Lippincott - DNA Structure, Replication, Repair Flashcards
1
Q
DNA
A
polymer of deoxyribonucleoside monophosphates covalently linked by 3’–>5’ phosphodiester bonds
2
Q
main bond in DNA
A
phosphodiester bond
3
Q
phosphodiester bond connects:
A
3’-hydroxyl group of one nucleotide to 5’ hydroxyl group of adjacent nucleotide
4
Q
3’ end
A
end with the free hydroxyl
5
Q
5’ end
A
end with the free phosphate
6
Q
what enzyme family cleaves DNA
A
deoxyribonucleases
7
Q
what enzyme family cleaves RNA
A
ribonucleases
8
Q
orientation of single stranded DNA in double helix
A
antiparallel
9
Q
type of bond that mediates base pairing
A
hydrogen bond
10
Q
DNA - adenine pairs with:
A
thymine
11
Q
DNA - guanine pairs with:
A
cytosine
12
Q
DNA - thymine pairs with:
A
adenine
13
Q
DNA - cytosine pairs with:
A
guanine
14
Q
methods of DNA denaturation
A
altering pH (ionization), melting DNA
15
Q
number of H bonds between guanine and cytosine
A
3
16
Q
number of H bonds between adenine and thymine
A
2
17
Q
which bases are purines
A
adenine, guanine
18
Q
which bases are pyrimidines
A
thymine, cytosine
19
Q
number of rings in purines
A
2
20
Q
number of rings in pyrimidines
A
1
21
Q
what base pairing denatures at higher temperatures? why?
A
GC, because of greater number of H bonds
22
Q
process of reforming the double helix from single strands of DNA
A
renaturation or reannealing
23
Q
process of separating the double helix of DNA
A
denaturation
24
Q
major stuctural forms of the double helix
A
B form, A form, Z form
25
B form
right handed helix with 10 residues per turn, main form of chromosomal DNA
26
A form
right handed helix with 11 residues per turn, produced by dehydrating the B form
27
Z form
left handed helix with 12 residues per turn, occur naturally in regions with alternating purines and pyrimidines (ex. poly GC)
28
region where active DNA synthesis occurs
replication fork
29
DnaA protein
binds to specific nucleotide sequences at origin, causing AT rich regions in the origin to melt
30
DNA helicase
actively unwinds the double helix
31
SSB
single strand binding proteins; keep the ssDNA separated and protect it from nucleases
32
type of enzyme that counteracts supercoiling
DNA topoisomerases
33
DNA topoisomerase I
relax both negative and positive supercoils, does not use up ATP
34
DNA topoisomease II
relaxes both negative and positive supercoils, requires ATP
35
DNA gyrase
creates negative supercoils in order to counteract positive supercoils
36
enzyme that copies the DNA templates
DNA polymerase
37
DNA polymerase - direction of reading
3'-->5'
38
leading strand
3'-->5' strand of template; needs only one promoter, synthesized continuously
39
lagging strand
5'-->3' strand of template; needs multiple promoters; synthesized discontinuously
40
stretches of discontinuous DNA in lagging strand
okazaki fragments
41
RNA primer
short stretch of RNA required by DNA polymerase to begin replication
42
responsible for RNA primer synthesis
primase
43
responsible for catalysis of DNA chain elongation
DNA polymerase III
44
DNA polymerase - direction of synthesis
5'-->3'
45
substrates of DNA polymerase III
5' deoxyribonucleoside triphosphates
46
when each new deoxynucleoside monophosphate is attached to the growing chain by DNA polymerase III, what is released?
pyrophosphate
47
for DNA synthesis to occur, what 4 substrates must be present?
dATP, dTTP, dCTP, dGTP
48
2 main activities of DNA polymerase III
5'-->3' polymerase; 3'-->5' exonuclease
49
5'-->3' polymerase activity of DNA polymerase III
for synthesis of new DNA strand
50
3'-->5' exonuclease activity of DNA polymerase III
for proofreading
51
responsible for excision of RNA primer
DNA polymerase I
52
activities of DNA polymerase I that allows it to complete its function
[1] 5'-->3' exonuclease activity to remove the primer
[2] 5'-->3' polymerase activity to fill in the gap with deoxyribonucleotides
[3] 3'-->5' exonuclease acitivity to proofread
53
difference between 5'-->3' exonucleases and 3'-->5' exonucleases
5'-->3' exonucleases can remove groups of altered nucleotides (up to 10) in the 5'-->3' direction
54
exonucleases used by DNA polymerase III
3'-->5' exonuclease
55
exonucleases used by DNA polymerase II
3'-->5' exonuclease
56
exonucleases used by DNA polymerase I
3'-->5' exonuclease, 5'-->3' exonuclease
57
responsible for sealing nicks between okazaki fragments after excision and replacement of RNA primers
DNA ligase
58
DNA polymerases in prokaryote replication
DNA polymerases I, II, III
59
DNA polymerases in eukaryote replication
DNA polymerases alpha, epsilon, delta, beta, gamma
60
DNA polymerase alpha
has primase activity
61
DNA polymerase beta
for gap filling in DNA repair
62
DNA polymerase gamma
replicates mitochondrial DNA
63
DNA polymerase delta
elongates okazaki fragments in lagging strand
64
DNA polymerase epsilon
elongates leading strand
65
telomeres - structure
complexes of noncoding DNA + proteins at ends of chromsoomes
66
telomeres - function
mediate structural integrity, protect from nuclease attack, allow repair systems to distinguish ends of DNA
67
responsible for maintaining telomeric length
telomerase
68
reverse transcriptase
synthesize DNA from RNA template
69
classes of histones
H1, H2A, H2B, H3, H4
70
charge of histones at physiologic pH
+
71
make up core of histone beads
H2A, H2B, H3, H4
72
location and function of H1
bind to linker DNA between beads, facilitates packing of histones into more complex structures
73
effect of UV radiation on DNA
fusing together of pyrimidine to form pyrimidine dimers (ex. thymine dimers)
74
effect of high energy ionizing radiation on DNA
double strand breaks
75
principle of methyl-directed mismatch repair
recognition of the parent strand as the methylated strand --> repairs are then based on the parent strand
76
responsible for recognizing mismatch in methyl directed mismatch repair
Mut
77
enzyme involved in repair of damage from UV radiation
UV specific endonuclease
78
xeroderma pigmentosum
inability to repair UV damage, extensive mutation due to exposure to sunlight
79
involved in removal of abnormal bases
specific glycosylases
80
involved in recognition and repair of AP site
AP endonucleases (recognition of missing base), deoxyribose phosphate lyase (removal of base-free sugar phosphate), DNA polymerase, DNA ligase
81
deoxyribose phosphate lyase
removes the base-free sugar phosphate residue in repair of AP sites
82
methods of repair of double strand breaks
[1] nonhomologous end-joining repair
| [2] homologous recombination repair
83
nonhomologous end-joining repair
crude ligation of DNA on either end of double strand break; prone to mutation (some DNA is lost)
84
homologous recombination repair
use of homologous DNA as a template to restore lost DNA from double strand breaks
85
enzymes in homologous recombination repair
enzymes that perform genetic recombination between homologous chromosomes during meiosis
