Translation in Prokaryotes/Eukaryotes

Question 1

Where is the 16s rRNA found?

Answer 1

Small ribosomal subunit in prokaryotes

Question 2

What are the three ribosomal sites in prokaryotes?

Answer 2

A, P, and E

Question 3

What are the three functional centers of the ribosome?

Answer 3

1) Decoding center
2) Peptidyl transferase center
3) GTPase associated region (GAR)

Question 4

What is the decoding center?

Answer 4

Center at the A side where tRNA and mRNA pair

- 3 highly conserved bases in the rRNA at this site

Question 5

What is the PTC?

Answer 5

peptide bond forms here

in large subunit

5 conserved bases in rRNA that bind 3’ end of aminoacyl tRNA and peptidyl tRNA

Question 6

What is the GTPase associated region?

Answer 6

Binding site in 50S, made of 23S rRNA

translation factors with GTPase activity interact with GAR causing GTP hydrolysis

Conformation change in the protein alters translation

Question 7

What does peptidyl transferase do?

Answer 7

Catalyzes formation of peptide bonds

Between amino group of new amino acid and carbonyl of existing peptide chain

Question 8

What are IFs?

Answer 8

Initiation factors

Question 9

How many initiation factors are required in prokaryotes?

Answer 9

3

Called IF1, IF2, IF3

Question 10

Where do IF1 and IF3 bind?

Answer 10

small subunit of ribosome

Question 11

How does translation start?

Answer 11

Small 30S subunit binds mRNA

Question 12

What is the Shine-Dalgarno sequence?

Answer 12

Purine rich sequence in mRNA upstream of AUG complementary sequence on 16S rRNA

Aligns initiation in P site

Only important in prokaryotes

Each gene in a polycistronic mRNA has a Shine-Dalgarno sequence

Question 13

What does IF2 do?

Answer 13

It’s a GTPase

binds initiation tRNA (in prokaryotes, formyl-methionine)

facilitates initiation tRNA into the P site

also, to end the initiation phase, IF2 interacts with GAR (remember, what is GAR?) on 50S subunit, triggering GTP hydrolysis

causes conformation change, and the two ribosomal subunits associate

IFs fall off

Question 14

What are the steps of elongation in prokaryotes?

Answer 14

1) New aminoacyl-tRNA binds in the A site
2) Peptide bond forms
3) translocate

Question 15

How many elongation factors are there?

Answer 15

3

EF-Tu, EF-Ts, EF-G

Question 16

What does EF-Tu do?

Answer 16

Binds aminoacyl tRNAs

positions them in A site, so anticodon binds codon w/ hydrogen bonding

(if the wrong tRNA is put in, EF-Tu falls off with the tRNA still attached)

Interacts with GAR–hydrolysis of GTP results in release of EF-Tu

Question 17

What is EF-Ts?

Answer 17

Catalyzes the exchange of GTP for GDP so EF-Tu can bind another aminoacyl-tRNA

Question 18

What is EF-G?

Answer 18

Another GTPase required for translocation

binds ribosome, GTP is hydrolyzed
conformation of protein changes and moves it along mRNA

Question 19

What facilitates translation termination?

Answer 19

Release factors

Question 20

What are the release factors in prokaryotes?

Answer 20

RF1, RF2, RF3

Question 21

How do RF1 and 2 work?

Answer 21

Look like tRNAs and recognize stop codons in A site

changes conformation in the PTC, transforming the peptidyl transferase to an esterase

Question 22

How does RF3 work?

Answer 22

Another GTPase–promotes binding of RF1 and RF2 to ribosome

Question 23

What are trapped ribosomes?

Answer 23

If there is a mutated or damaged mRNA that has no stop codon,
translation goes all the way to the 3’ end and the ribosome is trapped
(RRF doesn’t bind to release)

Question 24

What is a tmRNA?

Answer 24

tmRNA – an RNA that has features of tRNA and mRNA
- charged with an alanine
- binds EF-Tu and SmpB – protein mimicking small arm
of tRNA

tmRNA enters the A site
- Ala incorporated into the peptide

Question 25

How are trapped ribosomes released?

Answer 25

the mRNA part of tmRNA is used as a template for translation

encodes 10 AAs and has a stop codon

this provides normal termination

Question 26

How does initiation occur in eukaryotes?

Answer 26

Ribosome scans mRNA until it finds a start codon

No Shine-Delgarno sequences!

Question 27

What is included in the pre-initiation complex in eukaryotes?

Answer 27

40s subunit and multiple eIFs (eukaryotic initation factors)

Question 28

What is eIF3?

Answer 28

Blocks ribosomal assembly and facilitates mRNA binding

Question 29

What is eIF2?

Answer 29

GTPase

binds charged Met-tRNA

Question 30

What is the cap binding complex?

Answer 30

Binds to most mRNA before they can bind pre-initiation complex

Question 31

What are the major proteins in the cap binding complex?

Answer 31

eIF4E = cap binding protein, binds 5’ cap–rate limiting stem in initiation

eIF4A = helicase (ATP dependent)