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Biochemistry 2 > DNA Metabolism > Flashcards

DNA Metabolism Flashcards

(57 cards)

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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?

24
Q

DNA Polymerase 1

Study These Flashcards
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
DNA Polymerase 3
fast multisubunit enzyme does most of the DNA synthesis in E.Coli major portion made up of 13 subunits and 2 beta clamps
26
What is the 3’ -> 5’ exonuclease in DNA Polymerase 1 for?
error checking
27
What is the 5’ -> 3’ exonuclease in DNA Polymerase 1 for?
Nick Translation removes RNA primer replaces with DNA nucleotides completes the synthesis of the lagging strand
28
What do beta clamps in DNA Polymerase 3 do?
allows the polymerase to hold on to DNA longer
29
DNA Replicase System/Replisome
all of the enzymes and proteins required for DNA synthesis
30
Helicases
separate DNA strands
31
Topoisomerase
relieve strain caused in DNA
32
DNA binding proteins
stabilize and protect DNA
33
primases
make RNA primers
34
What replaces primers with DNA?
DNA polymerase 1
35
DNA Ligase
repairs the nick after primer removal
36
Initiation
highly regulated, bring together all the pieces stage of replication
37
Elongation
synthesis of DNA stage of replication leading strand 5’ -> 3’ continuous lagging strand 3’ -> 5’ discontinuous
38
Termination
the end of replication check for errors
39
DnaA protein
binds at origin and starts initiation process
40
DnaB protein
helicase that helps unwind/open DNA
41
DnaC protein
helps DnaB to bind
42
DUE
DNA unwinding element AT rich region near origin
43
SSB
single stranded binding protein
44
DNA gyrase
type 2 topoisomerase
45
Dam methylase
methylate DNA to distinguish old and new strands methylates A in GATC sequence common at the origin
46
Initiation steps
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
Elongation—Leading strand
primase (DnaG) makes short RNA primer for DNA to attach to synthesis occurs continuously along replication fork in 5’ -> 3’ direction
48
Elongation — Lagging Strand
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
Elongation — Okazaki fragments
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
DNA ligase mechanism
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
Termination in E. Coli
2 replication forks meet at a termination point
52
Ter sequences
allow replication fork to enter but not leave
53
Termination in DNA
1. Topoisomerase 4 separates the helices 2. separated chromosomes then split into the new cells
54
In eukaryotic DNA replication the origin is?
less conserved in multiple sites
55
Cyclins
regulate the eukaryotic DNA replication process
56
Viral DNA encodes its own?
DNA polymerase
57
Acyclovir
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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