Part 1: Basic components required for protein synthesis

Question 1

Is transcription reversible?

Answer 1

Yes

(DNA ⇔ RNA)

Question 2

Is translation reversible?

Answer 2

• No
• You can only go from RNA ⇒ protein. You cannot determine the RNA sequence from a protein.

Question 3

Molecular biology is the study of:

Answer 3

• the mechanisms of transcription and translation
  
  • factors involved at each step
  • regulation

Question 4

Protein synthesis (translation) is the last opportunity to:

Answer 4

• regulate gene expression

Question 5

Why study protein synthesis?

Answer 5

1. Last opportunity to regulate gene expression
2. rapid response to stimuli (transcription sometimes takes too long)
3. many pharmaceutics impact translation (e.g. antibiotics)

Question 6

Meaning of “degnerate” genetic code:

Answer 6

• the genetic code is not reversible
• You can’t figure out from a protein sequence what the RNA sequence was.
  • because some amino acids have multiple three-letter codes (codons)

Question 7

UGA codes for:

Answer 7

• a stop codon
• selenocysteine

Question 8

Nonsense mutation:

Answer 8

• amino acid codon mutated to a termination codon (leads to truncation of protein)

Question 9

Missense mutation:

Answer 9

• amino acid codon changes in one nucleotide to code for a different amino acid

Question 10

Silent mutation:

Answer 10

• amino acid codon has a single nucleotide mutation that makes it in to another codon that codes for the same amino acid

Question 11

Messenger RNA (mRNA):

Answer 11

the code

Question 12

Transfer RNA (tRNA):

Answer 12

the adapter

(matches codons to amino acids)

Question 13

Structure of mammalian mRNA:

Answer 13

1. 5’ cap (required for binding of initiation factors)
2. 5’ UTR (untranslated region)
3. start codon (AUG - Methionine)
4. coding region
5. stop codon (UAA/UGA/UAG)
6. 3’ UTR (untranslated region; site of key regulatory sequences)
7. poly-A tail (protects mRNA from degradation and increases translational efficiency)

Question 14

The 5’ cap of mRNA is required for:

Answer 14

• binding of initiation factors

Question 15

AUG

Answer 15

• the start codon
• codes for methionine

Question 16

The 3’ UTR of mRNA contains:

Answer 16

• key regulatory sequences

Question 17

Role of the 3’ Poly-A tail in mRNA:

Answer 17

• untemplated polyadenylate sequence
• ~200 nucleotides
• protects mRNA from degradation
• increases translational efficiency

Question 18

Deletion of a base in an mRNA sequence will:

Answer 18

• change the reading frame
  
  • can introduce premature stop/termination codon; results in truncated protein

Question 19

Components of tRNAs:

Answer 19

1. D-loop
2. anticodon loop
3. T-loop
4. 3’ end (CCA)
   
   • vital for the addition of the amino acid to the tRNA
   • not coded for by DNA, added after translation of tRNA

Question 20

What parts of the tRNA are vital for correct amino acid binding to tRNA?

Answer 20

1. anticodon loops (recognizes correct amino acid)
2. 3’ CCA end (binds amino acids to tRNA)

Question 21

What enzymes recognize tRNAs and add the appropriate amino acid to them?

Answer 21

• aminoacyl tRNA synthetases

Question 22

aminoacyl tRNA synthetases:

Answer 22

• recognize the anticodon as well as other structural features in tRNA
• add appropriate amino acid to tRNAs
  
  • which depends on the anticodon sequence

Question 23

Process of aminoacylation:

Answer 23

1. aminoacyl tRNA synthetase recognizes tRNA and matching amino acid of tRNA anticodon
2. aminoacyl tRNA synthetase catalyzes reaction of amino acid to AMP intermediate
3. amino acid added to 3’ CCA end of tRNA

ATP DEPENDENT

Question 24

The two active sites of aminoacyl tRNA synthetase:

Answer 24

1. editing site
   
   • has higher affinity for incorrect amino acids. If an amino acid binds to the editing site, it is cleaved from the enzyme, and the enzyme continues to search for the correct amino acid
2. synthesis site

Question 25

Where does the fidelity of translation begin?

Answer 25

• aminoacyl tRNA synthetase
  
  • needs to find and bind the correct amino acid to tRNA.
  • editing active site is key to this

Question 26

Ribosome structure:

Answer 26

• Two-subunits
  
  • 60s and 40s (combine to 80s unit)
• Mostly made up of RNA
• Three tRNA binding sites (E, P, A)

Question 27

The ribosome is a ribozyme because:

Answer 27

• it induces peptide bond formation without the contribution of any protein

Question 28

Ribozyme:

Answer 28

• a piece of RNA that can perform catalytic reactions just like a protein

Question 29

A-site (aminoacyl site) of a ribosome:

Answer 29

• initial tRNA binding site on the ribosome for the next codon on the mRNA
• where new amino acids arrive

Question 30

P-site (peptidyl site) of a ribsome:

Answer 30

• site of peptide bond formation in the ribosome

Question 31

E-site (exit site) of a ribosome:

Answer 31

• site of tRNA release from ribosome

Question 32

What do the three tRNA binding sites of a ribosome help with?

Answer 32

• all three bind to the mRNA strand at the same time
  
  • helps maintain reading frame