16. Genetic code. Translation

Question 1

Genetic Code

Answer 1

• Function: Carries information from nucleic acids to proteins.
• TRIPLET genetic code - Each amino acid is encoded by a combination of 3 nucleotides (codons).
  -> DNA has 4 types of nucleotides.
  -> 1-nucleotide combinations can code for 4 amino acids.
• Nucleotide triplets are called CODONS
• Genetic code is COLLINEAR, SEQUENTIAL - arrangement of amino acids in polypeptide depends on sequence of codons in the RNA.
• Genetic code is NON-OVERLAPPING - Insertion or deletion of 1 nucleotide pair shifts the frame and leads to mutation
• Genetic code is SYNONYMOUS - Some AA have more than 1 codon
• Genetic code is UNIVERSAL - For all organisms

Question 2

Point Mutations

Answer 2

Definition: Changes of a single nucleotide.

Types of Point Mutations:
1. Substitution: Replacement of a nucleotide.
- Silent Mutations: Substitution results in a codon for the same amino acid, leaving protein unchanged due to synonymy of genetic code.
- Missense Mutations: Substitution results in a codon for a different amino acid. These can be harmful or create normal polymorphisms.
- Nonsense Mutations: Substitution converts a codon for an amino acid into a stop codon, prematurely terminating protein synthesis and often destroying the protein’s function.

Deletion: Loss of a nucleotide.

Insertion: Addition of a nucleotide.

Both deletions and insertions cause frameshift mutations, altering the reading frame. This results in a sequence of incorrect amino acids followed by a random stop codon, often rendering the protein nonfunctional, similar to nonsense mutations.

Question 3

Translation - what is neccessary?

Answer 3

• mRNA
• tRNA
• aminoacyl-tRNA synthetases
• rybosomes

Question 4

Translation - tRNA

Answer 4

• Function: match AA to codons
• Molecule has 4 loops, 3 of them give a secondary structure
• Tertiary structure is L-shaped
• 3’- end endes with CCA
• On opposite side, one of the large loops carries anticodon

Question 5

Translation - Aminoacyl-tRNA synthetase

Answer 5

• tRNA recognizes the codon on mRNA, but not AA.
• All tRNAs have the same 3’-end.
• A second adapter, aminoacyl-tRNA synthetase (activating enzyme) is needed.
• Aminoacyl-tRNA synthetase is a cytosolic enzyme that binds AA to its corresponding tRNA.
• The enzyme catalyzes covalent attachment of the AA to tRNA, driven by ATP hydrolysis.
• The resulting aminoacyl tRNA is released from the enzyme.
• Aminoacyl tRNA delivers its amino acid to a growing polypeptide chain on a ribosome.

Question 6

Ribosome

Answer 6

• R has 2 subunits linked by Mg2+
• at least one molceule of rRNA is in each subunit plus dozens of ribosomal proteins
• largest rRNA performs role of PEPTIDYL TRANSFERASE or RIBOZYME and forms peptide bond

Question 7

Stages of translation

Answer 7

INITIATION
-small subunit recognizes mRNA by its cap at 5’ end. P factor is involved
- tRNA that carries 1st AA joins the complex
- mRNA binds with its anticodon - the peptidyl region of the small subunit
- Large subunit joins
- Proteins that are called initiation factors are needed

ELONGATION
A second aminoacyl-tRNA enters the aminoacyl (A)-region with help of an elongation factor called a
transport factor. If the anticodon matches the codon, the transport factor leaves the mRNA, which lodges in the A-site.

A and P Sections:
- anticodons of the two tRNAs are contiguous in the small subunit.
- at the catalytic center of the peptidyl transferase, the two amino acids are also contiguous.

Peptide Bond Formation:
- Ribozyme peptidyl transferase forms a peptide bond between the two amino acids.
- Cleaves the amino acid in the P-site from its tRNA.
- tRNA in the A-site now carries the growing peptide.

Translocation:
- An elongation factor called
translocase moves the ribosome one codon in the 5’-3’ direction.
- mRNA in the P-site is pushed out of the ribosome.
- mRNA with the peptide in the A-site moves to the P-site.

Cycle Continuation:
- A-site is free and ready to receive the next aminoacyl-tRNA.
- cycle continues, peptide chain grows, and the ribosome moves toward the 3’-end of the mRNA.

Energy Usage:
- Ribosome uses energy from GTP for its functions.

TERMINATION
- occurs when ribosome reaches a stop codon.
- no mRNA for it but it is recognized by proteins called releasing factors. - they change the activity of peptidyl transferase and cause it to hydrolyze the bond betw the last mRNA and the AA
- copleted olypeptide is releases
- whole complex falls apart

Question 8

Summary - Enzymes of translation

Answer 8

1. Aminoacyl-tRNA synthetase
   - cytosolic enzyme
   - binds AA to the corresponding tRNA
2. Peptidyl-transferase (ribozyme)
   - forms the peptide bond
   - it is part of the ribosome
3. Translocase
   - causes the ribosome to move one codon in the 5’–3’ direction