DNA Metabolism

Question 1

DNA is the blueprint for?

Answer 1

all RNA and proteins

Question 2

DNA requires

Answer 2

high speed and high fidelity (lack of errors)

Question 3

Where does the complexity of DNA come from?

Answer 3

the need for compaction and low tolerance for errors

Question 4

DNA errors are problematic because

Answer 4

they can be passed on and cause disease

Question 5

DNA is constantly in a state of?

Answer 5

flux

Question 6

Basic Rules of DNA replication

Answer 6

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

Question 7

Nuclease

Answer 7

degrades DNA

Question 8

DNA Polymerase

Answer 8

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

Question 9

What does semiconservative replication mean?

Answer 9

DNA copies will have one old strand and one new strand

Question 10

Start point in DNA replication is known as the ?

Answer 10

origin

Question 11

Replication Fork

Answer 11

where active replication occurs
part of the DNA remains unwound

Question 12

What is the difference between the leading and lagging strands?

Answer 12

leading- synthesized continuously
lagging- synthesized discontinuously

Question 13

Okazaki Fragments

Answer 13

on lagging strand, get pieced together later

Question 14

Exonuclease

Answer 14

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

Question 15

Endonuclease

Answer 15

single cut in the middle of the strand

Question 16

Excinuclease

Answer 16

2 cuts at internal sites to remove a chunk of DNA

Question 17

DNA polymerase use 2 magnesium ions for?

Answer 17

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

Question 18

What are the 2 requirements for DNA polymerase?

Answer 18

a template strand and a primer strand

Question 19

Primers

Answer 19

small pieces of RNA
place for nucleotides to add on to

Question 20

Processivity

Answer 20

amount of DNA that can be added at once

Question 21

How often do errors occur in DNA synthesis?

Answer 21

every 1,000 to 10,000 bases added

Question 22

How many DNA polymerases are in E.Coli DNA replication

Answer 22

5

Question 23

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

Answer 23

2, 4, and 5

Question 24

DNA Polymerase 1

Answer 24

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

Question 25

DNA Polymerase 3

Answer 25

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

Question 26

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

Answer 26

error checking

Question 27

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

Answer 27

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

Question 28

What do beta clamps in DNA Polymerase 3 do?

Answer 28

allows the polymerase to hold on to DNA longer

Question 29

DNA Replicase System/Replisome

Answer 29

all of the enzymes and proteins required for DNA synthesis

Question 30

Helicases

Answer 30

separate DNA strands

Question 31

Topoisomerase

Answer 31

relieve strain caused in DNA

Question 32

DNA binding proteins

Answer 32

stabilize and protect DNA

Question 33

primases

Answer 33

make RNA primers

Question 34

What replaces primers with DNA?

Answer 34

DNA polymerase 1

Question 35

DNA Ligase

Answer 35

repairs the nick after primer removal

Question 36

Initiation

Answer 36

highly regulated, bring together all the pieces stage of replication

Question 37

Elongation

Answer 37

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

Question 38

Termination

Answer 38

the end of replication check for errors

Question 39

DnaA protein

Answer 39

binds at origin and starts initiation process

Question 40

DnaB protein

Answer 40

helicase that helps unwind/open DNA

Question 41

DnaC protein

Answer 41

helps DnaB to bind

Question 42

DUE

Answer 42

DNA unwinding element AT rich region near origin

Question 43

SSB

Answer 43

single stranded binding protein

Question 44

DNA gyrase

Answer 44

type 2 topoisomerase

Question 45

Dam methylase

Answer 45

methylate DNA to distinguish old and new strands methylates A in GATC sequence common at the origin

Question 46

Initiation steps

Answer 46

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

Question 47

Elongation—Leading strand

Answer 47

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

Question 48

Elongation — Lagging Strand

Answer 48

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

Question 49

Elongation — Okazaki fragments

Answer 49

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

Question 50

DNA ligase mechanism

Answer 50

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

Question 51

Termination in E. Coli

Answer 51

2 replication forks meet at a termination point

Question 52

Ter sequences

Answer 52

allow replication fork to enter but not leave

Question 53

Termination in DNA

Answer 53

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

Question 54

In eukaryotic DNA replication the origin is?

Answer 54

less conserved in multiple sites

Question 55

Cyclins

Answer 55

regulate the eukaryotic DNA replication process

Question 56

Viral DNA encodes its own?

Answer 56

DNA polymerase

Question 57

Acyclovir

Answer 57

act against herpes simplex virus higher affinity for viral kinase over human kinase chain terminator blocks addition of more nucleotides inhibits viral polymerase