Gene Expression II: The Genetic Code and Protein Synthesis

Gene Expression II: The Genetic Code and Protein Synthesis

Introduction

This topic explores how genetic information stored in DNA is used to direct the synthesis of proteins, focusing on the genetic code and the experimental evidence that led to its discovery. Understanding these processes is fundamental to cell biology, as proteins carry out most cellular functions.

The Genetic Code

Definition and Significance

• Genetic Code: The set of rules by which the nucleotide sequence of DNA (or RNA) is translated into the amino acid sequence of proteins.

• The genetic code is universal (with rare exceptions), triplet-based, and degenerate (multiple codons can specify the same amino acid).

• Codon: A sequence of three nucleotides in mRNA that specifies a particular amino acid or a stop signal during translation.

Key Terms

• Gene: A segment of DNA that encodes a functional product (polypeptide or RNA).

• Coding Strand: The DNA strand whose sequence matches the mRNA (except T is replaced by U).

• Template Strand: The DNA strand that is used as a template for mRNA synthesis.

• Frameshift Mutation: A genetic mutation caused by insertions or deletions of nucleotides that change the reading frame of the genetic code.

• Alternative Splicing: The process by which different combinations of exons are joined together to produce multiple mRNA variants from a single gene.

• One-Gene One-Polypeptide Theory: The concept that each gene encodes a single polypeptide chain.

Experimental Evidence for the Genetic Code

Beadle and Tatum Experiment

George Beadle and Edward Tatum used the bread mold Neurospora crassa to demonstrate the relationship between genes and enzymes.

• They exposed the mold to X-rays to induce mutations.

• Mutants unable to grow on minimal medium but able to grow on complete medium were isolated.

• By supplementing minimal medium with specific amino acids or vitamins, they identified which metabolic step was blocked in each mutant.

• This led to the One-Gene One-Enzyme Hypothesis, later refined to the One-Gene One-Polypeptide Theory.

Table: Beadle and Tatum's Experimental Design

Type	Growth on Minimal Medium	Growth on Supplemented Medium	Blocked Step
Wild Type	Yes	Yes	None
Class I Mutant	No	Yes (with ornithine)	Gene A (Ornithine synthesis)
Class II Mutant	No	Yes (with citrulline)	Gene B (Citrulline synthesis)
Class III Mutant	No	Yes (with arginine)	Gene C (Arginine synthesis)

Relationship Between DNA, mRNA, and Protein

• The sequence of DNA bases determines the sequence of mRNA, which in turn determines the sequence of amino acids in a protein.

• Transcription copies the template strand of DNA into mRNA, replacing thymine (T) with uracil (U).

• Translation reads mRNA codons to assemble amino acids into a polypeptide chain.

Triplet Nature of the Genetic Code

• There are four DNA bases (A, T, C, G) and 20 amino acids.

• A doublet code (two bases per codon) yields only 16 combinations, insufficient for 20 amino acids.

• A triplet code yields 64 possible codons ($4^3 = 64$), more than enough for all amino acids.

Frameshift Mutations and the Triplet Code

• Frameshift mutations (insertions or deletions) shift the reading frame, altering the downstream amino acid sequence.

• Experiments by Crick and Brenner showed that adding or removing three nucleotides restored the reading frame, supporting the triplet nature of the code.

Degeneracy and Nonoverlapping Nature of the Code

• The genetic code is degenerate: most amino acids are specified by more than one codon.

• The code is nonoverlapping: each nucleotide is part of only one codon, and the reading frame advances three nucleotides at a time.

Cell-Free Systems and Deciphering the Code

• Marshall Nirenberg and J. Heinrich Matthaei used cell-free systems to study protein synthesis.

• They added synthetic RNAs of known sequence to these systems and observed which amino acids were incorporated.

• Homopolymers (e.g., poly(U)) led to the identification of codons for specific amino acids (e.g., UUU codes for phenylalanine).

• Gobind Khorana synthesized RNAs with alternating sequences to further assign codons to amino acids.

Start and Stop Codons

• Of the 64 possible codons, 61 code for amino acids.

• AUG is the start codon (also codes for methionine).

• UAA, UAG, UGA are stop codons, signaling termination of translation.

Universality and Ambiguity of the Genetic Code

• The genetic code is nearly universal across all organisms.

• Each codon has a single meaning (unambiguous), but many amino acids are specified by multiple codons (degenerate).

Summary Table: Properties of the Genetic Code

Property	Description
Triplet	Three nucleotides per codon
Degenerate	Multiple codons for most amino acids
Nonoverlapping	Each nucleotide belongs to one codon
Unambiguous	Each codon specifies only one amino acid
Nearly Universal	Same code used by most organisms

Example: DNA to Protein Sequence

• Coding strand: 5'-ATGGGCTC-3'

• Template strand: 3'-TACCCGAG-5'

• mRNA: 5'-AUGGGCUCG-3'

• Protein: Met-Gly-Ser

Additional info: The notes above expand on the original slides by providing definitions, context, and tables for clarity. The tables are inferred from the experimental design and properties of the genetic code as described in the slides.