated from
the blood
• Griffith postulated that a substance (genetic material) from the
dead type S cells had transformed the type R cells into type S
• Griffith could not
determine the
biochemical
composition of
the transforming
substance

9.1 Properties and Identification of the Genetic Material
Avery, MacLeod, and McCarty Used Purification Methods
to Reveal That DNA Is the Genetic Material
• In the 1940s, Avery, MacLeod, and McCarty used Griffith’s
observations as part of an experimental strategy to biochemically
identify the genetic material
• Initial experiments indicated that only purified DNA could
convert R to S; however, purified DNA might still contain traces
of contamination that may be the transforming principle
• Enzymes that
break down
DNA, RNA, or
protein were
used to
degrade
potential
contaminants

9.1 Properties and Identification of the Genetic Material
Avery, MacLeod, and McCarty Used Purification Methods
to Reveal That DNA Is the Genetic Material

9.1 Properties and Identification of the Genetic Material
Avery, MacLeod, and McCarty Used Purification Methods
to Reveal That DNA Is the Genetic Material

9.2 Nucleic Acid Structure
Section 9.2 Learning
Outcomes
1. Outline the structural
features of DNA at 5 levels
of complexity
2. Describe the structure of
nucleotides, a DNA strand,
and the DNA double helix
3. Describe the directionality
of a DNA strand
4. List the complementary
bases

9.2 Nucleic Acid Structure
• DNA and RNA are nucleic acids, polymers
of nucleotides that are responsible for the
storage, expression, and transmission of
genetic information
• The structure of DNA can be considered at
different levels of complexity:
1. Nucleotides – the building blocks
2. Strand – a linear polymer
3. Double helix – the two strands
twisted together
4. Chromosomes – DNA associated
with different proteins
5. Genome – the complete complement
of genetic material in an organism

9.2 Nucleic Acid Structure
Nucleotides Contain a Phosphate, a Sugar, and a Base
• A nucleotide has 3
components: a pentose sugar,
a phosphate group, and a
nitrogen-containing base
• A numbering system identifies
particular carbons in the sugar
• A base is attached to the 1ʹ
carbon atom, and a phosphate
group is attached to the 5ʹ
carbon

9.2 Nucleic Acid Structure
A Strand Is a Linear Linkage of Nucleotides
with Directionality
• A strand is formed when nucleotides are covalently attached
• Key structural features of a DNA strand:
• Covalent bonds, called phosphodiester
bonds, link nucleotides together
• A sugar in one nucleotide is linked to a
phosphate group in the next nucleotide,
forming a sugar-phosphate backbone
• Bases project away from the
backbone
• Strands have directionality, based on
orientation of the sugar molecules
• The 5ʹ end has a free phosphate group
and the 3ʹ end has a free hydroxyl group

9.2 Nucleic Acid Structure
DNA Has a Double-Stranded, Antiparallel, Helical Structure
Formed by Complimentary Base Pairing of Nucleotides
Features of DNA:
• Double-stranded helix with outer
backbone and bases on the inside
• Stabilized by H-bonds between base pairs
• Base pairing is specific (AT/CG rule)
• Strands are complimentary to each other
• Strands are antiparallel
• One complete turn is 3.4 nm and
comprises ~10 base pairs
• Contains major groove and minor groove;
the major groove provides a binding site
for many proteins

9.2 Nucleic Acid Structure
DNA Has a Double-Stranded, Antiparallel, Helical Structure
Formed by Complimentary Base Pairing of Nucleotides

9.3 Discovery of the Double-Helix Structure of DNA
Section 9.3 Learning
Outcomes
1. Describe and interpret the
work of Franklin, Chargaff,
and Watson and Crick

9.3 Discovery of the Double-Helix Structure of DNA
X-ray Diffraction Studies Provided Key Information
Regarding DNA Structure
• X-ray diffraction was a key
experimental tool that led to
the discovery of the DNA
double helix structure
• In the 1950s, Rosalind Franklin
(a British biophysicist)
analyzed DNA diffraction
patterns which indicated
• a helical structure
• a uniform diameter (~2nm)
• diameter too big to be a
single strand

9.3 Discovery of the Double-Helix Structure of DNA
An Analysis of Base Composition in DNA Provided
Evidence for the AT/CG Rule
• In 1950, Erwin Chargaff (Austrian-born biochemist) analyzed the
base composition of DNA that was isolated from many different
species and found a pattern
• The amount of adenine
was similar to the
amount of thymine and
the amount of cytosine
was similar to guanine

9.3 Discovery of the Double-Helix Structure of DNA
Creating Ball-and-Stick Models Provided a Strategy to
Deduce the Structure of DNA
• James Watson and Francis Crick (both biologists) synthesized the
work of others to discover the structure of DNA
• the x-ray diffraction data of Franklin
• the base ratio data of Chargaff
• the ball-and-stick modeling approach
of Linus Pauling (American chemist
studying protein structure)
• Watson and Crick
published their work
in 1953

9.4 Overview of DNA Replication
Section 9.4 Learning
Outcomes
1. Describe the experiments
of Meselson and Stahl
2. Interpret the results of the
Meselson and Stahl
experiments
3. Explain how the double-
stranded structure of DNA
and the AT/GC rule allow
DNA to be replicated
semiconservatively

9.4 Overview of DNA Replication
Meselson and Stahl Considered 3 Proposed Mechanisms
of DNA Replication
• In the late 1950s, 3 different
models for DNA replication had
been proposed
• Semiconservative mechanism
• Conservative mechanism
• Dispersive mechanism
• Original strands are parent
strands and newly made strands
are daughter strands

9.4 Overview of DNA Replication
Meselson and Stahl Considered 3 Proposed Mechanisms
of DNA Replication
• In 1958, Matthew Meselson and Franklin Stahl devised an
experiment that used isotope labeling to differentiate among the
three proposed DNA replication mechanisms
• Nitrogen is found in DNA and occurs in a common light form
(14N) and a rare heavy isotope form (15N)
• E. coli grew in an environment with 15N to label DNA (existing
parent strands were formed with heavy 15N), then the bacteria
were switched to an environment with 14N (any newly made
daughter strands would be formed with light 14N)
• Samples were collected after
each generation
• The results were consistent with
the semiconservative mechanism

9.4 Overview of DNA Replication
Meselson and Stahl Considered 3 Proposed Mechanisms
of DNA Replication

9.4 Overview of DNA Replication
DNA Replication Proceeds According to the AT/GC Rule
• During replication,
the 2 parental strands
are separated and
serve as template
strands for the
synthesis of daughter
strands
• The result of DNA
replication is 2 double
helices with the same
base sequence as the
original DNA

9.5 Molecular Mechanism of DNA Replication
Section 9.5 Learning
Outcomes
1. Explain how the synthesis of
new DNA strands begins at
an origin of replication
2. Describe the functions of
helicase, topoisomerase,
single-strand binding
protein, primase, and DNA
polymerase at the
replication fork
3. Outline the key differences
between the synthesis of the
leading and lagging strands
4. List 3 reasons why DNA
replication is very accurate

9.5 Molecular Mechanism of DNA Replication
DNA Replication Begins at an Origin of Replication
• An origin of replication is a site
within a chromosome that serves as
a starting point for DNA replication
• The DNA strands are unwound,
forming an opening called a
replication bubble
• Within this bubble, 2 replication
forks are formed
• Replication proceeds outward from
the replication forks in both
directions (bidirectional replication)

9.5 Molecular Mechanism of DNA Replication
DNA Replication Begins at an Origin of Replication
• Bacterial
chromosomes are
relatively small and
circular with a single
origin of replication
• Eukaryotic
chromosomes are
larger and have a
linear structure with
multiple origins of
replication
Fig 11.13, Biology, Brooker

9.5 Molecular Mechanism of DNA Replication
DNA Replication Requires the Action of Several
Different Proteins
• DNA helicase, DNA topoisomerase, and single-strand binding
proteins are responsible for fork formation and movement
• DNA helicase uses energy from ATP to break H-bonds between
base pairs

9.5 Molecular Mechanism of DNA Replication
DNA Replication Requires the Action of Several
Different Proteins
• Two enzymes are needed to synthesize DNA strands during
replication: DNA polymerase and DNA primase
• DNA polymerase covalently links
nucleotides together
• Incoming nucleotides
are triphosphates;
pyrophosphate is broken
away and the energy
released is coupled to
the formation of a new
bond between
nucleotides

9.5 Molecular Mechanism of DNA Replication
DNA Replication Requires the Action of Several
Different Proteins
• DNA polymerase has 2 important functional constraints
1. DNA polymerase cannot begin synthesis on a bare template
strand; it can only extend a pre-existing strand
2. DNA polymerase synthesizes DNA in a 5’ to 3’ direction
• DNA primase makes a
complimentary primer
of RNA (10 to 12
nucleotides in length)
that can be extended
by DNA polymerase

9.5 Molecular Mechanism of DNA Replication
Leading and Lagging Strands Are Made Differently
• Daughter strands are synthesized differently at the replication fork
• The leading strand is made continuously, extending in the same
direction that the replication fork is moving
• The lagging strand is made as a series of small Okazaki fragments,
extending in the opposite direction as the replication fork

9.5 Molecular Mechanism of DNA Replication
Leading and Lagging Strands Are Made Differently
• Proteins involved with the synthesis of leading and lagging strands
in E. coli

9.5 Molecular Mechanism of DNA Replication
Leading and Lagging Strands Are Made Differently
Table 11.2, Biology, Brooker

9.5 Molecular Mechanism of DNA Replication
DNA Replication Is Very Accurate
• Permanent mistakes in DNA replication are extraordinarily rare
(ex: 1 mistake per 100 million nucleotides in bacteria)
• DNA replication has high fidelity due to
1. Hydrogen bonds between A/T and C/G are more stable than
between mismatched pairs
2. DNA polymerase is unlikely to catalyze bonds between
nucleotides if a mismatched base pair occurs
3. DNA polymerase can proofread to remove mismatched pairs

9.6 Molecular Structure of Eukaryotic Chromosomes
Section 9.6 Learning
Outcomes
1. Describe the structure of
nucleosomes and the
30-nm fiber, and describe
how the 30-nm fiber forms
loop domains
2. Outline the various levels of
compaction that lead to a
metaphase chromosome

9.6 Molecular Structure of Eukaryotic Chromosomes
• A typical eukaryotic chromosome can be hundreds of millions of
base pairs in length and must fit inside the nucleus, meaning
chromosomes must be folded and compacted
• Chromosome describes a discrete unit of genetic material whereas
chromatin refers to the complex of DNA and proteins that makes
up eukaryotic chromosomes
• Chromosomes are dynamic; they alternate between tight and loose
compaction states
• Fig 4.20 - Chromosomes were labeled with chromosome-specific dyes

9.6 Molecular Structure of Eukaryotic Chromosomes
DNA Wraps Around Histone Proteins to
Form Nucleosomes
• Eukaryotic DNA is first compacted by wrapping around a group of
proteins called histones, which forms structures called
nucleosomes
• The nucleosome is a repeating
structural unit that is 11 nm in
diameter
• Histone proteins contain many
positively charged amino acids
that interact with the negatively
charged phosphates of DNA
• Linker regions of DNA connect
adjacent nucleosomes

9.6 Molecular Structure of Eukaryotic Chromosomes
Nucleosomes Form a 30-nm Fiber
• Nucleosomes are organized into a more compact structure that is
30 nm in diameter
• Histone H1 (the green protein in the figure below) and other
proteins are important in the formation of the 30-nm fiber

9.6 Molecular Structure of Eukaryotic Chromosomes
Chromosomes Are Further Compacted by the
Formation of Loop Domains
• A third level of compaction involves
interactions between the 30-nm fibers
and proteins to form loop domains
• Proteins called CTCF can form loops
• CTCF = CCCTC binding factor, these
proteins bind to a larger DNA
sequence that contains CCCTC
• SMC proteins can also form loops
when the SMC proteins form a dimer
• SMC stands for structural
maintenance of chromosomes
• CTCF and SMC proteins may also be
preset together at loop domains

9.6 Molecular Structure of Eukaryotic Chromosomes
Nondividing Cells Contain Heterochromatin and
Euchromatin, Within Chromosome Territories
• The level of compaction of chromosomes is not uniform
• Heterochromatin is highly compacted whereas euchromatin is less
condensed (both can be observed with a light microscope)
• Euchromatin contains 30-nm fibers folded into loop domains
• In heterochromatin, the loop domains are compacted even further
which means that genes found within heterochromatin are usually
inactive
• In nondividing cells, each
chromosome occupies its
own discrete region in the
nucleus and usually does not
overlap with the territories
of other chromosomes

9.6 Molecular Structure of Eukaryotic Chromosomes
During Cell Division, Chromosomes Undergo
Maximum Compaction
• When a cell prepares
to divide, each
chromosome becomes
entirely condensed
• All euchromatin is
compacted to
heterochromatin,
which is further
condensed to form the
final (maximally
compacted) metaphase
chromosome

Chapter 9 Summary
9.1 Properties and identification of the genetic material
• Griffith’s bacterial transformation experiments (using R and S
strains) indicated the existence of a genetic material
• Avery, MacLeod, and McCarty used purification methods to reveal
that DNA is the genetic material
9.2 Nucleic acid structure
• Nucleotides contain a phosphate, a sugar, and a base
• A strand is a linear linkage of nucleotides with directionality
• DNA has a double-stranded, antiparallel, helical structure formed
by the complementary base pairing of nucleotides
9.3 Discovery of the double-helix structure of DNA
• X-ray diffraction studies provided key information regarding DNA
structure
• Analysis of base composition provided evidence of the AT/CG rule
• Creating ball-and-stick models provided a strategy to deduce the
structure of DNA

Chapter 9 Summary
9.4 Overview of DNA replication
• Meselson & Stahl considered 3 proposed replication mechanisms
• DNA replication is semiconservative and proceeds according to
the AT/GC rule
9.5 Molecular mechanism of DNA replication
• DNA replication begins at an origin of replication
• DNA replication requires the action of several different proteins
(DNA helicase, DNA topoisomerase, single-strand binding
proteins, DNA primase, DNA polymerase)
• Leading and lagging strands are made differently
• DNA replication is very accurate

Chapter 9 Summary
9.6 Molecular structure of eukaryotic chromosomes
• DNA wraps around histone proteins to form nucleosomes
• Nucleosomes form a 30-nm fiber
• Chromosomes are further compacted by the formation of loop
domains
• In nondividing cells, chromosomes contain heterochromatin
and euchromatin, and they are found within chromosome
territories
• During cell division, chromosomes undergo maximum
compaction