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BioChem > Lecture 6 > Flashcards

Lecture 6 Flashcards

1
Q

semiconservative

A

each DNA strand can act as a template for the synthesis of a perfect copy of the other strand

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2
Q

DNA polymerases direction

A

5’ to 3’.

3’ oxygen is the nucleophile

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3
Q

Origin of replication

A

point where replication begins and likely rich in AT bonds

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4
Q

Leading strand

A

continuously synthesized in the 5’ to 3’ direction

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5
Q

Lagging strand

A

synthesized in the 5’ to 3’ direction in a discontinuous manner

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6
Q

DNA ligase

A

required to join the discontinuous Okazaki fragments together into a continuous piece of DNA. Will join the final phosphodiester bond that DNA Poly I is not able to join.

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7
Q

exonuclease

A

nucleases that remove DNA only from the ends of DNA strands

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8
Q

endonuclease

A

degrade DNA from the interior of a DNA strand (hydrolyze the phosphodiester bond)

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9
Q

All E. coli DNA polymerases exonuclease direction

A

3’ to 5’

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10
Q

E. coli DNA polymerase I exonuclease direction

A

5’ to 3’ as well as 3’ to 5’

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11
Q

Processivity

A

number of nucleotides a polymerase will add before dissociation

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12
Q

Cofactors of DNA polymerase

A

2 magnesium ions

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13
Q

Which phosphate is attacked on the incoming nucleotide?

A

The alpha phosphate. Attacking is done by the 3’ hydroxyl of the growing DNA chain

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14
Q

Protein involved in Nick translation

A

DNA polymerase I

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15
Q

3 major areas of polymerase III

A

core polymerase, clamp loading complex, beta clamp

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16
Q

DnaG

A

primase

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17
Q

Primase

A

creates RNA primers on the Okazaki fragments to allow for DNA polymerase to function on the lagging strand. Also is operating on the leading strand.

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18
Q

DNA gyrase

A

topoisomerase. will introduce negative supercoils into DNA. occurs before the replication fork

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19
Q

DnaB

A

Helicase. Put onto the unwound single strand DNA by DnaC. Will travel in the 5’ to 3’ direction .

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20
Q

Helicase

A

hexametric ring. unwinds the DNA by hydrolyzing NTPs. These hydroxylations cause conformational changes, unwinding the DNA. On lagging strand going 5’ to 3’

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21
Q

SSB

A

single-strand binding protein will prevent reannealing. not specific

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22
Q

Helicase’s 3 conformations

A

ATP, ADP+P, and empty.

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23
Q

DNA ligase’s energy

A

from ATP hydrolysis to AMP + PPi or NAD+ to NMN+ + AMP. Adenylylation of both substrate and enzyme (sequential ping-pong mechanism).

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24
Q

Residue in DNA ligase

A

Lysine

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25
Q

Type of catalysis for DNA ligase

A

General base catalysis via the enzyme.

26
Q

oriC

A

the origin of replication

27
Q

DnaA

A

recognizes ori sequence; opens duplex at specific sites in origin

28
Q

DnaC

A

required for DnaB binding at origin (chaperone). will load DnaB onto the unwound segment of DNA.

29
Q

Dam methylase

A

methylates adenosine in a GATC sequences of oriC, first on template strand but eventually on parent strand. Methylates at the N6.

30
Q

DUE

A

DNA unwinding elements which have a consensus sequence. AT rich

31
Q

Consensus sequence

A

when comparing the residues across the common binding sites, we can determine which bases are most likely to be found in each position

32
Q

ATP DnaA

A

Active. Will bind to R sites and I sites. DNA will right hand wrap around DnaA induces positive supercoiling, unwinding the DNA at the AT rich DUE site.

33
Q

ADP DnaA

A

Not active. Can only bind to R sites.

34
Q

oriC and major groove

A

base specific interactions where the alpha 5 helix fits into the major groove. This is a location of low Kd. Also has backbone interactions and an arm that will anchor into the minor groove

35
Q

ATP hydrolysis of DnaC

A

releases DnaC from DnaB after DnaB is put onto the open single strand.

36
Q

hemimethylated

A

The origin has one strand that is methylated (template strand). This prevents replication from happening until full methylation.

37
Q

DNA polymerase III

A

Dimer which adds deoxyribonucleotides in a continuous fashion to create the leading stranding and a discontinuous fashion to the lagging strand. Does not have 5’ to 3’ exonuclease activity, so will dissociate when it sees the RNA primer.

38
Q

Residues important in SSB’s binding site

A

3 Trps and 1 Phe

39
Q

what makes the RNA primer

A

primase (DnaG) with association of DnaB.

40
Q

Beta Clamp

A

as the okazaki fragment reaches the previous fragment, a new clamp will load onto the next primer and associates with the lagging strand polymerase.

41
Q

Clamp loading complex

A

Moves the clamp

42
Q

How does Beta clamp associate?

A

Interactions between positively charged amino acids and the phosphate backbone, hydrophobic pocket wrapping itself around a base, and junction (?) *need to clarify junction

43
Q

Replisome

A

the complex of proteins located at the replication fork

44
Q

DNA polymerase I

A

removes the RNA primer and replaces it with DNA on a lagging strand (Okazaki fragment)

45
Q

Termination mechanism for replication

A

replication forks will travel until one reaches a termination sequence and will be trapped. When the other replication fork reaches the next sequence it encounters, this halts replication.

46
Q

Catenated

A

when the two circular chromosomes are interlinked

47
Q

Topoisomerase IV

A

separates the two catenated chromosomes

48
Q

Eukaryotic replication

A

multiple sites of replication but the points of replication occur more slowly. Thus overall still is completed within a reasonable time frame

49
Q

Mutations

A

permanent changes in the genomic nucleotide sequence

50
Q

Carcinogen

A

mutation at a position that causes cancer

51
Q

4 repair systems

A

Mismatch repair, base-excision repair, nucleotide-exicison repair, direct repair

52
Q

Mismatch repair

A

Monitors methylation of adenine residues (Dam methylase) to determine old vs new strand. Mut complex then discards the incorrect and uses to old strand to fix it

53
Q

Part of Mut complex that cuts the unmethylated strand

A

MutH, which has endonuclease activity

54
Q

Components of Mut system

A

Mut L and Mut S bind, and then Mut H binds to Mut L

55
Q

MutS mismatch recognition

A

Phe residue that pushes against the anti conformation bases, a mismatched pair will break, and then swing into the syn conformation and get caught by Glu.

56
Q

Two common types of repairs that require base-excision repair

A

Deamination and demethylation

57
Q

Enzymes used in base-excision repair and the mechanism

A

DNA glycosylases which cleave the N-glycosyl bond to generate an AP site. AP endonculease will remove the AP set and DNA polymerase I and Ligase will complete the repair

58
Q

Large distortions in the helical structure of DNA is repaired by what mechanism

A

Nucleotide excision repair

59
Q

Enzyme in Nucleotide excision repair and its mechanism

A

ABC excinuclease (Uvr proteins A, B, C, and D) hydrolyzes two phosphodiester bonds on either side of the distortion

60
Q

Example of an enzyme in direct repair

A

Methyl transferase - which accepts the methyl group and makes it an inactive enzyme.

61
Q

SOS repair system

A

DNA polymerase V can replicate DNA without a template, hoping to save the damaged DNA.

62
Q

Xeroderma pigmentosum

A

unable to repair pyrimidine dimers formed by UV light absorption

BioChem (14 decks)

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