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The structure of DNA
 Deoxyribonucleic acid
 DNA is made of nucleotides
 Each nucleotide is composed of phosphate,
sugar (deoxyribose) and a nitrogen base
 4 nitrogen bases – Adenine, Thymine, Guanine,
Cytosine (A,T,G,C)
 A-T, C-G
 Bases are linked by hydrogen bonds
Figure 16.5
Sugar–phosphate
backbone
Nitrogenous bases
5 end
Thymine (T)
Adenine (A)
Cytosine (C)
Phosphate
Guanine (G)
Sugar
(deoxyribose)
DNA
nucleotide
3 end
Nitrogenous base
Figure 16.7
C
5 end
G
C
Hydrogen bond
G
C
G
C
G
3 end
A
T
3.4 nm
A
T
C
G
C
G
A
T
1 nm
C
A
G
C
G
A
G
A
T
3 end
T
A
T
G
C
T
C
C
G
T
A
(a) Key features of
DNA structure
0.34 nm
5 end
(b) Partial chemical structure
(c) Space-filling
model
Base Pairing
DNA strands





Run in opposite directions
Helicase – unwinds helix
Topoisomerase – cuts and rejoins the helix
Ligase – brings together Okazaki fragments
DNA polymerases add nucleotides only to the
free 3end of a growing strand; therefore, a new
DNA strand can elongate only in the
5to 3direction
 Along one template strand of DNA, the DNA
polymerase synthesizes a leading 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 by DNA ligase
Figure 16.13
Primase
3
Topoisomerase
3
5
RNA
primer
5
3
Helicase
5
Single-strand binding
proteins
Figure 16.15b
Origin of
replication
3
5
RNA primer
5
3
3
Sliding clamp
DNA pol III
Parental DNA
5
3
5
5
3
3
5
Figure 16.17
Overview
Origin of
replication
Leading
strand
Lagging
strand
Leading
strand
Lagging
strand
Overall directions
of replication
Leading strand
DNA pol III
5
3
3
Parental
DNA
Primer
5
3
Primase
5
DNA pol III
4
Lagging strand
DNA pol I
35
3
2
DNA ligase
1 3
5
Protein Synthesis
1. Transcription
The transfer of genetic info. From DNA to
messenger RNA (mRNA)
2. Translation
The transfer of mRNA to protein
Genes are pieces of DNA that code for proteins
mRNA – Uracil instead of Thymine
Transcription
 DNA codes for single strand of mRNA
 This happens in the nucleus
 RNA polymerase binds to the promoter
region on DNA template
 Sigma factor recognizes binding site on
DNA
 mRNA detatches at the terminator region
of the DNA template
Transcription
Translation
 The transfer of mRNA into a protein
 This happens at the ribosome
 Every 3 base pairs of mRNA is called a
codon
 tRNA hold anti-codons and amino acids
 tRNA bring amino acids down to the
ribosomes using the corresponding anticodon.
Translation
Translation
The Genetic Code
Discovery of DNA – Rosalind
Franklin
Watson and Crick
Mutations
Sickle cell mutation
Prokaryotes vs. Eukaryotes
 In prokaryotes, translation of mRNA can
begin before transcription has finished
 In a eukaryotic cell, the nuclear envelope
separates transcription from translation
 Eukaryotic RNA transcripts are modified
through RNA processing to yield the
finished mRNA
 A primary transcript is the initial RNA
transcript from any gene prior to
processing
Comparing Gene Expression in Bacteria,
Archaea, and Eukarya
• Bacteria and eukarya differ in their RNA
polymerases, termination of transcription, and
ribosomes; archaea tend to resemble eukarya in
these respects
• Bacteria can simultaneously transcribe and
translate the same gene
• In eukarya, transcription and translation are
separated by the nuclear envelope
• In archaea, transcription and translation are
likely coupled
© 2011 Pearson Education, Inc.
Figure 17.4
DNA
template
strand
5
3
A C C
A A
A C
T
T
T
G G
T
C G A G
G G C
T
T
C A
3
5
DNA
molecule
Gene 1
TRANSCRIPTION
Gene 2
U G G
mRNA
U U
U G G C U
C A
5
3
Codon
TRANSLATION
Protein
Trp
Phe
Gly
Ser
Gene 3
Amino acid
Important vocabulary in
transcription
 The stretch of DNA that is transcribed is called a
transcription unit
 Transcription factors (sigma) – initiate the
binding of the RNA polymerase
 The completed assembly of transcription factors
and RNA polymerase II bound to a promoter is
called a transcription initiation complex
 A promoter called a TATA box is crucial in
forming the initiation complex in eukaryotes
Figure 17.8
1 A eukaryotic promoter
Promoter
Nontemplate strand
DNA
5
3
3
5
T A T A A AA
A T AT T T T
TATA box
Transcription
factors
Start point
Template strand
2 Several transcription
factors bind to DNA
5
3
3
5
3 Transcription initiation
complex forms
RNA polymerase II
Transcription factors
5
3
5
3
RNA transcript
Transcription initiation complex
3
5
RNA processing
• Enzymes in the eukaryotic nucleus modify
pre-mRNA (RNA processing) before the
genetic messages are dispatched to the
cytoplasm
• During RNA processing, both ends of the
primary transcript are usually altered
• Also, usually some interior parts of the
molecule are cut out, and the other parts
spliced together
• Each end of a pre-mRNA molecule is
modified in a particular way
– The 5 end receives a modified nucleotide 5
cap
– The 3 end gets a poly-A tail
• These modifications share several functions
– They seem to facilitate the export of mRNA
to the cytoplasm
– They protect mRNA from hydrolytic enzymes
– They help ribosomes attach to the 5 end
Figure 17.10
5
G
Protein-coding
segment
P P P
5 Cap 5 UTR
Polyadenylation
signal
AAUAAA
Start
codon
Stop
codon
3 UTR
3
AAA … AAA
Poly-A tail
RNA Splicing
• In some cases, RNA splicing is carried out by
spliceosomes
• Spliceosomes consist of a variety of proteins
and several small nuclear ribonucleoproteins
(snRNPs) that recognize the splice sites
Figure 17.12-3
RNA transcript (pre-mRNA)
5
Exon 1
Intron
Protein
snRNA
Exon 2
Other
proteins
snRNPs
Spliceosome
5
Spliceosome
components
5
mRNA
Exon 1
Exon 2
Cut-out
intron
Figure 17.13
Gene
DNA
Exon 1 Intron Exon 2 Intron Exon 3
Transcription
RNA processing
Translation
Domain 3
Domain 2
Domain 1
Polypeptide
Figure 17.15
3
Amino acid
attachment
site
5
Amino acid
attachment
site
5
3
Hydrogen
bonds
Hydrogen
bonds
A A G
3
Anticodon
(a) Two-dimensional structure
Anticodon
(b) Three-dimensional structure
5
Anticodon
(c) Symbol used
in this book
Figure 17.22
1 Ribosome
5
4
mRNA
Signal
peptide
3
SRP
2
ER
LUMEN
SRP
receptor
protein
Translocation
complex
Signal
peptide
removed
ER
membrane
Protein
6
CYTOSOL
What Is a Gene? Revisiting the Question
• The idea of the gene has evolved through the
history of genetics
• We have considered a gene as
– A discrete unit of inheritance
– A region of specific nucleotide sequence in a
chromosome
– A DNA sequence that codes for a specific
polypeptide chain
© 2011 Pearson Education, Inc.
Figure 17.26
DNA
TRANSCRIPTION
3
5
RNA
polymerase
RNA
transcript
Exon
RNA
PROCESSING
RNA transcript
(pre-mRNA)
AminoacyltRNA synthetase
Intron
NUCLEUS
Amino
acid
AMINO ACID
ACTIVATION
tRNA
CYTOPLASM
mRNA
Growing
polypeptide
3
A
Aminoacyl
(charged)
tRNA
P
E
Ribosomal
subunits
TRANSLATION
E
A
Anticodon
Codon
Ribosome
Concept 17.5: Mutations of one or a few
nucleotides can affect protein structure and
function
• Mutations are changes in the genetic material
of a cell or virus
• Point mutations are chemical changes in just
one base pair of a gene
• The change of a single nucleotide in a DNA
template strand can lead to the production of an
abnormal protein
© 2011 Pearson Education, Inc.
Figure 17.23
Wild-type hemoglobin
Sickle-cell hemoglobin
Wild-type hemoglobin DNA
C T T
3
5
G A A
5
3
Mutant hemoglobin DNA
C A T
3
G T A
5
mRNA
5
5
3
mRNA
G A A
Normal hemoglobin
Glu
3
5
G U A
Sickle-cell hemoglobin
Val
3
Types of Small-Scale Mutations
• Point mutations within a gene can be divided into
two general categories
– Nucleotide-pair substitutions
– One or more nucleotide-pair insertions or
deletions
© 2011 Pearson Education, Inc.
Substitutions
• A nucleotide-pair substitution replaces one
nucleotide and its partner with another pair of
nucleotides
• Silent mutations have no effect on the amino
acid produced by a codon because of
redundancy in the genetic code
• Missense mutations still code for an amino
acid, but not the correct amino acid
• Nonsense mutations change an amino acid
codon into a stop codon, nearly always leading
to a nonfunctional protein
© 2011 Pearson Education, Inc.
Insertions and Deletions
• Insertions and deletions are additions or losses
of nucleotide pairs in a gene
• These mutations have a disastrous effect on the
resulting protein more often than substitutions do
• Insertion or deletion of nucleotides may alter the
reading frame, producing a frameshift mutation
© 2011 Pearson Education, Inc.
Figure 17.24
Wild type
DNA template strand 3 T A C T T C A A A C C G A T T 5
5 A T G A A G T T T G G C T A A 3 
mRNA5 A U G A A G U U U G G C U A A 3
Protein
Met
Lys
Phe
Gly
Stop
Carboxyl end
Amino end
(b) Nucleotide-pair insertion or deletion
(a) Nucleotide-pair substitution
Extra A
A instead of G
3 T A C T T C A A A C C A A T T 5
5 A T G A A G T T T G G T T A A 3
3 T A C A T T C A A A C C G A T T 5
5 A T G T A A G T T T G G C T A A 3
Extra U
U instead of C
5 A U G A A G U U U G G U U A A 3
Met
Lys
Phe
Gly
Stop
Silent (no effect on amino acid sequence)
5 A U G U A A G U U U G G C U A A 3
Met
Stop
Frameshift causing immediate nonsense
(1 nucleotide-pair insertion)
T instead of C
A missing
3 T A C T T C A A A T C G A T T 5
5 A T G A A G T T T A G C T A A 3
3 T A C T T C A A C C G A T T 5T

5 A T G A A G T T G G C T A A 3A
A instead of G
U missing
5 A U G A A G U U U A G C U A A 3
Met
Lys
Phe
Ser
Stop
Missense
5 A U G A A G U U G G C U A A
Met
Lys
Leu
Ala
Frameshift causing extensive missense
(1 nucleotide-pair deletion)
A instead of T
3 T A C A T C A A A C C G A T T 5
5 A T G T A G T T T G G C T A A 3
U instead of A
5 A U G U A G U U U G G C U A A 3
Met
Nonsense
Stop
T T C missing
3 T A C A A A C C G A T T 5
5 A T G T T T G G C T A A 3
A A G missing
 A A
5 A U G U U U G G C U A A 3U
Met
Phe
Gly
Stop
No frameshift, but one amino acid missing
(3 nucleotide-pair deletion)
3
Chromosomal Alteration
•
•
•
•
•
Deletion
Duplications – hemoglobin, antifreeze
Inversions
Translocations
Transposons – jumping genes (corn)
Gene Expression
• Gene expression is the act of going from
genotype to phenotype
• DNA to mRNA to Protein
• Genes are regulated by turning on and off
transcription
 The
lac operon in E.coli is the method by
which E. coli make enzymes that metabolize
lactose
 Regulatory gene – produces the repressor
 Repressor binds to the operator when lactose
is absent
 No Transcription – RNA polymerase cannot
bind to the promoter
 When
lactose is present, it binds to the
repressor pulling it off the operator
 RNA polymerase binds the promoter –
transcription begins
 Lactose-digesting enzymes are made
Regulatory
gene
DNA
Promoter
Operator
lacI
lacZ
No
RNA
made
3
mRNA
RNA
polymerase
5
Active
repressor
Protein
(a) Lactose absent, repressor active, operon off
lac operon
DNA
lacI
lacZ
lacY
lacA
RNA polymerase
3
mRNA
5
mRNA 5
-Galactosidase
Protein
Allolactose
(inducer)
Inactive
repressor
(b) Lactose present, repressor inactive, operon on
Permease
Transacetylase
 Trp
operon. E.coli will make tryptophan
from scratch, but if it is in the surroundings,
the E.coli will absorb it.
 Different from the lac operon
trp operon
Promoter
Promoter
Genes of operon
DNA
trpE
trpR
trpD
trpC
trpB
trpA
C
B
A
Operator
Regulatory
gene
3
RNA
polymerase
Start codon
Stop codon
mRNA 5
mRNA
5
E
Protein
Inactive
repressor
D
Polypeptide subunits that make up
enzymes for tryptophan synthesis
(a) Tryptophan absent, repressor inactive, operon on
DNA
No RNA
made
mRNA
Protein
Active
repressor
Tryptophan
(corepressor)
(b) Tryptophan present, repressor active, operon off
Proximal control elements are located close to
the promoter
 Distal control elements, groupings of which are
called enhancers, may be far away from a gene
or even located in an intron
 Some transcription factors function as
repressors, inhibiting expression of a particular
gene by a variety of methods
 A particular combination of control elements can
activate transcription only when the appropriate
activator proteins are present

Promoter
Activators
DNA
Enhancer
Distal control
element
Gene
TATA box
General
transcription
factors
DNAbending
protein
Group of mediator proteins
RNA
polymerase II
RNA
polymerase II
Transcription
initiation complex
RNA synthesis
Enhancer
Control
elements
Promoter
Albumin gene
Crystallin
gene
LENS CELL
NUCLEUS
LIVER CELL
NUCLEUS
Available
activators
Available
activators
Albumin gene
not expressed
Albumin gene
expressed
Crystallin gene
not expressed
(a) Liver cell
Crystallin gene
expressed
(b) Lens cell
Types of Genes Associated with Cancer
• Cancer can be caused by mutations to genes that
regulate cell growth and division
• Tumor viruses can cause cancer in animals
including humans
© 2011 Pearson Education, Inc.
Cancer Genes
• Oncogenes are cancer-causing genes
• Proto-oncogenes are the
corresponding normal cellular genes
that are responsible for normal cell
growth and division
• Conversion of a proto-oncogene to an
oncogene can lead to abnormal
stimulation of the cell cycle
Evidence That DNA Can Transform Bacteria
• The discovery of the genetic role of DNA began
with research by Frederick Griffith in 1928
• Griffith worked with two strains of a bacterium, one
pathogenic and one harmless
© 2011 Pearson Education, Inc.
• When he mixed heat-killed remains of the
pathogenic strain with living cells of the harmless
strain, some living cells became pathogenic
• He called this phenomenon transformation, now
defined as a change in genotype and phenotype
due to assimilation of foreign DNA
© 2011 Pearson Education, Inc.
Figure 16.2
EXPERIMENT
Living S cells
(control)
Living R cells
(control)
Heat-killed
S cells
(control)
Mixture of
heat-killed
S cells and
living R cells
Mouse healthy
Mouse dies
RESULTS
Mouse dies
Mouse healthy
Living S cells
Animation: Hershey-Chase Experiment
Right-click slide / select “Play”
© 2011 Pearson Education, Inc.
Figure 16.4-3
EXPERIMENT
Phage
Radioactive
protein
Empty
protein
shell
Radioactivity
(phage protein)
in liquid
Bacterial cell
Batch 1:
Radioactive
sulfur
(35S)
DNA
Phage
DNA
Centrifuge
Pellet (bacterial
cells and contents)
Radioactive
DNA
Batch 2:
Radioactive
phosphorus
(32P)
Centrifuge
Radioactivity
Pellet (phage DNA)
in pellet