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Biochem FINAL > Chapter 36: RNA Synthesis and Chapter 37: Regulation in Prokaryotes > Flashcards

Chapter 36: RNA Synthesis and Chapter 37: Regulation in Prokaryotes Flashcards

1
Q

3 similarities between transcription and replication

A
  • Both use DNA as template
  • Phosphodiester bonds formed in both cases
  • Both synthesis directions are from 5’ to 3’
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2
Q

Replication and Transcription: # of strands?

A

Replication: Double strands
Transcription: Single strand

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3
Q

Replication and Transcription: Substrate?

A

Replication: dNTP
Transcription: NTP

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4
Q

Replication and Transcription: Primer?

A

Replication: Yes
Transcription: No

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5
Q

Replication and Transcription: Enzyme?

A

Replication: DNA Polymerase
Transcription: RNA Polymerase

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6
Q

Replication and Transcription: Product?

A

Replication: dsDNA
Transcription: ssRNA

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7
Q

Replication and Transcription: Base pair?

A

Replication: A-T, G-C
Transcription: A-U, T-A, G-C

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8
Q

Genes encoding for enzymes of metabolic pathways are grouped in clusters on the chromosome - called _____.

A

Operons

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9
Q

Operons allow…

A

Coordinated regulation and gene expression

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10
Q

A regulatory sequence adjacent to an operon determines whether it is transcribed is called _____.

A

‘Operator’

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11
Q

Regulatory proteins interact with operators to control _____.

A

Transcription of the genes

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12
Q

What does RNA polymerase need to carry out transcription?

A
  1. DNA template
  2. Activated precursors in the form of the 4 nucleotides (ATP, GTP, UTP, CTP)
  3. Divalent metal ions- Mg2+ or Mn2+
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13
Q

What enzyme carries out transcription?

A

RNA polymerase

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14
Q

What is the difference between polycistronic and monocistronic operons?

A

Polycistronic can make/transcribe several genes because it has multiple genes controlled by 1 operon.
Monocistronic can only make 1 gene (operon only controls 1 gene).

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15
Q

What are the two strands of DNA called and what is the difference between them?

A

Coding strand and template strand:

  • Coding strand looks like the mRNA
  • Template strand used to make mRNA (complementary to mRNA)
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16
Q

How do nucleotides get added to the growing nucleotide chain? (direction and what attacks)

A
  • Grows in the 5’ to 3’ direction.

- 3’ OH of the growing chain attacks the inner most phosphoryl group of the incoming nucleotide.

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17
Q

In prokaryotes, ___ RNA polymerase synthesizes the 3 major classes of RNA: ______, _______, ______.

A 
In prokaryotes, 1 RNA polymerase synthesizes the 3 major classes of RNA: 
messenger RNA (mRNA)
ribosomal RNA (rRNA)
transfer RNA (tRNA).
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18
Q

What is the structure of RNA polymerase?

A

Multisubunit protein= 1 omega, 2 beta, 2 alpha, 2 beta’, 1 sigma
*everything but sigma is core enzyme, adding sigma makes holoenzyme

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19
Q

What are the functions of the subunits of RNA polymerase: alpha?

A

Assembly, activation of enzyme by regulatory proteins

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20
Q

What are the functions of the subunits of RNA polymerase: beta?

A

Binds NTPs, interacts w/ sigma, forms catalytic site with beta’

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21
Q

What are the functions of the subunits of RNA polymerase: beta’?

A

Binds nonspecifically to DNA, forms catalytic site with beta

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22
Q

What are the functions of the subunits of RNA polymerase: sigma?

A

Recognizes promoter in DNA, decreases affinity for nonpromoter regions

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23
Q

What directs RNA to proper initiation site?

A

Promoters - specific DNA sequences

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24
Q

What are the 2 DNA sequences that act as a promoter in E. coli?

A
  1. -10 sequence (Pribnow sequence)

2. -35 sequence

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25
Q

What is the difference between strong and weak promoters?

A
  • Strong promoters - closely match the consensus sequence
  • Weak promoters - have multiple substitutions at consensus sequences
  • *other sequences upstream of promoter and action of transcription factors can enhance promoter effectiveness
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26
Q

The 3 phases of transcription of prokaryotes are:

A
  1. initiation- RNA-pol. recognizes promoter and starts transcription
  2. elongation- RNA strand is continuously growing
  3. termination- RNA-pol. stops synthesis and RNA is separated from DNA template
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27
Q

First step in initiation:

A

RNA-pol recognizes -35 sequence, slides to -10 region, then opens DNA duplex.

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28
Q

How long is the unwound region during initiation?

A

About 17 +/- 1 base pair

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29
Q

What has to happen to unwind the DNA during initiation?

A
  • RNA polymerase searches for/binds promoter.
  • RNA pol. and promoter undergo conformational change from closed complex (DNA double stranded) to open complex (unwound)
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30
Q

What is the rate-limiting step of initiation/transcription?

A

Conformational change allowing DNA unwinding

31
Q

After DNA is unwound, __________ can take place.

A

Elongation can take place

32
Q

The first nucleotide on the RNA transcript is always a __________.

A

Purine triphosphate

*GTP more often than ATP

33
Q

Does RNA polymerase need a primer to start RNA synthesis?

A

No, can start de novo.

34
Q

What begins the process of elongation?

A

The release of the sigma subunit.

35
Q

Why does releasing the sigma subunit allow elongation to start?

A

Release causes a conformational change of core enzyme, so it can slide on DNA template toward 3’ end.

36
Q

What is the transcription bubble?

A

Region containing RNA polymerase, DNA, and RNA product (40ntds).
*transcription bubble moves along DNA as DNA is unwound/rewound; RNA product extrudes from complex.

37
Q

What is an intermediate in RNA synthesis?

A

A DNA-RNA hybrid helix of approximately 8 nucleotides.

38
Q

What happens during termination?

A

RNA-pol. stops moving on DNA template.

RNA transcript falls off from transcription complex.

39
Q

Termination occurs in either _______ or ________ manner.

A

Either rho-dependent or rho-independent manner.

*Both types involve signals on newly synthesized RNA

40
Q

How is termination triggered at rho-dependent termination sites?

A

Rho binds to ssRNA chain, destabilizing RNA-DNA hybrid and terminating transcription.
*has helicase activity and uses ATP

41
Q

How does termination occur in rho-independent termination?

A

The termination signal on the RNA transcript forms stem-loop structures that causes polymerase to pause after the hairpin, terminating the transcription.

42
Q

What is the termination signal?

A

A stretch of 30-40 nucleotides on the RNA transcript.

Made of many GCs followed by series of U.

43
Q

What are the weakest hydrogen bonding basepairs?

A

rU-dA

44
Q

What are 2 antibiotics that inhibit prokaryotic transcription?

A
  1. Rifamycin

2. Actinomycin

45
Q

When genes are organized into operons, _____ can be transcribed from the same ______ and at the same time.

A

Multiple genes can be transcribed from the Same promoter

46
Q

What is transcription controlled by?

A

The binding of regulatory factors.

Regulatory proteins help in activating or repressing gene transcription.

47
Q

What is the benefit of organizing the genome into operons?

A

More efficient

48
Q

What are the 2 types of transcription factors?

A
  1. repressors

2. activators

49
Q

What are repressor transcription factors?

A

DNA binding proteins that decrease the efficiency of transcription at the promoter

50
Q

What are activator transcription factors?

A

DNA binding proteins that increase the efficiency of transcription at the promoter

51
Q

What is an example of an inducible operon?

A

Lac operon - genes code for enzymes that break down lactose

52
Q

What does it mean to be an inducible operon?

A

Operon is usually off but an be stimulated/activated.

53
Q

When is transcription on and off in the lac operon?

A

Off in the absence of digestable lactose

On when there’s lactose that needs to be digested

54
Q

What happens when the lac operon is off?

A
  1. lacI (repressor) transcribed making active repressor.
  2. Repressor binds to operator, blocks polymerase.
  3. No transcription.
55
Q

How does the lac operon get turned on?

A
  1. Lactose binds lacI repressor, inhibiting its binding to operator.
  2. Polymerase can bind, so genes needed to digest lactose are transcribed.
56
Q

When is lactose used?

A

Only used when glucose is low.

57
Q

What happens when glucose is low?

A

Levels of cAMP build up.

58
Q

What does cAMP bind to?

A

CAP - regulatory protein that is only active when cAMP binds to it.

59
Q

What happens after CAP and cAMP bind?

A

CAP binds to promoter and stimulates RNA Polymerase to bind - speeds up transcription.

60
Q

What happens when glucose levels rise?

A

cAMP levels drop so no longer binds to CAP.

CAP can’t bind to promoter so transcription slows down.

61
Q

How is the lac operon regulated?

A

Positive gene regulation (2 levels):

  1. presence of lactose determines if transcription can occur
  2. CAP in active form determines how fast transcription occurs.
    * * See table in notes for summary
62
Q

What is an example of a repressible operon?

A

(Controlled by negative gene regulation)

Trp operon - ON most of the time

63
Q

How does negative gene regulation occur?

A

TrpR gene (repressor gene) ON all the time- produces inactive repressor protein

64
Q

During elongation, free NTPs added sequentially to _____ RNA strand.

A

3’OH of nascent

65
Q

When Trp present it binds to repressor, repressor becomes active and can…

A

Block transcription

66
Q

Inhibits prokaryotic transcription: Actinomycin is an antibiotic that..

A

intercalates btw bases of the DNA, preventing DNA from being used as a template

67
Q

Inhibits prokaryotic transcription: Rifamycin is an antibiotic that…

A

binds pol. preventing RNA from exiting.

68
Q

RNA polymerase requires which of the following for initiation: a DNA primer, an RNA primer, supercoiled DNA or nicked DNA

A

None of the listed

69
Q

In transcription, the 3’-hydroxyl group:

  • attacks the α-phosphorous group on an incoming nucleotide
  • binds to a Mg2+ in the active site
  • binds to the 5’ ribose
  • attacks the 5’ hydrogen of the incoming nucleotide
  • is not involved in any reaction
A

Attacks the α-phosphorous group on an incoming nucleotide

70
Q 
If the consensus for σ70 is TATAAT, which sequence would correspond to the strongest promoter?
A.  TATGGA
B.  TTTAAT
C.  AATGAA
D.  CAAGAG
E.  TCCGGA
A

TTTAAT because it most closely matches (strong promoter)

71
Q 
The eukaryotic enzyme that synthesizes mRNA is:
A.  RNA polymerase I
B.  RNA polymerase II
C.  RNA polymerase III
D.  reverse transcriptase
E.  RNA polymerase α
A

RNA pol II

72
Q

Under which conditions would the lac repressor, but NOT the cAMP activator protein, be bound to the lac operon?
A. high glucose, no or low β-galactosides
B. high glucose, high β-galactosides
C. no or low glucose, no or low β-galactosides
D. no or low glucose, high β-galactosides
E. this would never happen

A

High glucose, no or low β-galactosides

73
Q 
A common selective estrogen receptor modulator used in breast cancer therapy is:
	A.  tamoxifen
	B.  α−amanitin
	C.  streptomycin
	D.  chymostatin
	E.  regulafen
A

Tamoxifen

74
Q

Signals for termination of transcription are present on the:
A. DNA downstream of the termination site
B. DNA near the promoter region
C. newly synthesized RNA that is still hybridized to DNA
D. newly synthesized RNA that is no longer in the transcription bubble
E. protein being synthesized

A

Newly synthesized RNA that is no longer in the transcription bubble

Biochem FINAL (6 decks)

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