RNA

Question 1

Bacterial RNA pol: contains the catalytic site

Answer 1

beta subunit

Question 2

Bacterial RNA pol: Recognizes promoters; required for the initiation of transcription

Answer 2

sigma subunit

Question 3

Proks: Initiates transcription

Answer 3

Holoenzyme (a2BB’sigma)

Question 4

Proks: Carries out transcription

Answer 4

Core enzyme (a2BB’)

Question 5

What is also needed for RNA pol.-catalyzed reactions?

Answer 5

Divalent cation

Question 6

Promoters in bacterial genes usually include ~ __ bp upstream of the initiation site and are ___ rich

Answer 6

45 bps, A-T rich

Question 7

Proks: Specific sequence elements in typical promoters (bp location)

Answer 7

-35 Region; Pribnow (-10)

Question 8

What is a closed promoter complex?

Answer 8

When the sigma subunit binds to the core enzyme at a promoter site, however, a conformational change occurs and binding is stabilized

Question 9

What is an open promoter complex

Answer 9

When the two strands of DNA template unwind to produce an unpaired region containing approx. 12 bases.

Question 10

Supercoiling ahead of the transcription bubble

Answer 10

Positive

Question 11

Supercoiling behind the transcription bubble

Answer 11

Negative

Question 12

When does sigma subunit leave the transcription complex?

Answer 12

After about 9 bases are added

Question 13

Proks: Termination

Answer 13

rho independent or rho dependent

Question 14

Termination: DNA templates from which transcription terminates by this mechanism contain an inverted repeat (i.e. 2 palindromic) G-C rich regions followed by 8-10 A’s on the template strand (T’s on coding). Gives rise to a stem loop structure in the RNA transcript ending in a series of U’s.

What type of cells does this occur in?

Answer 14

Rho independent termination; proks

Question 15

Termination: a large hexameric protein binds the 5’ end of the new RNA transcript. Protein moves along the RNA strand toward the 3’ end using ATP. Polymerase concurrently slows down at a C-rich, G-poor sequence on the DNA template approx. 100 bases from the site of transcription termination. protein catches up to polymerase and uses its helicase function to unwind the RNA transcript from the DNA template strand.

What type of cells does this occur in?

Answer 15

Rho dependent termination; proks

Re: rho protein

Question 16

Rifampicin

• Target
• Function
• What is affected?
• What is not affected?
• What cells are vulnerable?

Answer 16

Target: Beta subunit of bacterial RNA pol
Function: prevents the formation of the first phosphodiester bond
-Affects: Initiation of prok. transcription
-Unaffected: Ongoing transcription
-Vulnerable: Proks

Question 17

Actinomycin D

• Target
• Function
• What is affected?
• What is not affected?
• What cells are vulnerable?

Answer 17

Target: intercalates between DNA strands (major groove)
Function: prevents unwinding of DNA template strands
Affects: initiation of transcription and ongoing transcription
Unaffected: n/a
Vulnerable: proks and euks

Question 18

Euks: what must occur before transcription can occur? Why?

Answer 18

two strands must be unwound; makes promoter region available for appropriate factors to bind

Question 19

Euks: transcribes the precursor large rRNAs (28S, 18S, 5.8S)

What is its location?

Answer 19

RNA Pol I; nucleolous

Question 20

Euks: transcribes the precursor mRNAs (hnRNAs), snRNA, miRNA

What is its location?

Answer 20

RNA Pol II, nucleus

Question 21

Euks: transcribes the precursors of small RNAs (tRNAs, 5s rRNAs)

What is its location?

Answer 21

RNA Pol III, nucleus

Question 22

Euks: promoter regions

Answer 22

CAAT box, GC box, TATA box, Inr (initiator element, pyrimidine rich)

Question 23

Promoter elements that dictate the site of transcription initiation

Answer 23

Basal elements

Question 24

Basal element which directs the binding of RNA pol II

Answer 24

TATA box

Question 25

Binds the TATA box, leading to the assembly of the remaining TFII protein factors

Answer 25

TATA binding protein (TBP)

Question 26

Promoter elements that dictate the rate of transcription initiation

Answer 26

Constitutive elements

Question 27

Constitutive elements (2)

Answer 27

CAAT box and GC box

Question 28

Promoter elements that dictate the specificity of transcription initiation. Mediate transcription in response to environmental signals

Answer 28

Inducible elements

Question 29

Not part of the promoter. regulate transcription by binding regulatory proteins which can either activate or repress transcription

Answer 29

Enhancers

Question 30

Formation of the Pol II pre-initiation complex is followed by: (4)

Answer 30

DNA melting, initiation, promoter clearance, and transcription elongation.

Question 31

During initiation, RNA pol II does not bind DNA directly but binds to:

Answer 31

proteins (first TBP then TFs then RNA poly) which are bound to DNA

Question 32

Euks: Necessary but not sufficient for effective transcription initiation

Answer 32

Basal apparatus

Question 33

Binding of the pol. is stabilized by a conromational change in the DNA caused by the binding of regulatory proteins to ___________(2) as well as ___________ (protein type) bound to enhancers

Answer 33

constitutive and inducible promoter elements; activator proteins

Question 34

Alpha-amanitin

• Target
• Function
• What is affected?
• What is not affected?
• What cells are vulnerable?

Answer 34

Target: RNA pol II (lesser extent for RNA pol III)
Function: inactivates RNA pol II
Affected: mRNA synthesis inhibited, liver failure and death (48 hours) - essential enzymes degraded and not replaced
Not affected: RNA pol I
Vulnerable: euks

Question 35

Euks: Termination

Answer 35

AAUAAA polyadenylation sequence