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MOLECULAR
BIOLOGY OF THE
GENE
Chapter 12
pp. 211-232
Major Contributors to DNA
Griffith
 Hershey and Chase
 Franklin and Wilkins
 Chargaff
 Watson and Crick

2
2
NUCLEOTIDE
(Building blocks of Nucleic Acids)

This is what a nucleotide would look like
in reality…….
NUCLEOTIDE
(often identified by their bases)

Here is how we
could draw it…..
P
S
B
BASES
(differs in each nucleotide)
Adenine (A)
 Cytosine (C)
 Guanine (G)
 Uracil (U)
 Thymine (T)
 Purines = double
ring
 Pyramidines =
single ring

Chargaff’s Rules
 The
amounts of A, T, G, and C in DNA:
 Identical in identical twins
 Varies between individuals of a species
 Varies more from species to species
 In
each species, there are equal amounts of:
A & T
G & C
 All
this suggests DNA uses complementary base
pairing to store genetic info
 Human chromosome estimated to contain, on
average, 140 million base pairs
11
Watson and Crick Model
Watson
and Crick, 1953
 Constructed
a model of DNA
 Double-helix
model is similar to a twisted ladder
 Sugar-phosphate
backbones make up the sides
 Hydrogen-bonded
 Received
bases make up the rungs
a Nobel Prize in 1962
15
3 end
P
P
P
P
P
P
• Therefore replication
takes place in opposite
directions
5 end
P
• Each strand of the
double helix is oriented
in the opposite
direction,
P
Figure 10.5B
Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings
3 end
5 end
A model for DNA replication: the basic concept
(layer 1)
A
T
C
G
T
A
A
T
G
C
(a) The parent molecule has two
complementary strands of DNA.
Each base is paired by hydrogen
bonding with its specific partner,
A with T and G with C.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
A model for DNA replication: the basic concept
(layer 2)
A
T
A
T
C
G
C
G
T
A
T
A
A
T
A
T
G
C
G
C
(a) The parent molecule has two
complementary strands of DNA.
Each base is paired by hydrogen
bonding with its specific partner,
A with T and G with C.
(b) The first step in replication is
separation of the two DNA
strands.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
A model for DNA replication: the basic concept
(layer 3)
T
A
T
A
T
A
C
G
C
G
C
T
A
T
A
T
A
A
T
A
T
A
T
G
C
G
C
G
C
G
A
T
C
G
T
A
A
C
G
(a) The parent molecule has two
complementary strands of DNA.
Each base is paired by hydrogen
bonding with its specific partner,
A with T and G with C.
(b) The first step in replication is
separation of the two DNA
strands.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
T
(c) Each parental strand now
serves as a template that
determines the order of
nucleotides along a new,
complementary strand.
A model for DNA replication: the basic concept
(layer 4)
T
A
T
A
T
A
C
G
C
G
C
T
A
T
A
T
A
A
T
A
T
A
T
G
C
G
C
G
C
G
A
T
A
T
A
T
C
G
C
G
C
G
T
A
T
A
T
A
T
A
T
A
T
C
G
C
G
C
A
G
a) The parent molecule has two
complementary strands of DNA.
Each base is paired by hydrogen
bonding with its specific partner,
A with T and G with C.
(b) The first step in replication is
separation of the two DNA
strands.
(c) Each parental strand now
serves as a template that
determines the order of
nucleotides along a new,
complementary strand.
(d) The nucleotides are connected
to form the sugar-phosphate
backbones of the new strands.
Each “daughter” DNA
molecule consists of one parental
strand and one new strand.
 DNA
replication is the process of copying a DNA
molecule.
is semiconservative, with each strand of
the original double helix (parental molecule) serving as
a template (mold or model) for a new strand in a
daughter molecule.
 Replication
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
DNA replication: A closer look
• DNA replication begins at specific sites
Parental strand
Origin of replication
Daughter strand
Bubble
Two daughter DNA molecules
Figure 10.5A
Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings
DNA
REPLICATION
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ee/0072437316/120076/micro04.swf::DNA%20Replication%2
0Fork
Replication: Prokaryotic
Prokaryotic
 Bacteria
Replication
have a single circular loop
 Replication
moves around the circular DNA
molecule in both directions
 Produces
two identical circles
 Cell
divides between circles, as fast as every 20
minutes
32
Replication: Prokaryotic vs. Eukaryotic
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origin
replication is
complete
replication is
occurring in
two directions
a. Replication in prokaryotes
replication fork
replication bubble
parental strand
new DNA
duplexes
b. Replication in eukaryotes
daughter strand
33
Replication Errors
Genetic
variations are the raw material for
evolutionary change
Mutation:
A
permanent (but unplanned) change in base-pair
sequence
 Some
due to errors in DNA replication
 Others
are due to to DNA damage
 DNA
repair enzymes are usually available to
reverse most errors
34
Function of Genes
Genes
Specify Enzymes
 Beadle
and Tatum:
 Experiments
on fungus Neurospora crassa
 Proposed that each gene specifies the synthesis of
one enzyme
 One-gene-one-enzyme hypothesis
Genes
Specify a Polypeptide
A
gene is a segment of DNA that specifies the
sequence of amino acids in a polypeptide
 Suggests that genetic mutations cause changes in
the primary structure of a protein
35
Overview of Protein Synthesis
DNA ---------> RNA ------> Protein
Transcription
Translation
DNA serves as a template to make
RNA (transcription), which then
carries the code for making a protein.
The code is deciphered to make the
protein (translation).
Gene 1
Gene 3
DNA molecule
Gene 2
DNA strand
TRANSCRIPTION
RNA
Codon
TRANSLATION
Polypeptide
Figure 10.7
Amino acid
Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings
Types of RNA
RNA
is a polymer of RNA nucleotides
RNA Nucleotides are of four types: Uracil,
Adenine, Cytosine, and Guanine
Uracil (U) replaces thymine (T) of DNA
Types of RNA
 Messenger
(mRNA) - Takes genetic message from
DNA in nucleus to ribosomes in cytoplasm
 Ribosomal (rRNA) - Makes up ribosomes which read
the message in mRNA
 Transfer (tRNA) - Transfers appropriate amino acid to
ribosome when “instructed”
39
Structure of RNA
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G
P
G
S
U
A
P
U
base is
uracil instead
of thymine
C
S
P
A
S
P
C
S
ribose
one nucleotide
40
RNA vs. DNA structure
41
The genetic code
• Virtually all
organisms share
the same genetic
code
Figure 10.8A
Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings
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on.swf
Fig. 17-7a-1
Promoter
Transcription
Factors bind so
RNA Polymerase
knows where to
go at TATA box
5
3
Start point
RNA polymerase
DNA
3
5
Fig. 17-7a-2
Promoter
5
3
Start point
RNA polymerase
3
5
DNA
1
Initiation
5
3
Unwound
DNA
3
5
RNA
transcript
Template strand
of DNA
Fig. 17-7a-3
Promoter
5
3
Start point
RNA polymerase
3
5
DNA
1
Initiation
5
3
3
5
Unwound
DNA
RNA
transcript
Template strand
of DNA
2
Elongation
Rewound
DNA
5
3
3
5
RNA
transcript
3
5
Promoter
5
3
Start point
RNA polymerase
3
5
DNA
1
Initiation
5
3
3
5
Unwound
DNA
RNA
transcript
Template strand
of DNA
2
Elongation
Rewound
DNA
5
3
3
5
3
5
RNA
transcript
3 Termination
5
3
3
5
5
Completed RNA transcript
3
Processing Messenger RNA
 Pre-mRNA,
is composed of
exons and introns.
 RNA
splicing:
 Primary


transcript consists of:
Some segments that will not be
expressed (introns)
Segments that will be expressed
(exons)
 Performed
by spliceosome
complexes in nucleoplasm


Introns are excised
Remaining exons are spliced back
together
 Result
is mature mRNA
transcript
54
Eukaryotic RNA is processed before leaving the
nucleus
 Modifications
to ends of
primary transcript:
 Cap
of modified guanine on
5′ end
The cap is a modified guanine
(G) nucleotide
 Helps
a ribosome where to
attach when translation begins

 Poly-A
tail of 150+ adenines on 3′
end
 Facilitates the transport of mRNA
out of the nucleus
 Inhibits degradation of mRNA by
hydrolytic enzymes.
Figure 10.10
Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings
Exon Intron
Exon
Intron
Exon
DNA
Cap
RNA
transcript
with cap
and tail
Transcription
Addition of cap and tail
Introns removed
Tail
Exons spliced together
mRNA
Coding sequence
NUCLEUS
CYTOPLASM
RNA Splicing
In
prokaryotes, introns are removed by “selfsplicing”—that is, the intron itself has the
capability of enzymatically splicing itself out
of a pre-mRNA
55
Aminoacyl t-RNA synthetase adds amino acids to tRNA
 tRNA molecules
have two binding sites
 One associates with the mRNA transcript
 The other associates with a specific amino acid
 Each of the 20 amino acids in proteins associates with
one or more of 64 species of tRNA
 tRNA
molecules come in 64 different kinds
 All very similar except that
 One end bears a specific triplet (of the 64 possible)
called the anticodon
 Other end binds with a specific amino acid type
 tRNA synthetases attach correct amino acid to the
correct tRNA molecule
 All tRNA molecules with a specific anticodon will always
bind with the same amino acid
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The structure of transfer RNA (tRNA)
3

A
Amino acid
C
attachment site
C
A
C
G
C
U
U
A
A
U C
*
C A C AG
G
G U G U *
C
* *
U C
* GA
G
G
U
A
*
A
*
*
5

G
C
G
G
A
U
U
U
A
A G *
* C U C
*
G
C G A G
A G G
*
C
C
A
G
A
Hydrogen
bonds
C
U
A G
Anticodon
(a
) Two-dimensional structure. The four base-paired regions and three loops are characteristic of all tRNAs,
as is the base sequence of the amino acid attachment site at the 3 end. The anticodon triplet is unique to
each tRNA type. (The asterisks mark bases that have been chemically modified, a characteristic of tRNA.)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Ribosomes
 Ribosomal
 Produced
 Combined
RNA (rRNA):
from a DNA template in the nucleolus
with proteins into large and small ribosomal
subunits
A
completed ribosome has three binding sites to
facilitate pairing between tRNA and mRNA
 The
E (for exit) site
 The
P (for peptide) site, and
 The
A (for amino acid) site
64
P site (Peptidyl-tRNA
binding site)
A site (AminoacyltRNA binding site)
E site
(Exit site)
Large
subunit
E
P
A
mRNA
binding site
Small
subunit
(b) Schematic model showing binding sites. A ribosome has an mRNA binding site and three tRNA
binding sites, known as the A, P, and E sites. This schematic ribosome will appear in later diagrams.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Steps in Translation: Initiation
 Components
necessary for initiation are:
 Small
ribosomal subunit
 mRNA transcript
 Initiator tRNA, and
 Large ribosomal subunit
 Initiation factors (special proteins that bring the above
together)
 Initiator
tRNA:
 Always
has the UAC anticodon
 Always carries the amino acid methionine
 Capable of binding to the P site
66
Steps in Translation: Initiation
Small
ribosomal subunit attaches to mRNA
transcript
 Beginning
of transcript always has the START
codon (AUG)
Initiator
tRNA (UAC) attaches to P site
Large
ribosomal subunit joins the small
subunit
67
Steps in Translation: Elongation
“Elongation”
refers to the growth in length of
the polypeptide
RNA molecules bring their amino acid fares
to the ribosome
 Ribosome
reads a codon in the mRNA
 Allows
only one type of tRNA to bring its amino acid
 Must have the anticodon complementary to the mRNA
codon being read
 Joins the ribosome at it’s A site
 Methionine of initiator is connected
of 2nd tRNA by peptide bond
to amino acid
70
Steps in Translation: Elongation
 Second
tRNA moves to P site (translocation)
 Spent initiator moves to E site and exits
 Ribosome reads the next codon in the mRNA
 Allows
only one type of tRNA to bring its amino acid
 Must
have the anticodon complementary to the mRNA codon
being read
 Joins the ribosome at it’s A site
 Dipeptide on 2nd amino acid is
of 3nd tRNA by peptide bond
connected to amino acid
71
Codon is translated
in a 5 to 3 direction.
The third base in
the code does not
always show a
complement
between codon and
anticodon =
WOBBLE. Wobble
still exists only
between purines
and pyrimidines
though.
Ribosomes build polypeptides
Next amino acid
to be added to
polypeptide
Growing
polypeptide
tRNA
molecules
P site
A site
Growing
polypeptide
Large
subunit
tRNA
P
mRNA
binding
site
A
mRNA
Codons
mRNA
Small
subunit
Figure 10.12A-C
Copyright © 2003 Pearson Education, Inc. publishing as Benjamin Cummings
TRANSLATION
(RNA is decoded)
Steps in Translation: Termination
 Previous
tRNA moves to P site
 Spent tRNA moves to E site and exits
 Ribosome reads the STOP codon at the end of the
mRNA
 UAA,
UAG, or UGA
 Does not code for an amino acid
 Polypeptide
is released from last tRNA by release
factor
 Ribosome releases mRNA and dissociates into
subunits
 mRNA read by another ribosome
74
Polysome (Polyribosome)
35
36
Gene Mutations

Point Mutations (Substitutions)
•Missense
•Nonsense

Frameshift Mutations
•Insertion
•Deletion
37
27
Figure 17.23 The molecular basis of sickle-cell
disease: a point mutation
Wild-type hemoglobin DNA
3
Mutant hemoglobin DNA
5
C
T
T
In the DNA, the
5 mutant template
strand has an A where
the wild-type template
has a T.
A
The mutant mRNA has
a U instead of an A in
one codon.
3
T
C
mRNA
A
mRNA
G
A
A
5
G
3
U
5
Normal hemoglobin
Glu
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
3
Sickle-cell hemoglobin
Val
The mutant (sickle-cell)
hemoglobin has a valine
(Val) instead of a glutamic
acid (Glu).
Figure 17.24 Base-pair substitution
Wild type
mRNA
A U G A A G U U U G G C U A A
5
Protein
3
Met
Lys
Phe
Amino end
Gly
Stop
Carboxyl end
Base-pair substitution
No effect on amino acid sequence
U instead of C
A U G A A G U U U G G U U A A
Met
Lys
Missense
Phe
Gly
Stop
A instead of G
A U G A A G U U U A G U U A A
Met
Lys
Phe
Ser
Stop
Nonsense
U instead of A
A U G U A G U U U G G C U A A
Met
Stop
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Figure 17.25 Base-pair insertion or deletion
Wild type
mRNA
Protein
5
A U G A A G U U U G G C U A A
Met
Lys
Gly
Phe
3
Stop
Amino end
Carboxyl end
Base-pair insertion or deletion
Frameshift causing immediate nonsense
Extra U
A U G U A A G U U U G G C U A
Met
Stop
Frameshift causing
extensive missense
U Missing
A U G A A G U U G G C U A A
Met
Lys
Leu
Ala
Insertion or deletion of 3 nucleotides:
no frameshift but extra or missing amino acid
A A G
Missing
A U G U U U G G C U A A
Met
Phe
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Gly
Stop
Figure 17.26 A summary of transcription and
translation in a eukaryotic cell
DNA
TRANSCRIPTION
1
RNA is transcribed
from a DNA template.
3
5 RNA
transcript
RNA
polymerase
RNA PROCESSING
2In eukaryotes, the
RNA transcript (premRNA) is spliced and
modified to produce
mRNA, which moves
from the nucleus to the
cytoplasm.
Exon
RNA transcript
(pre-mRNA)
Intron
Aminoacyl-tRNA
synthetase
NUCLEUS
Amino
acid
FORMATION OF
INITIATION COMPLEX
AMINO ACID ACTIVATION
tRNA
CYTOPLASM 3After leaving the
nucleus, mRNA attaches
to the ribosome.
mRNA
4 Each amino acid
attaches to its proper tRNA
with the help of a specific
enzyme and ATP.
Growing
polypeptide
Activated
amino acid
Ribosomal
subunits
5
TRANSLATION
5 A succession of tRNAs
E
A
AAA
UGGUU UA U G
Codon
Ribosome
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
add their amino acids to
Anticodonthe polypeptide chain
as the mRNA is moved
through the ribosome
one codon at a time.
(When completed, the
polypeptide is released
from the ribosome.)