Protein Synthesis by mRNA translation

Question 1

In which direction is the polypeptide chain growing?

Answer 1

N -> C

Question 2

What type of amino acids form the core?

Answer 2

Neutral, hydrophobic amino acids

Question 3

Which amino acids form salt bridges?

Answer 3

Acidic bases

Question 4

Which amino acids can form disulfide bridges?

Answer 4

Cysteine

Question 5

Bacterial ribosome

Answer 5

70S (50S,16S)

Question 6

Eukaryotic ribosome

Answer 6

80S (60S, 40S)

Question 7

What is the function of the large subunit in the ribosome?

Answer 7

Peptide bond formation, peptidyl transferase center

Question 8

What is the function of the small subunit in the ribosome?

Answer 8

Decoding interaction, find shine-dalgarno seq (bacterial), mRNA binding site

Question 9

EF-Tu

Answer 9

GTPase, brings the aa-tRNA. Hydrolysis of GTP makes EF-Tu release aa-tRNA in A-site. Also masks amino acid in tRNA so it doesnt react

Question 10

EF-G

Answer 10

Guides translocation of ribosome, also GTPase.

Question 11

What is wobble base-pairing

Answer 11

Third codon doesnt have to have correct watson-crick pairing

Question 12

Important sites of tRNA

Answer 12

Acceptor arm with exposed 3’ end (CCA) which is the amino acid attachment site
anticodon loop - basepairs to mRNA

Question 13

How does charging work?

Answer 13

Addition of AMP to tRNA by aatRNA synthase provides the high energy bond needed to create an ester linkage between AMP-tRNA and aa-tRNA

Question 14

aa tRNA synthase

Answer 14

Two classes depending which OH (2’ or 3’) they primarily attach aa group to. Has hydrolytic editing as proofreading; incorrect aa moves to editing site

Question 15

Protein synthesis initiation in bacteria

Answer 15

Shine-Dalgarno seq upstream of start codon. IF3 binds to E site in small subunit. IF2, IF1 and GTP binds to A-site, mRNA, f-Met to P-site. IF3 leaves so that large subunit can dock (IF2 in GTP form as signal to large subunit), IF2 hydrolyse and leave with IF1.

Question 16

IF1

Answer 16

Small initiation factor that help IF2 and 3. Blocks A-site.

Question 17

IF2

Answer 17

GTPase, looses affinity when in GDP state. Provides energy and works as signal molecule for large subunit to come in. Blocks A-site. Also binds to f-Met-tRNA to help it dock

Question 18

IF3

Answer 18

Large, blocks large subunit from binding to 30S initiation complex. Binds to E-site

Question 19

Protein synthesis initiation in eukaryotes

Answer 19

preinitiation-complex loops mRNA until it finds start codon, prompting eIF2 to hydrolyze GTP causing some eIFs to disappear. eIF5-GTP binds to A-site, which is signal for large subunit to come in. eIF5 hydrolyze GTP causing all remaining eIFs to leave.

Question 20

Which is the human homolog for IF2 in bacteria?

Answer 20

eIF5B

Question 21

Selection in ribosome

Answer 21

Small subunit stabilize mRNA+anticodon loop if its the correct pairing, so that EF-Tu is in the correct position to be hydrolyzed, if wrong aa-tRNA just leaves

Question 22

Proof-reading in ribosome

Answer 22

tRNA has to be rotated to into peptidyl transferase center. Incorrect tRNAs disappear - only correct base pairing can stand the strain?

Question 23

Explain peptide bond formation

Answer 23

NH2 in A site attacks CO in P-site, transferring the entre polypeptide chain to the tRNA in the A-site

Question 24

Peptide release in bacteria

Answer 24

RF1 and R2 release peptide from ribosome. RF3 releases RF1-2. RF3 hydrolyses and releases from ribosome.

Question 25

Which is the eukaryotic homolog for RF2

Answer 25

eRF1

Question 26

How does RFs work

Answer 26

Molecular mimicry, looks like tRNA so can go into A-site.

Question 27

What is ribosome recycling?

Answer 27

Removing the empty tRNAs, removing the mRNA and splitting the ribosome into its subunits so that it can participate in another round of protein synthesis. Done by RRF and EF-G.

Question 28

What is the primary determinant of secondary structure in a protein?

Answer 28

Hydrogen bonding [between backbone atoms]

Question 29

Aminoacyl-tRNA

Answer 29

tRNA covalently attached to aa at the 3' end of tRNA

Question 30

Chloramphenicol mechanism

Answer 30

Inhibits peptidyl transferase by binding to large subunit

Question 31

What are the start and stop codons for protein synthesis?

Answer 31

Start: AUG Stop: UAG

Question 32

Which eukaryotic initiation factor is homologous to bacterial IF3?

Answer 32

eIF1A

Question 33

Why is tRNA adenylated in tRNA charging?

Answer 33

To add a high energy bond

Question 34

What is special about glycine?

Answer 34

Is not chiral; more conformational freedom

Question 35

What is special about proline?

Answer 35

Less conformational freedom, cant really participate in secondary structures

Question 36

Which direction is alpha-helixes?

Answer 36

Right handed

Question 37

What is a possible way to regulate translation in prokaryotes?

Answer 37

High complimentary to 16S RNA (shine-dalgarno seq.), and proper spacing to start codon

Question 38

How is the ribosome recruited to eukaryotic mRNA?

Answer 38

It recognizes the 5' cap

Question 39

How does the polypeptide tunnel limit the conformation of the polypeptide chain?

Answer 39

It can only big enough for alpha helix, no beta or tertiary structures

Question 40

What is the GGQ?

Answer 40

A motif on class I release factors that stimulate polypeptide release from ribosome.