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MolBio > DNA RNA lect > Flashcards

DNA RNA lect Flashcards

1
Q

refers to the single units within nucleotides

A

nucleoside monophosphates

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1
Q

it serves as the precursor molecule during nucleic acid synthesis within the cell

A

triphosphate form

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2
Q

two long polynucleotide chains are coiled around central axis forming a __

A

right handed double helix

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3
Q

x-ray diffraction data shows that the DNA is a regular helix and the repeat distance is __

A

34 A*

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4
Q

average structure should be __

A

10 base pairs

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5
Q
  • more base pairs refer as ___
  • fewer base pairs refer as ___
A

more base pairs = overwound
fewer base pairs = underwound

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6
Q

denaturing agents

A

formamide or urea

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7
Q

site of interaction with many proteins that will bind to the specific nucleotides

A

binding or recognition sites

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8
Q

DNA molecule that exists in a very high relative humidity environment (92%)

A

B-DNA

Watson-Crick DNA

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9
Q

how many base pairs in each turn for B-DNA and the length of one turn of helix

A

10 base pairs
34A

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10
Q

DNA is dehydrated or under high salt conditions

A

A-DNA

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11
Q

which is short and thicker form of DNA?

A

A-DNA

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12
Q

how many base pairs in each turn for A-DNA and the repeat double helix

A

11 base pairs
24.6 A

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13
Q

a left handed, longer and narrower form of DNA in which it is known to occur in nature when there is a sequence of alternating purinepyrimidine

A

Z-DNA

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14
Q

how many base pairs in each helical turn for Z-DNA and the repeat helix

A

12 base pairs
45.6 A

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15
Q

Z-DNA is formed under conditions of __

A

high salt / presence of alcohol

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16
Q

DNA is duplicated __ cell division

A

before cell division

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17
Q

a stage in the cell cycle in which the replication undergo

A

S phase

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18
Q

structure that unwind the double helix in opposite directions

A

replication fork

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19
Q

phase in which the replication machinery moves along the parent dna strands and forms the daughter strands

adding of nucleotides

A

elongation phase

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20
Q

what phase does the two replication forks moving in opposite directions meet

A

termination phase

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21
Q

sites at which single stranded DNA is exposed and at which DNA synthesis occurs

A

replication forks

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22
Q

an enzyme that synthesize the short RNA sequences that are complementary to a single stranded piece of DNA which serves as its templates

A

primase

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23
Q

why there is a primase?

A

DNA polymerase cannot synthesize nucleotide without a based template

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24
Q

protein complex that serves as a processivity-promoting factor in DNA replication.

A

sliding clamp (beta clamp)

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25
Q

these protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand

A

sliding clamp

26
Q

major enzyme that is the one that polymerize the nucleic acid chain.

A

DNA polymerase

27
Q

enzyme responsible for sealing the nick between the new strands and the synthesized by polymerase III and polymerase I.

A

ligases

28
Q

these will proposed the semidiscontinuous replication mechanism

A

okazaki fragments

29
Q

okazaki fragments will linked this enzyme to form the second daughter strand

A

DNA ligase

30
Q

enzyme that harnesses the chemical energy from the ATP hydrolysis to separate the two DNA strands at the replication fork

A

helicase

31
Q

these proteins will bind selectively to single-stranded DNA as soon as it forms

A

Single-strand binding protein

32
Q

it allows enzymes to attach to the newly opened single strand and initiate elongation and these proteins are removed as DNA synthesis proceeds

A

Single-strand binding protein

33
Q

essential bacterial enzyme that catalyzes the ATP-dependent negative super-coiling of double-stranded closed- circular DNA

A

gyrase (topoisomerase TYPE 2)

34
Q

responsible for copying a short stretch of the DNA template strand to produce the RNA primer sequence

A

primase

35
Q

bind in a complex with the DNA polymerase

A

primases and alpha catalytic subunit

36
Q

subunits for eukaryotic primase

A
  • alpha catalytic subunit
  • accessary subunit
37
Q

synthesizes a stretch of 10–30 nucleotides of RNA.

A

polymerase-α subunit-primase complex

38
Q

broad class of enzymes that cleave off nucleotides one at a time from the three prime or five prime ends of DNA and RNA chains; it also functions to protect the sequence of nucleotides, which must be faithfully copied

A

exonucleases

exonuclease function gives the enzyme the capacity to proofread newly synthesized DNA

39
Q

First polymerase enzyme to direct during the initial synthesis

A

DNA polymerases III

40
Q

this is so called okazaki maturation process

A

DNA polymerase I

41
Q

uses its polymerase activity to fill in the gap left by the RNA with new DNA.

A

DNA polymerase I

42
Q

mass and number of subunits for the DNA polymerase I of E coli

A

mass: 103 kDa
subunits: 1

43
Q

mass and number of subunits for the DNA polymerase II of E coli

A

mass: 90
subunits: >4

44
Q

mass and number of subunits for the DNA polymerase III of E coli

A

mass: 830
subunits: >10

45
Q

This enzyme will add nucleotides to the end of a DNA strand in the absence of hydrogen base pairing with a template. it can synthesize polynucleotide chains without a template

A

terminal transferase

46
Q

the only dna polymerase that has 5’ - 3’ exonuclease activity

A

DNA Pol I

47
Q

often used in vitro as a method to introduce labeled nucleotides into DNA molecules. The resulting labeled products are used for DNA detection in hybridization analyses.

A

cut-and-patch nick translation

48
Q

responsible for the coupling of DNA replication. this is composed of DNA polymerase, sliding clamp, and clamp loader.

A

replisome

49
Q

responsible for holding catalytic cores onto their template strands.

A

sliding clamp

50
Q

recruiting DNA polymerase to the appropriate location on the DNA template. They localize specifically at the region where DNA synthesis needs to commence.

A

clamp loader and sliding clamp

51
Q

associated with the clamp loader and links this polymerases-clamp loader complex to the helicase.

A

Tau protein

52
Q

enzymes that modulate in the degree of DNA supercoiling. They can also convert one isomer of DNA to another

A

topoisomerases

53
Q

a topoisomerase enzymes transiently cleave and reseal one strand of duplex DNA in the absence of ATP

A

TP 1

54
Q

topoisomerase enzymes will cleave and relegate both DNA strands in the presence of ATP.

A

TP 2

55
Q
  • TTGGGG
  • TTAGGG
A
  • protozoans
  • vertebrates
56
Q

endonucleases that recognize specific base sequences and break or restrict the DNA polymer at the sugar-phosphate backbone

A

restriction enzymes

57
Q

most frequently used restriction enzyme in the lab

A

RE type II
- cleave the DNA directly at the binding site, producing fragments of predictable size.

58
Q
  • Analysis of gene rearrangements
  • Mutation detection
  • DNA recombination in vitro
  • Mapping a DNA fragment
A

uses of restriction enzymes

59
Q

the targets for several anticancer drugs. These __ inhibitors bring about cell death by interfering with the breaking and joining activities of the enzymes, in some cases trapping unfinished and broken intermediates

A

topoisomerase

59
Q

catalyze the addition of methyl groups to nitrogen bases, usually adenines and cytosines in DNA strands

A

methylation

60
Q

slipped structures, cruciform, and triple-helix

A

secondary structures

60
Q

the middle point of a temperature range where 50% of your DNA strands are denatured and the amount of denatured DNA is measured at an absorbance of __ nanometer.

A

melting temperature

260 nm

61
Q

DNA supercoiling is the __ winding of DNA helix axis that occurs when the double helix is under or over wound.

A

tertiary

MolBio (10 decks)

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