Module 1.1 DNA Replication

Question 1

Enzyme

Answer 1

molecules that catalyze chemical reactions within living organisms

lowers activation energy required for reaction

Question 2

DNA polymerases

features

Answer 2

• Require a template and a primer for DNA synthesis
• Use Deoxribonucleoside triphosphates as substrates and energy source for polymerization
• Only the complementary nucleotides can bind with high affinity
• Synthesize DNA in the 5’ -> 3’ direction

Question 3

DNA Synthesis

process

Answer 3

• DNA polymerase binds a single
  stranded DNA with primer
• Deoxribonucleoside triphosphates
  correctly base-pair with the template
  and bind DNA polymerase with high affinity
• Polymerase covalently links the
  incoming nucleotide to the 3’ end of a DNA strand

Question 4

DNA Synthesis

Replication Fork

structure

Answer 4

• Both strands are synthesized in the 5’-to-3’ direction.
• Leading strand is synthesized continuously.
• Lagging strand is synthesized discontinuously, creating Okazaki fragments

Question 5

DNA Synthesis

DNA ligase

function

Answer 5

catalyzes the formation of phosphodiester
bonds between the 3’ hydroxyl group of one nucleotide and the 5’ phosphate group of the adjacent nucleotide, joining the Okazaki fragments into a continuous strand to complete the lagging strand of DNA

uses ATP, releases AMP

Question 6

DNA Polymerase

P site

Answer 6

Catalytic site for polymerization reaction (where correct bp are added to DNA chain in polymerizing mode)

Question 7

DNA Polymerase

E site

Answer 7

catalytic site for exonucleolytic reaction (where incorrect bp are removed in editing mode)

Question 8

DNA repair #3

Strand-directed mismatch repair system

NOT DNA polymerase

Answer 8

• Detects noncomplementary base pairs in the DNA helix
• Identify the newly synthesized DNA strand
• In a prokaryotic cell, newly synthesized DNA is not methylated
• in a eukaryotic cell, newly synthesized DNA is transiently nicked (single-strand breaks)
• Removes replication errors in the new strand by using the original strand as a template

muts and mutL proteins

Question 9

Mutation rate

Answer 9

rate at which observable changes occur in DNA sequences

Question 10

DNA Polymerase

Pyrophosphate

Answer 10

the two extra phosphate groups on a nucleoside triphosphate (eg. dCTP) used by DNA polymerase as an energy source to bond nucleotide to growing chain

Question 11

DNA synthesis

Okazaki fragments

length in prokaryotes and eukaryotes

Answer 11

prokaryotes: 1000-2000 bp
eukaryotes: 100-200 bp

Question 12

Tautomer

Answer 12

Structural isomer of a nucleotide (eg. C*) that bind with wrong base pair

Question 13

DNA repair #2

Exonucleolytic proofreading

DNA polymerase

Answer 13

When DNA polymerase can’t continue elongation due to a mismatch, nuclease activity attached to DNA polymerase trims unpaired nucleotides 3’ to 5’ at E site

Question 14

DNA repair #1

Proofreading through binding

DNA polymerase

Answer 14

Nucleoside triphosphate pulled in by DNA polymerase to bind to DNA chain. DNA polymerase changes configuration so if the nucleoside triphosphate doesn’t fit well it won’t bind during the change

Question 15

Strand-directed mismatch repair system

mutS protein

functions

Answer 15

binds to mismatched base pair

Question 16

mutL protein

function

Answer 16

scans DNA near mismatched bp found by mutS for a nick to recognize new strand
triggers degradation of nicked strand through mismatched bp

Question 17

Error rate of DNA replication

TOTAL
DNA polymerization +
exonucleolytic activity +
strand-directed mismatched repair

Answer 17

1x10⁹ errors per nucleotide polymerized
DNA Polymerization: 1x 10⁵
Exonucleolytic activity: 1x10²
Strand-directed mismatched repair: 1x10²

Question 18

DNA repair enzymes

Helicase

Answer 18

unwinds DNA double helix

Question 19

DNA repair enzymes

single-strand binding protein

Answer 19

keeps separated DNA strands exposed

Question 20

sliding clamp

Answer 20

holds DNA polymerase on the DNA

Question 21

topoisomerase

Answer 21

prevents DNA tangling during replication

Question 22

DNA Primase

Answer 22

synthesizes short primers on the lagging strand