Mod 6 - structure and function of RNA

Question 1

what is RNA?

Answer 1

• ribonucleic acid
• the product of transcription from a DNA template
• several types of RNA that play a role in gene expression

Question 2

how does the chemical structure of RNA differ from DNA?

Answer 2

• Ribose instead of deoxyribose
• ribose contains 2’ - OH whereas deoxyribose lacks the oxygen - RNA = less stable than DNA
• uses uracil instead of thymine

Question 3

what is the role of mRNA?

Answer 3

• transfer of information from DNA to protei
• codes for proteins

Question 4

what is the role of rRNA and tRNA ?

Answer 4

protein synthesis

Question 5

what is the role of snRNA? (small nuclear RNA)

Answer 5

• processing of pre-mRNA
  -involved in splicing introns from pre-messenger RNA

Question 6

what is the role of snoRNA? (small nucleolar RNA)

Answer 6

• processing and modification of rRNA

Question 7

what are the RNA contents within a cell?

Answer 7

• single cell contains 10pg of RNA (10^-11g)
• 80-85% ribosomal RNA
• 10-15% low m/w species (tRNA, snRNA, etc)
• 1-5% mRNA

Question 8

what are some physical properties of RNA?

Answer 8

• generally single-stranded
• palindromic sequences allows for self-complementary base pairing, which allows it to fold into complex structures

Question 9

how does the lac operon control the amount of certain RNA’s?

Answer 9

• transcriptional-level control
• transcription can be turned on or off rapidly to control synthesis of RNA

Question 10

how is RNA abundance maintained apart from at the synthesis/transcriptional level?

Answer 10

• regulated degredation - taking advantage of RNA’s unstable structure to make it break down much faster
• can be achieved via transferrin receptor for mRNA
• translation efficiency - proteins controlling usage of certain RNA’s

all under the control of the UTR (untranslated region)

Question 11

How does the Transferrin Receptor work to control mRNA levels?

Answer 11

• TfR mRNA (transferrin receptor mRNA) codes for the transferrin receptors that transports Fe2+ (toxic) ions into the cell
• when intracellular Fe2+ content gets too high, TfR mRNA becomes degraded, meaning no more transferrin receptors can be coded for, so no more Fe2+ enters the cell.
• the protein IRE-BP (iron response element binding protein) protects the 3’ - UTR stem loop structure in the mRNA - keeps it stable
• Fe2+ binds to IRE-BP which forces it to dissociate from 3’ - UTR stem loop, leaving it exposed and unstable so it breaks down much more easily

Question 12

what is the function of the ferritin mRNA?

Answer 12

• regulates translation using RNA secondary structure
• ferritin binds to Fe2+ within the cell
• the ferritin mRNA has stem-loops in the 5’ UTR
• these IRE’s act as binding sites for IRE-BP
• when Fe2+ levels are high, they stop IRE-BP binding to IRE’s
• when Fe2+ levels are low, the IRE-BP binds to the IRE’s, which causes translation to be inhibited

Question 13

what are the 4 steps in RNA processing (pre-mRNA -> mature mRNA)

Answer 13

• transcription
• capping
• cleavage + polyadenylation
• splicing

Question 14

describe the process of mRNA capping

Answer 14

• adding GTP to the 5’ end of RNA
• linkage is from 5’ of the RNA to the 5’ phosphates of the GTP
• methylation occurs on the first 2 nucleotides and on the added G

Question 15

why is mRNA capping important?

Answer 15

• linked to transcription initiation
• increase stability of mRNA
• required for efficient splicing
• nuclear export + translation initation

Question 16

describe the process of 3’ cleavage and polyadenylation

Answer 16

precursor - signal sequence of AAUAA, G/U or a U rich region
- CPSF (cleavage and polyadenylation specificity factor) binds to AAUAA
- CstF (cleavage stimulatory factor) binds to G/U region
- these two factors recruit other factors such as cleaving factors and Poly-A polymerase (PAP)
- cleavage takes place at CA sequence
- polA tailing then occurs

Question 17

what are the 3 coserved sequence signals for pre-mRNA splicing?

Answer 17

5’ splice site - AGGU RAGU
3’ splice site - Y AGGU
branchpoint region - YNYURAY

(Y = pyrimidine)
(R = purine)
(N = any base)

Question 18

describe the 2-step process of splicing

Answer 18

• cleavage at 5’ splice site + lariat formation at branchpoint sequence
• 5’ phosphate of intron binds with free -OH of A residue of branchpoint
  (this is why the A of the branchpoint sequnce is the most important)
• cleavage at 3’ splice site - removal of intron region entirely

Question 19

what is a snRNP (snurp)?

Answer 19

small nuclear ribonuclear particles
- consists of snRNA and numerous proteins
- snurps involved in splicing are U1, U2, U4, U5, and U6

Question 20

what do the different snurps do?

Answer 20

U1 - attatches to exon 1 at the boundary between exon and intron
U2 - attatches at branchpoint
U4, U5, U6 - bind to exon 1, displaces U1

U2 then brings branchpoint into close proximity to exon 1 - U4 is displaced
U2, U5, U6 forms active site of spliceosome

Question 21

what is the function of RNA processing?

Answer 21

• increase stability + functional efficiency
• increase number of possible products that can arise from one gene

Question 22

what is a function of alternative splicing?

Answer 22

create isoforms - different proteins that arise from a single gene