3.12 Translation

Question 1

Central dogma

Answer 1

DNA to RNA to protein

Question 2

Genetic code is __. Why?

Answer 2

degenerate
More than 1 codon for many AA

Question 3

Wobble base is what position?

Answer 3

3rd

Question 4

What are the “non-sense codons”?

Answer 4

UAA
UAG
UGA

Question 5

Start codon for bacteria and eukaryotes

Answer 5

Bacteria = FMet
Eukaryotes = Met

Question 6

Define wobble base rule

Answer 6

a tRNA that recognizes a Pu at the 3rd position of the codon can recognizes the other Pu and vice versa w/ Py

Question 7

Inosine (hypoxanthine + ribose) can pair with what bases?

Answer 7

A, C or U

Question 8

5 overview steps for translation

Answer 8

1. Charging of tRNA with AA by tRNA synthetases
2. Initiation
3. Elongation
4. Termination
5. Post-translational processing

Question 9

The charging of tRNA to have AA attached to it is done by what enzyme?

Answer 9

tRNA synthetase

Question 10

How many ATP are used to charge tRNA?

Answer 10

2

Question 11

What site does charged initiator tRNA go to?

Answer 11

P site
(all others enter A site)

Question 12

Do bacteria or eukaryotes have a ribosome binding site?

Answer 12

Bacterial (shine-dalgarno sequence)

Question 13

What are the ribosome positioning mechanisms for eukaryotes?

Answer 13

Cap-dependent and cap-independent

Question 14

What are the bacterial ribosome subunits?

Answer 14

30S + 50S = 70S

Question 15

What are the eukaryotic ribosomal subunits?

Answer 15

40S + 60S = 80S

Question 16

What are the 3 sites on the ribosome and describe?

Answer 16

A = tRNA binding site and accepts charged tRNA
P = contains previous tRNA attached to the growing polypeptide
E = exit for uncharged tRNA

Question 17

Elongation of AA in bacteria is catalyzed by formation of peptide bonds by ___ rRNA

Answer 17

23S

Question 18

Where is the shine-dalgarno sequence located in bacteria?

Answer 18

5-10 nucleotides upstream of FMet (AUG)

Question 19

What IF binds to mRNA to position the ribosome in the correct place in bacteria?

Answer 19

IF-1 and IF-3

Question 20

What helps bind tRNA FMet to the P site in bacteria?

Answer 20

IF-2:GTP

Question 21

When does the 50S ribosome bind to 30S in bacteria?

Answer 21

With the removal of IF-1 and IF-2 and hydrolysis of GTP to GDP

Question 22

Bacteria initiation steps:

Answer 22

1. IF-1 and IF-3 bind to 30S subunit
2. IF-2:GTP recognizes tRNA with F-Met and helps it bind to P site
3. Triggers release of IF-3
4. IF-1, IF-2, and GDP are ejected
5. 50S subunit comes in = 70S subunit formed

Question 23

Bacteria elongation steps

Answer 23

1. EF-G with GTP enters ribosome and catalyzes ribosome translocation
2. EF-Tu + GTP brings in charged tRNA to A site
3. Hydrolysis of GTP kicks EF-Tu + GTP +Pi out of ribosome
4. EF-Tu is recycled, so GDP is displaced by EF-Ts to form EF-Tu/EF-Ts complex → EF-Ts is replaced with GTP → EF-Tu + GTP to bring in another charged tRNA
   A to P to E site
5. Peptide bond forms formed between AA (at carboxyl group) on P site and AA in A site
6. Translocation of growing peptide chain onto A site

Question 24

Termination in bacteria:

Answer 24

1. Uncharged tRNA causes RF-1 (UAA and UAG) or RF-2 (UAA or UGA) to come in
2. Ribosome release factor (RRF) and EF-G:GTP cause 70S dissociation

Question 25

Define polysomes

Answer 25

Complex of several ribosomes attached to mRNA - In bacteria

Question 26

2 reasons why transcription and translation occur simultaneously in bacteria

Answer 26

- Increases rate of protein synthesis - protect mRNA from nucleases

Question 27

Why are there pausing sites in transcription in bacteria?

Answer 27

RNAP moves faster than ribosomes, so by having RNAP pause it allows the ribosomes to catch up

Question 28

Is there a ribosome binding site in eukaryotes?

Answer 28

No

Question 29

rRNA and ribosomal proteins are assembled in the

Answer 29

Nucleus

Question 30

Where are the ribosomal subunits assembled in eukaryotes?

Answer 30

in the cytosol

Question 31

What does translation need in eukaryotes?

Answer 31

5'-cap, 3' poly A tail, and initiation factors

Question 32

What scans mRNA until it reaches AUG?

Answer 32

43S preinitiation complex

Question 33

What is the 43S preinitiation complex made of?

Answer 33

40S ribosome, eIF2-GTP, and tRNA Met

Question 34

When does the large ribosomal subunit bind in eukaryotes?

Answer 34

Once 40S subunit reaches the start codon

Question 35

Steps for initiation in eukaryotes:

Answer 35

1. Formation of 43S preinitiation complex 2. It then binds to 5’ cap 3. PABP binds to poly A tail 4. Initiation complex scans until it reaches AUG 5. 60S joins to form 80S ribosome

Question 36

Steps for elongation in eukaryotes:

Answer 36

1. EF-1A + GTP brings in charged tRNA to A site 2. Hydrolysis of GTP kicks EF-1A + GTP out of ribosome 3. EF-1A is recycled, so GDP is displaced by EF-1Balpha to form EF-1A/EF-1Balpha complex → EF-1B is replaced with GTP → EF-1A + GTP to bring in another charged tRNA

Question 37

Steps for termination in eukaryotes:

Answer 37

1. Uncharged tRNA causes RF-1 (UAA and UAG) or RF-2 (UAA or UGA) to come in 2. RF-3 aids in the activities of RF-1 and RF-2 3. Ribosome release factor (RRF) and EF-2:GTP cause 80S dissociation

Question 38

What are the post-translational modifications?

Answer 38

- Removal of Fmet or Met - processing - modification - chelation (metals)

Question 39

Why is enzyme degradation important?

Answer 39

Limits the activity and is a regulatory control

Question 40

Most proteins in bacteria degrade by

Answer 40

AAA+ ATPases

Question 41

Most eukaryotes degrade by

Answer 41

ATP-dependent Lysosomal protein turnover

Question 42

Why would proteins be degraded?

Answer 42

If they're defective or damaged they AA are recycled to prevent mishaps