RNA metabolism

Question 1

What is RNA?

Answer 1

ribonucleic acid

Question 2

How does RNA differ from DNA?

Answer 2

Hydroxyl group on the sugar (this is why not deoxyribo)
Has Uracil as pyrimidine instead of Thymine
Is single stranded

Question 3

What are the 3 RNA classes? Roles?

Answer 3

mRNA: encode the a.a. sequences of all the polypeptides found in the cell

tRNA (transfer): match specific a.a. to triplet codons in mRNA during prots synthesis

rRNA (ribosomal): constituents of ribosomes

Question 4

What do microRNAs do?

Answer 4

regulate expression of genes via binding to specific nucleotides sequences

Question 5

What is the direction of synthesis of RNA? is it the same direction as DNA?

Answer 5

5’ to 3’, yes it is

Question 6

What are the differences of RNA synthesis in comparison to DNA?

Answer 6

RNA does not require a primer

RNa uses only one strand as template (one strand is a non-template strand)
- The template strand is the one going from 3” to 5” because RNA is synthesized from 5’ to 3’

RNA uses only a segment of DNA as template

Question 7

What are the similarities in DNA replication and RNA synthesis?

Answer 7

Requirement of a template

Direction of syntehsis (5-3)

Addition of complementary nucleotides

Question 8

What ions are involved in RNA poymerase action, and how do they act?

Answer 8

2 Mg+ ions.

one Mg+ : facilitates the attack of 3’ hydroxyl roup on alpha (the one attached to the sugar) phosphate group of new coming ribonucleotide,

other Mg+: facilitates displacement of pyrophosphate

BBoth stabilize transition state

Question 9

What is promoter?

Answer 9

Specific DNA sequence that will initiate RNA polymerase binding and RNA synthesis

Question 10

What is the sequence on DNA that is part of promoter (pol II especially) of eukaryotes? where is it located?

Answer 10

-30 region of promoter sequence: TATAAA (tata box)

+1 region of promoter sequence: YYAN(TA)YY (Inr)

Question 11

What helps the RNA polymerase to locate the promoter?

Answer 11

Sigma subunit

Question 12

What are the 3 types of RNA polymerase? what do they synthesize?

Answer 12

Pol I: synthesis of rRNA
Pol II: synthesis of mRNA
Pol III: synthesis of tRNA, rRNA and specialized RNA

Question 13

What are the steps of RNA synthesis?

Answer 13

Assembly
Initiation
Elongation
Termination

Question 14

What are, in order, all the transcription prots involved in assembly, initiation and elongation?

Answer 14

INITIATION

• Polymerase II: catalysis RNA synthesis
• TBP (associated with TFIIA) : recognizes TATA box, transcription factor IIA will help with binding of TBP and TFIIB to promoter
• TFIIB: Binds to TBP, brings in Pol II and TFIIF to promoter
• TFIIE: recruits TFIIH
• TFIIF: Prevent Pol II to bind to nonspecific DNA sequences
• TFIIH: Unwinds DNA at promoter, phosphorylates Pol II, recruits nucletodies exciision repair prots

ELONGATION

• Elongation factors…

Question 15

What is the point of 5’ capping?

Answer 15

protext he RNA from ribonucleases that cleave RNA

Question 16

What is CTD

Answer 16

Carboxyl terminal domain , where there is capping

Question 17

What is longer, introns, or exons?

Answer 17

introns

Question 18

What is kept, introns or exons?

Answer 18

exons are kept

Question 19

What are the 2 ways of splicing?

Answer 19

Self splicing
Splicing with help of spliceosomes
Alternative splicing

Question 20

What is a spliceosome? How many?

Answer 20

RNA proteins called snRNPs (snurps… )
5 spliceosomes: U1,2,4,5,6
REQUIRES ATP

Question 21

Where and what do all the U spliceosome are/do?

Answer 21

U1: has sequence complementary to the 5’ end (beginning ) of intron

U2: has sequence complementary to (5’end) beginning of end of intron

U4,5,6: will bind after U1 and U2 are bond. They will create a complex

U1,4: will exit

splicing occurs….

Question 22

What sequence is a cleavage sequence ?

Answer 22

AAUAAA

Question 23

What enzymes/prots are involved in poly-A tail formation?

Answer 23

Poluadenylate polymerase

Endonucelases

Question 24

What results from alternative splicing?

Answer 24

multiple mRNA from one gene

Question 25

What does the processing imply after synthesis of RNA?

Answer 25

• Elimination of introns, joining exons
• Poly-adenylation of the 3’ end
• Capping the 5’ end

Question 26

What specific RNA acts more as a catalyst?

Answer 26

Ribosomal RNA