General Biology I

Chapter 11
Nucleic Acid Structure, DNA
Replication, and
Chromosome Structure
The Genetic Material:
• The Genetic material needs to:
• 1. Contain information to build and run
an entire organism.
• 2. Be copied accurately.
• 3. Be Transmitted, or passed from parent
to offspring, and cell to cell.
• 4. Account for the known variation
within and between species.
The Genetic Material:
• A series of experiments determined
what the Genetic Material was.
• Most scientists believed it would be
Proteins since they were known to be
much more variable than Nucleic
Acids.
• There were 20 amino acids and only 4
nucleotides.
The Genetic Material:
• Griffith (1928) set the stage for showing
what the Genetic Material would be.
• He worked with two strains of the
bacteria Streptococcus pneumoniae.
• The S strain was virulent and killed
mice with a pneumonia infection.
• The R strain was not virulent and a
mouse’s immune system would kill it.
The Genetic Material:
• Griffith first injected mice with the S
strain and saw that mice died.
• After death live S bacteria were found
in the blood.
• This established the virulence of the S
strain.
The Genetic Material:
• He then injected mice with the R strain and
saw that mice did not die (but dead bacteria
in blood).
• This established the non-virulence of the R
strain.
The Genetic Material:
• He then heat-killed the virulent S strain
and injected the dead S strain.
• The mice did not die, since the bacteria
were killed (and found in blood).
The Genetic Material:
• He then mixed the live R strain (which
did not kill mice) with the heat-killed S
strain (which did not kill mice) and
injected the mice with the mixture.
• Mice died, live S strain was recovered.
The Genetic Material:
• Something from the dead S strain had
been transferred to the live R strain,
transforming it into the live S strain.
• Whatever agent had transformed the R
strain to the S strain must be the
Genetic material.
• The hunt then began for this
Transforming Factor.
 The Genetic Material:
• In 1944 Oswald Avery et al. published the
results of their experiments.
• They took the live R Streptococcus
pneumoniae bacteria and mixed it with
heat killed S strain, like Griffith (#4).
• However, they first treated it with enzymes
to destroy some class (or another) of
organic molecules.
The Genetic Material:
• When they treated the heat-killed S
strain with proteases to destroy
proteins, and then added it to live R
bacteria, the mice still died.
• If the genes in the heat-killed S strain
were proteins, they should have been
destroyed and not able to transform the
live R strain into the S Strain.
• Genes could not be proteins.
The Genetic Material:
• When they treated the heat-killed S
strain with nucleases to destroy nucleic
acids, and then added it to live R strain,
the mice lived.
• Genes must consist of Nucleic Acids
since when they are destroyed, so is the
ability to transform the R strain to the
lethal S strain.
The Genetic Material:
• This was the first demonstration that
genes were Nucleic Acids.
• However, doubts about the purity of
the samples, and whether small
amounts of contaminating molecules
could have been altering the results left
doubts for some that genes were really
Nucleic Acids.
 The Genetic Material:
• The second demonstration of the nature of
genes was done by Hershey and Chase (1952).
• They used radioactive isotopes in viruses.
• Of all the organic molecules only Proteins
have Sulfur, so if they grow viruses in
radioactive 35S, only Proteins will be
“labeled.”
The Genetic Material:
• Only Nucleic Acids have Phosphorus.
• Viruses grown in radioactive 32P will
only “label” Nucleic Acids.
• So, they grew viruses in two separate
mixtures, one with 32P (nucleic acids)
and the other with 35S (proteins).
 The Genetic Material:
As an Aside…
• Viruses (i.e. bacteriophages) inject their
genes into bacteria and the genes use the
bacterial cell to produce more viruses.
• Whatever the “genes” are, they should be
found inside the bacterial cells after
infection.
• Are genes Proteins or Nucleic Acids?
The “gene”
 The Genetic Material:
• After growing viruses for several
generations in 35S (proteins) they infected
bacteria with these viruses.
• The bacteria did not contain 35S (proteins).
• Viral genes must not consist of Proteins
since the radioactive proteins were not
injected into the bacteria, nor found in the
next generation of viruses.
The Genetic Material:
• After growing viruses for generations in
32
P (nucleic acids) they infected bacteria
with these viruses.
• The bacteria contained 32P.
• Viral genes must consist of Nucleic
Acids since the radioactive Nucleic Acids
were injected into the bacteria and found
in the next generation of viruses.
The Genetic Material:
• This was the second and definitive
demonstration that genes were made of
Nucleic Acids (DNA).
• Since Viruses were well studied
genetically, it was accepted that genes
were made of DNA.
Structure of the Genetic Material
• Watson and Crick (1953), using information
from Rosalind Franklin, Erwin Chargaff, and
Maurice Wilkins, first described the correct
molecular structure of DNA.
• They described a DNA double helix with a
sugar-phosphate backbone and the
nitrogenous bases projecting inward in
complementary pairs.
The structure of Nucleic Acids
described by Watson and Crick.

Monomeric Subunits:
Nucleotides:
• Pentose Sugar
• Nitrogenous Bases
• Phosphate Group
Pentose sugar:

Ribose Deoxyribose
Found in: RNA DNA
DNA Backbone
Composed of
alternating Sugars
and Phosphates.
Four Nitrogenous Bases:
In DNA – ACG and T

In RNA – ACG and U

Nitrogenous Bases
• Purines: A and G
• Pyrimidines: C, U, and T
Base Pairing Relationships in DNA:
• A with T, and C with G.
Antiparallel
Structure:
• Two strands
in DNA run
in opposite
directions.
Differences between DNA & RNA

RNA DNA
Sugar: Ribose Deoxyribose
Bases: A,C,G & U A,C,G &T
# Strands: One Two
Watson-Crick Model
Link Between Structure & Function
Replication of DNA

• Three Possible Modes of

Replication were suggested by its
structure:
1. Conservative
Two old strands come back together
after Replication. Entire old
molecule conserved in one of two
new molecules.
2. Semiconservative
One new and one old strand form new
molecule. Half of the old molecule
is conserved in each of the new
molecules.
3. Dispersive
A patch-work of new and old forms
the new molecule. Old strand
dispersed in new strands.
 Meselson and Stahl (Ch. 11.3)
Were the first to demonstrate
Semiconservative DNA Replication
using density gradient centrifugation.
Grew Bacteria in heavy 15N, then
transferred them to normal 14N.
 Meselson and Stahl
After one generation in 14N medium, All
DNA was half 15N and half 14N (i.e. all int.),
ruling out Conservative* Replication.

*Conservative would have been

½ DNA heavy & ½ DNA light
 Meselson and Stahl
After two generations, half the DNA was
14
N/14N (light) and half was 15N/14N (int.),
ruling out Dispersive* Replication.

*Dispersive would have been all

the same weight (1 band)
DNA Replication
DNA Replication occurs when
the two strands open out, new
nucleotides line up opposite
the old complementary bases,
and DNA Polymerase
catalyzes their addition to the
new strand.
DNA Replication
• DNA Polymerases are large molecules.
• Most cells have multiple Polymerases,
(human cells have at least 15).
• Only one or two replicate
chromosomes, the rest are involved in
DNA repairs.
The Mechanism of DNA Replication
1. Helicase - Initiates Replication by
denaturing (unzipping) DNA using
energy from ATP.
The Mechanism of DNA Replication
• 2. Topoisomerase travels in front of
Helicase, relieving the supercoiling
caused by Helicase.
3. Single Strand Binding Proteins
These proteins coat single-stranded
DNA to keep it from renaturing
(reforming double helix).
4. Nucleoside Triphosphate precursors
Because of base-pairing relationships,
Nucleoside Triphosphates line-up
across from complementary bases in
old strand (red), which is the template
for the new strand.
 5. DNA Polymerase III –
Splits off last 2 high-energy
phosphates, polymerizing the
Nucleotide into the new
DNA strand.
 DNA Polymerase III

DNA Polymerase III has two limitations:

• It can’t start strands.

• It can’t add new Nucleotides to the 5’
end of growing DNA chains (can only
add to 3’ end of growing/new strand).
Primase overcomes first limitation of DNA
Polymerase III (i.e. it can’t start strands)
Primase replicates the first 12-20 Nucleotides
with RNA, (making the RNA Primer chain) on
which DNA Polymerase III can then build.
 Synthesis of Leading Strand
Template strand runs in the 3’→ 5’
direction (same as fork), so new strand is
built continuously (5’→ 3’ – adding to 3’
end) after a Primer Strand is produced.
 6. Okazaki Fragments
• Remember, the second limitation of
DNA Polymerase III is that it can
only add to 3’ end of growing chain
• This is overcome by building the
Lagging Strand in a discontinuous
fashion using Okazaki Fragments.
 Synthesis of Lagging Strand
Template strands runs in the 5’→ 3’
direction (opposite of fork) so if built
continuously, new strand would be
built in the wrong (3’→ 5’) direction
BUT DNA Polymerase
can only synthesize
in 5’→ 3’
direction.
 Okazaki Fragments
SO Lagging strand built discontinuously
in fragments (Okazaki fragments) each
built in 5’→ 3’ direction, but overall in
3’→ 5’ direction (same as fork).*

* Backwards leap frog

Okazaki Fragments
• After the first Okazaki fragment is built,
another primer then fragment is built.
• Each fragment is built in the 5’→ 3’
direction, but are laid down in the overall
3’→ 5’ direction (same as fork). *

*Backwards leap frog

 Okazaki Fragments
• Each fragment is laid down individually
or discontinuously and then connected
to others.
 7. DNA Polymerase I
(both strands)
• Follows Replication Fork, replacing
the Primer Strand with DNA &
correcting errors when found.
8. DNA Ligase
(only lagging strand)
Connects Okazaki Fragments by
closing last gap between fragments.
Animations:
• DNA Replication Video
http://www.youtube.com/watch?
v=4jtmOZaIvS0

• Many Others on YouTube, etc.

 Telomeres (have specialized form
of DNA Replication)

• The ends of Eukaryotic Chromosomes

are called Telomeres.
• They have special repeated
sequences that prevent the
ends of Chromosomes from
attaching to one another.
Telomeres (specialized form of
DNA Replication)
• The replication of Telomeres is
problematic since the replication of
the Lagging strand does not start at
the very end of the Chromosome
(because of DNA Polymerase III’s
limitations).
Telomeres
• As a result Telomeres, may shorten
over many rounds of Replication.
• Shortened Telomeres have been
implicated in aging.
Telomeres
• Some cells, including cancer cells,
have the enzyme Telomerase which
lengthens Telomeres.
• Telomerase attaches to the 3’ end of a
DNA strand.
Telomeres
• An internal RNA template is used
to line up DNA nucleotides and
extend the 3’ end of the
Chromosome.
Telomeres
• After the 3’ end is lengthened, it can be
long enough for DNA Polymerase to
attach and produce another Okazaki
Fragment (primase  RNA primer 1st).
• Okazaki fragment extends bottom
strand in 5’→ 3’ direction.
• Now the entire chromosome is longer.
Molecular Structure of Prokaryotic Chromosomes:

• Prokaryotic Chromosomes are circular

double strands of DNA with both ends
connected.
• Proteins do not regularly and permanently
attach to them.
• There is typically one main chromosome
in a cell, sometimes with “extra” small
circular chromosomes called Plasmids.
Molecular Structure of Eukaryotic Chromosomes:

• In contrast, Eukaryotic
Chromosomes consist
of both DNA and
Proteins.
• Many of the proteins
are Histones which
form Nucleosomes,
around which the DNA
is wrapped in a
groove.
Molecular Structure of Eukaryotic Chromosomes:
• Two copies each of
four Histones
compose
Nucleosomes.
• They contain many
positively charged
peptides to attract
and bind DNA.
Molecular Structure of Eukaryotic Chromosomes:
• A fifth Histone H1
binds linker DNA
which occurs
between the DNA
segments wrapped
around Nucleosomes.
• DNA wrapped
around Nucleosomes
resembles “beads on
a string.”
Molecular Structure of Eukaryotic Chromosomes:

• Adjacent
Nucleosomes are
organized into
thicker fiber, 30
nm in diameter.

c) From another book

Molecular Structure of Eukaryotic Chromosomes:
• The 30 nm fiber of each chromosome is
attached to a filamentous network of
proteins termed the Nuclear Matrix.
• The Matrix consists of protein fibers which
line the inner Nuclear Membrane (Nuclear
Lamina) and other fibers stretching
throughout the Nucleus.
Molecular Structure of Eukaryotic Chromosomes:
• Other Proteins
connect regions of
DNA to the
Nuclear Matrix,
and bend DNA
into Radial Loop
Domains
containing 25,000-
200,000 nbp
(nucleotide base
pairs).
Molecular Structure of Eukaryotic Chromosomes:

• DNA, and the Chromosomes they make up,

are thus anchored to specific regions in the
Nucleus.
• Chromosomes are not free to move within
the Nucleus, but are restricted to specific
regions by binding to the Nuclear Matrix.
Molecular Structure of Eukaryotic Chromosomes:
• During cell division,
Chromosomes condense
into thicker, shorter
structures by a series of
loops and bends, so they
can be moved without
tangling and breaking the
long DNA fibers.