Chapter 5: Protein Synthesis

1. Structure of Protein

Proteins are made up of amino acids (a.a) linked together by peptide bonds. A polypeptide chain is a long chain of a.a linked together in a specific order. Proteins can be made up of one or more polypeptide chains.

a. Isomers of a.a:

• Naturally occurring a.a exist in the L form. This is the important isomer in biology because only L isomers participate in protein formation.

b. Hydrophobicity of the side chain:

• The larger the non-polar side chain, the higher the hydrophobicity. This is because the larger surface area of the side chain in contact with water leads to stronger hydrophobic interactions.

c. Chemical properties of a.a:

• At pH = 7, the amino and carboxyl groups of a.a are ionized. The amino group (NH2) will accept a proton (H+) and become NH3+, while the carboxyl group (COOH) will donate a proton and become COO-.

d. Amino acid encoding:

• Triplet codon: Each a.a is encoded by one or more triplet codons on the mRNA molecule. A codon is a sequence of three consecutive nucleotides on mRNA.
• Met and Trp are the only 2 a.a with only 1 codon. Met is encoded by AUG, Trp is encoded by UGG.

e. Encoding rules:

• In a codon, if the third position is a pyrimidine (C or U) then the codons will all encode for the same amino acid. For example: CUU, CUC, CUA, and CUG all encode for the a.a Leucine.

2. The main stages of protein synthesis

Protein synthesis is the process of creating proteins from the genetic information encoded in DNA. This process consists of three main stages:

a. Transcription:

• DNA is transcribed into mRNA.
• The enzyme that catalyzes this process is RNA polymerase.
• The mRNA, after being synthesized, will move from the nucleus to the cytoplasm.

b. Translation:

• mRNA is translated into a polypeptide chain.
• Translation takes place on ribosomes.
• Ribosomes move along mRNA and read the triplet codons.
• Each codon encodes for a specific a.a.
• tRNA carrying the corresponding a.a to the codon arrives at the ribosome to connect to the forming polypeptide chain.

c. Protein folding:

• The polypeptide chain after being synthesized will be folded into the characteristic 3D structure of the protein.
• This 3D structure determines the function of the protein.

Notes:

• Protein synthesis is a complex process and is tightly controlled by many different factors, including:
• Transcriptional control: regulating the level of gene transcription.
• Translational control: regulating the level of mRNA translation.
• Protein folding: ensuring that the protein is folded correctly.
• Errors in the protein synthesis process can lead to serious diseases.

3. The significance of protein synthesis

Protein synthesis is the most important process in living organisms. Proteins play an important role in all life processes:

• Catalyzing chemical reactions (enzymes)
• Transporting substances
• Structure of the body (muscles, bones, skin…)
• Protecting the body (antibodies)
• Regulating cell activity…

Conclusion

Protein synthesis is a complex but necessary process for life. Understanding this process helps us explain biological mechanisms and apply them in medicine, agriculture…