7.

3 Translation HL

Structure of tRNA:

a) Amino acid which is specific to each tRNA (at the 3’end)

(b) CCA base sequence to which the amino acid is attached

(c) Complementary base pairing sequence

(d) 8 free bases non-pairing giving one loop of RNA.

(e) 7 free bases non-pairing giving second loop of RNA.

(f) Small open loop of RNA (variable in shape between different tRNA)

(g) Anti-codon (3 bases)

 Composed of a single chain of nucleotides

 At the 3' end of the tRNA there is the nucleotide sequence CCA to which the amino acid attaches
to.
 Has an anticodon of 3 bases that binds to the mRNA codon.
 Has double stranded sections:
 formed by base pairing
 via hydrogen bonds
 helical in shape.
 Has 3 loops of free bases non pairing (sometimes with an extra open loop which vary in shape
between different tRNA.
 Has a distinctive 3 dimensional structure

The role of tRNA-activating enzyme/ how does the tRNA attach to the correct amino acid?

1. There are many different types of tRNA

2. Each tRNA activating enzyme recognizes a specific tRNA
molecule
3. There are 20 different tRNA-activating enzymes as there are 20
different amino acids.
4. The different chemical properties and three dimensional
structure of each tRNA allows the tRNA-activating enzymes to
recognize their specific tRNA
5. Each tRNA enzyme binds a specific amino acid to the tRNA
molecule

1
 6. The tRNA-activating enzyme will bind the amino acid to the tRNA with the matching anticodon
at the 3’ end with CCA sequence.
7. Energy from ATP is needed during this process and phosphorylation takes place.
8. When the amino acid binds to the tRNA molecule a high energy bond is created. The energy
from this bond is used later on to bind the amino acids to the growing polypeptide chain during
translation.

Structure of Ribosomes

 made up of proteins and ribosomal RNA.

 70s in prokaryotes/ 80s in eukaryotes
 have two subunits: large and small subunits
 Large subunit has three binding sites for tRNA molecules ( E, P and A site). However, not more
than two tRNA molecules can bind to the ribosome at one time.
 A site: aminoacyl site - the position where the new tRNA binds codon
 P site: Peptidyl site – the position in which the amino acid on the tRNA adds to the
polypeptide.
 E site: Exit site – the position where the tRNA is released

 Small subunit has a binding site for mRNA

 Could be of two types:
 Free ribosomes: synthesize proteins for use primarily within the cell.
 Bound ribosomes (to RER): synthesize proteins primarily for secretion or for use in
lysosomes.

Translation

• Formation of a polypeptide
• Occurs in cytoplasm (ribosomes: free/bound)

2
 • Occurs in a 5'→3' direction
• Requires ATP
• Consists of 3 stages: initiation, elongation and termination.

Before initiation:

tRNA activating enzyme links the corresponding amino acid to the specific tRNA with the matching
anticodon.

Initiation:

1. Involves assembly of the components that carry out the process (tRNA, mRNA and ribosome).
2. Formation of the initiation complex:
• mRNA binds to the small subunit of the ribosome.
• ribosome slides along mRNA to the start codon
• the anticodon of 1st tRNA carrying methionine, pairs with the start codon ‘AUG’ by
complementary base pairing.
• the large subunit of the ribosome joins the complex and binds to the smaller one where
the 1st tRNA is at the P site.

Elongation: (formation of the polypeptide chain)

1. 2nd tRNA pairs with next codon at A site

2. Methionine is transferred to the amino acid of the 2nd tRNA
3. The two amino acids join by a peptide bond
4. Ribosomes move along the mRNA by one codon from 5' to 3' direction
5. This will shift the 1st tRNA to the E site without its amino acid, and the 2 nd tRNA to the P site.
6. The 1st tRNA is released at the E site.
7. another tRNA pairs with the next codon at A site.
8. Amino acids join at the P site by a peptide bond (the polypeptide chain form at the P site)
9. Ribosomes move along the mRNA by one codon
10. As this process continues, the polypeptide is elongated until a stop codon is reached.

Termination:

1. Termination starts when a stop codon is reached.

2. Disassembly of the components:
 mRNA and the ribosomes detach from one another.
 The polypeptide chain is released
 the tRNA return to be charged with more amino acid.
 the mRNA detaches from the ribosome

3
  the subunits of the ribosome separate

Many ribosomes can translate the same mRNA at the same time. They will all move along the mRNA in a
5'→3' direction. These groups of ribosomes on a single mRNA are called polysomes.

Translation can occur immediately after transcription in prokaryotes due to the absence of a nuclear
membrane.

Identification of polysomes in electron micrographs of prokaryotes and eukaryotes

4
Proteins structures:

Each amino acid has unique properties such as:

- Polar or nonpolar
- Basic or acidic
Acidic amino acids have R groups that tend to lose H + and become negative.
Basic amino acids have R groups that tend to gain H + and become positive.
- Some contain sulfur (S)

Interactions between R groups in proteins:

1. Hydrogen bonds
Can form between N-H and C=O groups, if they are brought close together. As a result,
two structures might form:
a) Α-helix
Develops when the polypeptide is wound into a right-handed helix and H bonds
form between adjacent turns of the helix.
b) β-pleated sheet
Develops when sections of polypeptide run parallel and H bonds form between
them. 5
There are four levels of protein structure:

Primary Structure:

• its amino acid sequence.

• Amino acids in the chain are joined by a peptide bond
• The sequence of amino acids will determine the structure of the 3D protein

Secondary Structure:

6
  Repeating regions within the protein
 Two forms: α-helices and β-pleated sheets.
 Due to hydrogen bonds between amino acids

Tertiary Structure:

• 3-D conformation of a polypeptide

• occurs as a result of the protein folding.
• stabilized by interactions between the R groups of different amino acids, which include:

1. hydrogen bonds
2. hydrophobic interactions:
hydrophilic polar amino acids orient to the outside, whereas hydrophobic non-polar amino acids
protected in the core
3. Ionic bonds: oppositely charged ions attract
4. Disulphide bridges: formed between sulphur-containing amino acids.

Ex. tRNA is a tertiary protein

Quaternary Structure:

• two or more polypeptide chains associate

• An example is haemoglobin which consists of four polypeptide chains.

7
• In some cases, some proteins can have a non-polypeptide structure called a prosthetic group.
The haem group in haemoglobin is a prosthetic group.

Quaternary proteins

2 or more polypeptides 2 or more polypeptides + prosthetic group

(non-polypeptide)
(Conjugated proteins)