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Biochemistry 2065 > DNA Replication and Repair > Flashcards

DNA Replication and Repair Flashcards

1
Q

genome

A

all the DNA in an organism, including genes and non coding parts

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2
Q

plasmids

A

accessory replicating DNA molecules

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3
Q

chromosome

A

a dna molecule with part or all of the genetic material of an organism

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4
Q

T/F a chromosome contains all the essential genetic information for life

A

true

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5
Q

T/F chromosomes are usually linear in humans and circular in bacteria

A

t

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6
Q

T/f plasmids are smaller than chromosomes

A

true

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7
Q

genes

A

parts of DNA that are transcribed

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8
Q

T/F virus genomes can be RNA or DNA

A

t

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9
Q

____ are the simplest cellular life forms, can be free-living or obligate endosymbionts of other host cells

A

prokaryotes (arcaea and bacteria)

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10
Q

prokaryotes genomes typically range from __ to ___ genes

A

400 to 9 000

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11
Q

T/F most genes in prokaryotes are found in a single circular chromosome

A

true

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12
Q

t/f some bacteria have multiple chromosomes and linear chromosomes

A

true

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13
Q

eukaryotic dna is wrapped around proteins called __

A

histones

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14
Q

dna wrapped around a histone is collectively called a __

A

nucleosome

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15
Q

the formation of nucleosomes contributes to the ___ of dna

A

packing

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16
Q

nucleosomes arrange into helical stacks called __

A

chromatin

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17
Q

folding of chromatin creates __

A

chromosomes

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18
Q

t/f chromosomes are the highest condensed structures

A

t

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19
Q

structure of chromatin during interphase and reason for this structure

A

loose; allowing DNA polymerase to get at the genes

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20
Q

during which cell stage is dna copied in preparation for mitosis?

A

interphase

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21
Q

in which stage of the cell cycle do chromosomes condense from chromatin? why?

A

metaphase ; to ease the separation of daughter cells

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22
Q

what % of the human genome is coding?

A

1.5%

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23
Q

protein coding DNA in humans is __%

A

2

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24
Q

how many exons/introns in bacterial genes

A

one exon, no introns

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25
Q

how many exons/introns in eukaryotic genes

A

multiple axons and introns

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26
Q

introns nad exons are ___ with a gene

A

nucleotide sequences

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27
Q

introns are removed by ___

A

RNA splicing

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28
Q

exons are covalently bonding to each other to make __

A

mRNA

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29
Q

DNA replication is semi-conservative, meaning :

A

each daughter cell gets a copy of DNA that is half from the parent and half newly made

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30
Q

the new DNA is assembled directly on a ___

A

pre-existing DNA template

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31
Q

role of helicase:

A

separates the dna strands making a fork with 2 template strands

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32
Q

role of single strand binding proteins (ssb)

A

stabilize the strands and prevent annealing

33
Q

role of primase

A

creates RNA primers, required to start replication

34
Q

role of DNA polymerase iii

A

binds at primer, builds the complementary strand from there

35
Q

role of DNA polymerase 1

A

removes primers as dns polymerase 3 approaches it

36
Q

dna polymerase 1 is especially important in the __ strand

A

lagging

37
Q

role of dna ligase

A

joins Okazaki fragments by joining phosphodiester bonds between adjacent nucleotides

38
Q

what enzymes unwinds dsdna in front of DNA polymerase?

A

helicase

39
Q

helicase is made of how many subunits?

A

3 different, 6 total

40
Q

t/f helicase is a hexamer

A

t

41
Q

SSbs are removed when ___ approaches

A

polymerase 3

42
Q

what is an RNA primer?

A

short RNA segment that allows the polymerase to start replication

43
Q

dna polymerase 3 catalyzes the step-by-step addition of __ to a dna strand

A

deoxyribonucleotide

44
Q

DNA polymerase makes dna in the ___ direction

A

5’ –> 3’

45
Q

DNA polymerase requires what 4 things?

A
  1. a template strand of dna
  2. a primer
  3. precursors
  4. mg 2+ cofactors
46
Q

primers initiate __

A

transcription

47
Q

what are precursors?

A

the building blocks of the dna product: the deoxyribonucleotide triphosphate

48
Q

DNA + dNTP =

A

dna + pyrophospate ion

49
Q

the strand elongation reaction catalyzed by polymerases is a nucleophilic attack by the ___ end of the growing strand to the ___ of dNTP

A

3’OH ; innermost phosphorus atom

50
Q

the 2 Mg increase the ___and help the position of __ in the active site

A

nucleophilicity of attacking OH; phosphates

51
Q

after attack by OH, a ___ bridge is formed and ___ is released

A

phosphodiester; pyrophosphate

52
Q

what happens to the released pyrophosphate that drives the polymerization forward?

A

hydrolyzed into 2 orthophosphates

53
Q

the basic structure of DNA polymerases resembles what anatomical structure/

A

an open right hand

54
Q

the “palm” of a dna polymerases contains ___

A

DNA, catalytically essential amino acids

55
Q

the “fingers” of dna polymerases are essential for __

A

nucleotide recognition and binding

56
Q

the “thumb” of dna polymerases are important to __

A

binding of the DNA substrate (dNTPs)

57
Q

the upper strand is the ___ strand; replication is ___

A

leading ; continuous

58
Q

the lower strand is the ___ strand ; replication is ___

A

lagging; discontinuous

59
Q

what part of DNA polymerase 1 removes the RNA primer?

A

the exonuclease

60
Q

dna polymerase 3 disengages when ___

A

the 2 okazaki fragments meet

61
Q

role of DNA ligase

A

joins the Okazaki fragments

62
Q

ligase catalyzes the formation of a phosphodiester bond between ___ at the end of one dna chain and the ___ at the end of the other

A

3’OH group; 5’ phosphoryl

63
Q

DNA damage can be thought of in what 2 ways?

A
  1. errors during replication

2. chemical changes to the nucleotides after replication

64
Q

what is non-watson-crick base pairing?

A

when dna incorporates the wrong nucleotide

65
Q

what is the effect of non-watson crick base pairing on the dna double helix?

A

local distortion

66
Q

what does it mean if a non-watson crick base pairing is mutagenic?

A

results in permanent changes in DNA sequence

67
Q

when a double helix containing a non-watson-crick base pairing is replicated, the 2 daughter cells will have __ sequences because __

A

different; the mismatched base is likely to pair with its Watson crick partner

68
Q

the ___ subunit of DNA polymerase 3 core has ___ activity that can remove an incorrect nucleotide

A

epsilon; exonuclease

69
Q

exonuclease

A

enzyme that removes successive nucleotides from the end of a polynucleotide molecule

70
Q

alfatoxin

A

hydrocarbon molecule and a toxin produced by molds that grow on food, like peanuts

71
Q

in the cell, aflatoxin is converted to an activated form that can modify ___ in DNA

A

guanine residues

72
Q

aflatoxin frequently leads to the conversion of a G-C into a ___ mutation

A

A-T

73
Q

mis-matches in dna can be repaired by a process called __

A

mis-match repair

74
Q

2 enzymes __ and ___ can recruit an enzyme __ that cuts the single strand near the mis-match. A __ then cuts away the single strand with the mis-match

A

MutS and MutL; MutH; exonuclease

75
Q

electromagnetic radiation, such as UV light induces ___ between adjacent pyrimidines along one strand of DNA

A

cross-links

76
Q

pyrimidine dimers are the primary cause of ___ in humans

A

melanomas

77
Q

the ____ repair system can recognize and excise thymine dimers

A

UvrABC excinuclease

78
Q

high fidelity in dna replication is maintained by what 3 things?

A
  1. accuracy of DNA polymerase
  2. proof-reading
  3. mismatch repair

Biochemistry 2065 (19 decks)

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