Biomolecules

Introduction to Biochemistry

• Definition: The study of molecules and their reactions in living organisms.
• Key Areas:
  • Structures, functions, and interactions of biomolecules.
  • Major classes include proteins, carbohydrates, lipids, and nucleic acids.
  • Foundational concept: Chemical basis of life.

Amino Acids

• Structure: Amino acids contain an alpha carbon (α) bonded to:
  • A carboxylate group (-COO-)
  • A protonated amino group (-NH3+)
• Physiologic pH: At physiological pH, amino acids exist as zwitterions (neutral molecules) with equal positive and negative charges.

Common Amino Acids

• There are 20 common amino acids; each has:
  • A name
  • A 3-letter abbreviation
  • A 1-letter code
• Variation: 19 out of 20 amino acids differ only in their side chain (R group).

Classes of Amino Acids

• Amino acids can be classified based on the polarity of their side chains:
  • Hydrophobic: Nonpolar side chains (e.g., Glycine, Alanine, Valine).
  • Polar, Neutral: Have some affinity for water but are not ionic (e.g., Serine, Threonine).
  • Positively Charged: Basic side chains that attract hydroxide anions in water (e.g., Lysine, Arginine, Histidine).
  • Negatively Charged: Acidic side chains that contain ionized carboxyl groups (e.g., Aspartate, Glutamate).

Protein Structure

• Four Levels of Protein Structure:
  1. Primary Structure: Sequence of amino acids in a polypeptide chain; held together by peptide bonds.
  2. Secondary Structure: Local folds in the polypeptide chain (e.g., α-helix, β-pleated sheet); stabilised by hydrogen bonding between backbone amide hydrogens and carbonyl oxygens.
  3. Tertiary Structure: The overall 3D shape of the protein, created by side chain interactions, including salt bridges, hydrogen bonds, hydrophobic interactions, and disulfide bridges.
  4. Quaternary Structure: The assembly of multiple polypeptide chains into a single protein complex, maintained by the same interactions as tertiary structure.

Biological Functions of Proteins

• Proteins, or "of first importance", play crucial roles in biological processes:
  • Enzymes: Biological catalysts that accelerate reactions.
  • Antibodies: Defense mechanisms against pathogens.
  • Transport Proteins: Carry substances across membranes.
  • Regulatory Proteins: Involved in signaling pathways.
  • Structural Proteins: Provide support and shape to cells and organisms.

Lipids

• Energy Source: Lipids yield 9 kcal of energy per gram; triglycerides store energy.
• Cell Membrane Components: Include phosphoglycerides, sphingolipids, and steroids.
• Classes of Lipids:
  • Fatty Acids: Can be saturated or unsaturated; have hydrocarbon chains.
  • Glycerides: Formed by the esterification of glycerol with fatty acids (e.g., triglycerides).
  • Complex Lipids: Include sphingolipids and steroids.

Fatty Acids

• Structure: Long chain carboxylic acids, typically 10-20 carbons.
• Saturation: Saturated fatty acids contain no double bonds; unsaturated fatty acids have one or more.

Melting Points

• The presence of double bonds in fatty acids lowers melting points, affecting physical state (oil vs. fat).

Carbohydrates

• Definition: Composed of carbon, hydrogen, and oxygen, often following the formula (CH2O)n.
• Types:
  • Monosaccharides: Simple sugars (e.g., glucose, fructose).
  • Disaccharides: Two monosaccharides linked (e.g., sucrose, lactose).
  • Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen).

Glycosidic Bonds

• Formed between monosaccharides during condensation reactions.

Nucleic Acids

• Types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
• Function:
  • DNA stores genetic information, while RNA is involved in protein synthesis.
• Nucleotide Structure: Composed of a nitrogenous base, pentose sugar, and phosphate group.
• DNA Structure: Double helix with antiparallel strands and specific base pairing between adenine-thymine and guanine-cytosine.

Central Dogma of Molecular Biology

• Outlines the flow of genetic information:
  • DNA -> RNA (transcription)
  • RNA -> Protein (translation)