W1 CELLULAR LEVEL ORGANISATION

Chemical Level of Organisation

• Atoms and Atomic Structure
  • Matter: Anything with mass and volume; made of atoms.
  • Atoms: Basic units of matter, join to form chemicals with varied properties.
  • Subatomic particles:
    • Protons: Positive charge, 1 mass unit.
    • Neutrons: Neutral, 1 mass unit.
    • Electrons: Negative charge, very small mass.
  • Nucleus: Contains protons and neutrons.
  • Electron Cloud: Area around nucleus, contains electrons.
  • Atomic Number: Number of protons defines the element.

Electron Shells and Energy Levels

• Electron Shells: Layers of electrons, outermost shell (valence shell) determines bonding.
• Atomic Weight: Average mass based on isotopes.
• Isotopes: Atoms of the same element with different neutron numbers; can be radioactive (radioisotopes).
• Electron energy levels (shells): Lower shells fill first; outermost (valence) shell critical for chemical bonding.
• Reactivity: Determined by electron arrangement.

Molecules and Compounds

• Molecule: Two or more atoms joined by strong bonds.
• Compound: Atoms of different elements joined by bonds (not all molecules are compounds).
• Molecular Weight: Sum of atomic weights in a molecule/compound.

Chemical Bonds

• Ionic Bonds: Formed by transfer of electrons from donor (forms cation) to acceptor (forms anion).
  • Attraction between positive (cation) and negative (anion).
• Covalent Bonds: Atoms share electrons.
  • Single, double, or triple depending on pairs shared.
• Hydrogen Bonds: Weak, between slightly positive and slightly negative regions of molecules.
  • Important in water (surface tension).
• Nonpolar Covalent: Equal sharing.
• Polar Covalent: Unequal sharing creates polar molecules (e.g. water).

States of Matter

• Solid: Constant volume and shape.
• Liquid: Constant volume, shape changes.
• Gas: Changes volume and shape.

Chemical Reactions

• Involves formation or breaking of bonds.
• Reactants: Entering materials; Products: Produced materials.
• Metabolism: All chemical reactions in the body.
• Energy: Capacity for work (kinetic = motion, potential = stored).
• Chemical Energy: Potential energy in chemical bonds.

Types of Reactions

• Decomposition (Catabolism): Breaks bonds, e.g. AB \rightarrow A + B.
  • Hydrolysis: AB + H_2O \rightarrow AH + BOH.
• Synthesis (Anabolism): Forms bonds, e.g. A + B \rightarrow AB.
  • Dehydration Synthesis: AH + BOH \rightarrow AB + H_2O.
• Exchange: Involves both decomposition and synthesis, e.g. AB + CD \rightarrow AD + CB.
• Reversible Reactions: Can proceed in either direction (A + B \leftrightarrow AB), seek equilibrium.

Enzymes

• Protein catalysts: Lower activation energy needed for reactions.
• Saturation Limits: Max speed determined by substrate availability.
• Cofactors: Ions/molecules needed for enzyme function; coenzymes are non-protein organic cofactors (e.g. vitamins).
• Specificity: Only catalyse specific reactions.
• Regulation: Controlled by other chemicals.
• Denaturation: Loss of enzyme shape/function due to heat or pH changes.

Inorganic vs Organic Compounds

• Inorganic Compounds: Usually lack carbon; include water, acids, bases, salts.
• Organic Compounds: Always contain carbon and hydrogen; include carbohydrates, lipids, proteins, nucleic acids.

Properties of Water

• Body content: Makes up 2/3 of body weight.
• Solution: Solvent (liquid) + solutes (dissolved substances).
• Universal Solvent: Many substances dissolve in water.
• Reactivity: Participates in many reactions (hydrolysis, dehydration).
• High Heat Capacity: Absorbs/retains heat.
• Lubrication: Reduces friction in body tissues.

Aqueous Solutions

• Dissociation: Ionic compounds separate in water; ionisation produces ions.
• Hydration Spheres: Water surrounds ions, keeping them in solution.

Electrolytes

• Definition: Inorganic ions that conduct electricity in solution.
• Imbalance: Can disrupt vital functions.

Hydrophilic vs Hydrophobic

• Hydrophilic: Water-loving; ions and polar molecules.
• Hydrophobic: Water-fearing; nonpolar molecules (fats, oils).

Colloids and Suspensions

• Colloid: Solution with large molecules, e.g. plasma.
• Suspension: Large particles settle out, e.g. whole blood.

pH and Homeostasis

• pH: Measure of hydrogen ion (H^+)$ concentration.
• Neutral pH: 7.0 (pure water).
• Acidic: pH < 7 (high (H^+)).
• Basic (Alkaline): pH > 7 (low (H^+)).
• Blood pH: 7.35–7.45.
• Inverse scale: More (H^+) = lower pH; less (H^+) = higher pH.

Acids, Bases, Salts, Buffers

• Acids: Proton donors, increase (H^+) in solution.
• Bases: Proton acceptors, remove (H^+)$$ from solution.
• Strong acids/bases: Dissociate completely.
• Weak acids/bases: Incomplete dissociation, help balance pH.
• Buffers: Stabilise pH; e.g. carbonic acid–bicarbonate system.

Macromolecules of Life

• Monomers and Polymers
  • Monomer: Single subunit.
  • Polymer: Chain of monomers.

Carbohydrates

• Elements: C, H, O (1:2:1 ratio).
• Monosaccharides: Simple sugars (glucose, fructose, galactose).
• Disaccharides: Two monosaccharides (sucrose, maltose).
• Polysaccharides: Many sugars (glycogen, starch, cellulose).
• Isomers: Same formula, different structure.

Lipids

• Types: Fats, oils, waxes.
• Mainly hydrophobic (insoluble in water).
• Fatty acids: Long chains, may be saturated (no double bonds) or unsaturated (one or more double bonds).
  • Monounsaturated: One double bond.
  • Polyunsaturated: Two or more double bonds.
• Eicosanoids: Cannot be made by body; derived from diet (arachidonic acid).
  • Leukotrienes: Immune system.
  • Prostaglandins: Local hormones.
• Glycerides: Fatty acids + glycerol (mono-, di-, triglycerides); energy, insulation, protection.
• Steroids: Four-ring structure (e.g. cholesterol, sex hormones, corticosteroids, bile salts).
• Phospholipids/Glycolipids: Diglyceride + phosphate/sugar; key for cell membranes.

Proteins

• Most abundant/important organic molecules.
• Elements: C, H, O, N.
• Amino acids (20 types): Monomers of proteins.
• Peptide bond: Link between amino acids (forms polypeptides).
• Functions:
  • Support (structural)
  • Movement (contractile)
  • Transport (carrier proteins)
  • Buffering (pH)
  • Metabolic regulation (enzymes)
  • Coordination/control (hormones)
  • Defence (antibodies)
• Levels of Structure:
  • Primary: Amino acid sequence.
  • Secondary: Spirals/pleats (hydrogen bonds).
  • Tertiary: 3D folding.
  • Quaternary: Multiple polypeptide chains.

Enzymes (Revisited)

• Catalysts: Lower activation energy, unchanged after reaction.
• Active site: Binds substrate.
• Specificity, saturation, regulation.
• Cofactors/Coenzymes: Assist enzyme function.
• Denaturation: Loss of function by heat/pH.
• Glycoproteins: Protein + carbohydrate (enzymes, hormones, antibodies, plasma membranes).
• Proteoglycans: Protein + polysaccharide (increase viscosity).

Nucleic Acids

• RNA: Involved in protein synthesis.
• DNA: Stores genetic info, directs protein synthesis.
• Structure: Chains of nucleotides (pentose sugar, phosphate, nitrogenous base—A, G, C, T/U).
  • Pyrimidines: Cytosine, thymine (DNA), uracil (RNA).
  • Purines: Adenine, guanine.

High-Energy Compounds

• Derived from nucleotides.
• Phosphorylation: Addition of phosphate group; stores energy.
• ATP (Adenosine Triphosphate): Three phosphates, main energy currency.
• ADP (Adenosine Diphosphate): Two phosphates.
• AMP (Adenosine Monophosphate): One phosphate.
• ATPase: Enzyme converting ATP to ADP, releasing energy.