protein synthesis: translation

Question 1

Draw the 2D structure of tRNA

Answer 1

google it duh

Question 2

Why are there so many modified bases in tRNA?

Answer 2

decreases the likelihood of successful pairing: if they were unmodified bases you wouldn’t get the bulb at the end of each arm and therefore the tRNA would not function as desired

Question 3

which part of the amino acid binds tRNA?

Answer 3

CARBOXYL GROUP

Question 4

Describe the mechanism of amino acid binding?

Answer 4

when you attach AMP to a carboxylic group, you remove the negative charge from COO-. the O becomes attached to the phosphorus of AMP ****

Question 5

what is the function of tRNA?

Answer 5

bind amino acids that are specific to their anticodon and transport them to the ribosome for addition to the ppc during protein syntehsis

Question 6

what are the 4 distinct domains of the tRNA?

Answer 6

anticodon loop
dihydrouracil loop
acceptor arm
ribothymine-pseudouracil-cytosine variable arm

Question 7

What is the structure and function of the anticodon loop?

Answer 7

contains anticodon triplet complementary to a specific codon

Question 8

How can multiple codons code for 1 amino acid?

Answer 8

due to the wobble effect, 1 tRNA molecule binds multiple codons e.g. AUA, AUC and AUU (to code for isoleucine)
anticodon loop can contain inosine in the 3rd position, and since recognition of the 3rd base by the tRNA is less dicrimnatory, and inosine can form weak bonds with C, U and A, any of these can appear in the codon and the correct amino acid will be incorporated
decreases risk of malicious mutations + improves translational accuracy

Question 9

What is the structure and function of the dihydrouracil group?

Answer 9

contains many dihydrouracil residues in the loop that bind together, with 3/4 bps stabilising the tertiary structure

the stability of this regions affects the stability/binding affinity of the whole molecule for ribosomal sites

Question 10

What is the structure and function of the acceptor arm?

Answer 10

contains the 5’ and 3’ terminal residues, witht he 3’ residue containing the CCA somain

the OH group of the A is where amino acids are attached by amnoacyl-tRNA transferase in tRNA charging

mostly composed of C-G base pairs due to their increased stability compared to A-T

Question 11

What is the composition of the T arm? and what occurs in organisms whose tRNA doesn’t contain it?

Answer 11

ribothymine
pseudouracil
cytosine

reduced EF-Tu binding and aminoacylation

Question 12

What molecule activates amino acids for addition to the peptide?

Answer 12

aminoacyl-tRNA synthetases

Question 13

what are some strategies used by aminoacyl-tRNA synthetases to create specificity?

Answer 13

having unique ions in their binding sites
e.g. Zn in threonyl-tRNA synthetase to distinguish between threonine and valine since the hydroxyl group side chain of threonine will interact with Zinc whereas the methyl group side chain of valine will not

therefore the wrong amino acid cannot bind to the wrong synthetase

Question 14

How does tRNA charging work?

Answer 14

ATP and amino acid react to form aminoacyl adenylate catalyst = aminoacyl-tRNA synthetase

COO- of amino acid is linked to phosphoryl group of AMP molecule to produce pyrophosphate (hydrolysed to release energy for reaction) and an intermediate

OH of adenine on tRNA can attack carbon of amino acid as there is no negative charge to repel it

aminoacyl is transferred to CCA domain on specific tRNA = aminoacyl-tRNA

Question 15

how does the enzyme ensure the correct tRNA has bound to the correct amino acid?

Answer 15

enzymes can read several points of tRNA to make sure it is the correct tRNA-aa combo, not just the anticodon

active site checks polarity + H bonding and discriminates on size being too big i.e. having 1 too many methyl groups

then has an editing site, smaller than active site, only amino acids that are too small e.g. only 1 methyl group, can enter this. then it is removed because if it can fit it is too small

Question 16

What is the purpose of the variable loop?

Answer 16

allows the 2ry structure to twist into the 3ry structure by giving extra ‘length’ to the arms.

Question 17

In prokaryotes, which initiator brings tRNA to the P site?

Answer 17

IF2

Question 18

What is the action of IF2?

Answer 18

hydrolyses GTP, triggering the conformational change in the P site to release initiation factors and allow tRNA to bind the large subunit of the ribosome

Question 19

In eukkaryotes, which initiator brings tRNA to the P site?

Answer 19

eukaryotic elongation factor type 1

Question 20

What hydrolyses GTP in protein synthesis in eukaryotes to initiate the process?

Answer 20

GTPase, elongation factor U (EF-Tu)

Question 21

What is the mechanism of elongation in eukaryotes?

Answer 21

N terminus of amino acid in A site nucleophillically attacks C terminus of the amino acid in the P site. catalyst = intrinsic peptidyl transferase activity of ribosome

go look at your essay

Question 22

where do initiation factors not bind?

Answer 22

the SD box

Question 23

what does the breakdown of GTP allow at the initiation of translation?

Answer 23

dissociation of the IFs from the initiator tRNA

Question 24

what is the translation initiation site in most eukaryotes?

Answer 24

Kozak sequence

Question 25

why is the initiation sequence of translation so important?

Answer 25

integral for protein regulation and overall cellular health
has implications in human disease.

Question 26

what is the ribosomal binding site?

Answer 26

5’ cap of mRNA
or internal ribosome entry site (IRES)