How Genes Work: From DNA to Protein and Mutation Chapter 16

How Genes Work

Introduction to Gene Expression

Understanding how genes function at the molecular level is central to modern biology. While the roles of DNA, heredity, chromosomes, and genes were established, the process by which genetic information is converted into functional molecules—known as gene expression—remained unclear for many years. Gene expression is the process of converting information in DNA into functioning molecules within the cell, primarily proteins.

What Do Genes Do?

The One-Gene, One-Enzyme Hypothesis

Beadle and Tatum pioneered the study of gene function by creating defective genes and observing their effects on phenotype. Nonfunctioning alleles, called null or loss-of-function alleles, were generated in bread mold (Neurospora crassa) using irradiation. Mutants unable to synthesize certain compounds revealed that each gene contains the information to make a specific enzyme. This led to the one-gene, one-enzyme hypothesis, later refined to the one-gene, one-polypeptide hypothesis as it became clear that not all proteins are enzymes and some proteins are composed of multiple polypeptides.

• Null allele: A nonfunctioning version of a gene.

• Genetic screen: A technique to identify mutants with specific defects.

• Example: Srb and Horowitz used a three-step metabolic pathway for arginine synthesis to show that each mutant lacked a different enzyme, supporting the hypothesis.

The Genetic Code Hypothesis

Francis Crick proposed that the sequence of bases in DNA acts as a code, with different combinations specifying the 20 amino acids. A gene is a stretch of DNA that specifies the amino acid sequence of a protein. However, the information in DNA is not directly translated into protein; instead, an intermediary is required.

RNA as the Intermediary

Jacob and Monod suggested that RNA serves as the link between genes in the nucleus and protein synthesis in the cytoplasm. Messenger RNA (mRNA) carries genetic information from DNA to the site of protein synthesis. The enzyme RNA polymerase synthesizes RNA using a DNA strand as a template, copying the code by matching complementary nucleotides.

The Central Dogma of Molecular Biology

The central dogma summarizes the flow of genetic information in cells:

• DNA codes for RNA, which codes for proteins.

• Genes are stretches of DNA that code for proteins.

• DNA sequence codes for RNA sequence; RNA sequence codes for amino acid sequence in proteins.

The Roles of Transcription and Translation

• Transcription: The process of using a DNA template to make a complementary RNA molecule (copying information).

• Translation: The process of using information in mRNA to synthesize proteins (interpreting nucleotide language into amino acids).

Linking Genotypes to Phenotypes

An organism’s genotype is determined by the sequence of bases in its DNA, while its phenotype is the product of the proteins it produces. Different alleles of the same gene have different DNA sequences, resulting in proteins with different amino acid sequences and, consequently, different phenotypes.

Modifications to the Central Dogma

Not all genes code for mRNAs that are translated into proteins; some RNAs have important functions on their own. Additionally, in some viruses, information can flow from RNA back to DNA via the enzyme reverse transcriptase.

The Genetic Code

Structure and Properties of the Genetic Code

The genetic code specifies how a sequence of nucleotides codes for a sequence of amino acids. George Gamow predicted that each "word" in the code contains three bases, known as a triplet code, which is the minimum needed to specify 20 amino acids.

• Codon: A group of three bases that specifies a particular amino acid.

• Crick and Brenner confirmed that codons are read in triplets, and the reading frame is critical for correct translation.

Cracking the Code

Nirenberg and Leder determined which codons code for each amino acid. There is one start codon (AUG) that codes for methionine and signals the start of protein synthesis, and three stop codons (UAA, UAG, UGA) that signal the end of the protein-coding sequence. The remaining 60 codons code for amino acids.

Analyzing the Code

• Redundant: All but two amino acids are encoded by more than one codon.

• Unambiguous: Each codon codes for only one amino acid.

• Non-overlapping: Codons are read one at a time.

• Nearly universal: Most organisms use the same code.

• Conservative: Codons for the same amino acid often share the first two bases.

The Value of Knowing the Code

Understanding the genetic code and the central dogma allows biologists to predict the amino acid sequence from a DNA sequence and vice versa. Due to redundancy, multiple DNA sequences can code for the same amino acid sequence.

Types and Consequences of Mutation

Definition and Types of Mutation

A mutation is any permanent change in an organism’s DNA, resulting in a modification of its genotype and potentially creating new alleles. Mutations can be classified as:

• Point mutations: Changes in one or a small number of bases.

• Chromosome-level mutations: Larger-scale changes affecting chromosome structure or number.

Point Mutations

• Missense mutations: Change an amino acid in the protein.

• Silent mutations: Do not change the amino acid sequence due to redundancy in the code.

• Frameshift mutations: Shift the reading frame, altering the meaning of all subsequent codons.

• Nonsense mutations: Change a codon specifying an amino acid into a stop codon.

Mutations can be beneficial (increase fitness), neutral (no effect), or deleterious (decrease fitness). Most point mutations are neutral or deleterious. Some mutations outside coding regions can affect phenotype by altering gene expression.

Chromosome Mutations

• Inversion: A chromosome segment breaks off, flips, and rejoins.

• Translocation: A segment breaks off and attaches to another chromosome.

• Deletion: A segment is lost.

• Duplication: A segment is present in multiple copies.

Chromosome mutations, like point mutations, can be beneficial, neutral, or deleterious. Cancer cells often exhibit deleterious chromosome mutations, which can be visualized using a karyotype (the complete set of chromosomes in a cell).

Summary Table: Consequences of Point Mutations

Type of Mutation	Effect on Protein	Potential Impact
Missense	Changes one amino acid	Variable (beneficial, neutral, or deleterious)
Silent	No change in amino acid	Usually neutral
Frameshift	Alters reading frame	Usually deleterious
Nonsense	Introduces premature stop codon	Usually deleterious

Additional info: The central dogma can be summarized by the following equations:

• Transcription: $\mathrm{DNA} \rightarrow \mathrm{RNA}$

• Translation: $\mathrm{RNA} \rightarrow \mathrm{Protein}$