Lecture 11 and 12 (ch13&14)

Genetic Code and Translation

Introduction

The genetic code and translation are central processes in molecular genetics, enabling the conversion of genetic information stored in DNA into functional proteins. This process involves several steps and components, including mRNA, tRNA, ribosomes, and various enzymatic factors.

Structure and Function of Proteins

Amino Acids: Building Blocks of Proteins

• Amino acids are organic molecules that serve as the monomers of proteins. There are 20 common amino acids found in proteins.

• Each amino acid has a similar structure: an amino group (–NH2), a carboxyl group (–COOH), a hydrogen atom, and a unique R group (side chain) attached to a central carbon atom.

• Polarity and chemical properties of the R group determine the behavior and function of each amino acid.

• Example: Glycine has a hydrogen as its R group, making it the simplest amino acid.

Levels of Protein Structure

• Primary structure: The linear sequence of amino acids in a polypeptide chain.

• Secondary structure: Local folding patterns such as alpha helices and beta sheets, stabilized by hydrogen bonds.

• Tertiary structure: The overall three-dimensional shape of a single polypeptide, determined by interactions among R groups.

• Quaternary structure: The assembly of multiple polypeptide chains into a functional protein complex.

• Example: Hemoglobin is a quaternary protein composed of four polypeptide subunits.

Genetic Code

Properties of the Genetic Code

• The genetic code uses mRNA nucleotides as "letters" to spell out instructions for protein synthesis.

• Each "word" in the code, called a codon, consists of three nucleotides (triplet code).

• The code is non-overlapping and continuous, meaning codons are read one after another without gaps or overlaps.

• The code is degenerate: multiple codons can specify the same amino acid.

• The code is (almost) universal across organisms.

Codons and Amino Acids

• A codon specifies an amino acid in a protein, except for "stop" codons which signal termination of translation.

• There are 64 different codons (61 coding for amino acids, 3 for stop signals).

• Only 20 amino acids are encoded, so the code is degenerate.

• Start codon: AUG (codes for methionine, initiates translation).

• Stop codons: UAA, UAG, UGA (terminate translation).

• The code is nearly universal, with rare exceptions in some organisms and organelles.

Table: Codon Possibilities

Word length (nucleotides)	Number of possible words
1	$4^1 = 4$
2	$4^2 = 16$
3	$4^3 = 64$

Degeneracy and Wobbling

• Degeneracy: Some amino acids are specified by more than one codon (synonymous codons).

• Maximum degeneracy is six codons for some amino acids (e.g., Serine, Arginine, Leucine).

• Wobble hypothesis: The third nucleotide in a codon is less critical for tRNA recognition, allowing flexibility and fewer tRNAs than codons.

• Example: Inosine in tRNA can pair with A, U, or C in the third codon position.

tRNA Charging

tRNA Structure and Function

• tRNAs are adaptor molecules that bring specific amino acids to the ribosome during translation.

• Each tRNA has a characteristic cloverleaf structure and contains rare modified bases.

• Each amino acid is recognized by a specific aminoacyl-tRNA synthetase, which attaches the correct amino acid to its tRNA.

tRNA Charging Mechanism

• Charging is the process of linking a tRNA molecule to its corresponding amino acid.

• Two-step process:

  1. Amino acid is activated by attachment of AMP, forming aminoacyl adenylate.

  2. Aminoacyl group is transferred to the 3' hydroxyl group of the terminal adenosine of tRNA, resulting in charged aminoacyl-tRNA.

• Equation: $ext{Amino acid} + ext{tRNA} + ext{ATP} ightarrow ext{Aminoacyl-tRNA} + ext{AMP} + ext{PP}_i$

Translation

Translation Overview

• Translation is the process by which ribosomes synthesize proteins using mRNA as a template.

• Occurs in three main stages: Initiation, Elongation, and Termination.

Translation Initiation

• In bacteria, the Shine-Dalgarno sequence helps ribosome binding to mRNA.

• Initiator tRNA (charged with methionine) binds to the P site of the ribosome.

• Initiation factors (IF1, IF2, IF3) assist in assembly of the initiation complex.

• GTP hydrolysis triggers joining of the large ribosomal subunit and release of initiation factors.

Translation Elongation

• Ribosome selects aminoacyl-tRNA complementary to the mRNA codon at the A site.

• Peptide bond forms between amino acids, catalyzed by peptidyl transferase activity of the ribosome.

• Ribosome translocates, moving the growing peptide to the P site and freeing the A site for the next tRNA.

Translation Termination

• Stop codons (UAA, UAG, UGA) signal the end of translation.

• Release factors recognize stop codons and promote release of the polypeptide chain.

• Ribosome dissociates and is recycled for further rounds of translation.

Polyribosomes (Polysomes)

• Multiple ribosomes can simultaneously translate a single mRNA molecule, forming a polyribosome or polysome.

• This increases the efficiency of protein synthesis.

Translation in Prokaryotes vs. Eukaryotes

Comparison of Translation Mechanisms

Feature	Prokaryotes	Eukaryotes
Ribosome size	70S (30S + 50S)	80S (40S + 60S)
Initiation sequence	Shine-Dalgarno	Kozak sequence (some genes)
Location	Cytoplasm	Cytoplasm (translation), Nucleus (transcription)
mRNA structure	Polycistronic	Monocistronic
Ribosome association	Free-floating	Often associated with endoplasmic reticulum

Post-Translational Modifications (PTMs)

Protein Modifications and Stability

• After translation, proteins may undergo post-translational modifications (PTMs) such as phosphorylation, methylation, acetylation, and glycosylation.

• PTMs can affect protein folding, stability, activity, and cellular localization.

• Protein folding is assisted by chaperone proteins, which help maintain proper structure and prevent aggregation.

• Misfolded proteins can form amyloid aggregates and cause diseases such as prion disorders.

Additional info:

• Exceptions to the universal genetic code exist in some mitochondria, bacteria, and viruses.

• Inosine in tRNA is a modified base that allows wobble pairing, increasing the efficiency of translation.

• Svedberg units (S) measure the sedimentation rate of ribosomal subunits during centrifugation.