DNA Introduction, Structure, Replication, and Repair Flashcards Preview

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Flashcards in DNA Introduction, Structure, Replication, and Repair Deck (80):
1

Macromolecule that stores and expresses genetic information

-DNA and RNA

Nucleic Acids

2

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

RNA (HIV)

3

What are four functions associated with DNA?

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

4

Joins two parental DNA segments to form a hybrid molecule

Recombination

5

Nucleic acids are polymers of

Deoxyribonuleotides or ribonucleotides

6

What are the three components of a nucleotide?

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

7

Allows DNA recognition by proteins that control gene expression

Base methylation

8

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

DNA Methylation

9

Blocks expression of virulence genes and prevents disease development in mice

Inactivation of DNA Adenine Methylase (dam)

10

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

Nucleosides

11

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

Position C-5 on the sugar

12

What do we call the RNA nucleosides?

Adenosine, Guanosine, Cytidine, Uridine

13

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

Nucleoside analogs

14

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

HIV

15

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

Block further DNA synthesis

16

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

Phosphodiester bond

17

Enzymes that cleave polynucleotide chains by hydrolyzing phosphodiester bonds

Nucleases

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

Exonucleases

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Only cleave internal phosphodiester bonds

Endonucleases

20

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

Restriction enzymes

21

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

10

22

Proteins that regulate gene expression bind to the

Major groove

23

Histone proteins found in chromatin bind to the

Minor groove

24

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

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

25

How many H bonds are between
1.) A and T
2.) G and C

1.) 2
2.) 3

26

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

-when a molecule has fewer helical turns than relaxed DNA

Negative Supercoils

27

Can force DNA into a negative supercoil

Histones

28

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

Topoisomerases

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

Topoisomerase I

30

Cuts both strands of the double helix and requires ATP

Topoisomerase II

31

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

DNA gyrase

32

Drugs that inhibit topoisomerases are used in

-Lead to cell death

Chemotherapy and as antibiotics

33

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

Nucleoid

34

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

Chromatin

35

Small basic proteins rich in Arg and Lys

-5 types

Histones

36

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

Nucleosome

37

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

-extended, active form of DNA

Euchromatin

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

Histone modifications

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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

Solenoid

40

DNA replication is semiconservative, meaning replicated DNA molecules contain

1 new strand and 1 parental strand

41

Molecular machine in prokaryotes that carries out DNA replication

Replisome

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

DNA Helicase

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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

Primase (RNA polymerase)

44

Continuously synthesized at the replication fork on the lagging strand

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

Primers

45

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

Leading strand

46

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

Lagging strand

47

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

2.) Which proofread?

1.) DNA Polymerase III

2.) DNA Polymerases I and III

48

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

DNA polymerase I

49

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

DNA Ligase

50

Has many origins of replication and is linear

Eaukaryotic DNA replication

51

What are the three eukaryotic DNA polymerases?

Polymerase alpha, delta, and epsilon

52

Contains a primase activity and synthesizes hybrid RNA/DNA primers

alpha polymerase

53

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.

Polδ

54

Synthesizes the bulk of leading strand DNA.

Polε

55

What performs DNA replication in mitochondria?

Polγ

56

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

Telomeres

57

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

Telomerase

58

Telomerase inhibitors can limit

Cancer cell proliferation

59

Cancer cells typically display

Indefinite cell division and uncontrollable telomerase

60

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

Mutations

61

Agents that damage DNA

Mutagens

62

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

Methylation

63

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

Mismatch repair

64

One of the biggest causes of cancer in humans

-accounts for 90% of patients with Lynch syndrome

Defects in the MMR

65

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

Base Excision Repair

66

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

Base excision repair

67

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.

Nucleotide excision repair (NER)

68

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

Global Genomic NER

69

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

Transcription-Coupled NER

70

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.

Transcription-coupled NER

71

Used to remove pyrimidine dimers caused by UV light

NER

72

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.

Single-strand breaks (SSBs)

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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

Double-strand breaks (DSBs)

74

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.

Failure to repair DSBs

75

What are the two different repair pathways of DSBs?

1.) Non-homologous end-joining (NHEJ) repair
2.) Homologous recombination

76

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

NHEJ repair

77

NHEJ is very

-Leads to the accumulation of random genetic mutations

Error Prone

78

NHEJ can also lead to

Chromosomal translocations

79

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.

Homologous recombination

80

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

Homologous recombination

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