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Biochemistry 2 > DNA Metabolism > Flashcards

DNA Metabolism Flashcards

1
Q

DNA is the blueprint for?

A

all RNA and proteins

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2
Q

DNA requires

A

high speed and high fidelity (lack of errors)

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3
Q

Where does the complexity of DNA come from?

A

the need for compaction and low tolerance for errors

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4
Q

DNA errors are problematic because

A

they can be passed on and cause disease

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5
Q

DNA is constantly in a state of?

A

flux

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6
Q

Basic Rules of DNA replication

A

semiconservative
begins at origin and travels both directions
goes 5’ -> 3’ and is semi discontinuous

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7
Q

Nuclease

A

degrades DNA

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8
Q

DNA Polymerase

A

makes DNA
phosphoryl group transfer is the fundamental reaction
can only add to an existing chain

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9
Q

What does semiconservative replication mean?

A

DNA copies will have one old strand and one new strand

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10
Q

Start point in DNA replication is known as the ?

A

origin

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11
Q

Replication Fork

A

where active replication occurs
part of the DNA remains unwound

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12
Q

What is the difference between the leading and lagging strands?

A

leading- synthesized continuously
lagging- synthesized discontinuously

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13
Q

Okazaki Fragments

A

on lagging strand, get pieced together later

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14
Q

Exonuclease

A

degrades from the end of the DNA strand
can be 5’ or 3’ end

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15
Q

Endonuclease

A

single cut in the middle of the strand

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16
Q

Excinuclease

A

2 cuts at internal sites to remove a chunk of DNA

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17
Q

DNA polymerase use 2 magnesium ions for?

A

1 for stabilizing the 3’ oxygen
1 for coordinating the incoming nucleotide

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18
Q

What are the 2 requirements for DNA polymerase?

A

a template strand and a primer strand

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19
Q

Primers

A

small pieces of RNA
place for nucleotides to add on to

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20
Q

Processivity

A

amount of DNA that can be added at once

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21
Q

How often do errors occur in DNA synthesis?

A

every 1,000 to 10,000 bases added

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22
Q

How many DNA polymerases are in E.Coli DNA replication

A

5

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23
Q

Which DNA polymerases in E.Coli replication are used for DNA repair?

A

2, 4, and 5

24
Q

DNA Polymerase 1

A

1st discovered in E.Coli Replication
slow, steady, efficient
involved mainly in clean-up and finding the lagging strand
contains both 3’ -> 5’ and 5’ ->3’ exonucleases
single subunit

25
Q

DNA Polymerase 3

A

fast multisubunit enzyme
does most of the DNA synthesis in E.Coli
major portion made up of 13 subunits and 2 beta clamps

26
Q

What is the 3’ -> 5’ exonuclease in DNA Polymerase 1 for?

A

error checking

27
Q

What is the 5’ -> 3’ exonuclease in DNA Polymerase 1 for?

A

Nick Translation
removes RNA primer
replaces with DNA nucleotides
completes the synthesis of the lagging strand

28
Q

What do beta clamps in DNA Polymerase 3 do?

A

allows the polymerase to hold on to DNA longer

29
Q

DNA Replicase System/Replisome

A

all of the enzymes and proteins required for DNA synthesis

30
Q

Helicases

A

separate DNA strands

31
Q

Topoisomerase

A

relieve strain caused in DNA

32
Q

DNA binding proteins

A

stabilize and protect DNA

33
Q

primases

A

make RNA primers

34
Q

What replaces primers with DNA?

A

DNA polymerase 1

35
Q

DNA Ligase

A

repairs the nick after primer removal

36
Q

Initiation

A

highly regulated, bring together all the pieces
stage of replication

37
Q

Elongation

A

synthesis of DNA
stage of replication
leading strand 5’ -> 3’ continuous
lagging strand 3’ -> 5’ discontinuous

38
Q

Termination

A

the end of replication
check for errors

39
Q

DnaA protein

A

binds at origin and starts initiation process

40
Q

DnaB protein

A

helicase that helps unwind/open DNA

41
Q

DnaC protein

A

helps DnaB to bind

42
Q

DUE

A

DNA unwinding element
AT rich region near origin

43
Q

SSB

A

single stranded binding protein

44
Q

DNA gyrase

A

type 2 topoisomerase

45
Q

Dam methylase

A

methylate DNA to distinguish old and new strands

methylates A in GATC sequence common at the origin

46
Q

Initiation steps

A
  1. 8 DnaA proteins bind near origin and form a helix
  2. strain from this helix causes DUE to open
  3. DnaC loads DNA B, 1 on each strand
  4. DnaC is released after ATP hydrolysis
  5. SSB binds to single stranded DNA to stabilize and protect DNA
  6. DNA gyrase works ahead of helicase to relieve strain
  7. DNA polymerase 3 binds to end the initiation phase, releases DNA by hydrolyzing ATP
47
Q

Elongation—Leading strand

A

primase (DnaG) makes short RNA primer for DNA to attach to
synthesis occurs continuously along replication fork in 5’ -> 3’ direction

48
Q

Elongation — Lagging Strand

A

lagging strand loops back so synthesis can go 5’ -> 3’
primase makes a primer for each fragment that associates with the beta clamp
as fragments are made the beta clamp is released and the replication core moves to the next beta clamp

49
Q

Elongation — Okazaki fragments

A

synthesized 5’ -> 3’
1. as they are made primase makes next primer
2. enzyme loads primer with a beta clamp
3. once fragment is finished beta clamp is released
4. enzyme moves the replisome to the next beta clamp to make the next fragment

50
Q

DNA ligase mechanism

A
  1. DNA ligase is adenylated
  2. transfers AMP onto the 5’ end of the cut
  3. acts as a leaving group, kicked off by 3’ hydroxyl
51
Q

Termination in E. Coli

A

2 replication forks meet at a termination point

52
Q

Ter sequences

A

allow replication fork to enter but not leave

53
Q

Termination in DNA

A
  1. Topoisomerase 4 separates the helices
  2. separated chromosomes then split into the new cells
54
Q

In eukaryotic DNA replication the origin is?

A

less conserved
in multiple sites

55
Q

Cyclins

A

regulate the eukaryotic DNA replication process

56
Q

Viral DNA encodes its own?

A

DNA polymerase

57
Q

Acyclovir

A

act against herpes simplex virus

higher affinity for viral kinase over human kinase

chain terminator blocks addition of more nucleotides

inhibits viral polymerase

Biochemistry 2 (11 decks)

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