II. Post-transcription | 23. The genetic code; structure and function of tRNAs; aminoacyl-tRNA synthetases; codon- anticodon connections

Question 1

1. Genetic code
   a/ What is a genetic code?

Answer 1

a triplet code (3-nucleotide sequence = codon) which is read from specific starting point on the mRNA.

Question 2

1. Genetic code
   b/ How many possible codons can you find?

Answer 2

There are 64 possible codons in the genetic code where 61 of them specify individual amino acids.

Question 3

1. Genetic code
   c/ What does the codon table describe?

Answer 3

The codon table describes 20 amino acids
- 1 codon = 3 nucleotides = 1 amino acid

Question 4

1. Genetic code
   d/ List the “stop” codon(s)

Answer 4

The three codons: ‘’UAA, UGA, UAG’’ do not specify amino acids, but are referred to as ‘’stop codons’’.

Question 5

1. Genetic code
   e/ The role of “stop” codon(s)

Answer 5

They mark the carboxyl (-COOH) terminus of polypeptide chains.

Question 6

1. Genetic code
   f/ List the “start” codon(s)

Answer 6

methionine (AUG) is the ‘’start codon’’

Question 7

1. Genetic code
   g/ Which amino acid(s) only have 1 codon code for them?

Answer 7

AUG = methionine
UGG = Tryptophan

Question 8

1. Genetic code
   h/ What are the 5 characteristics of the genetic code?

Answer 8

1/ Degenerated
2/ Non-ambiguous
3/ Non-overlapping
4/ Non-punctuated
5/ Universal

Question 9

1. Genetic code
   h5/ Why is genetic code “universal”?

Answer 9

Each codon is the same in most known organism
(eg.: same in eukaryotes and prokaryotes)

Question 10

1. Genetic code
   h1/ Why is genetic code “degenerated”?

Answer 10

Because a single amino acid maybe coded by more than 1 codon (methionine = 1 codon, serine = 6 codons)

Question 11

1. Genetic code
   h2/ Why is genetic code “non-ambiguous”?

Answer 11

1 amino acid can be coded by several different codons, BUT each codon ONLY codes for one amino acid, not more

Question 12

1. Genetic code
   h3/ Why is genetic code “non-overlapping”?

Answer 12

reading of the codon sequence does not involve overlapping of codons – the genetic code is read sequentially -> one codon at a time

Question 13

1. Genetic code
   h4/ Why is the genetic code non-punctuated?

Answer 13

the message is read in a continuous sequence of nucleotides triplets until a stop codon is reached

Question 14

1. Genetic code
   I/ What is the rule of genome reading?

Answer 14

• Some genes are encoded by one of the strands, while others are by the other strand
• But there are no overlapping genes on the two strands

Question 15

2. Toolbox of protein synthesis

Answer 15

1. RNA
   - Messenger
   - Transfer
   - Ribosomal
2. Proteins
   - Ribosomal
   - Aminoacy-tRNA synthetase
   - Translation factors
3. Ribosome
   - Prokaryotic 70S
   - Eukaryotic 80S
4. Amino acids
5. Energy: ATP, GTP

Question 16

3. tRNA
   a/ What is the structure of tRNA?

Answer 16

• Terminal 5’-end: is phosphorylated (PO4-2 group)
• Acceptor stem: 5’-end base-pairs with 3’-end (has a specific amino acid attached to it – CCA)
• D-loop: contains dihydrouridine
• Anticodon loop: contains anticodon (sequence of 3
  nucleotides that are complementary to codons in the mRNA).

Question 17

3. tRNA
   b/ How are amino acids linked to tRNA?

Answer 17

Amino acids are linked to the 3’ A via an ester bond

Question 18

3. tRNA
   c/ Function of tRNA?

Answer 18

• Carries amino acid to the ribosome during translation.
• As each triplet code is read on the mRNA, the tRNA will deliver its amino acid to a growing polypeptide chain (mRNA -> tRNA anticodon -> protein).
• It serves as a physical link between the mRNA and the amino acid sequence

Question 19

4. Wobble
   a/ What is wobble?

Answer 19

Wobble is a phenomena that occurs when a base pairing is atypical, meaning base pairing between nucleotides other than A-U and G-C
- Occurs at 3rd position of the codon (mRNA) and 1st position of anticodon (tRNA)
- Wobble pairing follows its own rules – a G in the anticodon can pair with only C/U in the 3rd position of the codon

Question 20

4. Wobble
   b/ What is function of wobble?

Answer 20

allows fewer tRNAs to cover all the codons of the genetic codes while still ensuring that the coding is accurate = allows faster dissociation of tRNA from mRNA

Question 21

5. What is Codon-anticodon hybridization?

Answer 21

the complementary binding between codon- anticodon, since anticodon present a reverse + complementary nucleotide trio for the codon on the mRNA

Question 22

6. Aminoacyl-tRNA synthetases
   a/ What are Aminoacyl-tRNA synthetases?

Answer 22

The genetic code translating enzymes

Question 23

6. Aminoacyl-tRNA synthetases
   b/ What are the functions of Aminoacyl-tRNA synthetases?

Answer 23

They possess a double function
1. Activation of amino acids
2. Translation of genetic code

Question 24

6. Aminoacyl-tRNA synthetases
   c/ How do Aminoacyl-tRNA synthetases participate in activation of amino acid?

Answer 24

The formed ester linkage provides the energy for peptide bond formation
Hydrolysis of pyrophosphate makes the reaction irreversible

Question 25

6. Aminoacyl-tRNA synthetases c/ How do Aminoacyl-tRNA synthetases participate in Translation of genetic code?

Answer 25

- According to the 20 amino acids most organism hold 20 aminoacyl-tRNA synthetases => They bring together the appropriate tRNAs and amino acids

Question 26

6. Aminoacyl-tRNA synthetases d/ How is formation of aminoacyl occur?

Answer 26

1) Amino acid is first activated by linking its carboxyl group (-COOH) to AMP, forming adenylated amino acid. This linkage is driven by the hydrolysis of ATP (ATP  AMP) 2) The adenylated amino acid is transferred to a hydroxyl group (-OH) at the 3’-end of the tRNA molecule 3) Here, AMP will be released and COOH-group of amino acid with link OH-group of tRNA to give an ester bond

Question 27

6. Aminoacyl-tRNA synthetases e/ What is function of Function of anticodon loop?

Answer 27

the triplet at the tip of the anticodon loop base-pairs with the correspond codon in mRNA

Question 28

6. Aminoacyl-tRNA synthetases f/ What is the Function of acceptor stem?

Answer 28

located in the 3’- end of tRNA. Has the sequence CCA. => This is the site where the specific amino acid becomes attached and where tRNA becomes activated aminoacyl-tRNA