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Biochemistry > New: RNA Synthesis and Regulation > Flashcards

New: RNA Synthesis and Regulation Flashcards

1
Q

a DNA sequence that is transcribed

A

gene

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2
Q

central dogma

A

biological information flow from DNA to RNA irreversible except by viral reverse transcriptase; RNA to protein is always irreversible

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3
Q

housekeeping genes encode

A

proteins or RNA essential for normal activities of the cell

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4
Q

DNA is transcribed to ____ is translated to _____

A

RNA; protein

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5
Q

Exceptions to the central dogma

A

RNA–> DNA via reverse transcriptase

protein –> protein (prion protein)

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6
Q

Prions-proteinaceous infections particles do what to proteins

A

like a virus, prions cannot replicate themselves, it enters a cell then it converts normal proteins into prions

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7
Q

prion proteins are a

A

tightly packed beta sheet that is too stable

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8
Q

examples of prion-proteinaceous infectious particle diseases

A

bovine spongifrom encephalopathy; creutzfeldt-jakob; chronic wasting;

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9
Q

4 types of RNA

A

transfer (tRNA)
ribosomal (rRNA)
messenger (mRNA)
small/micro RNA

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10
Q

transfer RNA

A

carries amino acids to translation machinery; very stable

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11
Q

ribosomal RNA

A

makes up much of the ribosome; very stable; majority of cellular RNA

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12
Q

messenger RNA

A

encodes message from DNA to ribosomes
rapidly degraded by nucleases (clicker Q)
small fraction of steady-state RNA, but uses a large percentage of synthetic capacity of cell

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13
Q

small/micro RNA

A

participate in metabolic events; many have catalytic activity and are turned over rapidly

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14
Q

Transcription in E. coli RNA polymease catalyzes

A

DNA-directed RNA synthesis (transcription)

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15
Q

RNA pol is core of a larger

A

transcription complex

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16
Q

complex assembles at one end of a gene when transcription is

A

initiated

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17
Q

DNA is continuously unwound as RNA pol catalyzes a

A

processive elongation of RNA chain

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18
Q

transcription complex responds to specific ________ signals and disassembles

A

termination

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19
Q

the synthesis of RNA from DNA template is called

A

transcription

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20
Q

transcription is catalyzed by

A

RNA polymerase

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21
Q

RNA polymerase requires the following 3 things:

A
  1. a template (but uses T instead of U)
  2. Activated precursors in the form of the four ribonucleoside triphosphates ATP, GTP, UTP, CTP
  3. Divalent metal ions, either Mg2+, or Mn2+
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22
Q

How many subunits is RNA polymerase composed of

A

multiple

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23
Q

core enzyme

A

alpha2betabeta’omega participates in many of the transcription reactions

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24
Q

Beta subunit in RNA polymerase assists in

A

*DNA binding and catalysis

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25
Q

a subunits are scaffolding and interact with

A

other proteins that regulate transcription

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26
Q

omega subunit aids in restoring

A

denatured polymerase

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27
Q

sigma subunit is used for

A

*promoter recognition

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28
Q

RNA polymerazation chain elongation reaction

A

mechanism almost identical to that for DNA polymerase - growing RNA chain is base-paired to DNA template strand

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29
Q

Step one of RNA polymerase reaction is incoming ribonucleotide triphosphates (RTPs) form correct H bond to template and

A

new phosphodiester bond formed and PPi released

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30
Q

in RNA polymerase chain elongation reaction it is catalyzed in the 5’–>3’ direction, is highly processive and thermodynamically assisted by

A

PPi hydrolysis

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31
Q

transcription is initiated at ______ _____ on the DNA template

A

promoter sites

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32
Q

three stages of RNA synthesis are

A

initiation, elongation, and termination

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33
Q

how does RNA polymerase know where to start?

A

specific DNA sequences called promoters

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34
Q

in E. coli 2 DNA sequences that act as promoter for many genes are the -10 sequence and at the -35 sequence these are the

A

TATA or Pribow box

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35
Q

operon

A

transcription unit in which several genes are contranscribed from a single promote in prokaryotes

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36
Q

in ____ not every gene needs a promoter

A

E. coli

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37
Q

a genes start site is said to be _____ of its stop codon

A

upstream

38
Q

convention for double stranded DNA: coding and template strands are written in what direction?

A 
Coding strand (top) is written 5' --> 3' (also called 'sense')
template strand (bottom) is written 3'-->5'
39
Q

gene is transcribed from the

A

5’–>3’ end

40
Q

template strand of DNA is copied from

A

3’ –> 5’

41
Q

transcription complex assembles at a

A

promoter

42
Q

consensus sequences are found

A

upstream from transcription start sites

43
Q

strong promoters

A

match consensus sequence closely

44
Q

weak promoters

A

match consensus sequences poorly

45
Q

DNA-binding proteins bind to promoter sequences and direct RNA pol to the

A

promoter site

46
Q

the sigma subunit of prokaryotic RNA polymerases is required for promoter recognition and formation of the

A

complex

47
Q

what subunit recognizes the promoter

A

sigma subunit

48
Q

sigma subunit ___ the affinity of the core polymerase for specific promoter sequences

A

increases

49
Q

sigma subunit _____ the affinity of the core polymerase for nonpromoter regions

A

decreases

50
Q

**if a core polymerase lacks a sigma factore then it will bind to DNA

A

nonspecifically

51
Q

the sigma factor acts catalytically - one sigma can aid many polymeraes in finding

A

promoters

52
Q

e. coli has many different sigma factors that recongnize different consensus sequences at the

A

promoter

53
Q

RNA polymerase changes

A

conformation

54
Q

RNA polymerase rapidly searches for and bind promoter but initiation is

A

slow

55
Q

unwinding of DNA at the initiation site requires a conformational change with is often the

A

rate limiting step

56
Q

RNA pol (R) and promoter (P) shift from

A

closed complex (DNA ds) to open complex (18 bp DNA unwound - forms transcription bubble)

57
Q

RNA polymerase lacks a

A

helicase

58
Q

RNA polymerase can start RNA synthesis de novo which means

A

no primer needed

59
Q

transcription bubble is the

A

region containing RNA polymerase, DNA, and RNA product

60
Q

steps of initiation of transcription in E. coli

A
    1. RNA polymerase binds non-specifically to DNA
      1. holoenzyme conducts a 1-D search for promoter
      2. holoenzyme and promoter form a closed complex
      3. conformational change to open complex - transcription bubble form, short stretch of RNA made
      4. sigma subunit dissociates from core, other accessory proteins (NusA) bind to polymerase - promoter clearance, shift to elongation stage
61
Q

transcription termination

A

only certain regions of DNA are transcribed; transcription compexes assemble a promoters and disassemble at the 3’ end of genes at specific termination sequences

62
Q

two types of termination sequences

A
  1. unstable elongation complex

2. rho-dependent termination

63
Q

regions of the gene where the rate of elongation slows down or stops temporarily

A

pause sites

64
Q

pause is exaggerated when newly transcribed RNA can form what type of structure

A

hairpin

65
Q

hairpin may ________ RNA-DNA hybrid in elongation complex

A

destabilize

66
Q

Rho-dependant termination sites; rho triggers disassembly of the transcription complex at some pause sites by

A

binding RNA and destabilizing RNA-DNA hybrid

67
Q

Rho binds to ssRNA chain, destabilizing the RNA-DNA hybrid and

A

terminating transcription

68
Q

precursors of tRNA and rRNA are cleaved and chemically modified after

A

transcription

69
Q

the final mature RNA is cleaved from a larger

A

precursor

70
Q

many tRNA transcripts lack CCA sequence at the 3’ end of the strand, these nucleotides are added

A

post- transcriptionally

71
Q

the bases and riboses of tRNA and rRNA are modified for instance by the attachment of

A

methyl groups

72
Q

some antibiotics inhibit

A

bacterial transcription

73
Q

rifampicin inhibits initiation by binding to the polymerase and blocking the exit of the

A

nascent RNA

74
Q

actinomycin intercalates between the bases of the DNA double helix, preventing the DNA from

A

being used as a template

75
Q

example of an operon

A

lactose operon

76
Q

some mRNAs directly sense and respond to

A

metabolites

77
Q

riboswitches

A

bind small molecules that cause as structural change in the riboswitch that terminates the synthesis of the mRNA

78
Q

transcription and translation occur at the same time in prokaryotes which ______ in eukaryotes

A

can not happen

79
Q

gene expression in eukaryotes is influences by 3 important characteristics

A
  1. complex transcription regulation
  2. RNA processing, including extensive processing of mRNA precursors
  3. the nuclear membrane that separates the site of RNA synthesis from that of protein synthesis
80
Q

RNA synthesis is catalyzed by 3 RNA polymerases that differ in

A

DNA substrate specificity and location

81
Q

in eukaryotes, each type of polymerase has a distinct

A

promoter element

82
Q

in eukaryotes, the promoters bind to proteins, called trans-acting elements or transcription factors, that

A

regulate polymerase activity

83
Q

RNA pol 2 requires

A

complex regulation

84
Q

most genes transcribed by RNA pol 2have an A/T rich sequence called

A

TATA box

85
Q

TATA box is located

A

-24 to -32

86
Q

initiator element (Inr) is at the transcriptional

A

start site

87
Q

The TFIID complex initiates assembly of the

A

active transcription complex

88
Q

transcription factors for RNA polymerase 2 =

A

TFII

89
Q

in genes with a TATA box, the _____, a component of TFIID, binds to the TATA bos

A

TATA box binding protein (TBP)* key player

90
Q

TFIIH binds to the complex and phosphorylates the carboxyl-terminal domain (CTD) of the polymerase, facilitating the transition from

A

initiation phase to the elongation phase.

91
Q

multiple transcription factors interact with eukaryotic promoters and

A

enhancers

92
Q

a large complex called ______ acts as a bridge between enhancer-bound activators and proteins, including the polymerase, at the promoter

A

mediator

Biochemistry (6 decks)

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