Hebert 1-6 Flashcards

1
Q

what percentage of our genome is repetitive?

A

50%

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2
Q

what percent of our genes actually codes for protein?

A

1.5%

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3
Q

what are the 5 classes of DNA?

A

repetitive
heterochromatin
regulatory
intronic
coding

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4
Q

what are the 3 classes of RNA?

A

protein coding
catalytic
regulatory

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5
Q

what is the significance of AT-rich regions on DNA?

A

it is where the origin of replication can happen because it is easier to break 2 hydrogen bonds rather than the 3 found in GC regions

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6
Q

SS DNA binding proteins

A

keep DNA single stranded and protect from nucleases

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7
Q

how do eukaryotes differ from bacteria in DNA replication?

A

it occurs at multiple sites in eukaryotes and only a single site in bacteria

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8
Q

helicase

A

enzyme that unwinds DNA at both replication forks
-requires ATP

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9
Q

topoisomerase

A

cut a nick in supercoil strand so it can unwind then uses ligase to restitch it back together

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10
Q

type I vs type II topoisomerase

A

-type I doesn’t require ATP, cuts only one strand
-type II cuts both strands and allows a double strand to pass through the break

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11
Q

what is the significance of the OH on the 3’ end?

A

DNA polymerase III binds in order to continue making DNA

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12
Q

DNA polymerase III

A

-reads parental strand from 3-5
-synthesizes new DNA from 5-3

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13
Q

okazaki fragments

A

multiple RNA primers in the lagging strand

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14
Q

DNA polymerase I

A

-removes primers in 5-3 exonuclease activity

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15
Q

what enzyme fuses the DNA ends together after the okazaki fragments have been cut out

A

ligase

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16
Q

telomeres

A

-ensure that genes are fully replicated
-protect ends of chromosomes
-shorten with age

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17
Q

why don’t telomeres shorten in cancer cells?

A

these cells express telomerase

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18
Q

telomerase

A

-an enzyme comprised of protein and a short piece of RNA
-reverse transcriptase activity (can make DNA from RNA template)
-maintains telomere length
-expressed in primary cell lines which makes them immortal

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19
Q

what is the approximate length of DNA?

A

6.5 feet

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20
Q

how do histones work

A

histones are positively charged and DNA is negative so they attract each other
-H1 binds the DNA between the nucleosome beads

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21
Q

what histone modifications can impact gene expression?

A

acetylation, methylation, and phosphorylation

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22
Q

mismatch repair reduces the error of replication to how many errors per replication?

A

3.2

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23
Q

repairs bulky lesions as those caused by pyrimidine dimers

A

nucleotide excision repair

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24
Q

-removes only the problem base
-takes care of bases lost to deamination

A

base excision repair

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25
Q

how are double strand breaks repaired?

A

nonhomologous end-joining (error prone)
homologous recombination (less error prone)

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26
Q

protein coding rna

A

mRNA

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27
Q

catalytic RNA

A

rRNA
tRNA
snRNA
snoRNA
scaRNA

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28
Q

regulatory RNA

A

miRNA
riboswitch

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29
Q

RNA modifications enable ~_________________genes in the human genome to produce ~_____________different proteins.

A

30,000
100,000

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30
Q

what percentage of RNA in a cell is mRNA?

A

5%

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31
Q

monocistronic vs polycistronic mRNA

A

-eukaryotes (mono): RNA carries info from 1 gene
-prokaryotes (poly): RNA carries info from more than 1 gene (operon)

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32
Q

rRNA accounts for what percent in a cell?

A

80%

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33
Q

-has unusual bases and intrachain pairing
-3 sizes in prokaryotes
-4 sizes in eukaryotes

A

rRNA

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34
Q

what percent of RNA in a cell does tRNA account for?

A

15%

35
Q

-at least one for each amino acid
-has unusual bases and intrachain pairing
-needs to be processes to form clover structure

A

tRNA

36
Q

-some are spliceosomal (remove introns)
-has unusual bases and intrachain pairing
-base pairs with heterogenous nuclear RNA (hnRNA) to facilitate splicing

A

snRNA (small nuclear)

37
Q

small nuclear ribonucleoproteins (snRNPs)

A

part of the spliceosome which removes introns from pre-mRNA

38
Q

what is the leading genetic cause of infant mortality?

A

spinal muscular atrophy caused by mutations in the survivor of motor neurons protein which helps in snRNP biogenesis

39
Q

guide RNAs that determine where modification takes place by base pairing with the rRNA

A

snoRNA (small nucleolar)

40
Q

-guide RNAs found in a nuclear subdomain
-guide modifications found in snRNAs

A

scaRNA (small cajal body-specific)

41
Q

-base pair with specific mRNAs in the 3’UTR region and promote mRNA degradation or reduced translation
-around 400 different ones expressed in humans

A

miRNA (micro)

42
Q

-short sequences of RNA that can change conformation upon binding of small molecules
-folding can disrupt transcription
-common in bacteria

A

riboswitch

43
Q

Name two diseases that have poly Q expansion

A

-Huntington disease
-Spinocerebellar ataxia type I

44
Q

repeats induce gene silencing via DNA methylation

A

Fragile X syndrome

45
Q

repeats reduce mRNA stability and induce heterochromatin

A

Myotonic dystrophy

46
Q

repeats induce heterochromatin and decrease transcription

A

Friedreich ataxia

47
Q

non-template strand

A

coding, sense strand

48
Q

template strand

A

noncoding, antisense strand

49
Q

compare and contrast prokaryotic and eukaryotic transcription

A

-RNA polymerase: prokaryotes have 1 and eukaryotes have 3
-prokaryotes have a sigma factor and eukaryotes have general transcription factors
-eukaryotes have nucleosomes and higher order chromatin
-eukaryotes undergo extensive mRNA modification while prokaryotes have no modifications

50
Q
A
51
Q

RNA is complementary to which strand?

A

template, antisense

52
Q

RNA is identical to which strand?

A

coding, sense

53
Q

what portion of the holoenzyme reads the DNA and makes RNA? (prokaryote)

A

core enzyme

54
Q

what protein binds to the promotor region so that RNA polymerase can start transcription? (eukaryote)

A

transcription factor

55
Q

a protein that helps bacteria start transcription by allowing RNA polymerase to bind to gene promoters (prokaryote)

A

sigma factor

56
Q

what type of RNA does RNA polymerase I make?
(eukaryote)

A

rRNA

57
Q

what type of RNA does RNA polymerase III make?
(eukaryote)

A

tRNA
snRNA

57
Q

what type of RNA does RNA polymerase II make?
(eukaryote)

A

mRNA
snRNA

58
Q

Rifampin

A

inhibits prokaryotic transcription inititation

59
Q

Actinomycin D

A

blocks transcription elongation; the first antibiotic used to treat cancer

60
Q

a-amanitin

A

inhibits RNA polymerase II (eukaryotic)

61
Q

rho-dependent termination (prokaryote)

A

rho protein cause RNA polymerase to break away from the DNA

62
Q

rho-independent termination (prokaryote)

A

CG repeats are attracted to each other and forms hairpin structure which removes the RNA polymerase

63
Q

describe termination of eukaryote transcription

A

polyadenylation signal (AAUAA) activates enzymes that cleave RNA from RNA polymerase

64
Q

hnRNA (heterogenous nuclear RNA)

A

rna that has just been transcribed but has to undergo modifications before becoming mRNA

65
Q

what splices introns in hnRNA to make mRNA

A

SNRPs

66
Q

what is the major mechanism by which chromatin is remodeled?

A

modification of histone lysine acetylation

67
Q

binds to transcription factors and and increases transcription of genes

A

enhancer

68
Q

what are the three hnRNA modifications

A

5’ capping
splicing
poly A tail

69
Q

what is the purpose of the 5’ cap?

A

protects RNA from nucleases and allows for efficient translation initiation

70
Q

nonsense mutation

A

a codon for aa changed to stop codon

71
Q

missense mutation

A

a codon for one aa changed to codon for another aa

72
Q

silent mutation

A

mutation does not change desired aa

73
Q

transition

A

purine for purine or pyrimidine for pyrimidine

74
Q

transversion

A

purine for pyrimidine or pyrimidine for purine

75
Q

why cant transcription and translation take place concurrently in eukaryotes?

A

eukaryotes have introns so you have to splice them first

76
Q

where does eukaryotic translation take place?

A

cytoplasm

77
Q

A site

A

binds incoming charged tRNA

78
Q

P site

A

carries peptidyl tRNA with nascent peptide chain

79
Q

E site

A

occupied by empty tRNA about to leave

80
Q

large subunit

A

catalyzes formation of peptide bonds that link amino acids in proteins

81
Q

small subunit

A

binds mRNA; ensures proper pairing between codon and anticodon

82
Q

what sequence in prokaryotes initiates translation?

A

shine-delgarno sequence

83
Q
A