ribosomal structure

Question 1

how are bacterial ribosomes structured?

Answer 1

70S
50S (large subunit)
30S (small subunit)

Question 2

how are eukaryotic ribosomes structured?

Answer 2

80S
60S (large subunit)
40S (small subunit)

Question 3

what proportion of the ribosome is RNA?

Answer 3

2/3rds by mass

Question 4

why is rRNA highly conserved?

Answer 4

it is catalytic RNA, with essential function

Question 5

how are the large subunits held together?

Answer 5

60S subunits - held together with many protein-protein interactions on the outside of the ribosome
50S subunits - bacterial subunits have not so many protein-protein interactions

Question 6

where does RNA enter and exit the ribosome?

Answer 6

enters - right hand side

exits - left hand side

Question 7

what is the decoding box?

Answer 7

the location of codon-anticodon interactions

Question 8

where is the decoding box located?

Answer 8

on the smaller subunit of the ribosome, on the track of the mRNA as it is threaded through

Question 9

where is the peptidyl-transferase centre located?

Answer 9

on the large subunit, with no proteins anywhere near it

Question 10

how are the decoding box and peptidyl-transferase centre linked?

Answer 10

tRNAs bridge the gap between the subunits

Question 11

why are processing enzymes often found bound to the outside of ribosomes?

Answer 11

no enzymes can cleave the peptide until it pokes out of the peptide exit tunnel, which spans the body of the larger ribosomal subunit

Question 12

how does the process of translation differ between prokaryotes and eukaryotes?

Answer 12

the main difference is in initiation, the elongation process is ubiquitous

Question 13

which sites on the ribosome are mutually exclusive?

Answer 13

E site and A site

Question 14

what are the three steps of translation?

Answer 14

1 - binding of the aminoacyl-tRNA into the A site of the ribosome
2- peptide bond formation
3- translocation reaction

Question 15

what is required for binding of the aminoacyl-tRNA into the A site?

Answer 15

carrier protein (GTP) and elongation factor Tu 
[aa-RS-GTP-Tu]. this is the rate limiting step

Question 16

why does peptide bond formation require no input of energy?

Answer 16

breaks the ester bond formed between the Amino acid and tRNA

Question 17

what is the function of the translocation reaction?

Answer 17

frees up the A site in order to prepare it to receive incoming aa-tRNA
also moves the ribosome along the mRNA

Question 18

why must the movement of the mRNA relative to the ribosome be exact?

Answer 18

must be exactly 3 nucleotides to avoid frameshift

Question 19

in translocation, how does the tRNA move through the ribosome?

Answer 19

P/P -> E/E -> A/A

Question 20

why do tRNAs move via hybrid sites?

Answer 20

allows them to remain attached to eachother, minimising the loss of peptidyl-tRNA

Question 21

what is required for each step of translocation?

Answer 21

step one its spontaneous as it is exerted on tRNAs already in the hybrid state
step 2 requires EF-G and GTP
EF-G enters the A/A site, displacing tRNA from A/P -> P/P

Question 22

how does EF-G displace tRNA from A/P?

Answer 22

• EF-G is too big to fit in the A site
• it has five folded domains, part of this is inserted into the decoding box
• it can push tRNA that is already bound in the A site out of the site.

Question 23

what is the role of EF-Tu in translocation?

Answer 23

carries aa-tRNA into the ribosomal A site

Question 24

how do EF-Tu and EF-G exhibit molecular mimicry?

Answer 24

both factors occupy the same site on the ribosome at different stages of the cycle

Question 25

when does translocation end?

Answer 25

when a stop codon is reached - there are no tRNAs to enter the A site as no tRNA is cognate for stop codons

Question 26

what are release factors?

Answer 26

bind stop codons in the A site and displace tRNA from the E site

Question 27

what are the release factors for bacteria?

Answer 27

RF1 - recognises UAA + UAG

RF2 - recognises UAA + UGA

Question 28

which component exhibits peptidyl hydrolase activity?

Answer 28

peptidyl-transferase centre

Question 29

how does eukaryotic release factor work?

Answer 29

it has a GGQ (glycine-glycine-glutamine) box with a water molecule coordinated within

Question 30

what do ribosomal release factors trigger?

Answer 30

dissociation of the ribosome from the tRNA

Question 31

what permits the bacterial ribosomal subunits to recognise the initiation codon?

Answer 31

shine-delgarno recognition (RNA-RNA interaction)

Question 32

what does transformylase do?

Answer 32

puts a formyl group onto the amino of methionine that is attached to tRNAf

Question 33

what is the functional effect of adding a formyl group to methionine?

Answer 33

causes the growing polypeptide to lose the the positive charge on the NH3

Question 34

how is the fmet-tRNAf guided into the proper site on the ribosome?

Answer 34

IP3 blocks the E site
IF1 blocks the A site
this guides the fmet-tRNAf into the P site