Amino Acids and Proteins

Structure and Properties of Amino Acids

Amino acids are the fundamental building blocks of proteins. They share a common structure but differ in their side chains, which determine their properties and functions.

• Amino Acid Structure: Each amino acid contains a central carbon (the alpha carbon, Cα), an amino group (–NH2), a carboxyl group (–COOH), a hydrogen atom, and a unique side chain (R group).

• L-amino acids: Only L-amino acids are found in ribosomally synthesized proteins. D-amino acids are rare in nature.

• Alpha-amino acids: The term refers to the amino group being attached to the alpha carbon.

• Chirality: Most amino acids (except glycine) are chiral, meaning they exist in L- and D- forms. Proteins use L-amino acids.

• Classification: Amino acids are classified by their side chains as hydrophobic, hydrophilic uncharged, acidic, or basic.

• Isoelectric Point (pI): The pH at which an amino acid (or protein) has no net charge.

• Acid/Base Properties: Amino acids can act as acids or bases, and their charge changes with pH.

Example: Glycine is the simplest amino acid, with a hydrogen as its side chain.

Additional info: The general formula for an amino acid is:

Protein Structure and Function

Proteins are polymers of amino acids, folded into complex structures that determine their function.

• Four Levels of Protein Structure:

  • Primary: Sequence of amino acids.

  • Secondary: Local folding (e.g., alpha helix, beta sheet).

  • Tertiary: Overall 3D shape.

  • Quaternary: Association of multiple polypeptide chains.

• Interactions Determining Structure: Hydrogen bonds, ionic interactions, hydrophobic effects, disulfide bonds.

• Native Structure: The functional, folded form of a protein.

• Denaturation: Loss of native structure due to heat, pH, chemicals.

• Essential Amino Acids: Amino acids that must be obtained from the diet.

• Protein Examples: Keratin, collagen, hemoglobin, myoglobin, insulin.

• Protein Hydrolysis: Breaking peptide bonds to yield amino acids.

Example: Hemoglobin is a quaternary protein with four subunits, each binding oxygen.

Applications and Techniques

• Electrophoresis: Technique to separate proteins by charge and size.

• Proteins in Diet: Essential for growth and repair.

• Sickle-Cell Anemia: Caused by a mutation in hemoglobin, leading to altered protein structure.

Enzymes and Vitamins

Enzyme Structure and Function

Enzymes are biological catalysts that speed up chemical reactions in living organisms.

• Definition: Proteins (or RNA) that catalyze biochemical reactions.

• Turnover Number: Number of substrate molecules converted per enzyme per second.

• Cofactors: Non-protein helpers; can be metal ions or coenzymes.

• Seven Main Classes of Enzymes: Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, Ligases, Translocases.

• Lock-and-Key vs. Induced Fit: Models for enzyme-substrate interaction.

• Catalytic Mechanisms: Enzymes lower activation energy by proximity, orientation, and transition state stabilization.

• Catalytic Triad: A group of three amino acids (often Ser, His, Asp) found in some enzymes, e.g., acetylcholine esterase.

• Factors Affecting Activity: Substrate concentration, temperature, pH.

Example: Amylase catalyzes the breakdown of starch into sugars.

Enzyme Regulation and Inhibition

• Regulation Types: Allosteric, feedback/feedforward, competitive/noncompetitive, reversible/irreversible, covalent modification (zymogens, phosphorylation).

• Enzyme Inhibitors: Used as drugs to block enzyme activity.

Vitamins and Cofactors

• Vitamins: Organic molecules required in small amounts; often act as coenzymes.

• Lipid-soluble Vitamins: A, D, E, K.

• Water-soluble Vitamins: C, B3 (niacin), B5 (pantothenic acid).

• Examples: Vitamin C (ascorbic acid), Vitamin A (retinol), Vitamin D (calciferol), Vitamin E (tocopherol), Vitamin K (phylloquinone).

Additional info: Cofactors are essential for enzyme function, and deficiencies can lead to disease.

Nucleic Acids and Protein Synthesis

Structure of Nucleic Acids

Nucleic acids (DNA and RNA) store and transmit genetic information.

• Composition: Phosphate, sugar (ribose or deoxyribose), and nitrogenous base.

• Bases: Adenine (A), Thymine (T), Guanine (G), Cytosine (C), Uracil (U).

• Purines: A, G; Pyrimidines: C, T, U.

• Nucleoside: Sugar + base; Nucleotide: Sugar + base + phosphate.

• Phosphodiester Linkages: Connect nucleotides in a chain.

Example: DNA is a double helix with base pairing: G-C and A-T.

Replication, Transcription, and Translation

• Replication: DNA is copied by DNA polymerase at replication forks, using nucleoside triphosphates. Occurs in 5' to 3' direction, creating Okazaki fragments on the lagging strand.

• Transcription: RNA polymerase synthesizes RNA from DNA template. Initiation occurs at promoter (TATA box), termination in bacteria by hairpin structure.

• Translation: mRNA is decoded by ribosomes to synthesize proteins. tRNA brings amino acids, rRNA forms ribosome structure. Methionine (AUG) is the start codon; stop codons terminate translation.

• Ribosome Structure: Large and small subunits; A, P, and E sites for tRNA movement.

• Splicing: Introns are removed, exons are expressed in mature mRNA.

Example: The genetic code is a set of three-base codons; AUG codes for methionine.

Genomics and Genetic Engineering

Human Genome and Sequencing

The human genome contains all genetic information, organized into chromosomes.

• Genome Size: ~3 billion base pairs (haploid), 23 pairs of chromosomes.

• Protein-coding Genes: ~20,000 in humans.

• Sequencing Strategies: Shotgun sequencing, Sanger dideoxy sequencing, and next-generation sequencing (NGS).

• NGS: All methods allow rapid, parallel sequencing of DNA.

Example: Shotgun sequencing breaks DNA into fragments, sequences them, and assembles the genome.

Mutations and Genetic Diseases

• Mutation: Change in DNA sequence; includes point mutations, insertions, deletions.

• SNPs: Single nucleotide polymorphisms; many genetic diseases are linked to specific SNPs.

• Genetic Diseases: Caused by specific mutations in genes.

DNA Technology and Genetic Engineering

• PCR (Polymerase Chain Reaction): Technique to amplify DNA sequences.

• DNA Fingerprinting: Uses PCR and restriction enzymes to identify individuals.

• Recombinant DNA: Cutting and pasting DNA using restriction enzymes and DNA ligase.

• Genetic Engineering: Benefits include disease treatment, agriculture; concerns include ethics and safety.

• CRISPR-Cas9: Genome editing tool; Cas9 cuts DNA at specific sequences, guided by RNA. Allows precise genetic modifications.

Example: CRISPR-Cas9 can be used to correct genetic mutations or introduce new traits.

Summary Table: Key Biomolecules and Functions

Additional info: Table summarizes the main biomolecules discussed in chapters 18, 19, 26, and 27.