Protein Structure, Gene Function, and Mutations in Genetics

Protein Structure and Amino Acids

Amino Acids as Protein Subunits

Proteins are polymers made up of amino acids, which are linked together by peptide bonds. Each amino acid contains a central carbon atom (the alpha carbon), an amino group, a carboxyl group, a hydrogen atom, and a unique side chain (R-group) that determines its chemical identity.

• R-groups: Define the chemical properties and identity of each amino acid.

• Classification:

  • Nonpolar (hydrophobic): e.g., Glycine, Alanine, Valine

  • Polar (hydrophilic): e.g., Serine, Threonine

  • Positively charged (basic): e.g., Lysine, Arginine, Histidine

  • Negatively charged (acidic): e.g., Aspartic acid, Glutamic acid

• Peptide Bonds: Link amino acids between the carboxyl group of one and the amino group of another, forming a polypeptide chain.

Example: The sequence and chemical properties of amino acids determine the structure and function of proteins.

Levels of Protein Structure

Primary Structure

The primary structure of a protein is its unique sequence of amino acids.

• Primary level = amino acid sequence

• Encoded directly by the gene's nucleotide sequence.

Secondary Structure

Secondary structure refers to local folding of the polypeptide chain into structures such as alpha helices and beta sheets, stabilized by hydrogen bonds.

• Alpha helices and beta sheets are common motifs.

• Hydrogen bonds hold these structures together.

Tertiary Structure

The tertiary structure is the overall 3D conformation of a single polypeptide chain, resulting from interactions among R-groups.

• Includes hydrophobic interactions, ionic bonds, disulfide bridges, and hydrogen bonds.

Quaternary Structure

Quaternary structure exists only in proteins with more than one polypeptide subunit. Subunits associate through noncovalent bonds.

• Example: Hemoglobin is a protein with quaternary structure, composed of multiple polypeptide chains.

Gene-Protein Connection

How Are Proteins Connected with Genes?

Genes encode the sequence of amino acids in proteins. Mutations in genes can alter protein structure and function, leading to genetic disorders.

• Example: Phenylketonuria (PKU)

  • Autosomal recessive disorder

  • Defect in the gene encoding phenylalanine hydroxylase

  • Results in inability to convert phenylalanine to tyrosine

  • Can cause intellectual disability if untreated

One Gene-One Enzyme Hypothesis

Beadle and Tatum's experiments with mold (Neurospora) demonstrated that each gene encodes a specific enzyme, supporting the "one gene-one enzyme" hypothesis.

• Mutant strains unable to synthesize specific amino acids unless supplemented

• Genetic analysis used to determine biochemical pathways

Genetic Analysis in Mold: Prototrophs vs. Auxotrophs

Definitions

• Prototrophs: Wild-type strains that can grow on minimal medium.

• Auxotrophs: Mutant strains that require supplementation with specific nutrients.

Genetic experiments supplement minimal medium with amino acids to identify which biosynthetic step is blocked in mutants.

Mutations: Types and Effects

Types of Mutations

• Insertions/Deletions (Indels): Addition or removal of DNA nucleotides.

• Point Mutations (Substitutions): Change of a single nucleotide.

Point Mutation Outcomes

• Missense Mutation: Changes one amino acid to another.

• Nonsense Mutation: Converts a codon to a stop codon, truncating the protein.

• Silent Mutation: Alters a nucleotide without changing the amino acid (due to code redundancy).

• Synonymous: Similar chemical properties.

• Non-synonymous: Different chemical properties.

Classifying Point Mutations by Molecular Change

• Transition: Purine to purine (A↔G) or pyrimidine to pyrimidine (C↔T).

• Transversion: Purine to pyrimidine or vice versa.

Inheritance and Location of Mutations

• Somatic mutations: Occur in non-reproductive cells; not inherited.

• Germline mutations: Occur in reproductive cells; can be passed to offspring.

How Do Mutations Occur?

Sources of Mutation

• Spontaneous mutations: Result from natural biological processes (e.g., replication errors, tautomeric shifts).

• Induced mutations: Caused by external factors (e.g., chemicals, radiation).

Error Rates in Humans

• Translation errors: $1 \times 10^{-3}$ to $1 \times 10^{-4}$ amino acids

• Transcription errors: $1 \times 10^{-4}$ to $1 \times 10^{-5}$ nucleotides

• Replication errors: $1 \times 10^{-10}$ nucleotides (with proofreading)

• ~3 x 109 nucleotides in the human genome

Mechanisms of Spontaneous Mutation

• Replication errors: Wrong nucleotide inserted, slippage in repeat regions.

• Tautomeric shifts: Cause anomalous base-pairing.

• Depurination: Loss of a purine base, leading to random nucleotide insertion.

• Deamination: Conversion of amino group to keto group (e.g., cytosine to uracil).

Table: Types of Point Mutations and Their Effects

Type of Mutation	Molecular Change	Effect on Protein
Missense	Single nucleotide change	One amino acid replaced by another
Nonsense	Single nucleotide change	Codon changed to stop codon; truncated protein
Silent	Single nucleotide change	No change in amino acid sequence
Frameshift	Insertion/deletion (not in multiples of 3)	Alters reading frame; changes downstream amino acids

Genetic Analysis: Determining Biochemical Pathways

Use of Mutant Strains

• Mutants blocked at different steps in a pathway can be rescued by supplementing with intermediate compounds.

• Order of biochemical steps determined by which supplement restores growth.

Example: Arginine biosynthesis in Neurospora studied using mutants (Srb and Horowitz experiment).

Summary Equations

• Mutation Rate Equation: $\text{Mutation Rate} = \frac{\text{Number of mutations}}{\text{Total number of nucleotides}}$

• Peptide Bond Formation: $\text{Amino acid}_n + \text{Amino acid}_{n+1} \rightarrow \text{Peptide bond} + H_2O$

Additional info:

• Assigned reading: Chapter 14.8 (pp. 277, 279-281) covers gene mutation, DNA repair, and transposition.

• BRCA1 gene example illustrates the importance of silent vs. missense mutations in disease risk.