Exam 2 Review

Question 1

replication at the begining of mitosis results in what

Answer 1

sister chromatids, joined at centromere

Question 2

what connects nucleosomes

Answer 2

histone h1

Question 3

describe reaction of incoming nucleoside triphosphate

Answer 3

the incoming nucleoside triphosphate base pairs with its partner on the template strand, it is covalentyl attached to the free 3’ hydroxyl end of the growing DNA strand

Question 4

new DNA strand synthesized how by what

Answer 4

5’ to 3’ by DNA polymerase

Question 5

where does energy for polymerization come from

Answer 5

hydrolysis of high energy phosphate bond in incoming nucleoside triphosphate and release of pyrophosphate

Question 6

polymerase adds incorrect nucleotide, what happens

Answer 6

mispaired nucleotide removed by proofreading, correcly paired3’ end allows additon of next nucleotide

Question 7

steps of rep fork replication

Answer 7

local opening of helix, RNA primer syntheisis, leading strand begins, RNA primers start lagging strand syn, fork continues to open

Question 8

telomerase extends which end via what

Answer 8

3’ end via its bound RNA template

Question 9

in telomere, what completes the lagging strand

Answer 9

DNA polymerase a

Question 10

reaction for a nicked double helix

Answer 10

step 1 - ATP hydrolyzed, AMP placed on 5’ phosphate, other strand binds to the AMP
step 2 - AMP released, makes continuous DNA strand

Question 11

deamination changes what to what

Answer 11

C to U

Question 12

deamination results in what after replication

Answer 12

one sequence is unchanged, one is mutated to where a G has been changed to an A

Question 13

depurination does what

Answer 13

removes A

Question 14

depurination results in what after replicaiton

Answer 14

one sequence unchanged, another single base deletion where AT nuc was deleted

Question 15

describe base excision repair

Answer 15

uracil NDA glycosylase removes deaminated nuc, AP endonuclease adn phosphodiesterase remove sugar phosphate, DNA polymerase adds new nucleotide using bottm strand as template, DNA ligase seals the break

Question 16

describe nucleotide excison repaur

Answer 16

excision nuclease finds site around damage to cut, helicase removes where the nuclease cut (12 nt gap), DNA polymerase adds new nucleotides using bottom strand as template, ligase seals break

Question 17

probes labeled by synthesizing them with what conjugated to what

Answer 17

nucleotides conjugated to fluorophoes

Question 18

DNA primase does not require what

Answer 18

base paired 3’ end as a starting point

Question 19

lagging strand rep steps

Answer 19

new rna prmer syn by primase, DNA poly adds nucleotides to 3’ end of new RNA primer to syn okazaki frag, poly finishes okazaki frag, prev RNA primer removed by nucleases and replaced with DNA, nick sealed by ligase

Question 20

For which cell type(s) in your body is the deletion of telomerase inconsequential?

Answer 20

cells that are dying frequenctly or being replaced

Question 21

UV radiation causes what, explain

Answer 21

causes pyrimidine dimer formation, two pyrimidines fuse together

Question 22

differences in bacterial vs human nucleotide excision

Answer 22

bacteria - 12 nt gap
human - helicase unwinds DNA duplex, excision leaves 30 nt gap

Question 23

Hae iii results in what

Answer 23

blunt ends

Question 24

Eco RI results in what

Answer 24

sticky ends

Question 25

Hindiii results inw ath

Answer 25

sticky ends

Question 26

Question 1: Which of the following is a palindromic restriction site (all written 5’ to 3’) that would appear most frequently in a bacterial genome with 60% GC content? A) CCCAATTCCC B) CGCTATAGCG C) GGCCGGCC D) CCATGG E) GGAAGG

Answer 26

D

Question 27

plamid and DNA fragment are cut by what

Answer 27

same restriction enzymes

Question 28

Ifweusethesamerestrictionenzyme to cut both plasmid and the fragment, what other reaction product can we get from the Ligation reaction?

Answer 28

self ligated plasmid,

Question 29

ligation of fragments with staggered overhangs reaciton

Answer 29

2 sticky ends + ligase and ATP = joined

Question 30

conversion of staggered to blunt ends what happens

Answer 30

staggered end filled in by DNA poly + dNTPs; ligase adn ATP join the two

Question 31

first cycle of amplificaiton describe it

Answer 31

heat to separate strands, cool to anneal primers, DNA syntheisis

Question 32

what does pcr do

Answer 32

amplifies target region exponentially, doubel stranded

Question 33

explain generation of labeled DNA probes

Answer 33

start with purified fragment of duplex DNA, denature and anneal with mix of hexanucletides, add DNA polymerase and 32P labeled nucleotides, DNA polymerase incorporates 32p nucleotides, resulting in a population of readiolabeled DNA molecules that contain seq from both strands

Question 34

Question 2: The Stokes Shift explains the phenomenon of why a fluorophore will absorb photons at a shorter wavelength than it emits them. A) True B) False

Answer 34

true

Question 35

difference between ddntp and dntps

Answer 35

ddntp has 3' H that prevents strand extension at 3' end

Question 36

process of DNA sequencing

Answer 36

start with single strand DNA fragment to be sequenced, add primer, add small amounts of LABELED ddntps and excess amounts of unlabeled dntps, gives you mix of DNA products each containing a chain terminatiing ddntp labeled with specific flurorscent marker

Question 37

How many copies of each gene does a diploid (2n) human cell have?

Answer 37

2

Question 38

You are testing a new method of detecting trisomy 21 in gametes via FISH. What would you design your DNA probe to target?

Answer 38

I would want to target a sequence that is specific to chromosome 21

Question 39

you are testing a new method of detecting trisomy 21 in gametes via fish How would you control for the non-specific binding of your probes?

Answer 39

-ensure the chosen sequence is highly specific to chromosome 21, - use two different probes each labeled with different phlorophore, for different chromosomes, can help confirm that we actually targeted chromosome 21

Question 40

You are testing a new method of detecting trisomy 21 in gametes via FISH... What are the expected FISH results if a metaphase cell you are testing is positive or negative for trisomy 21?

Answer 40

if negative - there will be two signals on chromosome 21, since there is just 2 copies of it if positive - there will be 3 signals on chromosome 21 bc there are 3 copies of it

Question 41

Fluorophores absorb photons at a what wavelength to achieve excitation

Answer 41

shorter wavelength

Question 42

florophores emit photons at what wavelength

Answer 42

longer wavelength

Question 43

what is the mechanism for the repair of depurinated nucleotides? why

Answer 43

base excision repair (ap endonuclease will recognize the site as a missing purine)

Question 44

What strategy could we use to ensure get a higher frequency of recombinant DNA ligations?

Answer 44

inc conc of plasmid and fragment

Question 45

: What is the minimum number of ATP molecules required to for DNA Ligase to ligate a single DNA fragment cut with EcoRI into a single plasmid also cut with EcoRI?

Answer 45

2, one on each DNA end

Question 46

How can we ensure that only bacteria that contain our plasmid of interest are replicated?

Answer 46

use an antibiotic selection marker (resisitance gene) which allow the bacteria that took up recombinant DNA to survive and kills all the others