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Biochemistry-Exam 2 > Qiao > Flashcards

Qiao Flashcards

0
Q

Alpha amanitin affects what process in the central dogma?

A

Transcription

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1
Q

What is the central dogma?

A

DNA to RNA to Protein

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2
Q

T or F:Mutation rates are very low

A

True (1 per billion)

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3
Q

What are caretaker genes?

A

Genes involved in DNA repair or genes that maintain the fidelity of chromosome segregation. These genes control the stability of the genome and prevent accumulation of mutations

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4
Q

What are gatekeeper genes?

A

Genes that directly regulate the growth of tumor either by inhibiting growth or promoting death

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5
Q

T or F: The incidence of cancer grows exponentially with age

A

T

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6
Q

What is an overactivity mutation and what does it activate?

A

Single mutation event creates an oncogene to promote cell transformation

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7
Q

What is an underactivity mutation and what does it activate?

A

First mutation event inactivates tumor suppressor gene and second event inactivates the second copy. These two mutations functionally eliminate the tumor suppressor gene.

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8
Q

What are the two general types of cancer-critical mutations?

A

Overactivity mutation and underactivity mutation

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9
Q

Why is DNA more stable than RNA?

A

Lacking the OH which makes it more stable less chemically active

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10
Q

What is the 2’ angle?

A

The addition of a OH to 2’ on the sugar changes the angle of the ring and increases the activity of the acid

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11
Q

What type of bonds covalently link DNA together?

A

3’ to 5’ Phosphodiester bond

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12
Q

T or F: There is the same amount of information in the major groove as in the minor groove

A

T

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13
Q

Where are the phosphate groups in the DNA double helix?

A

On the outer backbone

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14
Q

What stabilizes the double helix?

A

Hydrogen bonds between bases. AT with 2 H bonds and GC with 3 H bonds.

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15
Q

What does dactinomycin (actinomycin D) do?

A

Intercalates into the narrow groove of the DNA thus interfering with DNA and RNA synthesis.

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16
Q

What is Tm?

A

The temperature at which one half of the helical structure is lost. Defined as the DNA melting temperature.

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17
Q

What characterizes the bonding at transcription sites? At telomere sites?

A

Tx sites usually have lots of AT bonds in order to be less tightly held. Teleomers, which are not supposed to be exposed to Tx, are more tightly held by GC bonds.

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18
Q

What is renaturation?

A

Reannealing of the double helix.

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19
Q

T or F: DNA is semi-conservative

A

T; one complete strand given to daughter and one held on

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20
Q

What are the three activities of DNA pol I?

A

Polymerase activity and 2 exonuclease activities (5’ and 3’)

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21
Q

T or F: DNA replication is bidirectional in both bacterial and eukaryotic cells

A

T

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22
Q

T or F: The DNA fork is asymmetric

A

T

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23
Q

What was the Meselson-Stahl experiment?

A

Showed that DNA replication is semi-conservative using nitrogen isotopes in E.Coli replication

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24
Q

What are theta forms?

A

The replication intermediates or replication bubbles

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25
Q

What are the two characteristics of prokaryotic DNA?

A

Circular and single origin

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26
Q

T or F: Eukaryotic cells have multiple points/origins of replication

A

T

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27
Q

What are the four requirements for DNA polymerase I in bacteria?

A

Template (strand to be copied), Primer with a free 3’-OH end, and dNTP (dinucleotide triphosphates) (usually with a Mg++ salt)

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28
Q

Why are triphosphates used for DNA replication?

A

Stability of the triphosphate is very low making it very likely to react. Makes forming DNA highly energetically favorable.

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29
Q

T or F: Every known DNA polymerase requires a primer

A

T

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30
Q

Arthur Kornberg discovered what? What three enzymatic properties did this thing have?

A

DNA polymerase I. 5’ to 3’ DNA polymerizing activity. 3’ to 5’ exonuclease activity. 5’ to 3’ exonuclease activity.

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31
Q

T or F: The PPi removed from the triphosphate nucleotide is eventually hydrolyzed (pyrophosphate to 2 Pi)

A

T

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32
Q

Which direction does the nacent DNA replicated strand form?

A

5’ to 3’

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33
Q

Describe the structure and function of each component of DNA polyermase

A

Resembles a hand with DNA in palm. The palm site is the active site, binds metal ions, primer terminus is located here, and alpha phosphate of the incoming dNTP is held here. The fingers contact the single strand template and the incoming dNTP. Thumb contacts the duplex DNA.

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34
Q

What are the two important sites on DNA polymerase?

A

P: polymerase active site. E: The exonuclease active site for proof-reading

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35
Q

Describe the 3’ to 5’ exonuclease activity of DNA polymerase

A

Excises mismatched pairs during DNA synthesis.

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36
Q

What is the mutation rate in DNA?

A

About 1 in a billion

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37
Q

What are okazaki fragments?

A

The lagging strand of DNA is synthesized in short segments in the 5’ to 3’ direction approximately 1000 nt in bacteria and 200 nt in eukaryotes

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38
Q

What is processivity?

A

The length of the Okazaki fragments.

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39
Q

Name the 7 components necessary for DNA replication in bacteria

A

ori binding protein (DnaA), DNA helicase (hexameric) (DnaB), single stranded DNA binding protein (SSB), Primase, DNA polymerases, DNA ligase, and DNA topoisomerase/gyrase.

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40
Q

Describe the initiation of DNA bacterial replication

A

Originated at the AT rich region known as oriC. DnaA binds to 9 bp DnaA boxes using ATP which causes unwinding and allows helicase to bind. Helicase is activated and moves a defined distance in 5’ to 3’ and interacts with primase DnaG. Primase then synthesizes a short RNA primer for DNA polymerase III to activate.

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41
Q

T or F: Helicase uses ATP and performs hydrolysis

A

T

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42
Q

T or F: DNA Helicase provides unlimited processivity

A

T

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43
Q

Describe the structure and function of DNA helicase

A

Hexameric ring protein that catalyzes ATP dependent unwinding of dsDNA to generate the replication fork

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44
Q

What explains the ability for helicases to provide nearly unlimited processivity?

A

The structure changes with cyclical manner and surrounds DNA (i.e. perpetual changes that feed into each other, i.e. ATP binding to hydrolysis and back)

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45
Q

Describe the function of SSB

A

Aids helicase by binding cooperatively to DNA to remove the hairpin structure of single stranded DNA. Covers 8 nucleotides but keeps bases exposed. It is a tetramer and also involved in DNA repair and recombination.

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46
Q

T or F: DNA Primases have unlimited processivity

A

False; very limited and usually synthesize 12 nucleotide chains or less

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47
Q

T or F: Primase is a RNA polymerase

A

T

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48
Q

What is the function of DNA topoisomerase?

A

Resolves DNA winding and prevents tangling during replication by cutting the DNA backbone. Positive supercoiling occurs in from the replication bubble.

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49
Q

What are type I DNA topoisomerases?

A

Enzymes that reversibly cut one stand of double helix. Has both nuclease and ligase activities and DO NOT require ATP.

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50
Q

What are Type II topoisomerases?

A

Enzymes that tightly bind to DNA double helix and make transient double strand breaks. Allows another strand of DNA to pass through the break and reseals the break.

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51
Q

What is camptothecin (CPT)?

A

Attacks topoisomerase I and causes toxicity in the S phase.

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52
Q

What is doxorubicin?

A

Also known as adriamycin, used in breast cancer to inhibit Topo II activity.

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53
Q

What are the two types of Topo II?

A

Topo IIalpha is expressed in proliferating cells and Topo IIbeta has a developmental role.

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54
Q

T or F: Topo II is required for daughter chromosome separation?

A

T

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55
Q

Describe the structure of DNA polymerase III

A

Alpha subunit that has polymerase activity. Epsilon site that has 3’ to 5’ exonuclease activity for proof-reading. Gamma/Delta subunit: clamp loader. Beta is sliding clamp. The core subunit is made of alpha and epsilon. And more..

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56
Q

T or F: DNA Polymerase III is fully processive

A

F, only about 10-15 nucleotides are incorporated at a time.

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57
Q

What is the clamp loader?

A

Multi-protein complexes that binds the primer-template junctions and possess the DNA-dependent ATPase activity.

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58
Q

What subunits in E.Coli are the clamp loaders in DNA pol III?

A

Gamma and Tao

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59
Q

How many proteins make up the holoenzyme of DNA Pol III?

A

10

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60
Q

What components make up the replisome?

A

DNA Pol III holoenzyme, DnaB Helicase, DnaG primase, and SSB

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61
Q

What components make up the Primosome?

A

DnaB, Helicase, and DnaG primase

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62
Q

How many bacterial DNA polymerases are there?

A

5

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63
Q

What is the function of bacteria DNA Pol I?

A

RNA primer removal and DNA repair.

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64
Q

What is the function of bacteria DNA Pol II?

A

DNA repair

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65
Q

What is the function of bacteria DNA Pol III?

A

Principal DNA replication enzyme

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66
Q

What is the function of bacteria DNA Pol IV?

A

DNA repair

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67
Q

What is the function of bacteria DNA Pol V?

A

DNA Repair

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68
Q

Which bacterial DNA polymerases are involved in DNA repair?

A

Pol I, II, IV, V

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69
Q

What is the function of Cytosine arabinoside?

A

Anticancer chemotherapy by blocking DNA replication as an analog.

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70
Q

What is adenine arabinoside?

A

An anti-viral agent.

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71
Q

What is zidovudine (AZT, ZDV)?

A

A chemically modified nucleoside analog with a different sugar moiety that terminates DNA chain elongation

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72
Q

What are the two components of elongation stage?

A

Leading strand synthesis and Lagging strand synthesis.

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73
Q

Describe leading strand synthesis

A

RNA primer is synthesized by primase and DNA polymerase III can synthesize processively until it reaches the terminus.

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74
Q

Describe lagging strand synthesis

A

Pol III is partially dissasembled and new RNA primer is synthesized. Pol III is reassembled on the primer. Primase is closely associated with DnaB helicase to make RNA primers on the ssDNA of the lagging strand. Each synthesized Okazaki fragment is joined while at the same time the primer portion is removed by DNA Pol I.

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75
Q

The four steps of lagging strand synthesis in bacteria?

A

RNA primer of 4-12 nt, DNA Pol III performs bulk chain elongation, 5’ RNA removed by DNA Pol I (5’ to 3’ exonuclease activity), DNA ligase joins 5’ PO4 on the chain made by DNA Pol III to the 3’-OH on the chain made by DNA Pol I (after primer removal)

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76
Q

What are DNA polymerase delta, PCNA, and RFC responsible for?

A

Extending the 10 nucleotides of RNA followed by 10-20 nucleotides of DNA in okazaki fragments.

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77
Q

What does DNA ligase do?

A

Uses ATP to link the 3’ OH to the 5’ PO3– to make a phosphodiester bond.

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78
Q

T or F: Leading strand synthesis is continuous

A

T

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79
Q

What determines lagging strand processivity?

A

The sliding clamps and clamp loaders

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80
Q

What is the average length of Okazaki fragments?

A

~1kb

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81
Q

T or F: Lagging and leading strands are synthesized simultaneously

A

T

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82
Q

Where are the major differences between DNA replication in prokaryotes and eukaryotes?

A

Machinery, replication origin, and linear DNA

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83
Q

The helicase proteins in eukaryotes are?

A

MCM proteins

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84
Q

The polymerases in Eukaryotes that elongate the DNA chain?

A

Pol delta and Pol epsilon

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85
Q

The primase for RNA primer synthesis in Eukaryotes?

A

Primase-Pol alpha

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86
Q

The 3’ to 5’ nuclease proteins in eukaryote?

A

Pol delta, Pol epsilon, and Pol gamma

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87
Q

The sliding clamp in eukaryotic DNA replication?

A

PCNA

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88
Q

The clamp loader in eukaryotes?

A

RFC

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89
Q

The SSB proteins in eukaryotes?

A

RPA

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90
Q

The DNA ligase in eukaryotes?

A

Lig 1

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91
Q

The DNA topoisomerases in eukaryotes?

A

Topo I and II

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92
Q

Proteins that deal with primer removal in eukaryotes?

A

RNAse H and FEN 1

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93
Q

What is the function of Pol alpha?

A

Contains primase and initiates DNA synthesis

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94
Q

What is the function of Pol beta?

A

Repair

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95
Q

What is the function of Pol gamma?

A

Replicates mitochondria DNA

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96
Q

What is the function of Pol delta?

A

Elongates okazaki fragments of the lagging strand

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97
Q

What is pol epsilon?

A

Elongates the leading strand

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98
Q

What eukaryote DNA polymerases have proof-reading activity?

A

Pol gamma, delta, and epsilon

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99
Q

What are three diseases caused by homozygous mutation of pol gamma?

A

Opthalmoplegia, Alper syndome, and other neurodegenerative disorder

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100
Q

What type of repair is Pol beta responsible for?

A

Base excision repair

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101
Q

T or F: Pol beta mutation is found in a high percentage of tumor

A

T

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102
Q

What is the longest portion of the cell cyle?

A

G1

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103
Q

What are the 4 (5) portions of the cell cycle?

A

G1, S, G2, M (G0)

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104
Q

Control of the cell cyle is governed by what group of proteins?

A

Cyclins and cdc (cell division cycle) gene products (some code for kinases).

105
Q

When in the cell cycle does DNA synthesis occur?

A

S phase

106
Q

What are the three checkpoints in the cell cycle?

A

Start checkpoint G1/S to check if environment is favorable. G2/M checkpoint to check if environment is good and DNA is replicated. Metaphase to anaphase transition to check if all the chromosomes are attached to the spindle

107
Q

What are the origins of replication shaped like in eukaryotes?

A

Bubbles!

108
Q

What are ARS?

A

Autonomously replicating sequences in yeast (has about 400 in 12 chromosomes)

109
Q

How long does S phase take?

A

About 8 hours in mammals

110
Q

How far apart are DNA replication origins and what is the rate of DNA synthesis?

A

30-300 kb and 50 bp/sec

111
Q

T or F: THe chromatin structure can affect the DNA replication timing

A

T

112
Q

What are the 5 classes of histones?

A

H1, H2A, H2B, H3, and H4.

113
Q

What is the charge of histone? Why?

A

Positive at physiologic pH due to high lysine and arginine content.

114
Q

T or F: Calcium ions are usually associated with histones

A

F; Magnesium ions are

115
Q

Describe the structure of a histone

A

Octomer with two of H2A, H2B, H3, and H4. DNA is wound around nearly twice. H1 is the linker to the DNA chain between histone beads

116
Q

Name three diseases caused by trinucleotide repeat expansions

A

Huntington’s disease, Kennedy’s disease, and spinocerebellar ataxia.

117
Q

What are the possible causes of trinucleotide repeat expansions?

A

Strand slippage during replication, unequal strand exchange between chromatids, or oxidative damage

118
Q

What is the end-replication problem in linear eukaryotic DNA?

A

The 5’ end of the lagging strand where the last RNA primer is removed cannot be filled in because there is no addition to the 5’ end anymore. Would cause chromosomal loss. Doesn’t happen in circular DNA.

119
Q

What is the answer to the end-replication problem?

A

Telomerase

120
Q

What type of enzyme is telomerase?

A

A ribonucleoprotein. Composed of a RNA subunit (TR) with the 4C and 2 A sequence (gives the product a 4 G and 2 T sequence) and a protein subunit called TERT.

121
Q

What is the function of TERT?

A

Reverse transcriptase to copy the GGGGTT seqeuence onto the Telomere. IN HUMANS, this sequence is TTAGGG in the DNA

122
Q

T or F: Telomeres have a 3’ overhang

A

T

123
Q

What is the Hayflick limit?

A

The number of times a normal human cell population will divide until cell division stops. Telomeres get shorter with each division

124
Q

What is the function of telomerase?

A

To maintain the length of telomeres

125
Q

T or F: Telomeres shorten with age

A

T

126
Q

What is TA-65?

A

A compound that turns on hTERT to maintain or lengthen telomeres. hTERT is usually off except in immune, egg, sperm, and malignant cancer-forming cells.

127
Q

What are three factors that accelerate telomere loss?

A

Perceived stress, smoking, obesity.

128
Q

T or F: Telomerase activation is often associated with cancer

A

T

129
Q

T or F: Telomeres are nucleoprotein complexes

A

T

130
Q

What human protein associates with telomers?

A

Human Shelterin in the shelterin complex

131
Q

What proteins make up the T-loop of telomeres?

A

Pot1 binds to ssDNA while TRF1 and 2 bind to telomere dsDNA, both with very high specificity.

132
Q

What is ALT?

A

Alternative lengthening of Telomers. Telomerase inhibitors are found in 85-90 percent of tumors and ALT is found in 10 percent of tumors.

133
Q

X-rays can lead to what two types of DNAdamage?

A

Base-excision repair and Recombinational repair (HR, EJ)

134
Q

Oxygen radicals lead to what type of damage repair?

A

Base-excision repair

135
Q

Alkylating agents lead to what type of DNA repair?

A

Base-excision repair

136
Q

Spontaneous reactions lead to what type of DNA repair?

A

Base-excision repair

137
Q

Base-excision repair can be used to remedy what 4 types of mutation?

A

Uracil in DNA, Abasic site, 8-oxoguanine, SSB

138
Q

Uracil insertion in DNA is repaired by what mechanism?

A

Base-excision repair

139
Q

Abasic sites are repaired by what type of repair?

A

Base-excision repair

140
Q

8-Oxoguananine is repaired by?

A

Base excision repair

141
Q

Single strand breaks are repaired by?

A

Base excision repair

142
Q

UV light leads to what type of repair?

A

Nucleotide-excision repair

143
Q

Polycyclic aromatic hydrocarbons in DNA lead to what type of repair?

A

Nucleotide excision repair

144
Q

(6-4)PP, Bulky adduct, and CPD are all repaired by?

A

Nucleotide excision repair

145
Q

Anti-tumor agents like cis-Pt and MMC are repaired by what mechanism?

A

Recombinational repair

146
Q

Interstrand cross-links are repaired by?

A

Recombinational repair

147
Q

Double strand breaks are repaired by what?

A

Recombinational repair

148
Q

Replication errors are fixed by what mechanism?

A

Mismatch repair

149
Q

A-G mismatch is repaired by?

A

Mismatch repair

150
Q

T-C mismatch is repaired by?

A

Mismatch repair

151
Q

Insertion/Deletion are repaired by what mechanism?

A

Mismatch repair

152
Q

What is a point mutation?

A

A single base change

153
Q

What is a transition mutation?

A

Purine to purine or pyrimidine to pyrimidine

154
Q

What is a transversion mutation?

A

Purine to pyrimidine or vice versa

155
Q

What are the three mechanisms of chromosome rearrangement?

A

Translocation, inversions, and deletions

156
Q

T or F: Microsatellite DNA and tandem repeats change in length at a rate that is many orders of magnitude higher than the average rate of point mutations

A

T

157
Q

What diseases are associated with expansion of microsatellites in the 5’ UTR?

A

Huntington’s disease and fragile-X syndrome

158
Q

What are the 5 general mutations in DNA (codons)?

A

Missense (AA substitution), Neutral (Change in AA but no effect on the protein function), Silent (different codon, same AA), Nonsense (premature stop codon), Frame shift (indel that leads to ORF shift)

159
Q

What are the 3 causes of DNA damage?

A

Mistakes in replication, spontaneous mutation, induced mutation via environment

160
Q

What are the two types of spontaneous DNA damage?

A

Base loss and deamination of base

161
Q

What is base loss?

A

N-glycosyl linkage to deoxyribose is hydrolyzed (base is removed from sugar).

162
Q

What is an AP site?

A

Base loss that leads to a site without a base component of the nt

163
Q

What is deamination of a base?

A

Deamination of C to U happens 100 times/cell/day and can lead to C to T transition

164
Q

What three conversions are deamination responsible for (single mech)?

A

C to U, A to hypoxanthine, G to xanthine

165
Q

T or F: Thymine can be deaminated

A

F

166
Q

Describe the structural differences of G to xanthine and A to hypoxanthine

A

Xanthine is G with 2 carbonyls, hypoxanthine is adenine with no amine group and a carbonyl instead

167
Q

What is the common source of DNA deamination?

A

Nitrous acid (HNO2)

168
Q

Deaminated C can lead to what outcomes?

A

Mutation where we now have a AU instead of CG. Unchanged

169
Q

Depurinated A can lead to what two outcomes?

A

Unchanged or AT pair deletion.

170
Q

In a depurination of A, what enzymes would be responsible for mutation leading to AT excision?

A

Pol epsilon, Pol delta, and possibly Pol alpha

171
Q

UV-C is what wavelengths? What does it do?

A

180-290 nm and is germicidal, not found in sunlight b/c absorbed in ozone

172
Q

UV-B is what wavelength? Effect?

A

290-320 nm, major lethal and mutagenic fraction of sunlight

173
Q

UV-A wavelengths? Effects?

A

320nm-visible, creats ROS but very few pyrimidine dimers

174
Q

When exposed to UVB at 260 nm, what is likely to happen to DNA?

A

Adjacent pyrimidines are covalently linked to make cyclobutane pyrimidine dimer (CPD) or thymine dimers.

175
Q

What is a thymine dimer?

A

T-T crosslink due to UV

176
Q

What is a CPD?

A

cyclobutane pyrimidine dimer arising from the C=C double bond between pyrimidines

177
Q

What are 6-4 PPs?

A

Pyrimidine to pyrimidine cross-links between the 6 and 4 carbons of two bases

178
Q

Pyrimidine dimers affect the DNA helix how?

A

7-9 degree bend

179
Q

6-4 PPs affect the DNA helix how?

A

Bends 44 degrees

180
Q

What is mesothelioma?

A

Asbestos damages mesothelial cells in the lining of the chest interior surfaces and leads to cancer

181
Q

What is G-T transversion and smoking link?

A

Cigarette smoke byproducts like PAH (polycyclic aromatic hydrocarbon) e.g. benzo(a)pyrene epoxide lead to G to T transversion in many hotspots like p53

182
Q

Vinyl chloride causes?

A

Liver angiosarcoma

183
Q

Benzene causes?

A

Acute leukemias

184
Q

Arsenic causes?

A

Skin carcinomas and bladder cancer

185
Q

Asbestos causes?

A

Mesothelioma

186
Q

Radium causes?

A

Osteosarcoma

187
Q

What is the Ames test?

A

Mutated salmonella to not produce histidine have to mutate to survive in the presence of a chemical. Use liver puree to simulate body conditions

188
Q

Platin compounds do what?

A

Use platinum to recognize guanosine on DNA and prevent hydrogen binding by crosslinking the Gs. Typically intrastrand links are more deadly than interstrands

189
Q

Doxo and Daunorubicin does?

A

Insert aromatic compound into the base stacking to prevent DNA replication

190
Q

What are the 4 general cellular responses to DNA damage?

A

Checkpoint activation, DNA damage repair, Apoptosis, DNA damage tolerance

191
Q

Checkpoint activation leads to what processes?

A

Signal transduction, transcriptional regulation, cell cycle arrest

192
Q

What are the three major types of DNA repair?

A

Direct reversal of damage, Excision, Recombinational

193
Q

What are the three types of Excision repair?

A

Mismatch repair, base excision repair, and nucleotide excision rpair

194
Q

T or F: Photolysase is present in humans

A

F

195
Q

What is photolyase?

A

Binds to UV photoproduct and absorbs blue light to split the photoproduct. T-T and 6-4 PPs are reversed to normal bases

196
Q

What do humans use instead of photolyase?

A

Nucleotide Excision repair

197
Q

What are the 4 steps of photolyase repair?

A

Enzyme recognizes damage, light absorption by chromophore excites enzyme, chromophore donates electron to cyclobutyl dimer, dimer is destabilized back to monomeric pyrimidine

198
Q

What is an example of direct reversal of damage to DNA?

A

O6- alkyltransferase (AGT) directly removes methyl groups from guanosine to a cysteine in the enzyme in an irreversible reaction

199
Q

Mismatch repair tells the proper strand by?

A

Looking for methylation on the parent strand

200
Q

What is required for mismatch repair?

A

Parent strand, Mut proteins, polymerase and ligase

201
Q

What disease is caused by Mut mutation?

A

Hereditary nonpolyposis colorectal cancer (Lynch syndrome)

202
Q

AGT is also known as?

A

O6-methylguanine-DNA methyltransferase (MGMT)

203
Q

T or F: Mismatch repair can repair a O6-methylguanine to T pair

A

F

204
Q

Elevated O6meG-T pairs are repaired by?

A

AGT can remove the methyl and then mismatch can be performed.

205
Q

T or F: O6-meG is highly mutagenic in MMR deficient cells?

A

T especially if AGT is lacking.

206
Q

T or F: O6-meG can bind with thymine

A

T; hard for MMR to fix

207
Q

What do DNA glycosylases do?

A

Catalyze the hydrolysis of the N-glycosylic bonds linking altered bases t the deoxyribose-phosphate backbone

208
Q

What does apyrimidinic endonuclease do?

A

Nicks the backbone at AP sites

209
Q

T or F: DNA pol beta has lyase activity

A

T

210
Q

Describe the steps of base excision repair

A

Remove the base using a gylcosylase, use an AP endonuclease to nick backbone, use lyase to remove the backbone, polymerase and DNA and cNTP to fill in the blank

211
Q

AP endonucleases are important in generating a?

A

3’ OH terminus in the DNA backbone

212
Q

What are N-glycosylase?

A

Specific to modified bases to remove them from the backbone

213
Q

MutY mutation (a N-glycosylase) leads to what type of cancer?

A

MutY

214
Q

Damage recognition in NER of UV damage is done by?

A

XPC-HR23B or CSB/CSA-RNA polymerase holoenzyme

215
Q

What proteins are recruited in NER after activiation?

A

TFIIH, XPG, XPA, XPB and more to assemble repair complexes

216
Q

Double incisions to remove nucleotides are performed by?

A

XPG (24 nts) and XPF (32 nts).

217
Q

About how many proteins are needed for NER?

A

~25 proteins

218
Q

What is the only mechanistic difference between NER and BER?

A

Use of a lysase before incision endonuclease in BER

219
Q

What is xeroderma pigmentosum caused by?

A

Mutation in NER pathways

220
Q

What is Cockayne’s syndrome caused by?

A

mutations in NER (XPB, XPD, and XPG)

221
Q

What is trichothiodystrophy caused by?

A

XPB and XPD mutations in the NER pathways

222
Q

What are the symptoms of xeroderma pigmentosum

A

Light sensitivity and damage due to NER mutation in genes

223
Q

Symptoms of Cockayne’s syndrome?

A

Premature aging, dwafism, facial and limb abnormality, neuronal abnormality

224
Q

Symptoms of trichothiodystrophy?

A

Premature aging of tissue, brittle hair, facial abnormality, short statue and light sensitivity in some cases.

225
Q

What are the four origins of DSBs?

A

Ionizing radiation, ROS, V(D)J recombination, meiosis

226
Q

List the steps of homologous recombination

A

Uses undamaged sister chromatid as template. Happens in S-G2 phase to generate ssDNA. Strand invasion occurs to form the Holliday junction. Branches migrate and resolve

227
Q

Non-homologous end joining is acheived by?

A

Ku heterodimers bind to DNA ends and recruits kinases to processes the ends and Ligase 4 joins them

228
Q

T or F: DNA repair pathways can be a potential therapeutic to target in cancer cells as compared to healthy cells?

A

T

229
Q

MSH 2, 3, and 6 mutations affect what and what repair?

A

Colon cancer, MMR

230
Q

MLH1 and PMS2 symptoms are manifested where and what repair?

A

Colon cancer, MMR

231
Q

Xeroderma pigmentosum is what and what repair process?

A

Skin cancer, UV sensitivity, and neuro defects, NER

232
Q

XP variant is what?

A

UV sensitivity and skin cancer that is caused by tranlesion synthesis by DNA pol eta

233
Q

Ataxia telangiectasia is?

A

Leukemia, lymphoma, gamma sensitivity, and genome instability caused bt ATM protein which is a kinase activated by DSB

234
Q

BRCA2?

A

Breast, ovarian, and prostate cancer; repair by HR

235
Q

Werner syndrome?

A

Premature aging, cancer, genome instability; caused by accessory 3’ exonuclease and DNA helicase

236
Q

Bloom syndrome?

A

Cancer, stunted growth, genome instability; accessory helicase for replication

237
Q

Fanconi anemia

A

Cogenital abnormalities, leukemia, genome instability; DNA interstrand cross-link repair

238
Q

46 BR patient

A

Hypersensitivity to DNA damaging agents, genome instability; DNA ligase I

239
Q

In euk DNA replication, what is responsible for processivity?

A

PCNA

240
Q

What are the substrate requirements for DNA ligase?

A

5’ PO3– and 3’ OH. Duplex DNA strand with template, ATP and Mg ions.

241
Q

Describe the relationship of Pol alpha, delta, and epsilon

A

Pol alpha starts replication by extending the primer. Pol epsilon takes over leading strand and Pol delta takes over lagging strand

242
Q

What are the two types of recombination?

A

Homologous and Site-specific; homologous is generic and site specific has enough of a stretch of similarity

243
Q

What is the difference between meiotic recombination and normal HR?

A

Mre11 and Spo11 intentionally cause a DSB

244
Q

T or F: Chromosome cross-over in HR is varied depending on how the DNA is cut after heteroduplex replication

A

T

245
Q

What pols are required for HR replication?

A

Delta and epsilon

246
Q

BRCA 1/2 are important to what steps of the HR?

A

Pre-synapsis

247
Q

What is RPA?

A

A ssDNA binding protein that is important in end processing for HR

248
Q

What is site-specific recombination?

A

Mobile genetic elements with transposases are moved between non-homologous sites in DNA. This can alter DNA order and new information can be added

249
Q

Give an example of V(D)J recombination

A

Immunoglobin diversity in which the proteins are picked and removed/added depending on function of B cell

250
Q

ATR does what in cell cycle?

A

Blocks entry into M phase

251
Q

p53 mutation is often found in what cancer syndrome?

A

Li-Fraumeni

252
Q

p53 responds to what and signals what?

A

Hyperproliferative signals, DNA damage, telomere shortening, hypoxia and cuases cell cycle arrest, senescence and apoptosis.

253
Q

What is AT (ataxia telansomething)?

A

Mutation in ATM affecting ATM signaling an ATM NHEJ. Develops tumors of lymphoid origin like non-Hodgkins B-cell lymphoma or T-cell leukemia

254
Q

What is ATR-Seckel syndrome?

A

ATR mutation in ATR signaling which causes dwarfism and microencephaly.

255
Q

What is FANCD1 caused by?

A

BRCA2 mutation which leads to acute myleoid leukemia and head and neck squamous cell carcinoma

256
Q

NBS syndrome?

A

Caused by NBS1 mutation leading to ATM signaling issues and ATM dependent NHEJ issues, cause tumors of the lymphoid origin

257
Q

What is ATLD caused by?

A

MRE11 mutation which leads to mild AT (ataxia telangiectasia)

258
Q

What are gatekeeper genes?

A

tumor suppresor genes that control proliferation, differentiation, and apoptosis

259
Q

What are caretaker genes?

A

DNA maintenance genes that affect the rate at which cells accumulate mutant genes

Biochemistry-Exam 2 (14 decks)

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