GET BELLY FLOPPED

Question 1

Name 7 parts of protein synthesis macheinery

Answer 1

1) Ribosomes
2) mRNA (codons)
3) tRNAs (adpaters)
4) Amino acids
5) Aminoacyl tRNA synthetases (join aa to tRNA)
6) ATP (provides energy fro aminoacylation)
7) GTP (Induces conformational changes in protein factors and serves as an evergy source to drive the movement of ribosome)

Question 2

Subunits of ribosome prokaryotic and eukaryotic cells

Answer 2

50S + 30S = 70S (pro)

60S + 40S = 80S (Eu)

Question 3

Evidence for conservation of 2ndary strcuture in rRNA

Answer 3

Presence of compensating base changes (a 2nd mutation can restore base pairing)

Question 4

Example of ribotoxin

Answer 4

RICIN YEAHHHHHH

Question 5

Sequence of tRNA at amino acid attachment site

Answer 5

CCA-3’ the aa attaches to the A.

Question 6

Evidence for involvement of rRNA in protein synthesis

Answer 6

1) Antibiotics inhibit peptidyl transferase activity of ribosomes (e.g. erythromycin) bind directly to peptidyl transferase centre of 23S rRNA.
2) Naked 23S rRNA retains peptidyl tranferae activity
3) Colicin E3 is protein that inhibits growth of bacteria that lack Col plasmid.

Question 7

Charging of tRNA by amino-acyl tRNA synthetases

Answer 7

1) AA and ATP bind to synthetase to form an aminoacyl-adenylate intermediate
2) tRNA binds and aminoacyl tRNA formed
3) Aminoacyl tRNA dissociates from enzyme surface

Question 8

What are class I enzymes?

Answer 8

Catalytic domain is N-terminal and contains an ATP binding site consisting of alternative parallel B-sheets and A-helices

Question 9

What are class II enzymes?

Answer 9

Catalytic domain lies towards centre of molecule, comprises antiparallel B-sheets surrounded by A-helices.

Question 10

2 proofreading of aminoacyl-tRNA synthetases

Answer 10

1) Hydrolysis of ester bond of incorrect aminoacyl-AMP intermediate triggered by bind of the cognate tRNA.
2) Hydrolysis of ester bond of miss-matches aminoacyl-tRNA

Question 11

2 types of tRNA met

Answer 11

1) tRNA met f: Met residues attached to this are formylated and only used to start polypeptide chains
2) tRNA met m: Met residues attached are not formulated

Question 12

3 binding sites of ribosome

Answer 12

A site: Acceptor site of codon-directed binding of incoming aa tRNA
P site: Peptidyl site, holds codon directed peptidyl tRNA
E site: exit site, not associated with mRNA

Question 13

The roles of 3 initiation factors in prok (in 30S complex)

Answer 13

IF-3: Binds to 30S (prevents association with 50S)
IF-1: Binds near A site (driects fmet-tRNA to p site)
IF-2: Reacts with fmet-tRNA and GTP (Forms ternary complex)

Question 14

Roles of 3 eIFs in elongation in Euk

Answer 14

eIF4E: Binds 5’cap
eIF4A: ATP-dependent RNA helicase that removes 2ndary structure near 5’ end.
eIF-4G: scaffold subunit that links together the components of initiation complex

Question 15

Why is there a 75% reduction of protein synthesis during G2 to M transition

Answer 15

Due to cell cycle-dependent dephosphorylation of eIF-4E, lowers affinity of ribosomes for the cap

Question 16

The 3 steps of elongation

Answer 16

1) Codon-directed binding of the incoming aminoacyl tRNA
2) Peptide bond formation
3) Translocation of ribosome along mRNA in a 5’ to 3’ direction by length of one codon.

Question 17

Why is EF-Tu not present in initiation

Answer 17

Does not react with f met-tRNA

Question 18

What are the stop codons?

Answer 18

UAA, UGA UAG
RF-1 (UAA + UGA)
RF-2 (UAA+ UAG)

Question 19

Example of antibiotic inhibitors of protein synthesis

Answer 19

Streptomycin: Inhibit initiation and cause misreading of mRNA (proka)
Tetracycline: Binds to 30S subunit and inhibits binding of aminpacyl-tRNAs (proka)

Question 20

What is wobble base pairing

Answer 20

Allows some tRNAs to tolerate a mismatch at position 3 and allows tRNA to recognise for than one codon

Question 21

5 Translational control mechanisms

Answer 21

1) Regulation of activities of initiation/elongation factors by phos (P and E)
2) Blocking/opening of ribosome binding sites by reversible changes in 2ndary structure (P)
3) Autogenous regulation. Protein product binds to ribosome binding site in mRNA, stops initiation (P)
4) Reversible binding of a repressor protein to response element in 5’ UTR (E)
5) Differential stability of mRNA (E)