A-Level Biology Comprehensive Study Notes

Movement of Substances Into and Out of Cells

The Fluid Mosaic Model

Proposed in 1972 by S. J. Singer and G. L. Nicolson, this model describes the arrangement of molecules in the cell membrane. It is termed 'fluid' because phospholipids are in constant motion and 'mosaic' due to the scattered pattern of proteins when viewed from above. It is a 'model' because the molecules are too small to be seen even by the most powerful microscopes; thus, its structure is inferred from experimental behavior.

Components of the Cell Surface Membrane

1. Phospholipids: These are amphipathic molecules containing a polar, hydrophilic phosphate group 'head' (ionized) and two non-polar, hydrophobic fatty acid 'tails' (hydrocarbon chains). In water, they spontaneously form monolayers, micelles (spheres with heads outward), or bilayers. The bilayer is the fundamental structure of the membrane, with heads facing the aqueous environment inside and outside the cell while tails meet in the inner region, excluding water.
2. Cholesterol: Found within the phospholipid bilayer, it is hydrophobic. It reduces lateral movement of molecules, adds strength, and prevents leakage of ions. Crucially, it regulates fluidity; at high temperatures, it prevents the membrane from breaking up, while at low temperatures, it acts as "antifreeze" to prevent freezing.
3. Proteins:
      - Extrinsic (Peripheral): Located on the internal or external surface, bound by weak attractions. They provide mechanical support by attaching the membrane to the cytoskeleton.
      - Intrinsic (Integral): Embedded on one side or spanning the entire membrane (transmembrane). These act as enzymes (e.g., $ATP\,synthase$), protein channels (water-filled tubes for ions), carrier proteins (which change shape to move glucose/amino acids), or electron carriers in respiration and photosynthesis.
4. Glycolipids and Glycoproteins: Carbohydrates covalently bonded to lipids or proteins. Together they form the glycocalyx, which functions in cell recognition, stability, and cell-to-cell attachment to form tissues. They also act as receptors for hormones and neurotransmitters.

Transport Mechanisms

1. Simple Diffusion: Passive net movement of molecules from high to low concentration. Only very small molecules ($H_2O$, $O_2$, $CO_2$) or lipid-soluble nonpolar molecules (steroids) can pass directly through the lipid bilayer.
2. Facilitated Diffusion: Passive net movement from high to low concentration through specific channel or carrier proteins. The rate is limited by the number of available transport proteins.
3. Osmosis: The diffusion of water across a membrane from a region of higher water potential to lower water potential. Pure water has the highest water potential ($\Psi = 0\,kPa$). All solutions have negative values ($\Psi < 0$). The equation for water potential is:
   $\Psi = \Psi_s + \Psi_p$
      where $\Psi_s$ is solute potential and $\Psi_p$ is pressure potential.
4. Active Transport: Movement of molecules against a concentration gradient (low to high) using carrier proteins and energy from $ATP$. It involves a transmembrane $\text{ATPase}$ enzyme. A primary example is the $Na^+/K^+$ pump, which moves 3 $Na^+$ out and 2 $K^+$ in for every $1\,ATP$ hydrolyzed.
5. Bulk Transport: Movement of large molecules via vesicles. Endocytosis (taking in) includes pinocytosis (cell drinking) and phagocytosis (cell eating). Exocytosis is the reverse process, used for secreting hormones or digestive enzymes.

Biological Molecules and Water

Properties of Water

Water ($H_2O$) is a polar molecule; the oxygen atom is slightly negative ($\delta^-$) and hydrogen atoms are slightly positive ($\delta^+$). This polarity allows for electrostatic attractions called hydrogen bonds.
Key roles include:

• Excellent Solvent: Transports solutes and allows enzymatic reactions in solution.
• High Specific Heat Capacity: Buffers temperature changes, allowing enzymes to work in a narrow range.
• High Heat of Vaporization: Efficient cooling via sweating and transpiration.
• High Surface Tension: Allows cohesion (water sticking to itself) and adhesion (water sticking to surfaces like xylem walls), enabling water transport in tall trees.
• Metabolite: Involved in hydrolysis (breaking bonds with water) and condensation (forming bonds with the elimination of water).

Carbohydrates

Organic molecules containing $C$, $H$, and $O$ in the ratio $C_x(H_2O)_y$.

1. Monosaccharides: Single sugars like glucose ($C_6H_{12}O_6$), fructose, and galactose. Glucose exists as alpha ($\alpha$) (with $-OH$ on $C1$ below the ring) or beta ($\beta$) (with $-OH$ above the ring).
2. Disaccharides: Two monosaccharides joined by a glycosidic bond. Examples: Maltose ($\text{Glucose} + \text{Glucose}$), Sucrose ($\text{Glucose} + \text{Fructose}$), and Lactose ($\text{Glucose} + \text{Galactose}$).
3. Polysaccharides: Polymers of many sugars.
      - Starch: Plant storage; mixture of unbranched helical amylose ($1,4$ bonds) and branched amylopectin ($1,4$ and $1,6$ bonds).
      - Glycogen: Highly branched animal storage found in liver and muscle.
      - Cellulose: Structural component of plant cell walls; made of $\beta\text{-glucose}$ chains linked by hydrogen bonds to form high-tensile strength microfibrils.

Lipids

Hydrophobic compounds composed of $C$, $H$, and $O$.

• Triglycerides: Formed by one glycerol and three fatty acids via condensation. Saturated fatty acids have no $C=C$ double bonds; unsaturated have at least one, causing 'kinks' in the chain.
• Phospholipids: A triglyceride where one fatty acid is replaced by a phosphate group, creating a hydrophilic head and hydrophobic tails.
• Functions: Energy storage, thermal insulation, waterproofing (waxes), and hormone production (steroids like testosterone).

Proteins

Complex polymers made of amino acids ($CHONS$). There are 20 naturally occurring amino acids, each with a central carbon, an amino group ($-NH_2$), a carboxyl group ($-COOH$), and a variable $R$ group. At neutral $pH$, they exist as zwitterions.
Levels of Structure:

1. Primary: The unique sequence of amino acids.
2. Secondary: Folding into $\alpha\text{-helices}$ or $\beta\text{-pleated sheets}$ held by hydrogen bonds.
3. Tertiary: The final $3D$ shape held by hydrogen, ionic, disulphide bonds, and hydrophobic interactions.
4. Quaternary: Multiple polypeptide chains combined, often with a prosthetic group (e.g., the iron-containing haem group in haemoglobin).
   Types:

• Globular: Spherical, metabolic roles (e.g., haemoglobin, enzymes).
• Fibrous: Long strands, structural roles (e.g., collagen in bone/skin).

Enzymes

Mode of Action

Enzymes are globular proteins that act as biological catalysts by lowering the activation energy of a reaction. The Lock and Key Hypothesis suggests a rigid, complementary fit between the substrate and the enzyme's active site. The Induced Fit Hypothesis suggests the active site is flexible and molds around the substrate upon binding.

Factors Affecting Rate

• Temperature: Rate increases with kinetic energy until the optimum. Above $45\,^\circ C$, enzymes denature. The temperature coefficient $Q_{10}$ measures the increase for a $10\,^\circ C$ rise:
  $Q_{10} = \frac{\text{Rate at } (t + 10)\,^\circ C}{\text{Rate at } t\,^\circ C}$
• pH: Extreme $pH$ values disrupt ionic and hydrogen bonds, causing denaturation. Most work at $pH\,7.0\text{--}7.5$, but Pepsin works at $pH\,1.5$.
• Substrate Concentration: Rate increases until all active sites are saturated ($V_{max}$).
• Inhibitors:
    - Competitive: Similar shape to substrate; binds to the active site. Reversible by increasing substrate concentration.
    - Non-competitive: Binds to an allosteric site, changing the enzyme's shape. Permanent and independent of substrate concentration.

Cell and Nuclear Division

The Cell Cycle

Consists of three phases: Interphase, Mitosis, and Cytokinesis.

1. Interphase:
      - $G_1$: Organelle duplication.
      - $S$: $DNA$ replication (semi-conservative).
      - $G_2$: Error checking.
2. Mitosis (Nuclear Division):
      - Prophase: Chromosomes supercoil and become visible; spindle fibers form.
      - Metaphase: Chromosomes line up at the equator; spindle fibers attach to centromeres.
      - Anaphase: Centromeres divide; sister chromatids are pulled to opposite poles.
      - Telophase: Nuclear envelopes reform around groups of chromosomes.
3. Cytokinesis: Division of the cytoplasm. In animals, a cleavage furrow forms. In plants, a phragmoplast or cell plate is laid down.

Meiosis

A reduction division producing four haploid ($n$) gametes from one diploid ($2n$) cell.

• Meiosis I: Homologous chromosomes pair up (bivalents). Crossing over occurs at chiasmata, where alleles swap between maternal and paternal chromatids. Independent assortment at Metaphase I and II further increases genetic variation.
• Meiosis II: Similar to mitosis; sister chromatids separate.

Cancer

Uncontrolled cell division resulting from mutations in genes that regulate the cell cycle (oncogenes). Tumors can be benign (localized) or malignant (metastatic, spreading via blood/lymph to form secondary tumors). Carcinogens include $UV$ radiation, tobacco tar, and asbestos.

Transport in Humans

The Circulatory System

Mammals have a double circulation:

1. Pulmonary: Heart to lungs and back.
2. Systemic: Heart to body and back.

Blood Vessels

• Arteries: Thick, elastic walls; carry blood at high pressure away from the heart.
• Capillaries: Walls one cell thick; facilitate exchange of substances between blood and cells.
• Veins: Larger lumen, thinner walls, and valves to prevent backflow; carry low-pressure blood toward the heart. Squeezed by skeletal muscle contraction.

Haemoglobin and Gas Transport

Haemoglobin ($Hb$) is a globular protein with four haem groups. It displays a sigmoid (S-shaped) Oxygen Dissociation Curve (ODC) due to cooperative binding.

• Bohr Effect: High $CO_2$ and low $pH$ (acidic) cause the ODC to shift to the right, facilitating oxygen unloading in respiring tissues.
• Myoglobin: Found in muscle; has a much higher affinity for oxygen than $Hb$, acting as an oxygen reservoir.
• Foetal Haemoglobin: Has a higher affinity for oxygen than maternal $Hb$ to extract oxygen from the placenta; ODC is shifted to the left.
• $CO_2$ Transport: $85\%\,\text{as}\;HCO_3^-$ (hydrogencarbonate), $10\%\,\text{as carbaminohaemoglobin}$, and $5\%\,\text{dissolved in plasma}$. The Chloride Shift maintains electrical balance in red blood cells.

The Heart and Cardiac Cycle

1. Atrial Systole: Atria contract, pushing blood into ventricles.
2. Ventricular Systole: Ventricles contract; atrioventricular valves close ("lub"); semi-lunar valves open.
3. Ventricular Diastole: Ventricles relax; semi-lunar valves close ("dub").
   Control of heart rate is myogenic, initiated by the Sinoatrial Node (SAN). It is also regulated by the medulla oblongata via the sympathetic (increases rate) and parasympathetic (decreases rate) nervous systems, and hormones like adrenaline.

Nervous Control

Structure of Neurones

• Sensory: Receptors to CNS.
• Relay: Connect sensory and motor in CNS.
• Motor: CNS to effectors.
  Most axons are insulated by a myelin sheath (made of Schwann cells), with gaps called nodes of Ranvier. This allows saltatory conduction, increasing impulse speed by up to 50 times.

Nerve Impulses

• Resting Potential: Inside is $-70\,mV$ due to the $Na^+/K^+$ pump and faster leakage of $K^+$ ions.
• Action Potential:
    1. Depolarisation: $Na^+$ voltage-gated channels open; inside reaches $+30\,mV$.
    2. Repolarisation: $Na^+$ channels close; $K^+$ channels open, allowing $K^+$ to flow out.
    3. Hyperpolarisation: Potential briefly goes below $-70\,mV$ before returning to resting state.
• Refractory Period: Time when the axon is unresponsive, ensuring one-way transmission and discrete impulses.

Synapses

The gap between neurones is the synaptic cleft.

1. Action potential triggers $Ca^{2+}$ influx.
2. Vesicles release Acetylcholine (Ach) into the cleft.
3. Ach binds to receptors on the post-synaptic membrane, opening $Na^+$ channels and triggering a new action potential.
4. Acetylcholinesterase hydrolyzes Ach to stop continuous stimulation.

Sexual Reproduction

Gametogenesis

• Spermatogenesis: Continuous production of sperm in seminiferous tubules. Regulated by $FSH$ (Sertoli cells) and $LH$ (Leydig cells produce testosterone).
• Oogenesis: Production of eggs. Primary oocytes are formed before birth but frozen in Prophase I. Each month at puberty, one matures into a Graafian follicle.

Menstrual Cycle

Regulated by $FSH$, $LH$, oestrogen, and progesterone.

• Ovulation (day 14) is triggered by an $LH$ surge.
• Corpus Luteum forms after ovulation, secreting progesterone to maintain the uterine lining.

Fertilisation and Development

Involves Capacitation, the Acrosome Reaction (digesting jelly coat), and the Cortical Reaction (prevention of polyspermy). The resulting zygote implants in the uterus. The Placenta forms to facilitate exchange ($O_2$, nutrients, waste) and secretes $hCG$ and progesterone to maintain pregnancy.

Ecology and Human Impact

Ecological Concepts

An Ecosystem is a self-contained unit comprising a Community (biotic) and its Habitat (abiotic). A Niche is the specific role of a species in its ecosystem. Energy flows from Producers (autotrophs) to Consumers (heterotrophs). Only about $10\%$ of energy is transferred between trophic levels; the rest is lost as heat during respiration or through waste.

The Nitrogen Cycle

1. Nitrogen Fixation: $N_2$ gas to ammonia by Rhizobium (in legumes) or Azotobacter (free-living).
2. Nitrification: Ammonium to Nitrite (Nitrosomonas) then to Nitrate (Nitrobacter).
3. Ammonification: Organic waste to ammonium by decomposers.
4. Denitrafication: Nitrates to $N_2$ gas by Pseudomonas in anaerobic (waterlogged) conditions.

Human Impact and Conservation

• Negative Impacts: Overpopulation, deforestation (leads to soil erosion, flooding, and global warming), industrial/agricultural pollution, mining, and invasive species (e.g., water hyacinth).
• Greenhouse Effect: Trapping of heat by $CO_2$ and $CH_4$, leading to Global Warming.
• Conservation:
    - In situ: On-site (National Parks).
    - Ex situ: Off-site (Zoos, seed banks, botanical gardens).
    - Organizations: EMA (environmental standards), CAMPFIRE (community wildlife management), and CITES (regulation of international trade in endangered species like the African elephant and white rhino).

Health and Disease

Alcohol and Tobacco

• Alcohol: A depressant that slows brain function. Long-term use causes brain shrinkage or Wernicke-Korsakoff Syndrome (thiamine deficiency) and liver diseases: Fatty Liver, Hepatitis, and Cirrhosis.
• Tobacco: Contains Nicotine (addictive, raises heart rate), Tar (carcinogenic, causes chronic bronchitis, emphysema, and lung cancer), and Carbon Monoxide (reduces oxygen transport).

Global Diseases

• Malaria: Caused by Plasmodium via the Anopheles mosquito. Prevalent in the tropics.
• Tuberculosis (TB): Bacterial ($M. tuberculosis$). Air-borne; linked to poverty and HIV.
• HIV/AIDS: Retrovirus destroying T helper cells ($CD4^+$). Causes a syndrome of opportunistic infections.
• Cholera: Water-borne; caused by Vibrio cholerae. Leads to severe dehydration through toxins.
• Ebola: Zoonotic virus; causes severe haemorrhagic fever and is highly contagious through body fluids.