Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

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

Exam II (lecture 14-16) Flashcards

You may prefer our related Brainscape-certified flashcards:
Biology 101 flashcards
1
Q

Central dogma

A

DNA (replication)

Transcription (reversible)

RNA

Trnaslation

Protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Prescence of of 2’-OH group

DNA vs RNA

A

DNA: no

RNA: yes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Both DNA and RNA nucleotides are joined by

A

phosphodiester bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

DNA vs RNA secondary structure

A

DNA: double helix

RNA: many types

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Stability RNA vs DNA

A

DNA: stable

RNA: easily degraded

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

RNA secondary structure

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Helical portions of RNA have the overall geometry of

A

an A-form duplex

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Double helical characteristic of RNA

A

right handed helical conformation dominated by base-stacking interactions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

non-watson-crick interactions contribute to

A

secondary RNA structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

unusual interactions contribute to the 3D RNA folding

A

U:A:U base triple

C:G:C base triple

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what group contributes to stabilization of 3D RNA folding

A

2’-OH group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Base stacking

A

also contributes to stability of the 3D RNA structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

transcriptome

A

entire set of RNA transcripts produced in a cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

transcription

A

Enzymatic RNA synthesis directed by a DNA template

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

genes have different

A

rates of expression

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

RNA polymerases

A

Synthesize RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

RNA synthesis direction

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

RNA polymerase use

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

RNA polymerase adds nucleotides

A

to the 3-OH end ONLY

(same as DNA polymerases)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Does RNA polymerase require a primer?

A

NO

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Does the product remain with the template (RNA polymerase)

A

NO

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Is DNA or RNA synthesis more accurate

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Prokaryotes RNA polymerase

A

single RNA Pol

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Eukaryotes RNA polymerase

A

atleast 3 RNA Pol’s

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Where does the RNA polymerase attach

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

what signals the end of transcription?

A

terminator

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Transcription unit

A
  • sequence of nucleotides in DNA that encodes for a single RNA molecule
  • promoter
  • RNA coding sequence
  • terminator
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

nontemplate =

A

coding = sense strand is NOT transcribed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

template=

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

promoter

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

template strand

A

may vary for different genes along the chromosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

initation involves

A

binding of promoter and the formation of transcription bubble

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

No initation in vivo

A

Bacterial RNA polymerase core

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

sigma factor

A

directs the core enzyme to specific binding sites on the DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions