RNA Flashcards
Bacterial RNA pol: contains the catalytic site
beta subunit
Bacterial RNA pol: Recognizes promoters; required for the initiation of transcription
sigma subunit
Proks: Initiates transcription
Holoenzyme (a2BB’sigma)
Proks: Carries out transcription
Core enzyme (a2BB’)
What is also needed for RNA pol.-catalyzed reactions?
Divalent cation
Promoters in bacterial genes usually include ~ __ bp upstream of the initiation site and are ___ rich
45 bps, A-T rich
Proks: Specific sequence elements in typical promoters (bp location)
-35 Region; Pribnow (-10)
What is a closed promoter complex?
When the sigma subunit binds to the core enzyme at a promoter site, however, a conformational change occurs and binding is stabilized
What is an open promoter complex
When the two strands of DNA template unwind to produce an unpaired region containing approx. 12 bases.
Supercoiling ahead of the transcription bubble
Positive
Supercoiling behind the transcription bubble
Negative
When does sigma subunit leave the transcription complex?
After about 9 bases are added
Proks: Termination
rho independent or rho dependent
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?
Rho independent termination; proks
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?
Rho dependent termination; proks
Re: rho protein
Rifampicin
- Target
- Function
- What is affected?
- What is not affected?
- What cells are vulnerable?
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
Actinomycin D
- Target
- Function
- What is affected?
- What is not affected?
- What cells are vulnerable?
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
Euks: what must occur before transcription can occur? Why?
two strands must be unwound; makes promoter region available for appropriate factors to bind
Euks: transcribes the precursor large rRNAs (28S, 18S, 5.8S)
What is its location?
RNA Pol I; nucleolous
Euks: transcribes the precursor mRNAs (hnRNAs), snRNA, miRNA
What is its location?
RNA Pol II, nucleus
Euks: transcribes the precursors of small RNAs (tRNAs, 5s rRNAs)
What is its location?
RNA Pol III, nucleus
Euks: promoter regions
CAAT box, GC box, TATA box, Inr (initiator element, pyrimidine rich)
Promoter elements that dictate the site of transcription initiation
Basal elements
Basal element which directs the binding of RNA pol II
TATA box
Binds the TATA box, leading to the assembly of the remaining TFII protein factors
TATA binding protein (TBP)
Promoter elements that dictate the rate of transcription initiation
Constitutive elements
Constitutive elements (2)
CAAT box and GC box
Promoter elements that dictate the specificity of transcription initiation. Mediate transcription in response to environmental signals
Inducible elements
Not part of the promoter. regulate transcription by binding regulatory proteins which can either activate or repress transcription
Enhancers
Formation of the Pol II pre-initiation complex is followed by: (4)
DNA melting, initiation, promoter clearance, and transcription elongation.
During initiation, RNA pol II does not bind DNA directly but binds to:
proteins (first TBP then TFs then RNA poly) which are bound to DNA
Euks: Necessary but not sufficient for effective transcription initiation
Basal apparatus
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
constitutive and inducible promoter elements; activator proteins
Alpha-amanitin
- Target
- Function
- What is affected?
- What is not affected?
- What cells are vulnerable?
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
Euks: Termination
AAUAAA polyadenylation sequence
