Chapter 12: DNA
The Structure of DNA
Important Contributors to the Genetic Code
DNA Replication
Activating Prior Knowledge
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
List the eight characteristics of living things.
List the five elements found in nucleic acids.
Name the monomer of nucleic acids.
Identify the three parts of the monomer mentioned in question
three.
Name two examples of nucleic acids.
Identify two differences between prokaryotic and eukaryotic cells.
Which organelle serves as the site of protein synthesis?
Name the monomers of proteins.
Which organelle modifies, sorts, and packages proteins?
Which organelle serves as an intracellular highway?
Do you remember any of the eight
characteristics of living things?
1. Living things are based on a universal genetic code (DNA)
2. Living things grow and develop
3. Living things respond to their environment (stimulus)
4. Living things reproduce
5. Living things maintain a stable internal environment
(homeostasis)
6. Living things obtain and use material and energy
(metabolism)
7. Living things are made up of CELLS
8. Taken as a group, living things evolve over time
Nucleic Acids
 Large, complex organic compounds that store
information in cells, using a system of four compounds
to store hereditary information, arranged in a certain
order as a code for genetic instructions of the cell.
 Elements: Carbon, Hydrogen, Oxygen, Nitrogen,
Phosphorus
 Monomer: Nucleotide
1. Phosphate group
(Phosphoric Acid)
2. 5-carbon (pentose) sugar
(Deoxyribose or Ribose)
3. Nitrogenous Base
Nucleic Acids
 Nucleotides combine, in DNA to form a double helix, and in
RNA a single helix
 The sides of the ladder are made
up of the phosphate group and
the sugar and the rungs of the
ladder are nitrogen bases
 Examples of Nucleic Acids:
1. Deoxyribonucleic Acid (DNA)
2. Ribonucleic Acid (RNA)
Nucleic Acids and Dehydration Synthesis
Two categories of cells
Prokaryotic
-No Nucleus
Eukaryotic
-Nucleus
-Unicellular -Complex
-Cell wall
(plants and
bacteria)
-Membrane bound
organelles
-Smaller Ribosomes -Cell membrane -Multicellular
less complex
-DNA
- Ribosomes larger
-Cytoplasm
and complex
-DNA is circular
-Ribosomes
-DNA is X shaped
-Living
things
0.1-10µm
10-100µm
-Less complex
Proteins
 Elements: Carbon, Hydrogen, Oxygen, Nitrogen
 Monomer: AMINO ACID (20 different kinds)
 Each amino acid has a central carbon atom bonded to 4
other atoms or functional groups
Organelles
 Organelle that serves as the site of protein synthesis?
 Ribosomes (Rough ER)
 Organelle that modifies, sorts and packages proteins?
 Golgi Apparatus
 Organelle that serves as an intracellular highway?
 Endoplasmic Reticulum (ER)
DNA Structure
Section 12.2: The Structure of DNA
NOVA Journey into a Human (Interactive)
Discovery of DNA (4 min) video clip
Learn Genetics Tutorial
Deoxyribonucleic Acid is a polymer
formed from units called nucleotides.
 Each nucleotide monomer is made
up of three parts:
a) 5-carbon sugar
(deoxyribose)
b) phosphate group
c) nitrogen base
b.
c.
a.
There are 4 nitrogenous
bases found in DNA:
Purines (2 rings)
a) Guanine (G)
b) Adenine (A)
Pyrimidines (one ring)
a) Thymine (T)
b) Cytosine (C)
Nucleotides
Rosalind Franklin
 In the 1950s, British scientist Rosalind
Franklin used a technique called X-ray
diffraction to get information about the
structure of the DNA molecule.
 X-ray diffraction revealed an X-shaped
pattern showing that the strands in DNA
are twisted around each other like the coils
of a spring.
 The angle of the X-shaped pattern
suggested that there are two strands in
the structure.
 Other clues suggest that the nitrogenous
bases are near the center of the DNA
molecule.
Watson & Crick
 At the same time, James Watson, an American
biologist, and Francis Crick, a British physicist,
were also trying to understand the structure of
DNA.
 Early in 1953, Watson was shown a copy of
Franklin’s X-ray pattern. The clues in Franklin’s
X-ray pattern enabled Watson and Crick to
build a model that explained the specific
structure and properties of DNA.
 They built the first correct 3-D model of
the DNA molecule.
Erwin Chargaff
 Erwin Chargaff discovered that the percentages of
adenine [A] and thymine [T] bases are almost equal
in any sample of DNA.
 The same is true for the other two nucleotides,
guanine [G] and cytosine [C].
 The observation that [A] = [T] and [G] = [C]
became known as one of “Chargaff ’s rules.”
Watson and Crick
 In the double-helix model of DNA,
the two strands twist around each other
like spiral staircases.
 The double helix accounted for Franklin’s
X-ray pattern and explains Chargaff’s
rule of base pairing and how the two
strands of DNA are held together.
 What they knew. . .
 DNA is made of two strands.
 Each strand has a sugar-phosphate
backbone.
 The bases are in the middle connected
through hydrogen bonds
Deoxyribonucleic Acid:
 The DNA polymer looks
like a twisted ladder, with
the 5-carbon sugar and
phosphate group making
up the sides of the ladder
and the nitrogen bases
are the steps/rungs.
Nitrogen bases pair according to
certain rules
 Purines pair with pyrimidines
 Guanine pairs with Cytosine
 Adenine pairs with Thymine
The nitrogen bases are held
together by HYDROGEN bonds.
Deoxyribonucleic
Acid (DNA):
Structure of DNA
The DNA strands are
ANTIPARALLEL
 They run in opposite directions.
 One strand is arranged 5’ to
3’ while the other strand is
3’ to 5’
 5’ and 3’ refer to the carbon
atoms in the deoxyribose sugar.
Check your understanding…
 DNA is a long molecule made up of units called
nucleotides. Each nucleotide is made up of three basic
Deoxyribose
Phosphate group
Nitrogenous base
parts: __________,
__________,
&__________.
(5 C sugar)
Nitrogenous bases
 There are 4 kinds of ______________
in DNA.
pair
 They _______
according to two rules:
Purines always pair with ___________
Pyrimidines and
1) ________
Cytosine and _________
Thymine pairs
2) Guanine pairs with _________
with adenine.
Comprehension Question
If Cytosine makes up 22% of the nucleotides in a
sample of DNA from an organism, then adenine
would make up what percent of the bases?
A. 22
Answer is C:
B. 44
• C pairs with G for a total of 44%
• 100-44 = 56% (for A and T)
C. 28
•
Divide
by
2
for
the
%
of
A
D. 56
E. Not enough information is provided to
determine the answer to this question
DNA Replication
Section 12.3
PBS DNA Workshop
Learn Genetics Tutorial
DNA Replication
 Because each of the two strands of the DNA
double helix has all of the information to
reconstruct the other half, the strands are said
to be complementary.
 Each strand of the double helix serves as a
template to make the other strand.
DNA Replication Practice
A T C C G A T G A T T
T A G G C T A C T A A
RNA Transcription Practice
- Uracil (U) replaces Thymine (T)
A T C C G A T G A T T
U A G G C U A C U A A
Illustration of DNA Replication
DNA Replication (1:04 min)
DNA Replication
PBS: The Nuts and Bolts of DNA Replication
DNA Replication
 DNA replication is carried out by a series of
enzymes.
a) They separate (unzip) the two strands of the
double helix.
b) DNA polymerase adds new nucleotides.
DNA Replication
Biointeractive - Short clip of DNA
Replication (1 min)
DNA Replication
How does it replicate?
1. Helicase - is an enzyme that separates the two DNA
strands by breaking the hydrogen bonds in the middle.
DNA Replication (3:56)
DNA Replication
2.
DNA Polymerase: adds nucleotides to the single
stranded DNA according to base pairing rules.
 DNA polymerase only moves in one direction,
from 5’ to 3’ for the new strand formation
DNA Replication
 Leading Strand: the 5’ to 3’ strand, DNA polymerase can add
nucleotides to make one continuous strand.
 Lagging Strand: the 3’ to 5’ strand, DNA polymerase moves in
the opposite direction.
 DNA polymerase forms short segments of DNA called
Okazaki fragments.
DNA Replication
3.
Ligase: uses covalent bonds to connect Okazaki
fragments together in the lagging strand.
DNA Replication 3D (3:27)
DNA Replication Summary
1.
2.
3.
The double helix unzips with helicase down the middle as base pairs
separate.
DNA polymerase adds the correct complimentary nucleotide to each
exposed strand. Ligase connects all fragments.
A complimentary strand is created for each original strand in the double
helix.
DNA Replication Process
3D Animation (5:45)
Important Contributors to the
Genetic Code
Section 12.1: Identifying the Substance of Genes
The Secret of Life - The Discovery of DNA
(9 min)
PBS Episode 1 of 5 - DNA The Secret of Life
(54 min)
The Genetic Code:
 To truly understand genetics, scientists realized they had to discover
the chemical nature of the gene.
 If the molecule that carries genetic information could be identified,
it might be possible to understand how genes control the inherited
characteristics of living things.
Griffith’s Experiments:
 The discovery of the chemical nature of the gene began in 1928
with British scientist Frederick Griffith, who was trying to figure
out how certain types of bacteria produce pneumonia.
 Griffith isolated two different strains of the same bacterial species.
 Both strains grew very well in culture plates in Griffith’s lab, but
only one of the strains caused pneumonia.
Griffith’s Experiments:
 The disease-causing bacteria (S strain) grew into smooth colonies
on culture plates, whereas the harmless bacteria
(R strain) produced colonies with rough edges.
Griffith’s Experiments:
 When Griffith injected mice with disease-causing bacteria, the
mice developed pneumonia and died.
 When he injected mice with harmless bacteria, the mice stayed
healthy.
 Perhaps the S-strain bacteria produced a toxin that made the
mice sick? To find out, Griffith ran a series of experiments.
Griffith’s Experiments:
 First, Griffith took a culture of the S strain, heated the cells to kill
them, and then injected the heat-killed bacteria into laboratory
mice.
 The mice survived, suggesting that the cause of pneumonia was
not a toxin from these disease-causing bacteria.
Griffith’s Experiments:
 In Griffith’s next experiment, he mixed the heat-killed, S-strain
bacteria with live, harmless bacteria from the R strain and injected
the mixture into laboratory mice.
 The injected mice developed pneumonia, and many died.
Griffith’s Experiments:
 The lungs of these mice were filled with the disease-causing
bacteria. How could that happen if the S strain cells were dead?
 Griffith reasoned that some chemical factor that could change
harmless bacteria into disease-causing bacteria was transferred
from the heat-killed cells of the S strain into the live cells of the R
strain.
Griffith’s Experiments:
 He called this process transformation, because one type of
bacteria had been changed permanently into another.
 Because the ability to cause disease was inherited by the offspring
of the transformed bacteria, Griffith concluded that the
transforming factor had to be a gene.
Avery, McCarty, and MacLeod:
 A group of scientists at the Rockefeller Institute in New York, led
by the Canadian biologist Oswald Avery, wanted to determine
which molecule in the heat-killed bacteria was most important for
transformation.
 Avery and his team extracted a mixture of various molecules from
the heat-killed bacteria and treated this mixture with enzymes that
destroyed proteins, lipids, carbohydrates, and some other
molecules, including the nucleic acid RNA.
 Transformation still occurred.
Avery, McCarty, and MacLeod:
 Avery’s team repeated the experiment using enzymes that would
break down DNA.
 When they destroyed the DNA in the mixture, transformation did
not occur.
 Therefore, DNA was the transforming factor.
Hershey and Chase:
 Hershey and Chase studied viruses—nonliving particles that can
infect living cells.
 The kind of virus that infects
bacteria is known as a
bacteriophage, which means
“bacteria eater.”
Hershey and Chase:
 When a bacteriophage enters a bacterium, it attaches to the
surface of the bacterial cell and injects its genetic information into
it.
 The viral genes act to produce many new bacteriophages, which
gradually destroy the bacterium.
 When the cell splits open, hundreds of new viruses burst out.
Hershey and Chase:
 American scientists Alfred Hershey and Martha Chase studied a
bacteriophage that was composed of a DNA core and a protein
coat.
 They wanted to determine which part of the virus – the protein
coat or the DNA core – entered the bacterial cell.
Hershey and Chase:
 Hershey and Chase grew viruses in cultures containing
radioactive isotopes of phosphorus-32 (P-32) sulfur-35 (S-35)
Hershey and Chase:
 Since proteins contain almost no phosphorus and DNA contains
no sulfur, these radioactive substances could be used as markers,
enabling the scientists to tell which molecules actually entered the
bacteria and carried the genetic information of the virus.
Hershey and Chase:
 If they found radioactivity from S-35 in the bacteria, it would
mean that the virus’s protein coat had been injected into the
bacteria.
 If they found P-32 then the DNA core had been injected.
Hershey and Chase:
 The two scientists mixed the marked viruses with bacterial cells,
waited a few minutes for the viruses to inject their genetic
material, and then tested the bacteria for radioactivity.
Hershey and Chase:
 Nearly all the radioactivity in the bacteria was from phosphorus
P-32 , the marker found in DNA.
 Hershey and Chase concluded that the genetic material of the
bacteriophage was DNA, not protein.
 Hershey and Chase’s experiment with bacteriophages confirmed
Avery’s results, convincing many scientists that DNA was the
genetic material found in genes—not just in viruses and bacteria,
but in all living cells.
Rosalind Franklin:
 In the 1950s, British scientist Rosalind Franklin used a technique
called X-ray diffraction to get information about the structure of
the DNA molecule.
 X-ray diffraction revealed an X-shaped pattern showing that the
strands in DNA are twisted around each other like the coils of a
spring.
 The angle of the X-shaped pattern suggested that there are two
strands in the structure.
 Other clues suggest that the nitrogenous bases are near the center
of the DNA molecule.
Watson and Crick:
 At the same time, James Watson, an American biologist, and
Francis Crick, a British physicist, were also trying to understand
the structure of DNA.
 They built three-dimensional models of the molecule.
 Early in 1953, Watson was shown a copy of Franklin’s X-ray
pattern. The clues in Franklin’s X-ray pattern enabled Watson and
Crick to build a model that explained the specific structure and
properties of DNA.
Watson and Crick:
 In the double-helix model of DNA, the two strands twist around
each other like spiral staircases.
 The double helix accounted for Franklin’s X-ray pattern and
explains Chargaff’s rule of base pairing and how the two strands of
DNA are held together.
Erwin Chargaff:
 Erwin Chargaff discovered that the percentages of adenine [A] and
thymine [T] bases are almost equal in any sample of DNA.
 The same thing is true for the other two nucleotides, guanine [G]
and cytosine [C].
 The observation that [A] = [T] and [G] = [C] became known as
one of “Chargaff’s rules.”
Chapter 13:
RNA and Protein Synthesis
Transcription and Translation
RNA: Ribonucleic Acid
Section 13.1: RNA
DNA and RNA (6:57)
HOW DNA IS USED TO MANUFACTURE PROTEINS
Genetic
Code
(genes)
Intermediates
Molecules that
express our
genes
RNA = Ribonucleic Acid
 Consists of a long chain of
macromolecules made up of
nucleotides.
a) 5-carbon sugar (ribose)
b) phosphate group
c) nitrogen base
3 differences between DNA and RNA:
1. RNA is single stranded, DNA is
double stranded
2. RNA contains uracil in place of thymine
3. 5-carbon sugar is ribose in RNA,
deoxyribose in DNA
Amoeba Sisters: DNA vs. RNA (4:43)
3 main types of RNA:
1. Messenger (mRNA)
-instructions for making proteins
2. Ribosomal (rRNA)
-found in ribosomes (where proteins are made)
3. Transfer (tRNA)
-transfers amino acids to the ribosome
mRNA
rRNA
tRNA
RNA Synthesis: Transcription
 The process by which a molecule of DNA is copied into a
complementary strand of RNA (mRNA).
RNA Synthesis: Transcription
 All 3 types of RNA are synthesized from DNA in the nucleus
and then used to synthesize proteins in the ribosome.
 Protein synthesis is a two step process:
1) Transcription: DNA  mRNA (nucleus)
2) Translation: mRNA  amino acids  proteins (ribosome)
DNA Transcription and Protein Assembly (3:01)
RNA Synthesis: Transcription
 mRNA must bring the genetic information from DNA in the
nucleus to the ribosome in the cytoplasm.
 An enzyme, RNA polymerase , attaches to the DNA molecule
and separates the double helix.
 The enzyme moves along the DNA
molecule and synthesizes a
complementary mRNA strand.
RNA Synthesis: Transcription
 Transcribe the given DNA sequence into a
complementary mRNA:
A T G C A A G TC A T T C C A G C T
U AC G UU CAG UAA G GU CGA
RNA Synthesis: Transcription
Creating mRNA
1. Double stranded DNA
2. RNA polymerase binds to DNA and assembles a single strand
of RNA
3. Single stranded mRNA
RNA Editing:
 The process of transcription takes place in the nucleus.
 The mRNA must be processed before leaving the nucleus.
1) Introns and exons are transcribed from DNA
2) Introns are cut out of the mRNA and exons are
spliced back together
3) A cap and a tail are added to the mRNA
RNA Editing:
 Introns: Intervening sequences –
pieces of the mRNA cut out and
discarded
 Stays IN the nucleus
 Exons: Expressed sequences –
the remaining pieces are spliced
back together to form the final
mRNA that leaves the nucleus
 EXiting the nucleus
 EXpressed
 Some introns are involved in regulating gene activity.
 Splicing is necessary for export of mRNA from nucleus
 Alternative RNA splicing allows some genes to produce different
polypeptides since some can encode more than one kind of polypeptide,
depending on which segments are treated as exons during RNA splicing
 Introns may facilitate recombination of exons between different alleles or even
between different genes.
 Exons shuffling can result in novel proteins or the evolution of new proteins.
 May allow for more crossing over between exons of alleles or for mixing and matching
of exons between nonallelic genes
Protein Synthesis
Section 13.2: Ribosomes and Protein Synthesis
Protein Synthesis:
 The information that DNA transfers to mRNA is in the form
of a code, which is determined by the way in which the four
nitrogenous bases are arranged in DNA.
 DNA directs the formation of proteins.
 The monomers of proteins are amino acids.
 There are 20 different amino acids.
 A peptide bond holds two amino acids together.
A water molecule is removed
when a peptide bond is formed
• dehydration synthesis!
Protein Synthesis:
 The mRNA produced in the nucleus during transcription
travels to the ribosome to begin the process of translation.
 Once at the ribosome, the mRNA is read 3 nucleotides at a
time.
 A codon is a combination of three sequential nucleotides on
mRNA.
Protein Synthesis:
 There are 64 different codons.
 Each codon specifies a particular
amino acid that is to be placed
in the polypeptide chain.
 AUG is the “initiator” codon.
 There are 3 “stop” codons.
Protein Synthesis:
 Translation involves mRNA, rRNA, and tRNA.
 Transfer RNA (tRNA) carries the amino acids to the ribosome.
(different tRNA for each amino acid)
 Ribosomal RNA (rRNA) makes up the major part of the ribosome.
 Three sequential nucleotides on a
tRNA molecule are called an
anticodon.
 The anticodon on the tRNA is
complementary to the codon of mRNA.
Protein Synthesis:
Protein Synthesis:
tRNA
UAG CUG AAU CGC UUA GUC CUA
mRNA
AUC GAC UUA GCG AAU CAG GAU
Protein Synthesis:
 Each codon & anticodon bind together, and a peptide bond
forms between the two amino acids.
 The polypeptide chain continues to grow until the ribosome
reaches a stop codon.
Protein Synthesis:
Protein Synthesis:
 A stop codon is a codon for which no tRNA molecule exists.
 The ribosome releases the newly formed polypeptide.
Protein Synthesis:
Protein Synthesis (DNA transcription, translation and folding)(2:17)
PBS Video: From DNA to Protein (3:24)
Central Dogma – flow of genetic information from DNA to RNA to Protein
DNA
Transcription
Nucleus
mRNA
Translation
(Ribosome)
Cytoplasm
Protein
Made of Amino Acids
The Central Dogma of Biology (2:51)
Mutations
Section 13.3
Mutations
Mutations are heritable changes in genetic
information.
 A mutation results from a mistake in duplicating
genetic information during DNA replication.

Types of Cells Affected
 Germ Mutation - affects a reproductive cell (gamete or
sperm/egg)
 Does not affect the organism
 Passed to offspring
 Somatic Mutation – affects body cells
(all cells except gametes)
 Not passed to offspring
Types of Mutations
 All mutations fall into two basic categories:
 Those that produce changes in a single gene are known as gene
mutations.
 Those that produce changes in a part of a chromosome, whole
chromosomes, or sets of chromosomes are known as chromosomal
mutations.
Ameoba Sisters – Mutations (7 min)
Mutagens
 Mutations can be caused by chemical or physical agents -
mutagens
 Chemical – pesticides, tobacco smoke, environmental
pollutants
 Physical – X-rays and ultraviolet light
Animated Intro to Cancer (12:07)
Gene Mutations
Mutations that involve changes in one or a few
nucleotides are known as point mutations because
they occur at a single point in the DNA sequence. They
generally occur during replication.
 If a gene in one cell is altered, the alteration can be
passed on to every cell that develops from the original
one.

Gene Mutations
 Point mutations include substitutions,
insertions, and deletions.
Substitutions
In a substitution, one base is changed to a different base.
 Substitutions usually affect no more than a single amino acid,
and sometimes they have no effect at all.

Substitution - Silent Mutation
 A change in one base pair has no effect on the protein produced by the
gene.
 This is allowed for by the redundancy in the genetic code.
 Example (as shown in picture):
 Both GGC and GGU code for the amino acid glycine.
 Thus, the mutation is “silent,” i.e. causes no change in the final protein
product.
Substitution - Missense Mutation
 A change in one base pair causes a single amino acid to be changed in
the resulting protein.
 The result is called “missense” since the code is now different.
 The effect of a missense mutation on the protein is unpredictable.
 In the following example, GGC has been changed to AGC, resulting
in a different amino acid.
Substitutions – Missense Example

In this example, the base cytosine is replaced by the
base thymine, resulting in a change in the mRNA
codon from CGU (arginine) to CAU (histidine).
Sickle Cell Anemia
 A missense mutation is the cause of the disease, sickle cell anemia.
 a change in one base pair alters one amino acid
 effects hemoglobin protein, causing red blood cells to take
on a strange shape
Sickle Cell Anemia
Substitution - Nonsense Mutation
 a change in a single base pair creates a stop codon.
 Because this kind of mutation creates a stop signal in the middle of a
normally functional gene, the resulting protein is almost always
nonfunctional
 hence the term “nonsense” mutation.
Substitution
Silent
Mutation
Missense
Mutation
Nonsense
Mutation
Insertions and Deletions
Insertions and deletions are point mutations in which one
base is inserted or removed from the DNA sequence.
 If a nucleotide is added or deleted, the bases are still read in
groups of three, but now those groupings shift in every codon
that follows the mutation.

Frameshift Mutation
 Insertions and deletions are also called frameshift
mutations because they shift the “reading frame” of the
genetic message.
 Frameshift mutations can change every amino acid that
follows the point of the mutation and can alter a protein
so much that it is unable to perform its normal functions.
Frameshift Mutation:
 Example:
 Deletion:
 THE FAT CAT ATE THE RAT
 THE FAT ATA TET HER AT
 Insertion:
 THE FAT CAT ATE THE RAT
 THE FAT CAR TAT ETH ERA T
Insertions
Deletions
Muscular Dystrophy
 Both Duchenne muscular dystrophy and Becker muscular dystrophy result from mutations of a
gene on the X chromosome that codes for the dystrophin protein in muscle cells; this protein
helps to stabilize the plasma membrane during the mechanical stresses of muscle contraction.
 About 2/3 of cases are due to deletion mutations.
 If the number of nucleotides deleted in the mRNA is not a multiple of three, this type of
FRAMESHIFT mutation results in a severely defective or absent version of the protein, resulting in
more rapid breakdown of muscle cells and the more severe DUCHENNE muscular dystrophy.
 If the number of nucleotides deleted in the mRNA is a multiple of three, the mutation does not
cause a frameshift and this typically results in a less defective version of the protein, less rapid
breakdown of muscle cells, and the milder BECKER muscular dystrophy.
 Up to one-fifth of cases of Duchenne muscular dystrophy are caused by a nonsense mutation (a
point mutation that results in a stop codon).
Muscular Dystrophy
 Because the dystrophin gene is on the X chromosome and
because the alleles for defective dystrophin are recessive, both
of these types of muscular dystrophy are much more common
in boys than in girls. Duchenne muscular dystrophy affects one
in every 3500 male babies.
Gene Mutations
Substitution
Frameshift Mutation