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Microbio 3220 > Exam 3 - Lecture 14 > Flashcards

Exam 3 - Lecture 14 Flashcards

1
Q

what is a genome?

A

all of the DNA present in a cell or virus

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2
Q

what is a genotype?

A

a specific set of genes an organism possesses

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3
Q

what is a phenotype?

A

collection of observable characteristics

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4
Q

how many sets of DNA do prokaryotes have? what about eukaryotes?

A
  • prokaryotes: haploid (1N)
  • eukaryotes: diploid (2N)
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5
Q

who did the first experiments proving DNA is the genetic material?

A

Fred Griffith

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6
Q

what was the bacteria used in the transformation experiments?

A

Streptococcus pneumoniae

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7
Q

explain the transformation experiment done with smooth and rough strains.

A
  • smooth cells (S strain) have capsules and kill the host mouse
  • rough cells (R strain) have no capsule and do not kill the host
  • heat-killed S strains do not kill the host
  • live R strain with heat-killed S strain kills the host because the unharmful R strain transformed with the DNA of the lethal S strain
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8
Q

what is a nucleoside? what is a nucleotide?

A
  • nucleoside: nitrogenous base + 5 carbon sugar (ribose)
  • nucleotide: nucleoside + phosphate
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9
Q

which strand of the DNA does the mRNA resemble?

A

the plus (+) strand

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10
Q

can RNA be double stranded?

A

yeap (folded in on itself)

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11
Q

what are the four major types of RNA?

A
  • messenger (mRNA)
  • ribosomal (rRNA)
  • transfer (tRNA)
  • small regulatory (sRNA)
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12
Q

where does replication complete in circular bacterial DNA?

A

the terminus

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13
Q

DNA synthesis only occurs in what direction?

A

5’ to 3’

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14
Q

DNA polymerase adds new bases to what end of the DNA?

A

the 3’ end

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15
Q

what are the three things DNA polymerase requires?

A
  • template
  • primer
  • dNTPs
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16
Q

how many DNA polymerases does E. coli have?

A

5

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17
Q

which DNA polymerase plays the major role in replication in E. coli?

A

DNA polymerase III

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18
Q

which DNA polymerase is involved in lagging strand synthesis in E. coli?

A

DNA polymerase I

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19
Q

what is the role of helicase?

A

unwinding DNA strands

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20
Q

what is the role of single-stranded binding proteins?

A

keeping the DNA strands apart for replication to occur

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21
Q

what is the role of DNA gyrase & topoisomerases?

A

alter DNA supercoiling to relieve tension from rapid unwinding of double helix

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22
Q

what is the role of primase?

A

synthesizes short complementary strands of RNA (~10 nucleotides) to serve as primers needed by DNA pol I

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23
Q

what is the role of ligase?

A

attaching two pieces of single stranded DNA together

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24
Q

which strand of the DNA is synthesized non-continuously? how about continuously?

A
  • lagging strand: non-continuously
  • leading strand: continuously
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25
Q

how many primers does the lagging strand need?

A

a primer is needed for every Okazaki fragment

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26
Q

which DNA polymerase removes and replaces the RNA primers with DNA?

A

DNA pol I

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27
Q

DNA ligase forms a bond between what in the lagging strand?

A

between the 3’-hydroxyl of the growing strand and the 5’-phosphate of an Okazaki fragment

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28
Q

minor mistakes in DNA synthesis can be corrected by __________ activity

A

exonuclease

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29
Q

which direction does exonuclease work in?

A

3’ to 5’

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30
Q

do all polymerases have exonuclease activity?

A

nah

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31
Q

which DNA polymerase(s) has/have exonuclease activity?

A

DNA pol III

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32
Q

what is catenation?

A

when two circular chromosomes do not fully separate after replication

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33
Q

how is catenation solved?

A

topoisomerases temporarily break DNA molecules so that the strands can separate and then are ligated back into circular formation

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34
Q

what is the end replication problem?

A

shortening of chromosomes after each round of replication

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35
Q

what enzyme solves the end replication problem?

A

telomerase

36
Q

what is another name for a cistron?

A

a gene

37
Q

what does CDS stand for in a gene?

A

coding DNA sequence

38
Q

which strand is the template strand: the sense or the anti-sense?

A

anti-sense strand

39
Q

which strand is the coding strand: the sense or the anti-sense?

A

sense strand

40
Q

what is the promoter?

A

the recognition/binding site for RNA polymerase (-35 and -10 regions)

41
Q

what is the leader sequence?

A
  • 5’ untranslated region that is transcribed into mRNA but not into amino acids
  • region between the +1 transcription start site and translation start site (ATG)
42
Q

what is the Shine-Dalgarno sequence?

A
  • sequence important for initiation of translation
  • ribosome binding site located in the 5’ UTR (typically 6-10 nucleotides upstream of start codon)
43
Q

what is the coding start region?

A

the DNA sequence 5’-ATG-3’ aka RNA sequence 5’-AUG-3’

44
Q

what does AUG code for in bacteria?

A

N-formylmethionine, a modified amino acid used to initiate protein synthesis in bacteria

45
Q

where does translation stop?

A

stop codon (UAG, UAA, UGA)

46
Q

what is a “trailer” in protein coding genes?

A

a 3’ untranslated region which contains a terminator sequence used to stop transcription

47
Q

what does the transcription terminator do? what kind of DNA sequence does it have?

A

its DNA sequence is a palindrome and as it’s transcribed, it forms a hairpin loop that knocks RNA polymerase off the DNA, stopping transcription

48
Q

put these components in order of 5’ to 3’:

  • coding region
  • leader
  • terminator
  • promoter
  • trailer
  • transcription start
A
  • 5’
  • promoter
  • leader
  • transcription start
  • coding region
  • trailer
  • terminator
  • 3’
49
Q

true or false: there are exons and introns in bacterial genes.

A

false; there are no introns or exons.

50
Q

true or false: bacterial transcripts can be polycistronic or monocistronic.

A

true

51
Q

operons are present on monocistronic or polycistronic transcripts?

A

polycistronic

52
Q

what is a polycistronic mRNA?

A

an mRNA that has directions for more than 1 polypeptide in it

53
Q

what enzyme carries out transcription?

A

RNA polymerase

54
Q

how many subunits does RNA polymerase have? what are they?

A
  • two
  • the core enzyme + the sigma factor = holoenzyme (RNA pol)
55
Q

what does the core enzyme do and how many proteins is it composed of?

A
  • catalyzes RNA synthesis
  • composed of 5 proteins
56
Q

what is the purpose of the sigma factor?

A

has no catalytic activity but helps core enzyme recognize the promoter

57
Q

what are the two nucleotide positions of the promoter?

A
  • 35 and -10 relative to transcription site (+1)
58
Q

what enzyme unwinds the DNA in transcription?

A

RNA polymerase

59
Q

in what direction does RNA polymerase read the template strand? why?

A
  • 3’ to 5’
  • so that the RNA is synthesized in the 5’ to 3’ direction
60
Q

match the following:

  1. RNA stem loop/transcription terminator
  2. stop codons (TAG, TAA, TGA)

a. transcription stop site
b. translation stop site

A

1a
2b

61
Q

what is Rho-independent transcription termination?

A
  • no proteins involved
  • DNA sequence alone results in termination of transcription
62
Q

what is Rho-dependent termination?

A
  • protein factor rho binds to the mRNA at the rut (rho-utilization) site
  • rho moves along the mRNA in same direction as RNA pol
  • RNA pol pauses at the rho terminator
  • rho catches up and knocks RNA pol off
63
Q

what is translation?

A

mRNA is translated into an amino acid sequence/polypeptide chain

64
Q

what is a codon?

A

a 3 bp long DNA code that specifies an amino acid

65
Q

what amino acid does AUG code for?

A

methionine (start codon)

66
Q

how many possible codons are there?

A

64

67
Q

how many sense codons are there? how about nonsense (stop) codons?

A
  • 61 sense codons
  • 3 stops codons
68
Q

up to how many different codons can code for the same amino acid?

A

six

69
Q

what is the anticodon sequence for the tRNA that brings Met (give it in 5’ to 3’)?

A

CAU

70
Q

are there exceptions to the genetic code?

A

yes, some protists only have one stop codon (UGA) and the other two code for Gln instead

71
Q

what are the 21st and 22nd amino acids found in some microbes?

A
  • selenocysteine Sec; U (UGA)
  • pyrrolysine; Pyl; O (UAG)
72
Q

true or false: some bacteria have exceptions to the start codon.

A

yeah

73
Q

what is the direction of polypeptide synthesis: C to N terminal or N to C terminal?

A

N terminal to C terminal

74
Q

what is the ribosome?

A

the site of translation

75
Q

which domain(s) of life has/have coupled transcription and translation?

A

bacteria and archaea

76
Q

what is a polyribosome?

A

mRNA with multiple ribosomes

77
Q

which end of tRNA carries the amino acid: 5’ or 3’?

A

3’

78
Q

a tRNA with an amino acid attached is also known as a __________ tRNA. one without an amino acid is known as an __________ tRNA.

A

charged; uncharged

79
Q

true or false: tRNA are recycled.

A

true

80
Q

what enzyme catalyzes the attachment of amino acids to tRNAs?

A

aminoacyl-tRNA synthetases

81
Q

true of false: recharging of tRNA does not cost energy.

A

false; it costs ATP

82
Q

what is the size of the bacterial ribosome? what about the subunits?

A

70S (30S + 50S subunits)

83
Q

what are the two types of rRNA in the ribosome?

A

16S and 23S rRNA

84
Q

what is the function of 16S rRNA?

A
  • binds to the Shine Dalgarno site to initiate protein synthesis
  • binds initiation factor 3 (protein) to the 3’ charged end of tRNA
85
Q

what is the function of 23S rRNA?

A

ribozyme that catalyzes peptide bond formation

86
Q

what amino acid does bacterial translation start with?

A

N-formylmethionine

87
Q

what amino acid does archaeal translation start with?

A

methionine

Microbio 3220 (24 decks)

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