Protein synthesis

Question 1

why #proteins produced= # needed?

Answer 1

Process of protein synthesis is very energetically demanding

Question 2

What is the adaptor hypothesis?

Answer 2

Kreek proposed that in order for mRNA to be translated in AA there need to be an adaptor molecule- each specific for one AA

Question 3

What does non-overlapping code mean

Answer 3

Thecodeisnon-overlapping. This means that successive triplets are read in order.

Question 4

_ base is the least important in binding to tRNA

Answer 4

3rd base is the least important in binding to tRNA

Question 5

__ codon establishes the reading frame

Answer 5

First codon establishes the reading frame

Question 6

__/__ codons code for amino acids

Answer 6

61/64 codons code for amino acids

Question 7

What are the 3 terminal codons?

Answer 7

UAA
UGA
UAG

Question 8

What’s the initiation codon?

Answer 8

AUG, also the Met codon

Question 9

What are the 2 AA that have only 1 codon

Answer 9

Met an Trp

Question 10

How’s the code different in mitochondria?

Answer 10

• UGA encodes for Trp instead of STOP

- AGA/AGG encode Stop instead of Arg

Question 11

What’s the cycle of protein synthesis in prokaryotes

Answer 11

1. tRNAs are aminoacetylated to activate amino acids
   
   2. Initiation: First codon recognizing tRNA brings in methionine and attaches to ribosomal subunit. Only after attachment of mRNA and tRNA to small ribosomal subunit, the large subunit bind
   3. Elongation. Next tRNAs with AA are brought in and peptide bond is formed until nonsense codon is reached
   4. Termination- translation stops when a stop codon is reached. The mRNA and proteins dissociate, are ribosomal units are recycled
   5. Protein folding. Post translational processing

Question 12

What’s the general structure of tRNA?

Answer 12

All tRNAs have clover leaf structure
Anti-codon arm is complimentary to codon
Amino acid arm has CCA sequence- it is added at post-transcriptional modification

Question 13

Where is CCA sequence on amino end of tRNA important?

Answer 13

Important in first step of translation which is aminoacylation of tRNA

Question 14

At which end is CCA sequence?

Answer 14

At 3’ end

Question 15

How does aminoacylation of tRNA occurs?

Answer 15

1. Carboxyl of amino acid attacks a phosphorus of ATP, forming 5-aminoacyl adenylate. 2 P are thrown away
2. Aminoacyl group is transferred to the tRNA. The mechanism of this step is somewhat different for the two classes of aminoacyl-tRNA synthetases. For class I enzymes, the aminoacyl
   group is transferred initially to the 2’-hydroxyl group of the 3’-terminal A residue, then to the 3’-hydroxyl group by a transesterification reaction. For class II enzymes, the
   aminoacyl group is transferred directly to the 3’-hydroxyl group of the terminal adenylate.

Question 16

What are the 2 tRNAs for met and where are they found?

Answer 16

In prokaryotes and mitochondria

- tRNA that brings first AA- formylmethionine by tRNAfMet
- All the others Met are brought in by tRNAMet

Question 17

Describe initiation in eukaryotes

Answer 17

1. eIF1A and eIF3 bind ot 40S subunit. The factor eIF1 binds to the E site. The charged initiator tRNA (with Met) is bound by the initiation factor eIF2, which also has bound GTP. elF5B binds forming pre-initiation complex
2. mRNA is brought in by elF4F. mRNA attachment to preinitiation complex also requires energy
3. This complex scans the bound mRNA, starting at the 5’ cap, until an AUG codon is
   encountered. Scanning requires an existence of tRNA already at P site
4. Large 60S ribosomal subunit comes in, accompanied by the release of many of the initiation factors

Question 18

How’s peptide bond formed?

Answer 18

This occurs by the transfer of the initiating N-formylmethionyl group from its tRNA to the amino group of the second amino acid, now in the A site. The -amino group of the amino acid in the A site acts as a nucleophile, displacing the tRNA in the P site to form the
peptide bond. This reaction produces a dipeptidyl-tRNA in the A site, and the now “uncharged” (deacylated) tRNAfMet remains bound to the P site. T
Peptidyl transferase catalyzes peptide bond formation
The tRNA at A site has more than 1 AAs. It has a growing peptide chain. tRNA at has to be pushed to P site. The one at P has to be pushed to E and thrown out of the system
Elongation factors help in peptide bond formation is called elongation factor P

Question 19

What does elongation factor P do?

Answer 19

Help in peptide bond formation

Question 20

How does elongation occur?

Answer 20

Elongation factor TU-GTP that comes in associated with energy providing GTP helps new tRNA to bring new AA to A site- GTP is converted to GDP
Once tRNA is brought to A site, the role of TU is done and it can leave

Question 21

How does translocation occur?

Answer 21

EF- G-GTP pushes empty tRNA to E site, tRNA containing peptide chain is pushed to P site. Energy is provided by GTP
EF- G-GDP leaves when this is done
A site becomes empty for another tRNA

Question 22

How does termination occur?

Answer 22

Termination happens when nonsense codon arrives to A site- no tRNA can come there
Release factor comes and binds to A site
It releases the synthesized peptide from tRNA that is present in the P site

Question 23

What is the role of RRF?

Answer 23

Ribosome recycle factor uses elongation factors and energy to dissociate translational machinery

Question 24

How can translation machinery be recycled?

Answer 24

After it is degraded IF-3 attached to small ribosomal subunit is left- another cycle of translation can be started again

Question 25

What are some of the post-translational modification of proteins?

Answer 25

– Enzymatic removal of formyl group from first residue, or removal of Met and sometimes additional residues – Acetylation of N-terminal residue

Question 26

What are signal sequences?

Answer 26

Sequences in proteins that are removed

Question 27

Which proteins are short lived?

Answer 27

v Proteins for rapidly changing needs are short-lived | v Defective proteins are short-lived

Question 28

What is the purpose of ubiquitin attachment?

Answer 28

Attachment of ubiquitin is common step that triggers degradation

Question 29

How's ubiquitin attached?

Answer 29

``` Ub first attached to E1 to SH group. E1 brings in Ub Ub is then transferred to E2 E3 is needed to transfer Ub from U2 to amino group of lysine Only Lysine can be ubiquitinated Can be just one, can be several Ub ```

Question 30

What happens after ubiquitin is attached?

Answer 30

This is how a cell recognizes a protein to be degraded It is brought to peroxisomes This decided how long a protein be functional

Question 31

What are the names of E1, E2 and E3 enzymes?

Answer 31

E1 – activating enzyme E2 – conjugating enzyme E3 – ligating enzyme

Question 32

How and where are amino acids attached to tRNA?

Answer 32

In the cytoplasm | They are covalently bonded at the expense of ATP

Question 33

Elongation in translation requires ___ factors

Answer 33

Elongation in translation requires elongation factors

Question 34

Which steps in protein synthesis require energy?

Answer 34

1. Bonding of AA to tRNA- ATP 2. Initiation- GTP 3. Movement of ribosome along the mRNA - GTP

Question 35

Protein synthesis begins at the __ end and proceeds by the stepwise addition of amino acids to the ___end of the growing polypeptide

Answer 35

Protein synthesis begins at the amino-terminal end and proceeds by the stepwise addition of amino acids to the carboxyl-terminal end of the growing polypeptide

Question 36

All organisms have __ tRNAs for methionine

Answer 36

All organisms have 2 tRNAs for methionine

Question 37

How does initiation differ in mitochondria and chloroplasts?

Answer 37

Polypeptides synthesized by mitochondrial and chloroplast | ribosomes begin with N-formylmethionine.

Question 38

To which site does tRNA carrying the first Met binds?

Answer 38

To P site

Question 39

Name the release factors

Answer 39

RF-1, RF-2, and RF-3