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BMS > DNA Introduction, Structure, Replication, and Repair > Flashcards

DNA Introduction, Structure, Replication, and Repair Flashcards

1
Q

Macromolecule that stores and expresses genetic information

-DNA and RNA

A

Nucleic Acids

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2
Q

In cellular organisms, genes are composed of DNA. Some viral genomes are composed of

A

RNA (HIV)

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3
Q

What are four functions associated with DNA?

A
  1. ) Replication
  2. ) Transcription
  3. ) Repair
  4. ) Recombination
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4
Q

Joins two parental DNA segments to form a hybrid molecule

A

Recombination

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5
Q

Nucleic acids are polymers of

A

Deoxyribonuleotides or ribonucleotides

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6
Q

What are the three components of a nucleotide?

A
  1. ) A base (Purine or pyrimidine)
  2. ) A pentose sugar
  3. ) A phosphate group
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7
Q

Allows DNA recognition by proteins that control gene expression

A

Base methylation

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8
Q

Salmonella typhimurium bacteria cause food poisoning and virulence is absolutely dependent upon

A

DNA Methylation

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9
Q

Blocks expression of virulence genes and prevents disease development in mice

A

Inactivation of DNA Adenine Methylase (dam)

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10
Q

Consist of a base linked to a pentose sugar via an N-linked glycosidic bond, but no phosphate group

A

Nucleosides

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11
Q

Nucleosides are converted to nucleotides by the addition of 1, 2 or 3 phosphate groups to

A

Position C-5 on the sugar

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12
Q

What do we call the RNA nucleosides?

A

Adenosine, Guanosine, Cytidine, Uridine

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13
Q

Can be potent drugs in anti-viral and anti-cancer therapy

A

Nucleoside analogs

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14
Q

The pyrimidine analogs 3ʼ-azido-2ʼ-deoxythymidine (AZT; zidovudine) and dideoxycytidine (ddC;zalcitabine) are used to treat

A

HIV

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15
Q

Nucleoside analogs are incorporated into growing DNA strands during viral or cellular DNA replication to

A

Block further DNA synthesis

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16
Q

Formed between the 3ʼ-hydroxyl group on the sugar of one nucleotide and the 5ʼ-phosphate group of the next nucleotide, releasing a pyrophosphate group

-Connects nucleotides to make nucleic acids

A

Phosphodiester bond

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17
Q

Enzymes that cleave polynucleotide chains by hydrolyzing phosphodiester bonds

A

Nucleases

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18
Q

Remove nucleotides from either the 5’ or 3’ ends of polynucleotide chains, depending on the specificity

A

Exonucleases

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19
Q

Only cleave internal phosphodiester bonds

A

Endonucleases

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20
Q

One type of endonucleases that cleave DNA in a sequence specific manner and that are particularly useful in molecular biology.

A

Restriction enzymes

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21
Q

The double helix has how many base pairs per helical turn?

A

10

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22
Q

Proteins that regulate gene expression bind to the

A

Major groove

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23
Q

Histone proteins found in chromatin bind to the

A

Minor groove

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24
Q

Certain anti-cancer drugs, such as dactinomycin (actinomycin D) exert their cytotoxic effect by

A

Intercalating into the minor groove, thereby disrupting DNA and RNA synthesis

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25
Q

How many H bonds are between

  1. ) A and T
  2. ) G and C
A
  1. ) 2

2. ) 3

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26
Q

Energetically favored and they facilitate DNA strand separation during replication, repair, recombination and transcription.

-when a molecule has fewer helical turns than relaxed DNA

A

Negative Supercoils

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27
Q

Can force DNA into a negative supercoil

A

Histones

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28
Q

Transiently break one or both DNA strands, pass the strand(s) through the break, and rejoin them.

A

Topoisomerases

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29
Q

Cuts a single strand of the double helix and does not require ATP

A

Topoisomerase I

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30
Q

Cuts both strands of the double helix and requires ATP

A

Topoisomerase II

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31
Q

Bacterial topoisomerase II that can introduce negative supercoils into relaxed DNA in addition to removing negative and positive supercoils

A

DNA gyrase

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32
Q

Drugs that inhibit topoisomerases are used in

-Lead to cell death

A

Chemotherapy and as antibiotics

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33
Q

In prokaryotes, DNA is associated with non-histone proteins that can condense DNA to form a

A

Nucleoid

34
Q

The complex of DNA in the nucleus with associated proteins is called

A

Chromatin

35
Q

Small basic proteins rich in Arg and Lys

-5 types

A

Histones

36
Q

In chromatin, DNA is wound around a histone octamer comprised of two molecules each of H2A, H2B, H3, and H4. This complex is called a

A

Nucleosome

37
Q

During interphase, when the cell is not dividing, chromatin can be distinguished as

-extended, active form of DNA

A

Euchromatin

38
Q

Affect the regional compaction of chromatin and the regulation of gene expression

A

Histone modifications

39
Q

As soon as eukaryotic DNA replication is completed, one unit of histone H1 binds the spacer DNA to promote the tight packing of nucleosomes. As a result, the chromatin winds into a helical tubular coil called the

A

Solenoid

40
Q

DNA replication is semiconservative, meaning replicated DNA molecules contain

A

1 new strand and 1 parental strand

41
Q

Molecular machine in prokaryotes that carries out DNA replication

A

Replisome

42
Q

Binds near the replication fork and uses ATP to force the DNA strands apart.

A

DNA Helicase

43
Q

Synthesizes a short primer (~10 nucleotides) in the 5ʼ to 3ʼ direction by copying the DNA template strand.

-Allows for DNA polymerase to begin replication

A

Primase (RNA polymerase)

44
Q

Continuously synthesized at the replication fork on the lagging strand

-Provide a free 3’-hydroxyl that serves as an acceptro for the first deoxyribonucleotide

A

Primers

45
Q

Synthesized continuously in the 5ʼ to 3ʼ direction toward the replication fork

A

Leading strand

46
Q

Synthesized discontinuously in short 5ʼ to 3ʼ Okazaki fragments directed away from the fork.

A

Lagging strand

47
Q
  1. ) Which polymerase(s) does most of the DNA synthesis?

2. ) Which proofread?

A
  1. ) DNA Polymerase III

2. ) DNA Polymerases I and III

48
Q

Functions in replication (primer removal and gap synthesis) and repair. Has 3’ to 5’ and 5’ to 3’ exonuclease activity

-Only polymerase with 5’ to 3’ exonuclease activity

A

DNA polymerase I

49
Q

Covalently joins Okazaki fragments by catalyzing the ATP-dependent formation of a phosphodiester bond between the leading and lagging strands

A

DNA Ligase

50
Q

Has many origins of replication and is linear

A

Eaukaryotic DNA replication

51
Q

What are the three eukaryotic DNA polymerases?

A

Polymerase alpha, delta, and epsilon

52
Q

Contains a primase activity and synthesizes hybrid RNA/DNA primers

A

alpha polymerase

53
Q

Synthesizes the bulk of lagging strand DNA, and displaces the 5ʼ ends of primers from Okazaki fragments, which are degraded by “flap exonuclease” FEN1 and other nucleases.

A

Polδ

54
Q

Synthesizes the bulk of leading strand DNA.

A

Polε

55
Q

What performs DNA replication in mitochondria?

A

Polγ

56
Q

Consist of short non-coding G-rich repetitive DNA sequences (TTAGGG) and associated proteins at the ends of linear chromosomes.

A

Telomeres

57
Q

A ribonucleoprotein complex with reverse transcriptase activity (hTERT): it synthesizes DNA using its RNA subunit as the template. It adds short DNA repeats to the 3ʼ-ends of linear chromosomes to prevent the loss of coding sequences

A

Telomerase

58
Q

Telomerase inhibitors can limit

A

Cancer cell proliferation

59
Q

Cancer cells typically display

A

Indefinite cell division and uncontrollable telomerase

60
Q

Stable changes in DNA sequence (substitutions, deletions, insertions) that can lead to a phenotypic change in the cell

A

Mutations

61
Q

Agents that damage DNA

A

Mutagens

62
Q

In prokaryotes, strand-specificity for mismatch repair (MMR) is provided by DNA

A

Methylation

63
Q

An endonuclease cleaves the newly synthesized strand on either side of the mismatch. A helicase and an exonuclease remove DNA from the newly synthesized strand between the site of incision and the mismatch. DNA Pol III fills the gap, followed by DNA ligase

A

Mismatch repair

64
Q

One of the biggest causes of cancer in humans

-accounts for 90% of patients with Lynch syndrome

A

Defects in the MMR

65
Q

Repairs spontaneously occuring DNA base modifications (e.g. base damage caused by deamination of cytosine into uracil, depurination, alkylation, oxidation etc).

A

Base Excision Repair

66
Q

The damaged base is recognized by a base-specific DNA glycosylase that cuts the N-glycosidic bond between the damaged base and the sugar deoxyribose and the base is released upon action of a helicase

A

Base excision repair

67
Q

Can remove an infinite number of lesions including photoproducts, chemical adducts and intrastrand DNA adducts. However, it is the only mechanism that can remove bulky DNA adducts.

A

Nucleotide excision repair (NER)

68
Q

What type of NER is used if the damage is in a transcriptionally inactive region of DNA?

A

Global Genomic NER

69
Q

What type of NER is utilized if the damage is in a transcriptionally active region of DNA?

A

Transcription-Coupled NER

70
Q

A gene-specific repair process that is triggered when a helix distortion caused by DNA damage blocks progression of RNA polymerase II along the transcribed (template) strand of the DNA double helix.

A

Transcription-coupled NER

71
Q

Used to remove pyrimidine dimers caused by UV light

A

NER

72
Q

Commonly caused by oxidative damage and are usually associated with loss of a single nucleotide, and by damaged 5ʼ- and/or 3ʼ-termini at the site of the break.

A

Single-strand breaks (SSBs)

73
Q

Can be induced by ionizing radiation (gamma- and X rays), oxidizing agents (e.g. bleomycin) or topoisomerase inhibitors used for chemotherapy (e.g. camptothecin), some plant and microbial products (e.g. aflatoxins in moldy peanuts) or mechanical stress

A

Double-strand breaks (DSBs)

74
Q

Can severely compromise genome stability and can lead to loss of chromosome fragments during mitosis, or chromosomal translocations that can induce cancer due to joining of the wrong DNA ends.

A

Failure to repair DSBs

75
Q

What are the two different repair pathways of DSBs?

A
  1. ) Non-homologous end-joining (NHEJ) repair

2. ) Homologous recombination

76
Q

The major pathway to repair DSBs, because it does not require any sequence homology. It can thus occur throughout the cell cycle without needing alingment with a homologous chromosome

A

NHEJ repair

77
Q

NHEJ is very

-Leads to the accumulation of random genetic mutations

A

Error Prone

78
Q

NHEJ can also lead to

A

Chromosomal translocations

79
Q

Non-mutagenic because it involves alignment of highly homologous DNA molecules, so that the information on the homologous sequence can be used to repair the broken DNA.

A

Homologous recombination

80
Q

Restricted to the S and G2 phases of the cell cycle, when a sister chromatid is present

A

Homologous recombination

BMS (62 decks)

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