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42 Pages
Lecture2-1
Course: CHEM 114C, Spring 2012School: UCSD
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Word Count: 960
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the BergTymoczkoStryer Biochemistry SeventhEdition CHAPTER28 DNAReplication,Repair,and Recombination Copyright2012byW.H.FreemanandCompany 1 Copying Genetic Information Overall error rate of DNA Replication = 1 bp per 3 x 109 bp DNA synthesis: 1 per 103 104 bp Proofreading: 1 per 106 107 bp Postreplication mismatch repair: 1 per 109 1010 bp 2 DNA Replication, Damage, & Repair 3 DNA Replication...
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the BergTymoczkoStryer
Biochemistry
SeventhEdition
CHAPTER28
DNAReplication,Repair,and
Recombination
Copyright2012byW.H.FreemanandCompany
1
Copying Genetic Information
Overall error rate of DNA
Replication = 1 bp per 3 x 109 bp
DNA synthesis: 1 per 103 104 bp
Proofreading: 1 per 106 107 bp
Postreplication mismatch repair:
1 per 109 1010 bp
2
DNA Replication, Damage, & Repair
3
DNA Replication
4
DNA Replication
5
DNA Replication
6
DNA Polymerase
7
Discovery of the Mechanism of Nucleic Acid Synthesis
The Nobel Prize in Physiology or Medicine 1959
Severo Ochoa (PNPase), Arthur Kornberg (DNA Polymerase I)
8
Note: Kornberg discovered DNA polymerase I and not polymerase III.
9
Tom Steitz and co-workers
in 1985 determined the
structure of the Klenow
fragment of DNA
polymerase I from
E. coli.
C-terminal fragment of
Polymerase I.
Has: Polymerase & 3 to 5
exonuclease activities.
Missing: 5 to 3
exonuclease activity.
10
DNA Polymerase I Structure
Multiple domains: Palm,
Fingers, Thumb, &
Exonuclease.
http://www.rcsb.org/pdb/explore/
11
Polymerases have similar structure
HIV-RT
Taq Polymerase
RB69 gp43
Rat Polymerase
12
13
DNA Polymerase Mechanism
1. DNA polymerases are templatedirected enzymes.
2. Require a primer with a free 3hydroxyl group.
3. Catalyze the nucleophilic attack
of the 3-OH terminus on the phosphoryl group of the dNTP to
be added.
4. Two metal ions are critical for
activity. Stabilize the negative
charge on the pentacoordinate
transition state.
14
Importance of Hydrogen Bonds
and Shape Complementarity
15
Minor-groove Interactions
1. Residues of the
enzyme form
hydrogen bonds with
the minor-groove
side of the base pair
in the active site.
2. Hydrogen bond
acceptors are: N3 of
purine & O2 of
pyramidine
16
Shape Selectivity
Binding of the correct dNTP induces a conformational
change, generating a tight pocket for the base pair.
17
18
Interaction of Polymerase with Template + Primer
Minor groove
interactions
19
Mapping of Cancer Mutations in Polymerase
20
Priming: Synthesis of an RNA primer by Primase
Primase is an RNA
polymerase that
synthesizes about 5
nucleotide long primer.
The RNA primer is
removed at a later stage
of replication.
21
Okazaki Fragments
1. DNA polymerase synthesize DNA in 5 3 direction.
2. Synthesis of the Lagging Strand is DISCONTINUOUS.
22
DNA Ligase Reaction
DNA ligase seals breaks in double-stranded DNA molecules
Require energy: ATP or NAD+ is hydrolyzed
23
Helicase Structure
1. The two strands of the
DNA must be separated to
act as templates.
2.Helicases use the energy
of ATP hydrolysis to
separate the duplex DNA.
3.Helicases are oligomers.
Purple: P-loop NTPase; Yellow oval: DNA binding
http://www.rcsb.org/pdb/explore/explore.do?structureId=1e0k
24
Nonhydrolyzable Analog of ATP
25
Helicase Asymmetry
1. AMP-PNP binds to
four subunits.
2. Nucleotide-binding
sites are not
identical: (i) Favor
binding (ii) Favor
catalysis
3. Six subunits differ
in their orientation
(three classes)
26
Helicase Mechanism
ADP + Pi
ADP + Pi
ADP + Pi
ADP + Pi
27
DNA Unwinding & Supercoiling
Take a linear 260 bp B-DNA. It has 25 turns (260/10.4).
You get a relaxed circle if you join the ends.
28
DNA Unwinding & Supercoiling
Linking number (Lk): The number of
times a that strand of DNA winds in
the right-handed direction around the
helix axis when the axis lies in a plane.
Twist (Tw): A measure of the of the
helical winding of the DNA strand
around each other ( almost the same as
turns).
Writhe (Wr): A measure of the coiling
of the axis of the double helix
(supercoiling).
Right-handed coil is assigned a
negative number and a left-handed coil
is assigned a positive number.
29
DNA Unwinding & Supercoiling
Now unwind the DNA by two turns and then join the ends.
30
DNA Unwinding & Supercoiling
Linking number (Lk): The number of
times that a strand of DNA winds in
the right-handed direction around the
helix axis when the axis lies in a plane.
Twist (Tw): A measure of the of the
helical winding of the DNA strand
around each other ( almost the same as
turns).
Writhe (Wr): A measure of the coiling
of the axis of the double helix
(supercoiling).
Right-handed coil is assigned a
negative number and a left-handed coil
is assigned a positive number.
31
DNA Unwinding & Supercoiling
Topoisomers: Molecules
differing only in linking
numbers.
Topoisomers of DNA can be
interconverted only by
cutting one or both DNA
strands and then rejoining
them.
Lk = Tw + Wr
32
Topoisomers: Negatively Supercoiled and Relaxed DNA
Most naturally occurring DNA are negatively supercoiled (already unwound).
They are easier to replicate.
33
Structure of Topoisomerase I
Enzymes that introduce or
remove supercoils in DNA
Discovered by James Wang
& Martin Gellert.
http://www.rcsb.org/pdb/explore/explore.do?structureId=1ej9
34
Two Types of Topoisomerase
Type I: Catalyze the relaxation of
supercoiled DNA. Thermodynamically
favorable process. Cleave just one
strand of DNA.
Type II: Utilize free energy from ATP
hydrolysis to add negative supercoils to
DNA. Cleave both strands of DNA.
Both types use key tyrosine residues to
form covalent links to the DNA.
35
Topoisomerase I Mechanism
1.
2.
3.
4.
DNA binds in the central cavity (20 diameter).
A key Tyr residue cleaves the DNA strand forming a covalent
intermediate.
The DNA is rotated in a controlled manner driven by the release of
energy stored because of the supercoiling.
The free hydroxyl group of the DNA attacks the phosphotyrosine
residue to reseal the backbone and release tyrosine.
36
Topoisomerase I Mechanism
37
Structure of Topoisomerase II
Couple the binding and
hydrolysis of ATP to the
directed passage of one
DNA double helix through
another, temporarily
cleaved DNA double helix.
Form dimers with a large
internal cavity.
Gates at the top and the
bottom of the cavity.
http://www.rcsb.org/pdb/explore/jmol.do?structureId=2ZBK&bionumber=1
38
Topoisomerase II Mechanism
Gate segment (G) and Transported segment (T)
39
Inhibitors of Topoisomerase II (DNA gyrase)
Used as antibiotics because they inhibit bacterial topoisomerase
more than the eukaryotic enzyme.
1.Novobiocin: Blocks the binding of ATP to gyrase.
2.Nalidixic acid: Interfere with the breakage and rejoining of DNA
chains.
3.Ciprofloxacin: Interfere with the breakage and rejoining of DNA
chains.
4.Camptothecin: Antitumor agent. Inhibits human topoisomerase I
by stabilizing the enzyme covalently linked to DNA.
40
Used to treat urinary tract infections
41
Treat Bacillus anthracis (anthrax) infection.
42
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