Translation and the Genetic Code: From DNA to Protein

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Translation and the Genetic Code

Overview of Gene Expression

Gene expression is the process by which information encoded in DNA is used to direct the synthesis of proteins, which perform most cellular functions. This process involves two main steps: transcription (DNA to RNA) and translation (RNA to protein).

Transcription: The DNA sequence of a gene is transcribed to produce messenger RNA (mRNA).
Translation: The mRNA sequence is decoded by ribosomes to synthesize a specific polypeptide (protein).
Central Dogma: DNA → RNA → Protein.

Diagram of gene expression from DNA to protein

The Structure and Properties of Amino Acids

The 20 Common Amino Acids

Proteins are polymers of amino acids. Each amino acid has a central carbon (the α-carbon) bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable R group (side chain) that determines its properties.

Amino Group (NH2): Basic group.
Carboxyl Group (COOH): Acidic group.
R Group: Unique for each amino acid; determines chemical nature (nonpolar, polar, acidic, or basic).

General structure of an amino acid Structures and classifications of the 20 amino acids

Peptide Bond Formation

Amino acids are joined by peptide bonds, forming polypeptide chains. The peptide bond is a covalent bond between the carboxyl group of one amino acid and the amino group of the next.

Polypeptide Directionality: Free amino group at the N-terminus (start), free carboxyl group at the C-terminus (end).
Protein Structure: The sequence and chemical properties of amino acids determine the protein's 3D structure and function.

Peptide bond formation between amino acids

The Genetic Code

Codons and the Triplet Code

The genetic code is read in groups of three nucleotides, called codons, on the mRNA. Each codon specifies one amino acid. With four possible RNA bases (A, U, G, C), there are 64 possible codons, which is sufficient to encode all 20 amino acids.

Triplet Code: Each codon consists of three bases.
Non-overlapping: Codons are read one after another without overlap.
Degeneracy: Most amino acids are encoded by more than one codon.
Start Codon: AUG (methionine) signals the start of translation.
Stop Codons: UAA, UAG, UGA signal termination of translation.

Genetic code table showing codons and corresponding amino acids

Experimental Evidence for the Triplet Code

Crick and Brenner's experiments with bacteriophage T4 mutants demonstrated that the genetic code is read in triplets. Insertions or deletions of one or two bases disrupted protein function, but insertions or deletions of three bases restored function, supporting the triplet nature of the code.

Mutagenesis: Proflavin-induced insertions (+) or deletions (-) in DNA.
Revertants: Combinations of three insertions or deletions restored the reading frame and wild-type function.

Combined Mutations	+/- Designations	Result
FC 0, FC 21	+ –	Wild-type revertant
FC 40, FC 1	+ –	Wild-type revertant
FC 58, FC 1	+ –	Wild-type revertant
FC 0, FC 40, FC 58	+ + +	Wild-type revertant
FC 1, FC 21, FC 23	– – –	Wild-type revertant
FC 0, FC 40	+ +	rII mutant
FC 1, FC 21	– –	rII mutant

Bacteriophage T4 structure Bacteriophage infecting E. coli Bacteriophage life cycle Table of proflavin-induced mutations and revertants

Deciphering the Genetic Code

The genetic code was deciphered using synthetic RNAs and cell-free translation systems. Nirenberg and Khorana synthesized RNAs of known sequences and observed which amino acids were incorporated into polypeptides, allowing them to assign codons to amino acids.

Poly-U Experiment: Poly-U RNA directed synthesis of polyphenylalanine, showing UUU codes for phenylalanine.
Repeating Copolymers: Used to determine codons for other amino acids.
Final Assignment: All 64 codons were assigned to specific amino acids or stop signals.

Genetic code table

Properties of the Genetic Code

Triplet: Each codon is three bases.
Non-overlapping: Each base is part of only one codon.
No punctuation: The code is read continuously.
Start/Stop Codons: Specific codons signal initiation and termination.
Degenerate: Multiple codons for most amino acids.
Nearly Universal: The code is conserved across almost all organisms.

Genetic code table

Translation: From mRNA to Protein

The Role of tRNA

Transfer RNAs (tRNAs) are adapter molecules that match codons in mRNA with the correct amino acids during translation. Each tRNA has an anticodon that base-pairs with a codon in the mRNA and an acceptor stem that attaches to a specific amino acid.

Anticodon: Three-nucleotide sequence complementary to the mRNA codon.
Charging: Aminoacyl-tRNA synthetases attach the correct amino acid to the tRNA.
Wobble: The third base of the codon allows for flexible pairing, enabling one tRNA to recognize multiple codons.

tRNA anticodon pairing with mRNA codon

The Ribosome and Translation

The ribosome is the molecular machine that synthesizes proteins by reading the mRNA and catalyzing peptide bond formation. It has three binding sites for tRNA: the A (aminoacyl), P (peptidyl), and E (exit) sites.

Initiation: Ribosome assembles at the start codon (AUG) on the mRNA.
Elongation: Amino acids are added one by one as the ribosome moves along the mRNA.
Termination: When a stop codon is reached, the completed polypeptide is released.

Directionality of Translation

Translation proceeds from the 5' to 3' end of the mRNA, synthesizing the polypeptide from the N-terminus to the C-terminus.

Summary Table: Key Features of the Genetic Code

Feature	Description
Triplet	Each codon is three nucleotides
Non-overlapping	Codons are read sequentially, without overlap
Degenerate	Most amino acids have more than one codon
Start Codon	AUG (methionine)
Stop Codons	UAA, UAG, UGA
Universal	Code is nearly universal among organisms

Additional info: The Nobel Prize in Physiology or Medicine 1968 was awarded to Holley, Khorana, and Nirenberg for their work on deciphering the genetic code.