Complete CAPE Biology Unit 1 Study Notes: Module 1

BIOLOGY UNIT 1: ASPECTS OF BIOCHEMISTRY

1. Water

The Structure of a Water Molecule

• Molecular Composition: Water ($H_2O$) consists of one oxygen atom covalently bonded to two hydrogen atoms. These are single covalent bonds where oxygen shares one electron with each hydrogen.
• Electron Configuration: Oxygen has six outer-shell electrons. Two are used for bonding, leaving four electrons organized into two non-bonding pairs.
• Polarity and Dipoles: Electrons in the covalent bonds are shared unequally. The oxygen atom pulls electrons toward its nucleus, gaining a small negative charge ($\delta-$), while hydrogen atoms gain small positive charges ($\delta+$). This unequal charge distribution creates a permanent dipole.
• Molecular Geometry: The two hydrogen atoms are positioned on one side of the oxygen atom, creating a V-shape with a bond angle of approximately $104.5^\circ$.

Hydrogen Bonding

• Definition: A weak electrical attraction between the $\delta+$ hydrogen of one water molecule and the $\delta-$ oxygen of another.
• Dynamic Nature: In liquid water, these bonds constantly break and reform as molecules move. In ice, each molecule is hydrogen-bonded to four neighbors in a stable lattice.
• Biological Importance: Hydrogen bonds are "long-distance" relative to covalent bonds and are crucial for the structure of proteins and DNA.

States of Water and Density

• Kinetic Energy:
  • Ice: Molecules have little kinetic energy, vibrating in fixed positions.
  • Liquid Water: Molecules move past each other, forming fleeting bonds.
  • Water Vapour: Molecules are far apart with minimal interaction.
• Structure of Ice: As water cools, molecules slow down and form the maximum four hydrogen bonds, creating a rigid, open lattice. This lattice holds molecules further apart than in liquid form.
• Density Anomaly: Water is most dense at $4\,^\circ\text{C}$. Ice is less dense than liquid water and floats. This insulates aquatic life below the surface and prevents bodies of water from freezing solid.

Thermal Properties of Water

• Specific Heat Capacity: The energy required to raise the temperature of $1\,\text{g}$ of a substance by $1\,^\circ\text{C}$. For water, this is $4.2\,\text{J/g}^\circ\text{C}$. High energy is needed to break hydrogen bonds before the temperature can rise, ensuring thermal stability in organisms and aquatic environments.
• Latent Heat of Vaporisation: The energy required to turn liquid into gas. Evaporation of water (like sweat) requires significant heat to break bonds, providing a powerful cooling mechanism for terrestrial organisms.
• Latent Heat of Fusion: The energy required to change water from solid to liquid ($300\,\text{J/g}$). This high value makes it difficult for cytoplasm to freeze, protecting cells from crystal damage.

Solvent and Chemical Properties

• Solvent Versatility: Water's dipoles attract ions (like $Na^+$ and $Cl^-$) and polar molecules (like glucose). The water molecules surround the solute, breaking ionic bonds or forming new hydrogen bonds to keep them in solution.
• Metabolic Reactions: Most chemical reactions in the body occur in solution so that ions/molecules can come into contact. Water also acts as a reactant in hydrolysis and a product in condensation.
• Cohesion and Surface Tension: Water molecules stick together (cohesion) allowing mass flow in xylem and blood vessels. High surface tension allows small organisms to walk on water.
• pH and Buffering: Pure water dissociates into equal parts $H^+$ and $OH^-$, giving it a neutral pH of 7.0. Biological fluids are often buffered between pH 7 and 8.

2. Carbohydrates

Monosaccharides (Simple Sugars)

• General Formula: $(CH_2O)_n$. They are soluble in water and taste sweet.
• Classification by Carbon Number:
  • Trioses (3C): e.g., Glyceraldehyde (first carbohydrate in photosynthesis).
  • Pentoses (5C): e.g., Ribose (RNA), Deoxyribose (DNA).
  • Hexoses (6C): e.g., Glucose, Fructose, Galactose.
• Glucose Structure: Exists in straight-chain or ring forms. Ring formation occurs between C1 and the oxygen on C5.
  • $\alpha$-glucose: The $-OH$ group on C1 is below the ring (opposite side of C6).
  • $\beta$-glucose: The $-OH$ group on C1 is above the ring (same side as C6).

Disaccharides and the Glycosidic Bond

• Formation: Two monosaccharides link via a condensation reaction (removing $H_2O$) to form a glycosidic bond.
• Common Disaccharides:
  • Maltose: $\alpha$-glucose + $\alpha$-glucose ($\alpha\,1-4$ bond).
  • Sucrose: $\alpha$-glucose + $\beta$-fructose ($\alpha 1-\beta 2$ bond). Used for transport in plants.
• Hydrolysis: The breakage of glycosidic bonds by adding water, catalyzed by enzymes like maltase or sucrase.

Polysaccharides (Complex Carbohydrates)

• Definition: Giant polymers made of thousands of monosaccharide monomers. Insoluble and ideal for storage.
• Starch (Plant Storage): Mixture of two polymers:
  • Amylose: $\alpha\,1-4$ glycosidic bonds; unbranched; coils into a compact spiral via internal hydrogen bonds.
  • Amylopectin: $\alpha\,1-4$ bonds with $\alpha\,1-6$ branches; less compact than amylose.
• Glycogen (Animal Storage): Similar to amylopectin but more highly branched. Stored in liver and muscles; easily mobilized into glucose.
• Cellulose (Structural): Polymer of $\beta$-glucose joined by $\beta\,1-4$ bonds. Alternate glucose units are rotated $180^\circ$. This makes the molecule straight. Hydrogen bonds between parallel chains form strong microfibrils and fibers.

Chemical Testing for Carbohydrates

• Benedict's Test (Reducing Sugars): Heated with Benedict's reagent (blue copper(II) sulphate). Reducing sugars (glucose, fructose, maltose) reduce $Cu^{2+}$ to $Cu^+$, forming a brick-red copper(I) oxide precipitate.
• Non-reducing Sugars (Sucrose): Shows negative Benedict's result. Must be hydrolyzed with acid, neutralized with alkali, and re-tested to show a positive result.
• Iodine Test (Starch): Iodine solution turns blue-black in the presence of amylose.

3. Proteins

Amino Acids

• Basic Structure: A central carbon atom bonded to an amino group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen atom, and a variable R-group.
• R-Groups: There are 20 different naturally occurring R-groups. They can be polar (hydrophilic), non-polar (hydrophobic), or sulfur-containing (cysteine).
• Peptide Bonds: Formed via condensation between the amino group of one acid and the carboxyl group of another. The resulting chain is a polypeptide.

Levels of Protein Structure

• Primary Structure: The unique sequence of amino acids in the polypeptide chain, determined by genes.
• Secondary Structure: Local folding into regular patterns held by hydrogen bonds between the C=O of one peptide bond and the N-H of another.
  • $\alpha$-helix: A right-handed spiral.
  • $\beta$-pleated sheet: Parallel or anti-parallel strands.
• Tertiary Structure: The overall 3D folding of the chain. Stabilized by:
  • Hydrogen bonds
  • Disulphide bridges: Covalent bonds between cysteine R-groups.
  • Ionic bonds: Between charged R-groups.
  • Hydrophobic interactions: Non-polar R-groups clustering in the center.
• Quaternary Structure: The association of two or more polypeptide chains (e.g., hemoglobin has four).

Globular vs. Fibrous Proteins

• Globular Proteins (e.g., Hemoglobin): Spherical, soluble, and metabolically active. Hemoglobin contains four polypeptide chains (two $\alpha$, two $\beta$), each with a prosthetic haem group containing iron ($Fe^{2+}$) to bind oxygen.
• Fibrous Proteins (e.g., Collagen): Long, insoluble, and structural. Collagen consists of three helical polypeptide chains wound like a rope (triple helix). Every third amino acid is glycine. Millions of molecules are cross-linked to form fibrils and fibers with high tensile strength.

4. Lipids

Triglycerides

• Composition: One glycerol molecule bonded to three fatty acids via ester bonds (formed by condensation).
• Saturation:
  • Saturated: No carbon-carbon double bonds in the tail; usually solid at room temperature.
  • Unsaturated: Contain one or more double bonds ($C=C$), creating "kinks" that prevent close packing; usually liquid (oils).
• Functions: Highly efficient energy store ($2\times$ energy of carbohydrates), thermal insulation, and protection.

Phospholipids and Cell Membranes

• Structure: Glycerol bonded to two fatty acids and one phosphate group.
• Amphipathic Nature: The phosphate "head" is negatively charged and hydrophilic; the fatty acid "tails" are non-polar and hydrophobic.
• Bilayer Formation: In water, they arrange with heads facing outward and tails inward, forming the basis of all biological membranes.

5. Cell Structure and Microscopy

Microscopy Concepts

• Magnification: $\frac{\text{image size}}{\text{actual size}}$.
• Resolution: The smallest distance between two points that can be distinguished. Limit of resolution is roughly $0.45 \times \text{wavelength}$.
• Light Microscope: Uses visible light; max resolution $200\,\text{nm}$; max useful magnification $\times 1400$. Can view living specimens.
• Electron Microscope: Uses electron beams; max resolution $0.5\,\text{nm}$; max magnification $\times 300,000$. Specimens must be dead and in a vacuum.

Organelles

• Nucleus: Contains chromatin (DNA + histones). The nucleolus produces rRNA.
• Endoplasmic Reticulum (ER): RER (with ribosomes) for protein synthesis; SER for lipid synthesis.
• Golgi Body: Modifies, sorts, and packages proteins into vesicles for secretion (exocytosis).
• Mitochondria: Site of aerobic respiration/ATP production. Features cristae (folds) and a matrix.
• Chloroplasts: Site of photosynthesis. Contains thylakoids (grana) and stroma.
• Lysosomes: Vesicles containing digestive enzymes.
• Centrioles: (Animal only) Organize microtubules for the spindle during division.
• Cell Walls: (Plant only) Made of cellulose microfibrils in a pectin matrix.

6. Cell Division

The Cell Cycle

• Interphase: G1 (growth), S (DNA replication), G2 (prep for mitosis).
• Mitosis: Division of the nucleus into two identical daughter nuclei.
  • Prophase: Chromosomes condense; spindle forms.
  • Metaphase: Chromosomes align at the equator.
  • Anaphase: Centromeres split; chromatids move to poles.
  • Telophase: Nuclear envelopes reform.
• Cytokinesis: Division of the cytoplasm.

Meiosis

• Purpose: Reduction division to produce four haploid gametes from one diploid cell.
• Meiosis I: Homologous chromosomes pair (bivalents) and separate. Includes crossing over at Prophase I.
• Meiosis II: Chromatids separate (similar to mitosis).
• Variation Sources: Independent assortment of bivalents and crossing over (chiasmata).

7. Membrane Transport

Passive Transport

• Diffusion: Net movement down a concentration gradient.
• Facilitated Diffusion: Movement through channel or carrier proteins (for ions/polar molecules).
• Osmosis: Diffusion of water through a partially permeable membrane down a water potential ($\psi$) gradient.
  • Water Potential Formula: $\psi = \psi_s + \psi_p$ ($\psi_s$ = solute potential; $\psi_p$ = pressure potential).

Active processes

• Active Transport: Moving substances against a gradient using ATP and carrier proteins (e.g., Sodium-Potassium pump).
• Bulk Transport: Endocytosis (engulfing) and Exocytosis (secreting) using vesicles.