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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
Type of catalysis for DNA ligase
General base catalysis via the enzyme.
26
oriC
the origin of replication
27
DnaA
recognizes ori sequence; opens duplex at specific sites in origin
28
DnaC
required for DnaB binding at origin (chaperone). will load DnaB onto the unwound segment of DNA.
29
Dam methylase
methylates adenosine in a GATC sequences of oriC, first on template strand but eventually on parent strand. Methylates at the N6.
30
DUE
DNA unwinding elements which have a consensus sequence. AT rich
31
Consensus sequence
when comparing the residues across the common binding sites, we can determine which bases are most likely to be found in each position
32
ATP DnaA
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
ADP DnaA
Not active. Can only bind to R sites.
34
oriC and major groove
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
ATP hydrolysis of DnaC
releases DnaC from DnaB after DnaB is put onto the open single strand.
36
hemimethylated
The origin has one strand that is methylated (template strand). This prevents replication from happening until full methylation.
37
DNA polymerase III
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
Residues important in SSB's binding site
3 Trps and 1 Phe
39
what makes the RNA primer
primase (DnaG) with association of DnaB.
40
Beta Clamp
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
Clamp loading complex
Moves the clamp
42
How does Beta clamp associate?
Interactions between positively charged amino acids and the phosphate backbone, hydrophobic pocket wrapping itself around a base, and junction (?) *need to clarify junction
43
Replisome
the complex of proteins located at the replication fork
44
DNA polymerase I
removes the RNA primer and replaces it with DNA on a lagging strand (Okazaki fragment)
45
Termination mechanism for replication
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
Catenated
when the two circular chromosomes are interlinked
47
Topoisomerase IV
separates the two catenated chromosomes
48
Eukaryotic replication
multiple sites of replication but the points of replication occur more slowly. Thus overall still is completed within a reasonable time frame
49
Mutations
permanent changes in the genomic nucleotide sequence
50
Carcinogen
mutation at a position that causes cancer
51
4 repair systems
Mismatch repair, base-excision repair, nucleotide-exicison repair, direct repair
52
Mismatch repair
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
Part of Mut complex that cuts the unmethylated strand
MutH, which has endonuclease activity
54
Components of Mut system
Mut L and Mut S bind, and then Mut H binds to Mut L
55
MutS mismatch recognition
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
Two common types of repairs that require base-excision repair
Deamination and demethylation
57
Enzymes used in base-excision repair and the mechanism
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
Large distortions in the helical structure of DNA is repaired by what mechanism
Nucleotide excision repair
59
Enzyme in Nucleotide excision repair and its mechanism
ABC excinuclease (Uvr proteins A, B, C, and D) hydrolyzes two phosphodiester bonds on either side of the distortion
60
Example of an enzyme in direct repair
Methyl transferase - which accepts the methyl group and makes it an inactive enzyme.
61
SOS repair system
DNA polymerase V can replicate DNA without a template, hoping to save the damaged DNA.
62
Xeroderma pigmentosum
unable to repair pyrimidine dimers formed by UV light absorption

BioChem (14 decks)

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