Protein synthesis

Question 1

what are the monomers of proteins?

Answer 1

amino acids

Question 2

what bonds form between amino acids?

Answer 2

peptide bonds

Question 3

what are the different structural levels of a protein?

Answer 3

• primary
• secondary
• tertiary
• quaternary

Question 4

what are the features of primary protein structure?

Answer 4

chain of amino acids

Question 5

what are the features of secondary structure?

Answer 5

• hydrogen bonds form
• amino acids fold into either alpha helix or beta pleated sheet

Question 6

what are the features of tertiary structure?

Answer 6

three dimensional folding pattern of secondary structures

Question 7

what are the festures of quaternary structure?

Answer 7

protein consisting of more than one amino acid chain

Question 8

what is the basic unit of the genetic code?

Answer 8

a codon (three nucleotides)

Question 9

how many possible codons are there?

Answer 9

64

Question 10

how many stop codons are there?

Answer 10

3

Question 11

what does the genetic code being degenerate and not ambiguous mean?

Answer 11

• degenerate means more than one codon may specify a particular amino acid
• not ambiguous means no codon specifies more than one amino acid

Question 12

what is the correct reading frame?

Answer 12

correct groupings of codons read together

Question 13

What are the main RNA classes involved in protein synthesis?

Answer 13

• rRNA
• tRNA

Question 14

how many amino aids can bind to one tRNA?

Answer 14

1

Question 15

where do ribosomes join with mRNA?

Answer 15

near the 5’ of mRNA

Question 16

what are the stages of translation?

Answer 16

• tRNA charging: binding of tRNAs to amino acids
• Initiation: assembly of the machinery at the ribosome
• Elongation of the polypeptide chain through addition of new amino acids at the C-ter
• Termination: protein synthesis ends at the stop codon and the machinery is released

Question 17

tRNA charging

Answer 17

• The CCA sequence is shared by all tRNAs
• The carboxyl group of the amino acid is attached to the nitrogenous base of A at the 3’ end of tRNA
• Specificity is determined by aminoacyl-tRNA synthetases
• Recognition of tRNA by the aminoacyl-tRNA synthetases is mediated by the nucleotide sequence
• Recognition of amino acid by the aminoacyl-tRNA synthetases is mediated by size, charge and R groups

Question 18

what components are required for protein synthesis?

Answer 18

• mRNA
• Small and large subunits of the ribosome
• Initiation factors (only 3 in prokaryotes)
• Initiator tRNA (Met-tRNAiMet)
• GTP

Question 19

what are the stages of initiation?

Answer 19

-The small (SSU) and large (LSU) ribosomal subunits need to be separate for the mRNA to bind the small subunit
- A 43S pre-initiation complex composed of SSU, Met-tRNAiMet and initiation factors recognise and bind the 5’ cap in the mRNA (different compared with bacteria!!!)
- The 43S pre-initiation complex scans the mRNA until the first AUG codon is found
- AUG is surrounded by a consensus sequence which helps the recognition: the Kozak sequence (ACCAUGG)
- After recognition, codon and anticodon (in the tRNA) bind
- Initiation factors are released
- LSU binds the complex

Question 20

what are the main roles of initiating factors in initiation?

Answer 20

-Preventing the large subunit (LSU) from attaching too early by binding to the small subunit (SSU).
- Recognizing and binding the 5’ cap of the mRNA.
- Recruiting the initiator tRNA, which carries methionine.
- Ensuring proper binding between the initiator tRNA and the start codon (AUG).
- Allowing the large subunit (LSU) to bind after everything is properly aligned.

Question 21

what does elongation require?

Answer 21

• The 80S initiation complex
• Charged tRNA (= with aa)
• Elongation factors
• GTP

Question 22

what are the three possible binding sites for tRNA on ribosomes?

Answer 22

Aminoacyl (A)
Peptidyl (P)
Exit (E)

Question 23

what are the three steps of elongation?

Answer 23

• Binding of a charged tRNA
• Peptide bond formation
• Translocation

Question 24

what occurs during the first stage of elongation?

Answer 24

Binding of a charged tRNA:
- A charged tRNA (carrying an amino acid) enters the A site of the ribosome.
- This process is helped by elongation factor eEF1a and GTP.
- The tRNA pairs with the matching codon on the mRNA, and eEF1a is released (as GDP).

Question 25

what happens during the second stage of elongation?

Answer 25

Peptide bond formation: - The amino acid in the A site forms a peptide bond with the one in the P site. - This reaction occurs in the large ribosomal subunit (LSU) and is catalyzed by 28S rRNA, which acts as a ribozyme. - The amino acid in the P site is released from its tRNA.

Question 26

what happens during the third stage of elongation?

Answer 26

Translocation: - The ribosome moves along the mRNA (from 5’ to 3’), shifting the tRNAs. - The tRNA in the P site moves to the E site (exit site) and is released back into the cytoplasm to be recharged. - This movement is powered by eEF2 and GTP hydrolysis.

Question 27

what happens during the termination stage of translation?

Answer 27

- Stop codon: Protein synthesis ends when the ribosome reaches a stop codon (no tRNA matches it, so the A site stays empty). - Release factors: Special proteins called release factors (RFs) handle the final steps: - eRF1 recognizes the stop codon. - eRF3 helps break the bond between the tRNA and the finished protein (using GTP). - Other RFs help release the tRNA, mRNA, and separate the ribosome.