DNA Replication And Repair

Question 1

What direction does DNA replication proceed?

Answer 1

5’ to 3’ direction

Question 2

Leading strand

Answer 2

DNA is replicated in one smooth, continuous process

Question 3

Lagging strand

Answer 3

DNA is replicated in small sections then fused together

Question 4

Primers

Answer 4

Short section of RNA which is complementary to the template strand and contains free 3’ OH group

Question 5

Helicase

Answer 5

Separates the DNA strands. Requires ATP.

Question 6

What reaction does DNA polymerase catalyze?

Answer 6

Hydrolysis of PPi to 2Pi that allows the incoming nucleotide to be bound to the strand.

Question 7

Primase

Answer 7

RNA polymerase that is required to initiate DNA synthsis

Question 8

Okazaki Fragments

Answer 8

Short sections of primer RNA plus DNA that form on the lagging strand. Will be joined together later.

Question 9

Replisome

Answer 9

Total proteins and enzymes required for DNA synthesis at a replication fork

Question 10

Topoisomerases

Answer 10

Acts to prevent the extreme supercoiling of the parental helix by breaking and rejoining DNA chains. Relieves the tension ahead of the replication fork.

Question 11

Type I topoisomerase

Answer 11

Makes a break/nick in a strand of DNA helix, passes the other strand thru the break to relax the coil. Removes 1 supercoil

Question 12

Type II topoisomerases

Answer 12

Requires ATP. AKA DNA gyrase in E. Coli Produce break in BOTH strands of DNA. 2 supercoils are removed in one step

Question 13

Single Stranded binding protein

Answer 13

Keeps the separated strands as single strands. Are displaced and reused as DNA is replicated

Question 14

DNA polymerase I

Answer 14

Removes RNA primers (5’ –> 3’ exonuclease activity) and fills in gaps with dNTP that matches the exposed DNA template. Edits/proofreads the strand (3’->5’ exonuclease activity), cleaving off any unpaired 3’ terminal nucleotide

Question 15

DNA polymerase III

Answer 15

Major replicative enzyme. Stays on the DNA molecule for long stretches of processing

Question 16

DNA ligase

Answer 16

Enzyme that catalyzes formation of phosphodiester bond b/t 2 Okazaki fragments

Question 17

Types of DNA mutations

Answer 17

Point mutations, insertions, deletions

Question 18

Point mutations

Answer 18

substitution of one base for another

Question 19

Insertion

Answer 19

Adding one or more nucleotides within a DNA sequence

Question 20

Deletions

Answer 20

Removal of one or more nucleotides with a DNA sequence

Question 21

Steps of DNA repair

Answer 21

Removal, filling of the gap, ligation

Question 22

Nucleotide excision repair

Answer 22

Removal of a group of nucleotides

Question 23

Base excision repair

Answer 23

Specific glysosylase that removes a damaged base by hydrolyzing an N-glycosidic bond

Question 24

What serves as substrates in DNA synthesis?

Answer 24

Deoxyribonucleotide triphosphates

Question 25

What do DNA polymerases require for activity?

Answer 25

Primer and template

Question 26

Ciprofloxin

Answer 26

Works on both Gram - and + bacteria. Effects the supercoiling of bacterial DNA gyrase

Question 27

Replisome

Answer 27

All factors required for DNA synthesis

Question 28

What 4 classes of DNA polymerase are found in the nucleus?

Answer 28

Alpha, beta, delt, sigma

Question 29

Where is gamma DNA polymerase found?

Answer 29

mitochondria

Question 30

What 2 classes of DNA polymerase are involved in DNA repair?

Answer 30

beta and sigma

Question 31

What two chemical reactions are used to disassociate histones from DNA?

Answer 31

Acetylation and phosphorylation

Question 32

What proteins dictate the phase of replication that the cell is in?

Answer 32

Cyclins (A and E involved in DNA synthesis)

Question 33

What two types of agents cause DNA damage?

Answer 33

physical and chemical

Question 34

What causes thymine dimers to form?

Answer 34

UV rays

Question 35

Why does a thymine dimer cause disfunction in DNA?

Answer 35

Distorts the helix, so the DNA cannot be replicated without error

Question 36

What is deamination?

Answer 36

Cytosine converts to uracil, ultimately leading to a C→T mutation

Question 37

Single Strand break

Answer 37

The phosphodiester bond is broken on a single strand of DNA, is easily repaired.

Question 38

Double strand break

Answer 38

2 single strand breaks occur near each other on opposite sides of the DNA. Is very hard to repair, and usually results in cell death

Question 39

When is excision repair used?

Answer 39

Used to repair bulky damages to DNA

Question 40

When is base excision repair used?

Answer 40

Small modifications to DNA bases

Question 41

Postreplication repair

Answer 41

is known as the SOS repair, error prone repair which occurs as a last ditch effort where a random nucleotide is inserted

Question 42

Xeroderma pigmentosum

Answer 42

Excision repair proteins have lost activity, so cannot repair damages, particularly those done by UV. Can have eye photosensitivity

Question 43

Ataxia Telangiectasia

Answer 43

Gamma irradiation sensitivity. Usually have lymphomas, Signs: ataxia, dilation of blood vessels in the skin, chromosomal aberrations

Question 44

Fanconi’s Anemia

Answer 44

Have a sensitivity to cross linking. Causes leukemias. Signs: hypoplastic pancytopenia, congenital abnormalities

Question 45

Bloom’s Syndrome

Answer 45

Sensitivity to UV. Causes leukemias. Signs: skin photosensitivity, usually a butterfly shaped rash on the face

Question 46

Cockayne’s Syndrome

Answer 46

Have a sensitivity to UV. Causes various tumor cancers. Signs: neurological defects, dwarfism

Question 47

10% of colorectal cancers are cased by what defect?

Answer 47

Mismatch repair is defective