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Biochemistry > 3.1-3.2 DNA and RNA Organization > Flashcards

3.1-3.2 DNA and RNA Organization Flashcards

1
Q

what does DNA fold to compress itself into?

A

a supercoil

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2
Q

how does circular prokaryotic DNA fold?

A

folds in on itself

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3
Q

how does linear eukaryotic DNA fold?

A

wraps around positively charged histone proteins

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4
Q

what do right handed DNA twists produce?

A

a negative supercoil

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5
Q

what do left handed DNA twists produce?

A

a positive supercoil

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6
Q

what is a linking number (Lk)?

A

a constant, the number of time a strand of DNA winds in the right handed direction around the helix axis

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7
Q

how is Lk calculated? in terms of Tw and Wr

A

Lk = Tw + Wr
linking number is twists plus writhes

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8
Q

what is Tw?

A

twist, the winding of DNA strands around each other

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9
Q

what is Wr?

A

writhes, the crossover of the double helix

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10
Q

relate changes in Tw and changes in Wr and why

A

changes in Tw = changes in Wr so that Lk stays constant

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11
Q

how is Lk calculated in terms of avergae base pairs per turn and total base pairs?

A

Lk = total base pairs/ average base pairs per turn

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12
Q

how is Lk shifted?

A

by DNA cleavage, the added or removing turns

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13
Q

what does removing turns make?

A

a negative supercoil

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14
Q

what does adding turns make?

A

a positive supercoil

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15
Q

what are topoisomers?

A

DNA that differ only in Lk

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16
Q

what is a nucleosome?

A

DNA wrapped around histone proteins

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17
Q

when DNA is not cleaved, describe Lk

A

constant

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18
Q

what do topoisomerases do?

A

cleave and reseal DNA to change Lk

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19
Q

what kind of supercoils aid in replication and transcription?

A

negative supercoils

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20
Q

describe why replication and transcription is easer with negative supercoils

A
  1. DNA must be unwound and separated in this process
  2. this is easier with fewer turns (like negative supercoils have)
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21
Q

describe most genomic DNA

A

negative supercoiled

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22
Q

why is positive supercoiled DNA not good for replication and transcription? how does topoisomerase help?

A

positive supercoiled DNA creates tension down the line, making the processes harder; topoisomerases release positive supercoils

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23
Q

during transcription, where does RNA polymerase enter and what does it form?

A

enters at the unwound region, forming a transcription bubble

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24
Q

when RNA polymerase enters at the unwound region forming a transcription bubble, what does it form? (2)

A
  1. negative supercoils upstream of transcription bubble
  2. positive supercoils downstream of transcription bubble
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25
Q

what do topoisomerases do?

A

relieve supercoiling

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26
Q

how many classes of topoisomerases are there?

A

2

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27
Q

describe type I topoisomerases (3)

A
  1. breakone strand of DNA
  2. change twists (Tw)
  3. not ATP-dependent
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28
Q

describe type II toposiomerases (3)

A
  1. break both strands of DNA
  2. change writhes (Wr)
  3. ATP-dependent
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29
Q

describe the structure of type I topoisomerases

A

monomeric

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30
Q

describe the structure and function of the structure of type II topoisomerases

A

dimeric; each monomer binds a strand of DNA

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31
Q

what are type II topoisomerases super important for? why? (2)

A

replication and transcription
1. negative supercoiling facilitates the start of transcription
2. positive supercoiling may inhibit replication of transcription
(topoisomerases relieve supercoiling)

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32
Q

give the 8 steps of the topoisomerase II mechanism

A
  1. topoisomerase in initial state
  2. enzyme opens and binds DNA strand
  3. enzyme breaks the first DNA strand
  4. enzyme then breaks the second strand
  5. enzyme crosses second strand through first strand using energy from ATP
  6. enzyme repairs break is 1st DNA strand
  7. enzyme releases second strand
  8. cycle repeats
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33
Q

what can inhibition of topoisomerases cause?

A

cell death

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34
Q

give 4 substances that inhibit type II topoisomerases and how

A
  1. aclarubicin: prevents binding of DNA
  2. ICRF-187: prevents DNA cleavage
  3. merbarone: prevents crossover
  4. etoposide: prevents release of DNA
    (just one of these substances can inhibit, don’t need all)
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35
Q

what does the hydroxyl at the 2’ carbon of RNA facilitate? how?

A

facilitates spontaneous degradation; in alkaline conditions, the OH- can deprotonate and cause intramolecular cleavage at the phosphodiester bond

36
Q

why is the spontaneous degradation capability of RNA advantageous for mRNA translation?

A

you can get a quick burst of translation with no lasting protein expression as the mRNA is degraded after time

37
Q

when auto-cleavage is prevented, what can RNA form?

A

secondary structures

38
Q

give an example of the secondary structures formed by RNA and its function

A

ribozymes: RNA molecules with catalytic activity

39
Q

give an example of a ribozyme and its function

A

Ribonuclease P; a ribozyme that cleaves nucleic acids

40
Q

what can RNA secondary structures form?

A

3-D structures from modified bases

41
Q

what is an example of a 3-D structure formed from secondaary RNA structures and what is the advantage?

A

tRNA; has specificity for amino acids

42
Q

histones bind DNA to form what?

A

nucleosomes

43
Q

what does a nucleosome contain?

A

DNA + 8 histones

44
Q

where does DNA connect on histones?

A

to the positively charged sections, since the DNA itself is negatively charged

45
Q

what is the point of nucleosomes?

A

keeps DNA organized and protected

46
Q

what do single stranded DNA binding proteins do?

A

protect single stranded DNA from nucleases, premature annealing, and formation of secondary structures

47
Q

what do SS DNA binding proteins contain that allows them to bind DNA?

A

contain a positively charged region that binds to negatively charged DNA

48
Q

what are SS DNA binding proteins selective for?

A

single stranded DNA

49
Q

what is a genome?

A

the complete set of genes of an organism

50
Q

is genome size proportional to the number of genes of an organism?

A

no!

51
Q

what is necessary for storage of the genome?

A

compaction

52
Q

what kind of chromosomes are more compacted?

A

mitotic

53
Q

give the 6 levels of organization from DNA up to chromosomes

A
  1. DNA
  2. nucleosomes
  3. chromatin
  4. looped chromatin
  5. condensed coils of chromatin
  6. chromosomes
54
Q

do humans have the most base pairs per chromosome?

A

nope

55
Q

is all DNA destined for transcription/translation?

A

nope

56
Q

what are the 2 types of sequences that DNA contains?

A

coding and noncoding sequences

57
Q

what is heterochromatin?

A

mostly noncoding portions of chromatin that are highly condensed

58
Q

what is heterochromatin important for?

A

chromosomal division and maintenance

59
Q

what is euchromatin?

A

gene-rich portions of chromatin that are less compacted; becomes YOU

60
Q

what are sister chromatids?

A

identical copies of DNA in a mitotic chromosome

61
Q

what is a kinetochore?

A

protein complex needed for separation of chromosomes

62
Q

how does the chromosome divide?

A

mitotic spindles attach to the kinetochore and pull sister chromatids apart

63
Q

what is a telomere?

A

heterochromatin that protects chromosomal ends from degradation

64
Q

what do telomeres contain? what do these form?

A

thousands of repetitive G-rich sequences that form the G-quadruplex structure

65
Q

what do proteins do after binding telomeres?

A

proteins bind telomeres to stabilize loop structures

66
Q

what is a promoter?

A

DNA sequence that occurs upstream of coding sequence

67
Q

what does a promoter do?

A

binds transcription factors that recruit RNA ploymerase to start transcription

68
Q

what is a coding sequence?

A

the actual gene to be transcribed

69
Q

what is a monocistronic gene in prokaryotes?

A

a promoter followed by a single coding region

70
Q

what is a polycistronic gene in prokaryotes?

A

a promoter followed by multiple coding regions

71
Q

how is a polycistronic gene transcribed? what does it form?

A

transcribed as a single RNA transcript but forms multiple proteins whose functions are usually related

72
Q

what does a polycistronic gene contain in terms of start and stop points for translation?

A

contains multiple start and stop points for translation

73
Q

what are operons?

A

polycistronic genes that contain coding sequences for proteins in a single pathway

74
Q

what are exons in DNA?

A

coding regions

75
Q

what are introns in DNA?

A

noncoding regions

76
Q

what do regulatory sequences bind in transcription of eukaryotic DNA?

A

regulatory sequences bind transcriptional regulatory proteins

77
Q

list and describe 2 regulatory sequences in eukaryotic DNA

A
  1. 5’ UTR: the 5’ untranslation region that facilitates interaction with translational proteins
  2. 3’ UTR: the 3’ untranslated region that facilitates termination of transcription by RNA polymerase
78
Q

what adds stability and translational efficiency to RNA? (2)

A
  1. the 5’ cap
  2. polyadenylation
79
Q

what does genetic recombination result in?

A

new proteins from the same gene sequence

80
Q

what do exons often encode?

A

functional domains

81
Q

what is exon shuffling?

A

when exons are deleted or inserted across genes

82
Q

what does exon shuffling allow for?

A

evolution of novel proteins

83
Q

what does alternative splicing result in?

A

produces different protein products with alternative structures and functions

84
Q

what does Hutchinson-Gilford progeria syndrome (HGPS) cause? how common is it?

A

rapid aging and death; occurs in 1 in 4 million

85
Q

what causes Hutchinson-Gilford progeria syndrome (HGPS)?

A

a mutation in the lamin A gene

86
Q

describe the HGPS mechanism of disease

A
  1. prelamin precursor is modified by the ICMT enzyme, which causes methylation of prelamin A
  2. this methylation is normally removed later by protease, forming the functional lamin
  3. but the mutation in the lamin A gene prevents demethylation
  4. toxic lamin accumulates in the nuclear membrane and damages nuclei leading to cell death

Biochemistry (20 decks)

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