BB451 exam 2 - DNA Replication, Recombination, Repair

Question 1

DNA structure

Answer 1

double helix, phosphodiester linkages of nucleotides, alternating sugar/phosphate links

Question 2

complementary base pairs held by

Answer 2

H bonds

Question 3

anti parallel

Answer 3

one strand 5’ to 3’ paired with other 3’ to 5’

Question 4

phosphodiester bonds

Answer 4

linkage between 5’ phosphate group of incoming nucleotide and 3’ hydroxyl of previous nucleotide in chain

Question 5

base pairings

Answer 5

AT with 2 H bonds

CG with 3 H bonds (harder to break)

Question 6

start with ___ only 1 phosphate added

Answer 6

start with triphosphate, only 1 phosphate added to the strand

Question 7

major and minor groove from…

Answer 7

asymmetric glycosidic linkage between deoxyribose sugar and each base in double helix

Question 8

3 major forms of DNA

Answer 8

A, B, Z

Question 9

A form DNA

Answer 9

right handed helix, franklin published, found only when dehydrated, more compressed/tilted, double stranded RNA (or RNA-DNA duplex)

Question 10

B form DNA

Answer 10

most common, right handed helix, Watson and Crick published, stole from Franklin, 10.5 base pairs per turn

Question 11

Z form DNA

Answer 11

left handed helix, marking location of genes in eukaryotic chromosomes

Question 12

semiconservative replication

Answer 12

each daughter has 1 new strand + 1 old strand

Question 13

DNA polymerase I function

Answer 13

5’ to 3’ DNA polymerase activity to make DNA
3’ to 5’ exonuclease activity (proofreading)
5’ to 3’ exonuclease activity (remove RNA primer)

Question 14

most abundant DNA polymerase

Answer 14

DNA polymerase I

falls off

Question 15

structure of DNA polymerase I

Answer 15

hand structure

Question 16

bacteria have ____ chromosomes

Answer 16

circular

Question 17

all DNA polymerases require a ___ to start DNA synthesis

Answer 17

primer formed by primase

Question 18

DNA polymerase II

Answer 18

repair mechanisms

Question 19

DNA polymerase III

Answer 19

responsible for most replication 
very processive - stays on (don't need as many as Pol I) 
fast - 1000 nucleotides/sec 
does have proofreading 
dimer

Question 20

subunits of DNA polymerase III

Answer 20

2 identical sets of subunits (dimer)
2 cores: where catalysis occurs
beta clamp/sliding clamp - hold to DNA
clamp loader - closes clamp around DNA

Question 21

helicase

Answer 21

pull strands apart using energy from ATP hydrolysis

fast enough to not slow down Pol III (1000 nucleotides/sec=100 turns/sec=6000 rpm)

Question 22

single strand binding protein

Answer 22

covers up bases and protects strand after pulled apart

Question 23

topoisomerase II (gyrase)

Answer 23

relieves tension, changes superhelical density

Question 24

topoisomerases can…

Answer 24

increase or decrease superhelical density

don’t usually bring it to 10.5 base pairs/ turn (relaxed)

Question 25

okazaki fragments

Answer 25

segments synthesized on lagging strand | must be combined together

Question 26

ligase

Answer 26

connects okazaki fragments (after Pol I removes primer) | biotechnologists use to join DNA fragments to create recombinant molecules

Question 27

___ is faster so..

Answer 27

leading strand is faster so lagging strand loops around --> trombone

Question 28

removal of RNA primers requires

Answer 28

Pol I's 5' to 3' exonuclease activity | -remove RNA at front end of enzyme as polymerase activity (at back of Pol I) fills in space behind it as it moves along

Question 29

topoisomerases...

Answer 29

change topological structure of DNA molecule

Question 30

supercoiling can occur when..

Answer 30

it has something other than 10.5 base pairs per turn

Question 31

tension relived by

Answer 31

supercoiling | -double strands twist over each other --> helix goes back to approximately 10.5 base pairs per turn

Question 32

2 types of topoisomerase

Answer 32

type 1 - cut one strand | type 2 - cut both strands (ex: gyrase)

Question 33

drugs that inhibit topoisomerases..

Answer 33

can be effective antibiotics | ex: naladixic acid, ciprofloxacin

Question 34

topoisomerase 7

Answer 34

only in E. coli/bacteria good for antibiotics unwinds strands, kill them, no effects on us

Question 35

linking number

Answer 35

L=T+W | twits + writhes

Question 36

twists (T)

Answer 36

number of times 2 helices cross each other

Question 37

writhes (W)

Answer 37

number of superhelical turns can be + or - when not 0, it is a superhelical, has superhelicity

Question 38

writhing occurs in an attempt of...

Answer 38

DNA to relax | relaxed = number of base pairs per twist = 10.5

Question 39

initiation of replication in E. coli occurs at

Answer 39

OriC (origin of replication) | contains 3 repeats of an AT rich sequence

Question 40

DNA A

Answer 40

several copies bind at origin of replication | DNA wraps around it --> superhelical tension --.strands come apart (AT only 2 H bonds, weak)

Question 41

DNA BC complex

Answer 41

bind when strands come apart from DNA A | dnaB = helicase, dnaC released

Question 42

DNA A released when

Answer 42

SSB and primase bind the exposed single strands

Question 43

eukaryotic chromosomes..

Answer 43

linear, multiple origins or replication

Question 44

telomeres

Answer 44

at linear ends, junk DNA | thousands of copies of repeats of short sequences

Question 45

telomerase

Answer 45

builds telomeres found predominantly in fetal and cancer cells and fertilized eggs, differentiated cells do not appear to have active telomerase reverse transcriptase -

Question 46

reverse transcriptase

Answer 46

telomerase use an RNA template (that it carries) to synthesize DNA other in retroviruses (HIV)

Question 47

deamination of adenine -->

Answer 47

hypoxanthine (chemical damage to DNA)

Question 48

oxidation damage to DNA -->

Answer 48

creation of 8-oxo-guanine

Question 49

aflatoxin

Answer 49

made by mold, from peanut butter | causes damage to DNA

Question 50

UV light causes..

Answer 50

dimerization of thymines

Question 51

lack of repair of DNA sliding (amid repeating sequences) -->

Answer 51

Huntington's disease

Question 52

proofreading

Answer 52

3' to 5' exonuclease activity, as DNA is being replicated

Question 53

mismatch repair

Answer 53

fix mismatches, after replication

Question 54

nucleotide excision repair

Answer 54

excision of group of nucleotides followed by replacement w/ correct ones by exonucleases ex: removal of thymine dimers (segment removed by nuclease) or remove aflatoxin

Question 55

base excision repair

Answer 55

uracil repair excision of damaged base, nicking by endonuclease, repair ex: remove U from DNA by uracil glycosylase

Question 56

deamination of cytosine

Answer 56

--> uracil --> GU base pairs

Question 57

mismatch repair in E. Coli

Answer 57

MutS recognizes mismatch MutL recruits MutH MutH nick newly synthesized strand to allow exonuclease removal of nucleotides around mismatch

Question 58

p53

Answer 58

critical protein for monitoring DNA for damage prior to division stop cell cycle is senses damage if repair cant be performed --> induce apoptosis

Question 59

which strand made error?

Answer 59

strand that is being copies is methylated | new strand with error is not