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BIOCHEMISTRY > EXAM2_L16_Transcription_makingRNA > Flashcards

EXAM2_L16_Transcription_makingRNA Flashcards

1
Q

4 similarities between transcription and replication

A
  1. req ssDNA template
  2. enzymes make nucleic acid chains w/ phosphodiester bonds
  3. 5’–>3’ elongation using the 3’ OH groups
  4. New strand made complimentary to template DNA strand
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2
Q

7 differences of replication vs transcription

A
  1. Uracil used instead of Thymine
  2. Transcription only occurs specific times/places in genome
  3. RNA product is displaced from the template
  4. only one DNA strand used as a template
  5. one to several thousand copies are made
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3
Q

4 classes of RNA’s

A

tRNA- transfers AA’s to ribosomes for protein synth.
mRNA- blueprint/code for building proteins
rRNA- ribosomes (links AA’s (peptidyl transferase active)
snRNA- euk’s only- used for mRNA splicing/processing

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4
Q

How many strands are used in TRANSCRIPTION?

What is the template strand?

Directionality of reading and writing the code?

What is a result of this directionality?

A

Template strand is the DNA strand that the code is read and copied from. The ribosome Prints the complementary sequence to the strand that it is reading from.

Reads 3’->5’
Writes 5’->3’

Thus the RNA has same sequence as the non-template strand (this is why the non-template strand is called “the coding strand”) because the new strand is an exact copy of the NEW RNA *****except for T’s are now U’s

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5
Q

What does +1 mean?
AUG?
UTR?

A

+1 = TRANSCRIPTION start site

AUG= TRANSLATION start site

UTR= un-translated region

Note: +1 is NOT same as 1st codon (ATG, methionine)

only copies a small portion of genome***

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6
Q

3 PROKARYOTIC TRANSCRIPTION events

A
  1. Initiation (bind RNApol, promotor melt, initial transcription)
  2. Elongation (RNApol changes, start transcription, unwind, elongation, reanneal)
  3. Termination (terminators, stop & release RNA)
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7
Q

PROKARYOTIC RNA Polymerase:

how many types? how many subunits? What are they?

What helps RNApol bind to DNA? Where?

When is RNApol activated?

A 
One RNApol w/ 6 subunits- holoenzyme
1. 2 alpha   (core)
2. 1 beta     (core)
3. 1 beta'    (core)
4. 1 omega (core)
5. 1 sigma (sigma subunit)
Sigma facilitates RNApol binding to DNA at -35 and -10 promotor elements

*RNApol Activated after sigma subunit dissociates

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8
Q

PROKARYOTIC TRANSCRIPTION:
What are the two important DNA sequences of the Promoter?
What are they made of?
Where are they located?
Which one is AT rich segment?
How far apart are they from each other?
What does this mean about the promotor sequence of prokaryotes? term?

A

“-10” and “-35” elements -> (6 nucleotides each)

  • located upstream of “+1” actual start site
  • 10 is AT rich segment
  • about 20 bp apart and about 7bp from +1

-This means that the PROMOTER sequence is the same for all prokaryotes so that RNApol can recognize and bind to it even though the messages are different.

Called a CONSENSUS SEQUENCE

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9
Q

4 steps of Prokaryotic transcription

A
  • INITIATION
    1. RNApol binds at -10 and -15 of DNA via SIGMA subunit
    2. RNApol separates dsDNA w/o helicase
    3. SIGMA unit released from RNApol
    • ELONGATION
      4. RNApol elongation (WITHOUT PRIMER)
      RNA code product is displaced from template via “termination signal”
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10
Q

2 types of termination in Prokaryotic transcription?

A

–rho-independent- palindrome/hairpin/derail
(AAAA on DNA and UUUU on RNA- Hairpin de-rails)

–Rho-Dependent- Rho protein & stem loop
Rho: (atp-dependent helicase activity)

-Rho binds to rho recognition site and finds paused RNApol at termination site & releases RNA transcript

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11
Q

Antibiotic inhibiting bacterial cell growth by inhibiting RNA synthesis.
What called?
What does it treat?
How?

A
  • Rifampicin (TuBerculosis-aka: Dactinomycin)

- Binds Beta subunit of RNApol (prokaryotic only)

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12
Q

4 EUKARYOTIC TRANSCRIPTION EVENTS:

A
  1. Init- bind TF’s & RNApol to PROMOTER site
  2. Elong- unwind/synth RNA transcript
  3. Term- Release
  4. Processing- 5’ cap, 3’ poly-A tail, Splicing
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13
Q

EUKARYOTIC RNA Polymerase:
How many? What types? What function of each?
What needed for initiation?

A

3 RNApol’s
RNApol1- transcribes 3 major rRNA’s
RNApol2- transcribes mRNA
RNApol3- transcribes tRNA & small rRNA

GTF’s (general transcription factors) needed to begin transcription

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14
Q 
PIC 
What is it?
How many Parts?
What parts and what do they do?
Where do they bind?
A

Pre-Initiation Complex (6 Parts)
1. TFIID (binds AT rich promoter-TATAbox)

-(has TBP “tata binding protein” acts like bacterial SIGMA subunit to find and bind to tata box)

  1. TFIIA- assist TFIID binding
  2. TFIIB- Orients polymerase
  3. RNApol II- bind GTF’s at promoter (carboxy held by GTFs)
  4. TFIIE- support RNApol II
  5. TFIIH- is recruited
  6. TFIIH- multisubunit- Helicase and Kinase activity
    (phosphorylates c terminal domain (CTD) of RNApol II
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15
Q

What TF’s does RNApol II require?

Which one is multisubunit? What are the two activities?

A

TFII -A,B,D,E,H

–TFIIH- multi-subunit:
-Helicase- atpase unwinds dna at initiation site
-Kinase- Phosphorylates C-terminal domain (CTD) of
RNApol II

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16
Q

What is the beginning elongation step for RNApol II in Eukaryotic transcription?

A

TFIIH phosphorylates the C-terminal Domain (CTD) of RNA pol II
-RNApol II releases GTF and STARTS Transcription

17
Q

What are the 3 post transcriptional processing events?

What is added and what are 2 functions?

Where does cut/addition take place?

What used for addition?

What 2 functions of tail?

A

For Stability:

  1. 5’ CAP addition (ADDs 7-methylguanosine at beginning)
    - protects from degrading nucleases
    - Attachment role later onto ribosome
  2. Splicing
  3. 3’ polyadenylation tail
    - Cut 10-35 nucleotides downstream from “AAUAAA”
    - Enzyme “poly(A) Polymerase” adds ~200 nucleotides (each time) to 3’ end produced by the cleavage to make poly A tail.
  • Stability of mRNA
  • Signal for export into cytoplasm
18
Q

RNA Splicing 5 steps:

what protein used?

A
  1. 5’ cut
  2. intron folds into lariat at branch point
  3. 3’ cut
  4. exons connected
  5. lariat degraded by nucleases
    (spliceosomes cut and connect) snRNA also
19
Q

Alternative splicing:

A

pre-mRNA’s contain multiple introns SO…
different mRNA’s can be produced from the same gene by different combining of 5’ and 3’ splicing

  • Fewer genes, Greater coding capacity, Less energy used
20
Q

prokaryotes and eukaryotes :

- What determines which DNA strand becomes the template? or which gene transcribed? or what direction?

A
  • Gene promoters located on both strands

- direction determined by promoter at the beginning of each gene and RNApol recognition of that promoter

21
Q

What is Eukaryotic RNA processing and Start Sequence?

A

5’ y-methguanosine cap, Splicing, 3’polyA tail

-10 TATA box

22
Q

What RNA polymerase for Prokaryotic?

A

Core enzyme: a2, B, B’, W

Holoenzyme: a2, B, B’, W, SIGMA

23
Q

What recognizes the prokaryotic and eukaryotic promoter region?

A

Prokaryotic: Sigma factor of (RNA pol holoenzyme)
Eukaryotic: TBP (TATA Binding Protein)

24
Q

TBP is a component of which transcription initiation complex? is this for pro or eu?

A

Eukaryotic Transcription

-TBP is a component of TFIID

25
Q

Which is polycistronic? Monocistronic? Which has continuous coding region? which has exons/introns?

A

PROKARYOTES:
polycistronic/continuous coding/Holoenzyme/sigma/1RNApol/-35&-10 promoter/ RNApol= (ABBwSigma)

EUKARYOTES:
-monocistronic/exons&introns/TFIID(TBP)/GTF’s/RNApol II/-10 TATAbox/5’cap/PolyAtail/RNApol 1,2(mRNA),3 (tRNA)

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