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BIO130 Section One Guide (5)

10 Pages
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Department
Biology
Course Code
BIO130H1
Professor
Kenneth Yip

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Chapter 5 DNA Replication, Repair, and
Recombination
(pg. 263-288, 292-304)
The Maintenance of DNA Sequences
Mutation Rates are Extremely Low
-Mutation rate rate at which observable changes occur in DNA sequences
oA single genes that encodes an average-sized protein ( 103 nucleotide pairs)
accumulates a mutation about once in about 106 bacterial cell generations
-Comparing amino acid sequences of the same protein in several species can provide
an estimate of mutation rates in mammals; because natural selection causes
mutations to vanish from the population, these tend to be underestimates
-Luckily, the sequence of one family of protein fragments (fibrinopeptides) does not
seem to matter, allowing the encoding genes to accumulate mutations without being
selected against
-Fibrinopeptides fragments 20 AA long that are discarded when the protein
fibrinogen is activated to form fibrin during blood clotting
oBecause the function of fibrinopeptides doesnt depend on its AA sequence, it
can tolerate almost any mutation
-Another way to estimate mutation rates is to compare DNA sequences between
related species
Low Mutation Rates are Necessary for Life as We Know It
-Deleterious mutations limit the number to essential proteins an organism can
encode (50,000)
oA mutation rate 10X high would limit an organism to about 5000 essential
genes
-Germ cells transmit genetic information from parent to offspring
-Somatic cells form the body of the organism
-Uncontrolled cell proliferation of somatic cells causes cancer, causing more than
20% of deaths each year in Europe and North America
- Multicellular organisms depend on the high fidelity their DNA sequences are
replicated and maintained for both the survival of their large number of genes (germ
cell stability) and the prevention of cancer caused by mutations in somatic cells
(somatic cell stability)
DNA Replication Mechanisms
-DNA is replicated at up to 1000 nucleotides/second
Base-Pairing Underlies DNA Replication and DNA Repair
www.notesolution.com
-DNA templating mechanism to copy nucleotide sequence of one DNA strand into
a complementary DNA sequence (through base-pairing with free nucleotides)
-DNA polymerase first nucleotide-polymerizing enzyme
oDeoxyribonucleoside triphosphates (dNTPs) served as substrates for this
enzyme
The DNA Replication Fork is Asymmetrical
-Replication fork region of replication that moves along the parental DNA double
helix
-DNA polymerases synthesize only in the 53 direction
-Leading strand is synthesized continuously 53
-Lagging strand synthesized discontinuously by polymerizing Okazaki
fragments (5-3 direction on the lagging strand, then joined together after their
synthesis to create long DNA chains)
The High Fidelity of DNA Replication Requires Several Proofreading
Mechanisms
-Generally, only 1 mistake occurs for every 109 nucleotides copied
oSometimes hydrogen bonds form between G + T in DNA, or C pairs with A
instead of G
-DNA polymerase performs the first proofreading step just before a new nucleotide
is added to the growing chain (the new correct nucleotide is always energetically
favourable)
oBecause DNA polymerases fingers tighten around the active site more
readily with correct than incorrect base-pairing, it allows the polymerase to
double-check the exact base-pair geometry before it catalyzes the addition
of the nucleotide
-The next error-correcting reaction (exonucleolytic proofreading) self-correction
oDNA molecules with a mismatched nucleotide at the 3-OH end of the primer
strand are not effective as templates because the polymerase cannot extend
such a strand
oThe correction of a mismatched nucleotide occurs by means of a separate
catalytic site
Either in a separate subunit or separate domain of the polymerase
molecule
oThe 3-5 proofreading exonuclease clips off unpaired residues at the
primer terminus
-In contrast, RNA polymerase enzymes involved in gene transcription dont need
efficient proofreading because errors in making RNA are not passed on to the next
generation
oThis allows them to start new polynucleotide chains without a primer
www.notesolution.com
oError frequency in RNA synthesis and mRNA translation is 1 mistake for
every 104 polymerization events; 100,000X greater than DNA replication
Only DNA Replication in the 5 3Direction Allows Efficient Error Correction
-If replication occurred in the 35 direction, dNTPs would be added to the growing
5-chain end. Mistakes in polymerization couldnt be hydrolyzed away because the
base 5-chain end would immediately terminate DNA synthesis.
A Special Enzyme Synthesizes Short RNA Primer Molecules on the Lagging
Strand
-DNA primase uses ribonucleoside triphosphates to form RNA primers on the
lagging strand
oprimers are 10 nucleotides long; made every 100-200 nucleotides on lagging
strand
oBecause RNA primers contain a properly base-paired nucleotide with a 3-OH
group at one end, it can be elongated by the DNA polymerase to begin an
Okazaki fragment
-Once the primer is later removed, DNA ligase joins 3 end to the 5 end of previous
one
-Why would an erasable RNA primer be preferred?
oThe argument that a self-correcting polymerase cannot start chains de novo
also implies its converse: an enzyme that starts chains anew cannot be
efficient at self-correction.
oThe use of RNA rather than DNA for priming allow the ribonucleotides in the
primer to mark these sequences as suspect copy to be efficiently removed
and replaced
Special Proteins Help to Open Up the DNA Double Helix in Front of the
Replication Fork
-DNA helicase proteins that hydrolyze ATP when they are bound to single strands
of DNA
oATP hydrolysis can change the shape of a protein molecule in a cyclical
matter that allows the protein to perform mechanical work
oDNA helicase uses this to propel itself rapidly along a DNA single strand
(1000 NP/s)
-Single-strand DNA-binding (SSB) proteins bind to exposed single-stranded
DNA without covering the bases
oStabilize the unwound, single-stranded conformation
oThey coat and straighten out single-stranded DNA on the lagging-strand
template, preventing formation of short hairpin helices (hairpins can impede
DNA synthesis)
www.notesolution.com

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Description
Chapter 5 DNA Replication, Repair, and Recombination (pg. 263-288, 292-304) The Maintenance of DNA Sequences Mutation Rates are Extremely Low - Mutation rate rate at which observable changes occur in DNA sequences 3 o A single genes that encodes an average-sized protein ( 10 nucleotide pairs) accumulates a mutation about once in about 10 bacterial cell generations - Comparing amino acid sequences of the same protein in several species can provide an estimate of mutation rates in mammals; because natural selection causes mutations to vanish from the population, these tend to be underestimates - Luckily, the sequence of one family of protein fragments (fibrinopeptides) does not seem to matter, allowing the encoding genes to accumulate mutations without being selected against - Fibrinopeptides fragments 20 AA long that are discarded when the protein fibrinogen is activated to form fibrin during blood clotting o Because the function of fibrinopeptides doesnt depend on its AA sequence, it can tolerate almost any mutation - Another way to estimate mutation rates is to compare DNA sequences between related species Low Mutation Rates are Necessary for Life as We Know It - Deleterious mutations limit the number to essential proteins an organism can encode (50,000) o A mutation rate 10X high would limit an organism to about 5000 essential genes - Germ cells transmit genetic information from parent to offspring - Somatic cells form the body of the organism - Uncontrolled cell proliferation of somatic cells causes cancer, causing more than 20% of deaths each year in Europe and North America - Multicellular organisms depend on the high fidelity their DNA sequences are replicated and maintained for both the survival of their large number of genes (germ cell stability) and the prevention of cancer caused by mutations in somatic cells (somatic cell stability) DNA Replication Mechanisms - DNA is replicated at up to 1000 nucleotidessecond Base-Pairing Underlies DNA Replication and DNA Repair www.notesolution.com
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