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molecular bio 2 Flashcards

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1
Q

Trombone model

A

2 DNA polymerases are connected to a set of proteins including a helicase at the replication fork. As the lagging strand is synthesized, the loop gets larger

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2
Q

Helicase

A

Unwind DNA and RNA

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3
Q

Beta clamp

A

Processivity-promoting in prokaryotes

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4
Q

DNA polymerase III

A

Replication polymerase in bacteria

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5
Q

DNA polymerase I

A

Clean-up polymerase in bacteria; has exonuclease activity; removes primers and fills in

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6
Q

Primers for DNA replication

A

RNA

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7
Q

Primase

A

Creates RNA primer; eukaryotes have this enzyme in the DNA polymerase alpha complex

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8
Q

Ligase

A

Connects nicked strands of DNA after primers removed

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9
Q

Looping

A

Allows for lagging and leading strand synthesis machinery to be nearby by looping the lagging strand

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10
Q

Okazaki fragment

A

DNA fragments on lagging strand

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11
Q

Processivity

A

Not releasing substrates

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12
Q

OriC

A

Origin of chromosomal replication

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13
Q

13-mer and 9-mer

A

Repeats with A-T around OriC that make it easier to open

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14
Q

Ter sites

A

Slow down replication fork on one side to prevent collisions

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15
Q

Unequal replication speed in prokaryotes

A

Caused by Ter sites

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16
Q

DNA polymerase alpha

A

Enzyme complex that includes RNA primase activity and places about 20 DNA nucleotides; on the lagging strand; does not have exonuclease activity

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17
Q

DNA polymerase epsilon

A

Leading strand replication enzyme

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18
Q

DNA polymerase delta

A

Continues where alpha left off; replaces alpha’s priming and DNA; lagging strand

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19
Q

Length of Okazaki fragment in eukaryotes

A

100-200

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20
Q

Length of Okazaki fragment in prokaryotes

A

1000-2000

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21
Q

Enzyme that gets rid of flap

A

Flap endonuclease

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22
Q

Why linear chromosomes lose length

A

Primers at each end will dissociate and cannot be replaced by DNA

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23
Q

Telomeres

A

Repeat sequences at the end of linear DNA to prevent important regions from being disturbed

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24
Q

How telomerase works

A

Has an RNA template; extends the end of the DNA, matching this template; DNA polymerase will make the other side

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25
Sheltering complex
Proteins that bind to the end of the linear chromosomal DNA to prevent single strand being degraded or binding with something
26
Germ cell
Sperm or egg
27
MMR
Mismatch repair; machinery follows behind replication machinery
28
NER
Nucleotide excision repair; responds to bulky, helix-distorting mutations; removes entire segment around the dimer (2 cuts)
29
BER
Base excision repair; most commonly a single base; fixes 8-oxoguanine, alkylated bases, deaminated bases
30
HR
Homologous recombination; uses homologous strands as templates
31
NHEJ
Non-homologous end joining; joining blunt ends created by double strand breaks
32
Replication slippage
Loops (more common in repeat zones) cause insertions when the new strand is folding up and is bonding to itself instead of the template
33
TNR
Trinucleotide repeat
34
Oxidative damage to DNA
G -> 8-oxoguanine, which can bind to A
35
UV-caused DNA damage
Thymine dimer (side by side)
36
Deamination
C -> U (amine group is NH2)
37
DNA damage from ionizing radiation
Double strand breaks
38
Topoisomerase
Removes knots and tangles from DNA
39
Nuclease
Enzyme with ability to cleave nucleotides
40
Nucleosome
2 turns of DNA wrapped around 8 histones
41
Hemimethylation
Half of bacterial DNA is methylated while it is being synthesized to remember which is which; later, bacterial chromosomes are fully methylated
42
The strand in prokaryotes that will be repaired
Non-methylated
43
Exonuclease
Enzyme that cleaves one nucleotide at a time at the end of a string of nucleotides
44
Direction DNA is read
3' to 5'
45
Direction DNA is synthesized
5' to 3'
46
First evidence of bidirectional replication
Labelled nucleotides were on each side of the replication fork
47
DNAa box
Binds to DNAa (protein), which kicks off replication
48
ORC protein
Complex that remains bound to replication origins throughout the cell cycle in eukaryotes
49
PCNA
Clamps DNA pol epsilon to the DNA; increases processivity
50
If the top strand is going from 5' to 3', is the top right portion leading or lagging?
Lagging
51
If the top strand is going from 3' to 5', is the bottom right portion leading or lagging?
Lagging
52
What is the sequence called in telomeres?
TER sequence
53
If the top strand is going from 3' to 5', is the top right portion leading or lagging?
Leading
54
If the top strand is going from 5' to 3', is the top left portion leading or lagging?
Leading
55
DNA Glycosylase
(BER) Recognizes damage, flips base out, removes it, 5'dRP is left
56
APE-1
(BER) Cuts the backbone after base is removed
57
Pol beta in SPBER
(BER) Remove 5'dRP, synthesizes
58
If 5'dRP gets oxidized what happens
Long path BER, pol beta displaces and creates flap, happens with multiple G's in a row
59
FEN
Flap endonuclease
60
Denaturing gel
Breaks H-bonds between DNA
61
Opposite of denaturing gel
Native gel
62
One of first chemotherapeutic drugs
The platinums; breaks DNA; cancerous cells die
63
Ames test
Mutagens tend to encourage growth around the chemical
64
DSB repair
Considered very deleterious; 3' overhangs are created (that are like 3-5kB long); sister chromatids are used if in S or G2 phase (homologous recombination)
65
Translesion polymerases
Only add a couple bases; beneficial because continue replication; add random bases
66
G1
Prepare for chromosomal replication; other contents are duplicated
67
S
Chromosomes duplicated
68
G2
2nd growth
69
SS annealing
After DSB when there is not a sister chromatid; microhomologous regions bind to each other after some trimming to make overhangs; this is worse than HR
70
NHEJ
Proteins bind to the ends; very error-prone
71
ATR/ATM
Triggered by DSB; can lead to apoptosis

molecular (7 decks)

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