biochem 7A - DNA structure, replication, and repair

Question 1

what bond links polymers of deoxyribonucleoside monophosphates

Answer 1

covalent 3-5 phosphodiester bonds

Question 2

3-5 phosphodiester bonds are cleaved by what

Answer 2

nucleases
(deoxyribonuelases for DNA)
(ribonucleases for RNA)

Question 3

strands of DNA are held together by what type of bonds

Answer 3

H-bonds

Question 4

AT how many H bonds

Answer 4

2H bonds

Question 5

GC how many H bonds

Answer 5

3H bonds

Question 6

when would a DNA strand have higher melting temp

Answer 6

more GC base pairs

Question 7

hands of DNA

Answer 7

A (right handed)
B (right handed)
Z (left handed)

Question 8

in prokaryotic DNA syntehsis, what base pairing is it almost exclusively that faciliate melting

Answer 8

AT base pairs

Question 9

DnaA protein

Answer 9

binds to origina and causes the AT rich regions to melt

Question 10

DNA helicase

Answer 10

undwinds the double helix

Question 11

ssDNA-binding proteins

Answer 11

keeps the strands apart and protect DNA from nucleases that degrade ssDNA

Question 12

topoisomerase 1

Answer 12

cut and rejoin one strand of double helix to remove supercoils

Question 13

topoisomerase II

Answer 13

cuts and rejoins both

Question 14

what direction does DNA polymerase read

Answer 14

3’ -> 5’

Question 15

what direction does syntehsis occur

Answer 15

5’->3’

Question 16

RNA primer catalzyed by what

Answer 16

primase

Question 17

RNA primer charactieristics

Answer 17

~10 nucleotide w free OH on 3’ end

Question 18

chain elongation in prokaryotic DNA synthesis is catalzyed by what

Answer 18

DNA polymerase III

Question 19

how does DNA pol III correct mismatch

Answer 19

has 3’-5’ exonuclease

Question 20

RNA is excised and the gap is filled by

Answer 20

DNA pol I

Question 21

how does eukaryotic DNA replication differ from prokaryotic

Answer 21

-has multple origins of replication
-RNA primers are removed by RNase rather than DNA polymerase

Question 22

G1 phase

Answer 22

cell prepares to initiate DNA synthesis, biosynthesis occurs (growth)

Question 23

S phase

Answer 23

DNA content doubled (DNA synthesis)

Question 24

G2 phase

Answer 24

biosynthesis for mitosis to occur (growth and preparation for mitosis)

Question 25

DNA pol alpha

Answer 25

-contains primase -initiates DNA synthesis

Question 26

DNA pol gamma

Answer 26

replicates michondria DNA

Question 27

DNA pol delta

Answer 27

elongates okazaki fragments of the lagging strand

Question 28

DNA pol epsilon

Answer 28

elongates the leading strand

Question 29

telomeres

Answer 29

-consist of several thousand tandem repeats of noncoding AGGGTT -GT strand longer than its complement leaving a few hundred nucleotides in length at the 3' end -complexes of noncoding DNA plus proteins located at the end of linear chromosomes -maintain structural integrity of the chromosome, preventing attack by nucleases -allow repair enzymes to distinguish between a true end from a break in dsDNA -in normal somatic cells, telomeres shorten with each successive division (once they shortened beyond a critical length, cell no longe table to divide and is said to be senescent

Question 30

what cells has telomerase and what does it do

Answer 30

stem and cancer cells maintains telomeric length in the cells

Question 31

reverse transcriptase function

Answer 31

enzyme that syntehsizses DNA from RNA

Question 32

are histones basic or acidic

Answer 32

basic

Question 33

nucleosomes

Answer 33

order DNA in structural units

Question 34

nucleosomes further arranged into what

Answer 34

chromosomes

Question 35

DNA damage

Answer 35

-hydrolysis -oxidation -methylation -UV light -ionizing radiation

Question 36

UV light leads to the formation of what

Answer 36

pyrimidine dimers (thymine dimers)

Question 37

Base Excision Repair (BER)

Answer 37

removes and replaces individual damaged bases

Question 38

Nucleotide excision repair (NER)

Answer 38

-removes and replaces damaged bulky lesions (2-30 nu) -recognizes physical distortion rather than specific base sequences (larger area)

Question 39

mismatch repair

Answer 39

removes nu that do not form correct base pairs

Question 40

Xeroderma pigmentosum (DNA repair disease)

Answer 40

-pyrimidine dimers formed in skin cells exposed to UV light -defects in excision repair due to a mutant UV-specific endonuclease

Question 41

ataxia telangiectasia

Answer 41

-defects in excision repair -neurodegenerative disease -poor coordination