AP Biology Mr.

Austin

UNIT 6
GENE EXPRESSION AND REGULATION
Topics: (click one to jump to that section)

(1)Proving DNA is the Genetic Material

(2)The Structure of DNA
(3)The Replication of DNA
(4)DNA vs. RNA

Self-Assessment Questions
UNIT 6.1 DNA STRUCTURE & REPLICATION

PROVING DNA IS THE

GENETIC MATERIAL
The Search for the Genetic Material
● In the early 1900s, scientists struggled to
identify which molecule contains the genes
that are involved in inheritance.
● In the mid 1800s, Gregor Mendel, the
father of genetics, discovered that
“heritable factors” were passed down from
parent to offspring.
● In 1910, Thomas Hunt Morgan proved
that genes are carried on chromosomes
and are the mechanical mechanism of
inheritance.
● This narrowed down the identity of the
Griffith’s Experiment
● In 1928, Frederick Griffith experimented with a bacterium that
causes pneumonia in mammals. He used two strains of the bacteria,
a pathogenic (disease-causing) one, and a nonpathogenic
(harmless) strain.
● He found that when the pathogenic bacteria were killed with heat
and then mixed with living nonpathogenic bacteria, the living cells
became pathogenic.
● He called this phenomenon transformation, now defined as a
change in genotype and phenotype due to the assimilation of
foreign DNA by a cell.
● Griffith did not know what the transforming “principle” was. It could
have been carbohydrates, proteins, or nucleic acids from the heat
Griffith’s
Experiment
● Bacteria of the
“S” (smooth)
strain are
pathogenic
because they
contain a sugar
capsule that
protects them
from an animal’s
immune system.
● The “R” (rough)
Avery-McCarty-Macleod Experiment
● In 1944, three scientists (Avery, McCarty, and MacLeod)
announced that the transforming “principle” from Griffith’s
experiment was DNA.
● In their experiment, they isolated different solutions containing the
heat-killed S bacteria cells and examined in which solutions
transformation still occurred with the R strain bacteria.
● Only the solutions with the S strain DNA still intact led to
transformation of the R strain bacteria.
● The scientific community was very skeptical of these findings. Many
scientists still supported the theory that proteins were the genetic
material.
Avery-McCarty-
Macleod
Experiment
Hershey-Chase Experiment
● Further support for DNA came from Alfred Hershey and Martha
Case in 1952, who performed experiments that showed DNA was
the genetic material of a bacteriophage known as T2.
○ A bacteriophage (or just “phage”) is a virus that infects
bacteria.
● T2 viruses are composed of almost entirely DNA and protein. When
they infect a bacteria cell (specifically E. Coli), T2 reprograms its
host cell to produce viruses, until the cell finally ruptures.
● Their experiment involved radioactively labeling the proteins and
DNA of T2 viruses and seeing which of the two were found in the
bacteria cells that were infected by the virus.
● The results showed that the viruses transferred their DNA, not their
Hershey-
Chase
Experiment
https://www.khanacademy.org/science/biology/dna-as-t
he-genetic-material/dna-discovery-and-structure/v/esta
blishing-dna-as-transformation-principle
In 1910, Thomas Hunt Morgan proved that
genes are carried on chromosomes. Label the
picture that shows what two types of
molecules make up a chromosome.

Interactive Notes
In Griffith’s experiment, neither living R cells
nor heat killed S cells caused a mouse to die
when given separately. However, a mixture of
the two given to a mouse did cause the
mouse to die. Come up with a possible
explanation.

Interactive Notes
What evidence did Avery, McCarty, and
Macleod have to support that DNA was the
transforming principle in Griffith’s
experiment?

Interactive Notes
Why do you think radioisotopes of sulfur and
phosphorus were used to trace proteins and
DNA in Hershey and Chase’s experiment?

Interactive Notes
How would Hershey and Chase’s results have
changed if they cultured the viruses in a
medium containing radioisotopes of nitrogen,
rather than sulfur and phosphorus?

Interactive Notes
THE STRUCTURE
OF DNA
The Structure of DNA
● Once most scientists were convinced
that DNA was the genetic material, the
challenge became to determine its
structure.
● By the 1950s, it was already known that
DNA is a polymer of nucleotides, each
consisting of a nitrogenous base, a five-
carbon sugar, and a phosphate group,
but the specific shape and 3-D structure
of DNA was still unknown.
Nucleotides
● Each nucleotide is composed of three
parts:
○ A phosphate group, a pentose
(5-carbon) sugar, and a nitrogen-
containing (nitrogenous) base.
● The pentose sugar found in DNA
nucleotides it is deoxyribose.
○ The carbon atoms in the pentose
sugar are numbered 1’ (“1 prime”)
to 5’
○ The nitrogenous base is bound to
the 1’ carbon and the phosphate (DNA) (RNA)
Nucleotides
● There are two families of
nitrogenous bases:
○ Pyrimidines are bases
with one ring and include
cytosine (C), thymine (T),
and uracil (U).
○ Purines are bases with
two rings and include
adenine (A), and guanine
(G).
● Thymine is found only in DNA,
and uracil only in RNA; the rest
Polynucleotides
● Nucleotides are joined together
by a series of dehydration
New
reactions to form a strand Covalent
Bond
(polymer) called a
polynucleotide.
● Covalent bonds are formed
between the 3’ carbon (of the
pentose sugar) of one nucleotide
and the phosphate group of the
next nucleotide.
● The link between the 3’ carbon
of one nucleotide and the 5’
Polynucleotides
Phosphodiester
● Polynucleotides have linkage
two ends: a 3’
(hydroxyl) end and a
5’ (phosphate) end.
● During DNA and RNA
synthesis, nucleotides
are added to the 3’ end
of the growing strand.

New nucleotides
added to the 3’ end
Franklin and Wilkins’ Contribution
● Rosalind Franklin, alongside her colleague
Maurice Wilkins, used X-ray crystallography
to study the 3-D structure of DNA.
○ X-ray crystallography produces images
with spots and smudges created by the
diffraction of X-rays passing through
molecules.
○ Mathematical equations translate the
patterns into information about the 3-D
shape of molecules.
● Franklin had concluded that there were two
outer sugar-phosphate backbones, with the
Watson and Crick’s Contribution
● At the same time, James Watson and
Francis Crick were also trying to uncover
the structure 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 width suggested that the DNA molecule
was made up of two strands, forming a
double helix.
Watson and Crick’s Contribution
● Using the X-ray measurements
and what was known about the
chemistry of DNA, Watson and
Crick developed a final model of
DNA, which they published in
1953.
● 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
Watson and Crick’s Contribution
● Watson and Crick determined that
adenine pairs only with thymine,
and guanine pairs only with
cytosine.
● This matched the finding of
biochemist, Erwin Chargaff, who in
1947 discovered that an organism’s
DNA base composition of adenine
always equals thymine, and the
same for cytosine and guanine.
○ This is known as Chargaff’s
rule.
Overview of DNA’s 3D Structure
● DNA is a double-stranded
molecule.
● Both strands are made up of a
backbone that is composed of
alternating sugar-phosphate
molecules. Sugar-
phosphate
● The two strands twist around backbone
each other, forming a double
helix, and are held together by
hydrogen bonds between the
nitrogenous bases.
DNA
Overview of DNA’s 3D Structure
● Between DNA strands there is
complementary base
pairing:
○ Cytosine (pyrimidine)
makes three hydrogen
bonds with guanine
(purine).
○ Adenine (purine) makes
two hydrogen bonds with
thymine (pyrimidine) in
DNA, or uracil in RNA.
Overview of DNA’s 3D Structure
● A DNA strand has two ends, a 5’
end and a 3’ end, based on the
orientation of the carbons in the
pentose sugar.
● The two strands that make up the
DNA double helix are
antiparallel, meaning they are
oriented in opposite directions.
○ One runs in the 5’→3’
direction, and the other runs
in the 3’→5’ direction
DNA in Prokaryotes vs. Eukaryotes
● The DNA inside prokaryotes is organized
into a single circular chromosome, but
in eukaryotes it is organized into linear
chromosomes.
● Bacterial cells, viruses, and some
eukaryotes also contain plasmids.
○ Plasmids are small, circular,
double-stranded DNA molecules
that are distinct from a cell's
chromosomal DNA.
○ Often, the genes carried in plasmids
provide bacteria with genetic
What are the three components of a
nucleotide?

Interactive Notes
Here is an image of two
nucleotides bonded together. Add
the following to the image:
● Draw a circle around a
nucleotide in the image above.
● Label a phosphodiester bond in
the image above.
● Label each nitrogenous bases
as either a purine or
pyrimidine.
● Draw an arrow on the end that
a third nucleotide would be
added to.
Interactive Notes
What are 3 things that Franklin’s X-ray
crystallography helped to uncover about the
structure of DNA?

1.
2.
3.

Interactive Notes
What are 3 things that Chargaff discovered by
analyzing the DNA base composition of
various species?
1.
2.
3.

Interactive Notes
Correct the following statements about DNA’s
3-D Structure:

1. DNA has two backbones made of alternating sugars

and nitrogenous bases.

2. Between the two strands of DNA, purines pair with

purines and pyrimidines pair with pyrimidines.

3. The two strands that make up DNA are held together

by covalent bonds.

Interactive Notes
How many hydrogen bonds are formed
between nitrogenous bases when they pair
together?

Interactive Notes
DNA is antiparallel. What exactly does that
mean?

Interactive Notes
Plasmids can be transferred between bacteria
cells that are in direct contact with one
another. Use the internet to look up what this
process is called and to draw what it looks
like.

Interactive Notes
What differences would you find in the DNA of
prokaryotes and eukaryotes?

Interactive Notes
UNIT 6.2 REPLICATION

THE REPLICATION
OF DNA
The Basic Principle of DNA Replication
● Conveniently, Watson and Crick’s model of DNA suggested the basic
mechanism of its replication!
● 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 Semiconservative Model
● 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 and the
dispersive model.
● The semiconservative model of
replication was proven in the late 1950’s
in an experiment done by Matthew
Meselson-Stahl Experiment
● In their experiment, DNA was radiolabeled with a heavy isotope of
nitrogen (15N). Then it was placed in a medium containing the
normal, lighter isotope of nitrogen (14N) and allowed to replicate.
○ This meant any new DNA molecules made during replication
would have to use the lighter nitrogen isotope.
● After one replication cycle, all the DNA molecules contained half the
heavy isotope and half the light isotope.
● After two replication cycles, half the DNA molecules contained only
the light isotope and the other half still contained a 50/50 mixture
of light and heavy isotopes.
Meselson-
Stahl
Experiment
Meselson-
Stahl
Experiment
Origins of Replication
● Replication begins at special sites called
origins of replication (ori), 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
● At the ends of each replication bubble is
a replication fork, a Y-shaped region
where new DNA strands are elongating.
● Replication proceeds in both directions
from each origin, until the entire
DNA Replication Complex
● The replication of DNA involves
over a dozen different proteins.
● Most of the proteins involved in
the replication of DNA are bound
together, forming a large protein
complex.
● Some of the major proteins
involved include:
○ DNA Polymerases DNA Replication
○ Primase Complex

○ DNA Ligase
○ Helicase
Unwinding the Double Helix
● Helicase is the enzyme that
unwinds the double helix at the
replication forks, separating the
two parental strands.
● This unwinding causes tighter
twisting and straining ahead of
the replication fork. An enzyme
called topoisomerase relieves
this strain.
DNA Polymerase
● Enzymes called DNA polymerases
catalyze the elongation of new DNA at
a replication fork by adding
nucleotides complementary to the
template strands.
● DNA polymerase can only synthesize
the new DNA strand in the 5’→3’
direction.
○ Meaning that it “reads” the
template strand in the 3’→5’
direction.
○ This also causes the two strands
Leading and Lagging Strands
● Along one template strand of DNA,
called the leading strand, DNA
polymerase can synthesize a
complementary strand continuously,
moving toward the replication fork.
● 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
Priming DNA Synthesis
● DNA polymerases cannot initiate
synthesis of a polynucleotide; they can
only add nucleotides to the 3’ end of
an already existing chain.
● DNA replication must begin with a
short primer or starter strand, usually
a short single strand of RNA,
synthesized by an enzyme called
primase.
● DNA polymerase then adds nucleotides
to the 3ʹ end of the primer and
continues until replication of that
Priming DNA Synthesis
● Only one primer is needed to synthesize the
leading strand, but for the lagging strand
each Okazaki fragment must be primed
separately.
● Another type of DNA polymerase replaces
the RNA primers with DNA.
 Proofreading and Repairing DNA
● DNA polymerases can make mistakes during replication, but most
errors are repaired.
● Two major repair mechanisms:
○ Proofreading: DNA polymerase has a proofreading function, and
if bases are paired incorrectly, the nucleotide is removed.
○ Mismatch repair: after replication, other proteins scan for
mismatched bases missed in proofreading and replace them
with correct ones.
DNA proofreading

Mismatch repair
To the right is a
piece of DNA.
Draw what it will
look like after it
replicates once,
and then a
second time.
Track the original
strands by
drawing them
thick and any new
strands draw thin. Interactive Notes
In Meselson and Stahl’s
experiment, 15N labeled DNA
was replicated in a 14N
medium, and then
centrifuged to separate the
DNA molecules by density. In
the microcentrifuge tubes to
the right, draw where bands
would appear for all three
proposed models of DNA
replication if DNA was
allowed to go through two
cycles of replication. Interactive Notes
Identify the name of the enzyme responsible
for the following actions during DNA
replication:
__________________ unwinds the DNA and separates the two
strands.

__________________ adds short strands of RNA nucleotides to the

DNA strands.
__________________ adds complementary DNA nucleotides to each
strand.
__________________ relieves coil tension upstream from the
replication fork.
__________________ joins Okazaki fragments together on the
lagging
Interactive Notes
strand.
Identify the name of the enzyme responsible
for the following actions during DNA
replication:
__ helicase _______ unwinds the DNA and separates the two
strands.

___primase_________ adds short strands of RNA nucleotides to

the
DNA strands.
_DNA polimerase_____ adds complementary DNA nucleotides to
each
strand.
____topoisomerase __ relieves coil tension upstream from the
replication fork.
__DNA ligase _______ joins Okazaki fragments together on the
lagging
Interactive Notes
Why is the complementary strand synthesized
continuously for one of the template strands,
while the other one is synthesized in short
fragments?

Interactive Notes
Label the origin of replication (ori), leading
strand, lagging strand, Okazaki fragments,
RNA primer, and the 5’ and 3’ ends of the DNA
in the replication bubble below.

Interactive Notes
A biochemist prepares a solution that contains
various molecules needed for DNA replication.
She then adds a DNA template strand, and
replication occurs. When she analyzes the
newly replicated DNA molecules, she finds
that some of the adenine nitrogenous bases
are paired to uracil instead of thymine. What
did she probably forget to add to the mixture?

Interactive Notes
During DNA replication, DNA polymerases on
average make a mistakes every 1 in 100,000
bases. However, errors in the completed DNA
molecule amount to only 1 in 10,000,000,000
bases. Why is the accuracy so much greater
in the completed molecule?

Interactive Notes
THE STRUCTURE &
FUNCTION OF RNA
The Structure of RNA 5’

● Both DNA and RNA are made of

nucleotide monomers that have
three components: sugar,
phosphate, and a nitrogenous
base
● In both DNA and RNA, the
nucleotides are connected by
covalent bonds to form a linear
3’
molecule with 3' and 5' ends,
with the nitrogenous bases
perpendicular to the sugar-
phosphate backbone.
The Structure of RNA
● DNA is a double stranded molecule made of
nucleotides that contain the pentose (5-carbon)
sugar deoxyribose, while RNA is usually a
single stranded molecule made of nucleotides
that contain the pentose sugar ribose.
The Structure of RNA
● The nitrogenous bases found in DNA and RNA can be either
pyrimidines (one ring) or purines (two rings).
○ DNA contains the bases thymine, adenine, guanine and
cytosine.
○ RNA contains the bases uracil (in lieu of thymine), adenine,
guanine, and cytosine.
● Both exhibit complementary base pairing:
○ cytosine pairs with guanine (C-G)
○ adenine pairs with thymine in DNA or uracil in RNA (A-T or A-U)
Complementary Base Pairing
Functions of RNA
● There are a huge variety of RNA molecules found in living organisms
that have a large variety of functions, including:
○ Messenger RNAs (mRNA), ribosomal RNAs (rRNA), and transfer
RNAs (tRNA) are involved in protein synthesis and gene
expression
○ MicroRNAs (miRNA) are involved in regulating gene expression
(help control what genes are expressed).
○ Ribozymes: enzymes made of RNA molecules that catalyze
specific chemical reactions
○ RNA is the genetic material in many types of viruses and, like
DNA, is responsible for the storage and transmission of their
heritable information.
The 3 Main Types of RNA
● There are three main types of
RNA, which are found in all
cells: rRNA, mRNA, and tRNA.
● Ribosomal RNA (rRNA): RNA
molecules that bind with
proteins to create ribosomes.
○ Each ribosome is made of
two pieces, a small subunit
and a large subunit.
○ Ribosomes are the site of
protein synthesis.
The 3 Main Types of RNA
● Messenger RNA (mRNA):
copies the genetic code
mRNA
from DNA and brings the
codon
information to ribosomes.
○ Every three nucleotides
on a mRNA strand is
called a codon.
○ Each codon specifies a
particular amino acid, Amino
acids
which can be
determined using a
codon chart.
Codon
Chart
The 3 Main Types of RNA
● Transfer RNA (tRNA): RNA
molecules that bring amino
acids to the ribosomes so
that a polypeptide chain
(protein) can be built from
mRNA.
○ Each tRNA binds to
specific amino acids and tRNA
contains an anticodon.
○ An anticodon is a
sequence of three
nucleotides that
What are three important differences between
the structure of RNA and DNA?

Interactive Notes
The following base composition data was
collected from the genome of an unidentified
organism:
33% A, 28% G, 27% T, and 12% C

Which of the following describes the structure of

the organism’s genetic material? Justify your
answer.
A. Double stranded DNA
B. Double stranded RNA
C. Single stranded DNA
D. Single stranded RNA
Interactive Notes
What are 4 functions of RNA?

Interactive Notes
Label the codon and
anticodon in the
diagram shown below.
In the box, write the
name of the amino
acid that would be
attached the tRNA
shown in the diagram.

Interactive Notes
SELF-ASSESSMENT
QUESTIONS
Self-Assessment Questions
1) In his work with pneumonia-causing bacteria and mice, Griffith found
that

A. the protein coat from pathogenic cells was able to transform

nonpathogenic cells.
B. heat-killed pathogenic cells caused pneumonia.
C. some substance from pathogenic cells was transferred to
nonpathogenic cells, making them pathogenic.
D. the polysaccharide coat of bacteria caused pneumonia.
E. bacteriophages injected DNA into bacteria.
Self-Assessment Questions
2) Tobacco mosaic virus has RNA rather than DNA as its genetic
material. In a hypothetical situation where RNA from a tobacco mosaic
virus is mixed with proteins from a related DNA virus, the result could
be a hybrid virus. If that virus were to infect a cell and reproduce, what
would the resulting "offspring" viruses be like?

A. tobacco mosaic virus

B. the related DNA virus
C. a hybrid: tobacco mosaic virus RNA and protein from the DNA virus
D. a hybrid: tobacco mosaic virus protein and nucleic acid from the
DNA virus
E. a virus with a double helix made up of one strand of DNA
complementary to a strand of RNA surrounded by viral protein
Self-Assessment Questions
3) Cytosine makes up 38% of the nucleotides in a sample of DNA from
an organism. What percent of the nucleotides in this sample will be
thymine?

A. 12
B. 24
C. 31
D. 38
E. It cannot be determined from the information provided.
Self-Assessment Questions
4) In an analysis of the nucleotide composition of DNA, which of the
following is true?

A. A=C
B. A = G and C = T
C. A+C=G+T
D. A+T=G+C
E. Both B and C are true
Self-Assessment Questions
5) A space probe returns with a culture of a microorganism found on a
distant planet. Analysis shows that it is a carbon-based life form that
has DNA. You grow the cells in 15N medium for several generations and
then transfer it to 14N medium. Which pattern in this figure would you
expect if the DNA were replicated in a conservative manner?
Self-Assessment Questions
6) Imagine the following experiment is done: Bacteria are first grown for
several generations in a medium containing the lighter isotope of
nitrogen, 14N, then switched into a medium containing 15N. The rest of
the experiment is identical to the Meselson and Stahl experiment.
Which of the following represents the band positions you would expect
after two generations?
Self-Assessment Questions
7) You are trying to support your hypothesis that DNA replication is
conservative; i.e., parental strands separate; complementary strands
are made, but these new strands join together to make a new DNA
molecule and the parental strands rejoin. You take E. coli that had
grown in a medium containing only heavy nitrogen (15N) and transfer a
sample to a medium containing light nitrogen (14N). After allowing time
for only one DNA replication, which band location would support your
hypothesis of conservative DNA replication?
Self-Assessment Questions
8) Using the experiment explained in the previous question, which
centrifuge tube would represent the band distribution obtained after
one replication showing that DNA replication is semiconservative?
Self-Assessment Questions
9) A biochemist isolates and purifies various molecules needed for DNA
replication. When she adds some DNA, replication occurs, but each DNA
consists of a normal DNA strand paired with numerous segments of DNA
a few hundred nucleotides long. What has she probably left out of the
mixture?

A. DNA polymerase
B. DNA ligase
C. nucleotides
D. Okazaki fragments
E. primase
Self-Assessment Questions
10) What is the basis for the difference in how the leading and lagging
strands of DNA molecules are synthesized?

A. The origins of replication occur only at the 5' end.

B. Helicases and single-strand binding proteins work at the 5' end.
C. DNA polymerase can join new nucleotides only to the 3' end of a
growing strand.
D. DNA ligase works only in the 3' → 5' direction.
E. Polymerase can work on only one strand at a time.
Self-Assessment Questions
11) The elongation of the leading strand during DNA synthesis

A. progresses away from the replication fork.

B. occurs in the 3' → 5' direction along the template strand.
C. produces Okazaki fragments.
D. depends on the action of DNA polymerase.
E. does not require a template strand.
Self-Assessment Questions
12) Synthesis of a new DNA strand usually begins with

A. an RNA primer.
B. a DNA primer.
C. an Okazaki fragment.
D. DNA ligase.
E. a thymine dimer.
Answers to Self-Assessment Questions
1) C 7) C
2) A 8) A
3) A 9) B
4) C 10)C
5) B 11)B
6) E 12)A