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Molecular Genetics > Exam II (lecture 14-16) > Flashcards

Exam II (lecture 14-16) Flashcards

1
Q

Central dogma

A

DNA (replication)

Transcription (reversible)

RNA

Trnaslation

Protein

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2
Q

ncRNA

A

the gene segment of a nucleic acid that carries the code for a particular protein or for a functional non-coding RNA (ncRNA)

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3
Q

Prescence of of 2’-OH group

DNA vs RNA

A

DNA: no

RNA: yes

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4
Q

Both DNA and RNA nucleotides are joined by

A

phosphodiester bonds

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5
Q

DNA vs RNA secondary structure

A

DNA: double helix

RNA: many types

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6
Q

Stability RNA vs DNA

A

DNA: stable

RNA: easily degraded

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7
Q

RNA secondary structure

A

enables RNA molecules to fold into many different shapes that lend themseleves to many different biological functions.

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8
Q

Helical portions of RNA have the overall geometry of

A

an A-form duplex

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9
Q

Double helical characteristic of RNA

A

right handed helical conformation dominated by base-stacking interactions

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10
Q

non-watson-crick interactions contribute to

A

secondary RNA structure

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11
Q

unusual interactions contribute to the 3D RNA folding

A

U:A:U base triple

C:G:C base triple

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12
Q

what group contributes to stabilization of 3D RNA folding

A

2’-OH group

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13
Q

Base stacking

A

also contributes to stability of the 3D RNA structure

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14
Q

transcriptome

A

entire set of RNA transcripts produced in a cell

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15
Q

transcription

A

Enzymatic RNA synthesis directed by a DNA template

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16
Q

genes have different

A

rates of expression

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17
Q

RNA polymerases

A

Synthesize RNA

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18
Q

RNA synthesis direction

A

5’-3’ (the template DNA is copied in the 3’ to 5’ direction)

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19
Q

RNA polymerase use

A

ribonucleoside 5’-triphosphates (rNTPs) to syntehsize RNA complementary to the template

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20
Q

RNA polymerase adds nucleotides

A

to the 3-OH end ONLY

(same as DNA polymerases)

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21
Q

Does RNA polymerase require a primer?

A

NO

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22
Q

Does the product remain with the template (RNA polymerase)

A

NO

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23
Q

Is DNA or RNA synthesis more accurate

A

DNA is more accurate (1/10,000 bases)

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24
Q

Prokaryotes RNA polymerase

A

single RNA Pol

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25
Q

Eukaryotes RNA polymerase

A

atleast 3 RNA Pol’s

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26
Q

Where does the RNA polymerase attach

A

initiates transcription at the promoter “upstream” of the information contained in the gene

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27
Q

what signals the end of transcription?

A

terminator

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28
Q

Transcription unit

A
  • sequence of nucleotides in DNA that encodes for a single RNA molecule
  • promoter
  • RNA coding sequence
  • terminator
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29
Q

nontemplate =

A

coding = sense strand is NOT transcribed

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30
Q

template=

A

coding = antiesense strand is transcribed and complementary and antiparallel to the RNA product

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31
Q

promoter

A

RNA polymerase binding site on the DNA. Will determine which strand is going to be transcribed

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32
Q

template strand

A

may vary for different genes along the chromosome

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33
Q

General transcription steps

A
  1. RNA polymerase binds the ptomoter (forming first a closed complex)
  2. Promoter melting (open complex)
  3. Transcription initiated within complex
  4. Promoter clearance and elogation complex
  5. RNA pol dissociation from DNA and recycling
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34
Q

initation involves

A

binding of promoter and the formation of transcription bubble

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35
Q

chemical mechanism of RNA synthesis

A

the addition of an rNTP to a growing transcript is a Mg2+ dependent reaction that produces a 5’-3’ phosphodiester linkage.

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36
Q

Bacterial RNA polymerase core

A

5 subunits: 2alpha, 1beta, 1beta (prime), omega

  • RNAPs look like “crab clows”
  • Capable of RNA synthesis on a DNA template
  • However
    1. no specificity for promoter
    2. no initation in vivo
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37
Q

No initation in vivo

A

Bacterial RNA polymerase core

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38
Q

sigma factor

A

directs the core enzyme to specific binding sites on the DNA

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39
Q

Core enzyme

A

2a, B’, B, w

Required for polymerization activity

40
Q

Sigma factor + core enzyme =

A

holoenzyme

2a, 1B, 1B’, 1w and sigma factor

41
Q

holoenzyme

A

required for correct initation of transcription: binding to promoter

42
Q

Rpo

A

RNA polymerase

43
Q

E. coli has several sigma factors that specify RNAP binding to particular promoters

A

Because different E. coli have sigma factors direct RNAP to different promoters, different sets of genes may be transcribed as “needed” by changing the sigma factor in the holoenzyme

44
Q

sigma factor 70/RpoD

A

“housekeeping genes” expressed in all growing cells

45
Q

consensus sequence

A

certain nucleotides that are particularly common at each position form a consensus sequence.

Bacterial promoters

46
Q

How is a consensus sequence determined?

A

by alligning all known examples and finding most common base at each position

47
Q

Consensus sequence of a sigma70 promoter

A

The sequence of most of the promoter is irrelevant; only short stretches of DNA are conserved

Structure/sequence identifies promoter - determines “strength”

48
Q

Features of E coli promoters recognized by sigma70 (optimal promoters).

-10 region and -35 region

A

consensus sequences (interaction sites for sigma 70)

49
Q

-10 region

A

5’-TATAAT-3’

50
Q

-35 region

A

5’-TTGACA-3’

51
Q

distance between -10 and -35 region

A

17bp

52
Q

upstream promoter (UP) element

A

promoters of certain highly expressed genes

(bound by one alpha subunits of RNA polymerase)

53
Q

mutations in the -10 and -35 regions of the promoter

A

affect the efficiency of RNAP binding and transcription initation

A change in just one base pair can decrease the rate of binding by several orders of magnitude

54
Q

structural changes lead to open complex.

A

transition to open complex and to elongation requires conformational changes in RNAP and changes of its association with DNA

  • place downstream duplex DNA in the active site cleft and then seprating the nontemplate and template strands.
55
Q

an open complex has:

A

several channels, which provide access to the core of the enzyme

56
Q

Initation is _ and produces short _

A

Primer independent; abortive transcripts

  1. the first 8-10 phosphodiester binds forms: high probability that the RNAP will release the transcript from the template without extending furhter
  2. Beyond 10 nts: the RNA becomes stable
  3. “release” of sigma
57
Q

Transcription elongation is

A

continuous until termination

58
Q

promoter clearance

A

RNA polymerase moves beyond the promoter region of the DNA to behin rapid elongation of the transcript.

59
Q

transcription termination

A

specific sequences in the template strand stop transcription.

60
Q

types of terminations

A
  1. intrinsic terminators
  2. Rho dependent termination
61
Q

intrinsic terminatiors (p-independent)

A

relies primarily on structures that form in the RNA transcript

62
Q

Rho dependent terminators

A

require rho (p) protein.

63
Q

Intrinsic terminators:
2 distinguishable features

A
  1. highly conserved segment of A residues in the template that are transcribed into U residues.
  2. RNA transcript with self-complementary sequences - formation of a hairpin structure, centered 15-20 nucleotides before the projected end of the RNA strand.
64
Q

Mechanism of intrinsic terminators

A

Hairpin disrupts several A-U base pairs (weak) in the RNA/DNA hybrid segment. May disturb important interactions between RNA and RNA polymerase, leading to dissociation of the transcript.

65
Q

Rho (p)-dependent terminators

A

CA-rich sequence called a rut (rho utilization) site in the template strand (50-90 bases) long.

66
Q

Rho (p) factor characteristics

A
  • hexameric helicase
  • binds to RNA very ealry in the transcription process
  • RNA binding domain is the center hole of the hexamer
  • ATPase activity, helicase activity
67
Q

RNA that include a rut site, recruit the p helicase which

A

migrates in the 5’ to 3’ direction along the mRNA and seperates it from the polymerase.

68
Q

Promters are recognized by

A

sigma70

69
Q

RNA polymerase has different

A

intrinsic affinities for promters of different sequence

70
Q

Different E.Coli sigma factors direct RNAP to different promoters

A

different sets of genes may be transcribed as “needed” nby changing the sigma in the holoenzyme

71
Q

rpoH

A

sigma 32

heat shock

72
Q

at 42 degrees C

A

induction phase - transiently increase of sigma32 levels

73
Q

at 46 degrees celsius

A

approx. 30% of all proteion are HSPs

74
Q

at 50 degrees C

A

sigma70 is inactivated, High levels of sigma32

75
Q

at 57 degrees celsius

A

RNAP core is inactivated

76
Q

Transcription factors

A

Activators and Repressors, control RNA polymerase function at a promoter

77
Q

Cis acting elements

A

promoter, operator, activator binding site, UP element

78
Q

Trans-acting factors

A

RNAP; repressor; activator

79
Q

negative control

A

repressor present, transcription off

80
Q

positive control

A

activator present, transcription on

81
Q

repressor inhibits transcription

A

prevents or decreases expression

82
Q

activator facilitates transcription

A

promotes or increases expression

83
Q

Activation and repressors can function by

A

DNA looping.

84
Q

regulators often work together for

A

signal intregation

85
Q

signal integration

A

control of a gene by multiple regulators in response to more than one environmental signal

86
Q

operon Lac

A

approx. 6000 bp

87
Q

Operon Lac

signal integration: environmental condition

A

Environmental: availability of glucose and lactose

88
Q

Lactose -metabolizing genes, are

A

under the control of an activator protein, needed for the efficienct transcription of the lac operon genes, even in the absemce of the Lac repressor.

89
Q

Lactose -metabolizing genes, are

A

under the control of an activator protein, needed for the efficienct transcription of the lac operon genes, even in the absemce of the Lac repressor.

90
Q

transcription initiation is the step most regulated

A

regulation at this point is the most energy efficienct, becuase it occurs before the investment of energy in mRNA

91
Q

Repressors can hinder transcription binding by DNA

A

at a site that prevents RNA polymerase binding or by preventing closed-to-open transition of the polymerase- promoter complex (negative regulation)

92
Q

Binding factors for transcription facors don’t need to be close to the transcirption start site.

A

Regulatory proteins that bind sites distant from the promoter exert their effects through DNA looping

93
Q

Activators promote RNA polymerase binding through

A

cooperativity or promote formation of the open complex by causing a conformational change in the promoter or the polymerase (positive regulation)

94
Q

promoters may be controlled by two or more transcription factors, allowing

A

inegration of signals from more than one environmental variable

95
Q

small signal molecules (effectors)

A

allosterically regulate the function of activators and repressors

96
Q

sets of genes that function in one pathway

A

are often controlled simultaneously.

Molecular Genetics (9 decks)

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