Ch. 12 Molecular Genetics
I.
DNA: The Genetic Material
A. DNA Structure
1. scientists knew genetic material was carried on
chromosomes in eukaryotic cells
a. 2 main components of chromosomes are
nucleic acid (DNA) and proteins
b. experimentation showed that DNA was the
genetic material
2. Nucleotides: building blocks of DNA
 Consist of three components: a nitrogenous base, a
sugar, and a phosphate group.
 Joined to one another via covalent bonds between the
sugar of one nucleotide, and the phosphate of the next 
sugar-phosphate backbone
 DNA has 4 nitrogenous bases: Adenine (A), Guanine (G),
Thymine (T), and Cytosine (C).
o Purines (double-ring): Adenine and Guanine
o Pyrimidines (single-ring): Thymine and Cytosine
o In RNA, thymine is replaced by Uracil (U)
3. Chargaff’s rule: within a species, the amount of
guanine nearly equals the amount of cytosine, and the
amount of adenine nearly equals the amount of
thymine.
C = G and T = A
4. double helix: twisted ladder shape of DNA formed by
two strands of nucleotides twisted around each other.
5. Watson and Crick: built first model of the double helix
in 1953:
a. two outside strands consist of alternating
deoxyribose and phosphate
b. cytosine and guanine bases pair to each
other by three hydrogen bonds
c. thymine and adenine bases pair to each other
by two hydrogen bonds
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 DNA: DeoxyriboNucleic
Acid
 RNA: RiboNucleic Acid
 Both are nucleic acids:
long chains (polymers) of
nucleotides.
 DNA is made up of two
strands: The nitrogenous
bases of the nucleotides on
different strands form
hydrogen bonds with one
another, creating the
double helix structure.
o This structure was
discovered by
Watson & Crick
o A purine must bond
with a pyrimidine to
maintain a uniform
thickness.
o A pairs with T and
G pairs with C.
(A-T & G-C)
 The sugar and phosphate groups form the “backbone”
of DNA and RNA.
 DNA has a 3’ (“three prime”) and a 5’ (“five prime”)
end.
 antiparallel orientation: the 2 strands of DNA run in
opposite directions to each other
top strand:
5’carbon-----------------------3’carbon
bottom strand 3’carbon------------------------5’carbon
B. Chromosome Structure
1. prokaryotes: DNA molecule is contained in the
cytoplasm and is composed of a ring of DNA and
proteins.
2. eukaryotes: DNA is organized into individual
chromosomes ranging from 51 to 245 million base
pairs.
3. to fit inside the nucleus, DNA coils tightly around a
group of beadlike proteins called histones b/c the
negative phosphate group of the DNA is attracted to the
positively charged histones.
4. nucleosome: structure formed by DNA coiled around
histones.
5. nucleosomes group together into chromatin fibers
which supercoil to make the chromosome structure.
II.
Replication of DNA
Main Idea: DNA replicates by making a strand that is
complementary to each original strand
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Complementary strands are separated.
Each strand serves as a template for a new complementary strand.
One DNA double helix has now been turned into two DNA helices, each with one
original strand and one new strand.
This method depends on specific base pairing.
A. Semiconservative Replication: proposed by Watson and Crick;
parental strands of DNA separate, serve as templates and
produce DNA molecules that have one strand of parental DNA
and one strand of new DNA.
1. unwinding: the double helix is unwound and unzipped
by the enzyme DNA helicase
a. hydrogen bonds between base pairs are
broken
b. single-stranded binding proteins keep the
strands separate during replication
c. RNA primase adds a short segment of RNA
called an RNA primer on each DNA strand
2. base pairing:
a. DNA polymerase: enzyme that adds the
appropriate nucleotides to the new DNA
strand on the 3’ end
b. Leading strand: half of original DNA where
replication occurs continuously in the 5’ to
3’ direction
c. Lagging strand: half of original DNA where
replication occurs in discontinuously in
small segments called Okazaki fragments in
the 3’ to 5’ direction.
i. DNA ligase: later connects the
Okazaki fragments together on the
lagging strand
d. b/c one strand is synthesized continuously
and the other is synthesized discontinuously,
DNA replication is said to be
semidiscontinuous as well as
semiconservative.
3. joining: when DNA polymerase comes to an RNA
primer on the DNA, it removes the primer and fills in
the place with free DNA nucleotides, then DNA ligase
links the two sections.
B. DNA replication in eukaryotes vs. prokaryotes
1. multiple areas of replication occur along eukaryote
chromosomes at the same time
2. these areas of origin look like bubbles in the DNA
strand.
3. prokaryotic DNA has one area of origin for replication.
III.
DNA, RNA and Protein
Main Idea: DNA codes for RNA, which guides protein synthesis.
DNA
RNA
Protein
 An organism’s phenotype (physical appearance) is
determined by the genetic information contained in its
DNA.
 First, a DNA strand is transcribed into RNA.
 Next, the RNA is translated into proteins and
enzymes.
 Finally, the proteins (and enzymes) perform many
functions that ultimately determine an organism’s
phenotype.
Transcription & Translation Overview
 Transcription
o A complementary strand of RNA is created from a
DNA template.
o The mRNA strand contains U’s in place of T’s.
o Translation
o Three bases of mRNA make up a codon.
o Each codon codes for a specific amino acid.
o Amino acids are put together to form a
ypolypeptide (protein).
A. How DNA serves as a Genetic Code
1. basic mechanism of reading and expressing genes is
from DNA to RNA to protein.
2. RNA: nucleic acid similar to DNA but has the sugar
ribose, the base uracil replaces thymine, and is usually
single-stranded. 3 types:
a. messenger RNA (mRNA): long strands of
RNA nucleotides formed complementary to
one strand of DNA.
i. Travel from the nucleus to the
ribosome to direct protein synthesis
b. Ribosomal (rRNA): associates with proteins
to form ribosomes in the cytoplasm
c. transfer (tRNA): small RNA nucleotides
that transport amino acids to the ribosome.
3. transcription: synthesis of mRNA from DNA
a. RNA polymerase: enzyme that unzips DNA
and initiates mRNA synthesis in the 5’ to 3’
direction
b. template: DNA strand being read
c. mRNA is synthesized as a complement to
the template DNA strand.
d. The base uracil is used instead of thymine
e. When finished, the mRNA is released and
moves out of the nucleus through nuclear
pores.
4. RNA processing: mRNA code is shorter than the DNA
code from which it was made.
a. introns (intervening sequences): DNA code
sequences that do not appear in the final
mRNA.
b. Exons: DNA codes sequences that do
appear in the final mRNA
c. Introns are removed in eukaryotes from the
pre-mRNA, have a protective cap on the 5’
end and have a tail of adenine nucleotides
added.
B. The Code
1. 20 amino acids are used to make proteins so DNA must
provide at least 20 different codes.
a. codon: 3-based code in DNA or mRNA that
is transcribed into the mRNA code.
2. translation: process by which the mRNA code is read
by the ribosome to make a protein
a. mRNA leaves the nucleus and enters
cytoplasm
b. 5’ end of the mRNA connects to a ribosome
c. tRNA is folded into a cloverleaf shape and
activated by attaching to a specific amino
acid.
d. The middle of the tRNA contains a 3-base
coding sequence (anticodon) that
complements a codon on the mRNA.
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 Translation takes place in the cytoplasm of the cell.
 The following are needed for translation to occur:
 Ribosomes (made of proteins and rRNA)
 Messenger RNA (mRNA, created during
transcription)
 Transfer RNA (tRNA)
 Anticodon: a triplet that is complementary to
an mRNA codon
 Amino acid: the building block of proteins
 Each tRNA molecule only carries one
anticodon and therefore one amino acid.
 The amino acids are added to the tRNA with
the help of an enzyme and ATP for energy.
The Steps of Translation
 Step 1: An mRNA molecule binds to a small
ribosomal subunit at the start codon.
 Step 2: A special initiator tRNA molecule binds to
the start codon via the anticodon.
 Step 3: A large ribosomal subunit binds to the small
one, creating a functional ribosome.
 Step 4: The ribosome moves down the mRNA and a
new tRNA molecule’s anticodon pairs with the next
codon.
 Step 5: The amino acid carried on the first tRNA
forms a peptide bond with the amino acid on the
second tRNA and detaches from the first tRNA.
 Step 6: The first tRNA is kicked out as the ribosome
moves down the mRNA molecule.
 Step 7: A new tRNA molecules binds to match with
the next codon sequence.
 Step 8: Steps 5-7 are repeated until a stop codon is
reached.
 Step 9: The polypeptide chain is released from the
last tRNA and the ribosome. The ribosome splits
back up into its two subunits.
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Main idea: Gene expression is regulated by the cell, and mutations
can affect this expression.
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 Gene expression can be regulated so that specific
kinds of proteins are only produced when and where
they are needed.
 Operon: a cluster of genes, including a promoter and
an operator, that regulates gene expression.
o Promoter: a stretch of nucleotides to which RNA
polymerase attaches to begin transcription.
o Operator: a DNA segment that can act as a switch
and determine whether RNA polymerase can bind to
the promoter.
 Repressor: a protein that binds to the operator to
block the attachment of RNA polymerase.
 Regulatory genes outside the operon code for the
repressors.
 Repressor Controlled Operons
o Positive control: Repressor is active when alone and inactive when
bound to a specific molecule.
 Ex: lac operon
 Negative control: Repressor is inactive when alone and active when
bound to a specific molecule.
 Ex: trp operon
 Activator Controlled Operons
 Activator: a protein that makes it easier for
RNA polymerase to bind to the promoter.
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 transcription factors: proteins that make sure a gene is
used at the right time and that proteins are used in the
right amounts. 2 types:
i. guides and stabilizes the binding of
the RNA polymerase to the promoter
ii. help control the rate of transcription
 structure of DNA: wrapped around histones to form
nucleosomes inhibits transcription
 Hox (homeobox) genes: control differentiation of cells
and are important for determining the body plan of an
organism.
 RNAi (interference): small segments of RNA that bind
to mRNA and prevent its translation.
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1. mRNA Breakdown
 Some mRNA’s have very short lifetimesvery few proteins are
synthesized from each mRNA
2. Translation Initiation
 Some genes have inhibitory proteins that prevent the translation of the
mRNA unless a certain molecule is present.
o Red blood cells are inhibited from producing hemoglobin
unless a supply of heme is present.
3. Protein Activation
 Some proteins must be cut into smaller, active final products.
o The hormone insulin must be cut from one long polypeptide
into two short chains that are bonded to one another by links
between sulfur atoms.
4. Protein Breakdown
 The cell can breakdown proteins when they are damaged or no longer
neededthe cell can respond to changes in its environment.
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A.
1. types of mutations:
a.point mutations: change in just one base pair
 substitution: one base is exchanged for another
 missense mutations: DNA codes for the wrong
amino acid
 nonsense mutations: amino acid codon is changed
to a stop codon which causes translation to stop
early (causes proteins to malfunction)
b. gain/ loss of nucleotides: causes frameshift
 insertions: addition of a nucleotide to a DNA
sequence
 deletions: loss of a nucleotide in a DNA sequence
c.large portions of chromosomes deleted or relocated on
the chromosome or to a different chromosome—causes drastic
effects of gene expression.
d.Tandem repeats: increase in the number of copies of
repeated codons
 Fragile X syndrome: CGG codons repeated
hundreds of times at the end of an X
chromosome (causes mental and behavioral
problems)
e.protein folding and stability: the change of one amino
acid for another can change the sequence of amino acids in
a protein which can affect the folding and stability of a
protein
 sickle-cell disease: caused by the codon for
a glutamic acid (GAA) changed to a valine
(GUA) in the protein. This change in
composition changes the structure of
hemoglobin proteins causes red blood cells
to abnormally fold.
f.mutagens: substances that cause mutations (ex.
Chemicals and radiation)
 point mutations are sometimes spontaneous:
DNA polymerase sometimes adds the wrong
nucleotides
 chemicals: change the structure of the bases
causing them to bond with the wrong base;
other chemicals take the place of nucleotides
which prevents replication.
 Radiation:
1.X-rays and gamma rays: highly
mutagenic; create free radicals
(energized atoms) that react violently
with other molecules (including DNA)
2.UV (ultraviolet) radiation: causes
adjacent thymine bases to bind
disrupting DNA structure and
replication.
2.
Contained only
in body cells of
an organism.
body-cell and sex cell mutations:
e. mutations become part of body (somatic)
cells if not repaired become part of the
genetic code and are passed on to future
daughter cells.
f. Somatic cell mutations are not passed on to
the next generation.
g. Neutral mutations: Some mutations don’t
cause problems (ex: unused sequences,
intron mutations, or mutation doesn’t change
the amino acid coded for).
h. Mutations that cause abnormal protein
production: cell may not be able to function
and cell death may occur; unregulated cell
cycle mutations may cause cancer.
i. Germ-lined (sex) cell mutations: passed on
to organism’s offspring and present in every
cell in offspring.
i. May not affect parent but drastically
affect the offspring