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BIO130 > Lecture 4 > Flashcards

Lecture 4 Flashcards

1
Q

what are initiator proteins?

A

several proteins that bind to DNA to unwind the double helix

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2
Q

where do initiator proteins bind?

A

to the origin of replication

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3
Q

what does helicase require?

A

ATP

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3
Q

what do initiator proteins require?

A

ATP

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4
Q

what is the job of initiator proteins?

A

help helicase bind

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5
Q

what are the two types of helicase?

A

one helicase the runs in the 5’ to 3’ direction and the other helicase that runs in the 3’ to 5’ direction

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6
Q

what is the job of ssbp?

A

prevent the two DNA strands from reannealing by preventing hydrogen bonds from forming

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7
Q

what does DNA polymerase require to begin transcription?

A

a bound primer

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8
Q

what is the job of primase?

A

make RNA primer

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9
Q

In what direction does primase synthesize the primer?

A

the in 3’ to 5’ direction

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10
Q

what are the steps in bacterial DNA replication?

A

1) Origin of replication
2) Binding of initiator
proteins
3) Unwinding by helicase
4) Binding of single-strand
binding protein
5) RNA primers made by
primase

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11
Q

what would happen if there were no sliding clamps?

A

DNA polymerase would constantly dissociate from the template strand

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11
Q

what is the job of DNA polymerase?

A

add nucleotides to the template stand in the 5’ to 3’ direction

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12
Q

what is the job of the sliding clamp?

A

hold DNA polymerase on the DNA template

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13
Q

how are the Okazaki fragments linked on the lagging strand?

A

DNA ligase enzyme glues the fragments together using phosphodiester bonds

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14
Q

how is the leading strand made in terms of continuity?

A

continuously

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15
Q

where does the leading strand start being made from?

A

a single RNA primer

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16
Q

how is the lagging strand made in terms of continuity?

A

discontinously

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17
Q

how many primers does the lagging strand have?

A

multiple

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18
Q

which strand is the predominant helicase on?

A

lagging strand

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19
Q

what is the primosome?

A

a group of enzymes involves in priming DNA including helicase and primase

20
Q

what are Okazaki fragments made of?

A

RNA primer and DNA

21
Q

what is the unwinding problem?

A

a DNA unwinds, it creates torsional strain

22
Q

which type of molecule is the unwinding problem common in?

A

circular chromosomes and large linear eukaryotic chromosomes

23
Q

how is the unwinding problem solved?

A

Solved by DNA topoisomerase

24
Q

what happens at the end of linear chromosomes?

A

during DNA replication on the lagging strand, DNA polymerase can not replicate the very end of the chromosome because there is no primer

25
Q

what is the direction of DNA replication?

A

bidirectional

25
Q

why is the shortening at the ends of linear chromosomes a problem?

A

loss of essential genetic information

26
Q

how does telomerase help the shortening of the ends of linear chromosomes?

A

adds repeated nucleotide sequences to the 3’ end of the parent strand

27
Q

what are the steps of telomere replication?

A

1) RNA template
2) Resembles: Reverse Transcriptase
3) Generates: G-rich ends
4) Adds nucleotides to:
3’ ends of parental
strand template

28
Q

how does loss of telomerase affect cell division?

A

inhibits cell division

29
Q

what type of cells is telomerase abundant in?

A

stem and germ cells

30
Q

which type of cell produces high levels
of telomerase?

A

cancer cells

31
Q

what is the error rate of RNA polymerase?

A

1 in 10^4

32
Q

what is the error rate of DNA polymerase?

A

1 in 10^9

33
Q

how many times does the genome change every time a cell divides?

A

three times

34
Q

what are the two mechanisms for proofreading DNA?

A

1) 3’ to 5’ exonuclease
2) stand directed mismatch repair

35
Q

what is the job of the 3’-5’ exonuclease?

A

remove incorrect nucleotides during DNA synthesis

36
Q

what is the job of stand-directed mismatch repair?

A

detects and repairs abnormalities after DNA synthesis has occurred

37
Q

after DNA synthesis, can DNA still get damaged?

A

yes

37
Q

what happens if there are defects in repair mechanisms?

A

it can lead to diseases

38
Q

what can DNA damage be caused by?

A

oxidation, radiation, heat, chemicals

39
Q

what is depurination?

A

loss of purine bases (adenine or guanine) from DNA, leaving a gap where the base used to be

40
Q

what are the two types of spontaneous DNA damage?

A

depurination, deamination

41
Q

what is deamination?

A

the removal of an amino group from a nucleotide base in DNA

42
Q

what are two general mechanisms of DNA repair?

A

base excision repair, nucleotide excision repair

43
Q

what happens to DNA that is left uncorrected?

A

the daughter cells inherit the mutation

44
Q

what is base miexcision repair?

A

correcting one modified base

45
Q

what is nucleotide excision repair?

A

correcting groups of modified bases

46
Q

what are the two mechanisms to repair double-stranded bond breaks?

A

non-homologous end joining, homologous recombination

47
Q

what is non-homologous end joining?

A

ligating broken parts together but there is a lack of insertion of nucleotide at the repair site

48
Q

what is homologous recombination?

A

uses a template to repair broken DNA strand

BIO130 (6 decks)

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