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BIOLCHEM 415 > Transcription > Flashcards

Transcription Flashcards

1
Q

central dogma

A

DNA is transcribed into RNA which is translated into proteins

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2
Q

gene

A

sequence of DNA or RNA that codes for a molecule that has a function

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3
Q

exon

A

actual protein coding region

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4
Q

intron

A

DNA sequence that is removed during RNA processing

only occurs in eukaryotes

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5
Q

5’-UTR and 3’-UTR

A

translation control

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6
Q

regions that are transcribed

A

exon
intron
5’-UTR
3-UTR

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7
Q

regions that are not transcribed

A 
promoter 
terminator 
enhancer 
silencer 
etc...
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8
Q

promoter

A

special DNA sequences that direct RNA Pol to the initiation site
bound by RNA polymerase for starting transcription

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9
Q

terminator

A

transcription termination

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10
Q

enhancer and silencer

A

regulate gene expression

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11
Q

how many base pairs make up the human genome?

A

over 3 billion

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12
Q

coding DNA

A

sequences that can be transcribed into RNA and translated into proteins
makes up ~2% of total DNA

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13
Q

non-coding DNA

A 
non-coding functional RNA 
cis- and trans-regulatory DNA sequences 
introns
pseudogenes
telomeres
centromeres
other repetitive sequences....
makes up ~98% of total DNA
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14
Q

non-coding functional RNA

A

many are critical elements in gene expression

types: ribosomal RNA (rRNA), transfer RNA (tRNA), microRNA, snRNA, long non-coding RNA, etc.

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15
Q

cis- and trans-regulatory DNA sequences examples

A

promoters, enhancers, silencers, 5’-UTR, 3’-UTR

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16
Q

pseudogenes

A

inactive copies of protein-coding genes

are often generated by gene duplication

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17
Q

RNA polymerase

A

enzyme responsible for transcription
requires NTP and Mg2+
synthesis is 5’ to 3’
either DNA strand can be used as a template for transcription
does NOT require a primer
is NOT evolutionarily related to DNA polymerase
lacks 3’ to 5’ exonuclease activity

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18
Q

coding strand

A

DNA strand that has the same sequence as the RNA product (except T instead of U)

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19
Q

template strand

A

DNA strand that has a different sequence than the RNA product

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20
Q

how many subunits does bacterial RNA polymerase have?

A

5 (α, β, β’, ω, σ^70)

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21
Q

holoenzyme

A

made up of subunits: α (2), β, β’, ω, σ^70

is required for initiating RNA synthesis

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22
Q

core enzyme

A

made up of subunits: α (2), β, β’, ω

carries out the actual RNA polymerase activity

23
Q

α subunit function

A

assembles core enzyme
interacts with regulatory factors
the C-terminal domain makes sequence-specific interactions at the UP element
contains determinants for interactions with regulatory factors

24
Q

β subunit function

A

takes part in all stages of catalysis

25
Q

β’ subunit function

A

binds to DNA — takes part in catalysis

26
Q

ω subunit function

A

is required to restore denatured RNA polymerase into its native form

27
Q

σ^70 subunit

A

takes part in promoter recognition (position RNA Pol for correct initiation)
decreases RNA Pol’s affinity for general DNA regions, which allows it to look for the promoter
makes sequence-specific contacts with the -10 and -35 regions
more than 1 is present in E. Coli
different ones recognize different promoters

28
Q

stages of bacterial transcription cycle

A

initiation
elongation
termination

29
Q

initiation

A

RNA Pol holoenzyme forms and locates a promoter – the polymerase unwinds the DNA at the place where transcription begins – transcription starts

30
Q

elongation

A

once RNA polymerase has synthesized ~ 10 RNA nucleotides, the σ^70 releases and the polymerase shifts into elongation mode
rate is approx. 50 nucleotides/second

31
Q

termination

A

when the polymerase encounters a termination signal, it leaves the DNA template and releases the RNA

32
Q

upstream promoter element (UP)

A

40-60 nucleotides upstream of the transcription start site

is A/T rich

33
Q

factors that affect the strength of a promoter

A

deviation from the consensus sequences
the distance between consensus sequences (17 bp is optimal)
transcription factors

34
Q

transcription bubble

A

is formed when the DNA duplex is unwound over a short distance (normally ~17 bps)

35
Q

backtracking

A

RNA Pol moves backwards when it becomes arrested
is a proofreading mechanism
strongly depends upon the stability of the RNA/DNA hybrid in the transcription bubble and the nature of the 3’-terminal residue (weaker hybrid = higher chance of arresting and backtracking)

36
Q

intrinsic termination

A

the termination lies within the RNA transcript itself

37
Q

intrinsic termination signal

A

the RNA product has a G/C rich palindromic sequence (which forms a hairpin), followed by several uracil residues
after the hairpin is formed: RNA Pol stalls, the RNA product is released, and the DNA double helix forms

38
Q

Rho-dependent termination

A

termination depends upon the Rho protein
requires:
naked, unstructured DNA, no coupled translation, and slowed or paused transcription

39
Q

Rho

A

hexameric helicase that specifically binds a stretch of 72 nucleotides on single stranded RNA (which is C-rich)
upon contact with the transcription bubble, it dissociates

40
Q

negative regulation

A

involves repressors

41
Q

ways negative regulation occurs

A

1) a repressor binds to the operator in the absence of a molecular signal – the external signal causes dissociation of the repressor to permit transcription
2) a repressor binds to the operator in the presence of a molecular signal – when the signal is removed, the repressor dissociates – transcription continues

42
Q

positive regulation

A

involves activators

43
Q

ways positive regulation occurs

A

1) an activator binds to the operator in the absence of a molecular signal – transcription proceeds; a signal is added – activator dissociates, transcription is inhibited
2) an activator binds to the operator in the presence of a molecular signal, it only dissociates when the signal is removed

44
Q

operon

A

a cluster of related genes that share a promoter and regulatory sequences
the genes are transcribed together, so that one mRNA can encode several different proteins
is a common way that prokaryotic genes are organized
1st example: lac operon

45
Q

lac operon

A

contains 3 genes for lactose metabolism: β-galactosidase (lacZ), lactose permease (lacY), and thiogalactoside transacetylase (lacA)
its expression is controlled by the lac repressor and glucose availability

46
Q

β-galactosidase (lacZ)

A

cleaves lactose to from glucose and galactose

47
Q

lactose permease (lacY)

A

transports lactose into the cell

48
Q

thiogalactoside transacetylase (lacA)

A

transfers an acetyl group from acetyl-CoA to β-galactosidase (lacZ)

49
Q

lac repressor

A

binds operators O1-O3 (primarily to operator O1), preventing RNA Pol from binding to the promoter
even with it present, transcription STILL OCCURS at a basal rate
dissociates from the operator when allolactose binds to it
has its own promoter
its transcription is independent of the transcription of the enzymes it regulates
is encoded by the gene lacI

50
Q

requirements for the strongest induction of the lac operon

A

low [glucose]
high [cAMP]
lactose is present

51
Q

trp operon

A

1st biosynthetic operon discovered
has 5 structural genes that encode enzymes for tryptophan synthesis
is regulated by repression and attenuation

52
Q

trp repressor

A

binds to DNA in the presence of tryptophan
high [tryptophan] – tryptophan binds to the repressor – repressor associates with the operator – gene expression for tryptophan synthesis is slowed

53
Q

attenuation

A

allows for a second level of regulation
responds to the concentration of charged tRNA^trp
is possible because in prokaryotes, transcription and translation occur simultaneously

54
Q

riboswitch

A

regulatory segment of mRNA that binds to a small molecule, resulting in a change in the production of proteins encoded by the mRNA
most known ones occur in prokaryotes
can regulate gene expression at many different levels

BIOLCHEM 415 (10 decks)

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