Cambridge International AS Level Biology (9700)

Revision Notes (2025-2027 Syllabus)

March 30, 2025

Contents

1
1 Cell Structure

All organisms are composed of cells. Understanding cell structure and function is fundamental
to biology.

1.1 Characteristics of Living Organisms and The Cell Theory

• Living organisms share characteristics: Movement, Respiration, Sensitivity, Growth, Re-

production, Excretion, Nutrition (MRS GREN).

• Cell Theory:

1. All living organisms are composed of one or more cells.

2. The cell is the basic structural and functional unit of life.
3. All cells arise from pre-existing cells.

• Cells separate their internal chemistry from the external environment using a cell surface
membrane (plasma membrane). This membrane is partially permeable, controlling
the movement of substances.

1.2 Microscopy

Units of Measurement

Microscopy requires specific units:

• Metre (m): Base unit.

• Millimetre (mm): 1 × 10−3 m (10−3 m)

• Micrometre (µm): 1 × 10−6 m (10−6 m) or 1 × 10−3 mm (10−3 mm)

• Nanometre (nm): 1 × 10−9 m (10−9 m) or 1 × 10−3 µm (10−3 µm)

Typical cell sizes: Animal cells (≈ 5 µm to 40 µm), Plant cells (≈ 40 µm), Bacteria (≈ 1 µm),
Ribosomes (≈ 25 nm).

Light Microscopy

• Uses visible light as the radiation source.

• Specimens are often thin sections, mounted on slides, and stained to improve contrast.

• Temporary mounts: Quick preparations of fresh material (e.g., cheek cells, onion epi-
dermis). Stains like methylene blue (animal) or iodine in potassium iodide (plant) are
used.

2
Electron Microscopy (EM)

• Uses a beam of electrons instead of light.

• Electrons have a much shorter wavelength than light, allowing for higher resolution.

• Resolution: The ability to distinguish between two points that are very close together.
Higher resolution means greater detail can be seen.

• Magnification: The number of times larger an image is compared to the actual size of
the object.

• EM requires a vacuum, so specimens must be dehydrated (dead).

• Transmission Electron Microscope (TEM): Electrons pass through a very thin spec-
imen. Provides high resolution images of internal structures (ultrastructure). Stains often
use heavy metals.

• Scanning Electron Microscope (SEM): Electrons scan the surface of a specimen, and
reflected electrons are detected. Produces 3D-like images of surfaces. Resolution is lower
than TEM.

Magnification and Resolution

Image size (I)

• Magnification (M) = . Formula: M = AI . Can be rearranged: A = I
Actual size (A) M
or I = M × A. Ensure units are consistent before calculating.

• Resolution Limit: Light microscope ≈ 200 nm. Electron microscope ≈ 0.5 nm (TEM).
Objects smaller than half the wavelength of the radiation used cannot be resolved.

• Increasing magnification beyond the resolution limit only results in a larger, blurry image.

Measuring Size with a Microscope

• Eyepiece Graticule: A scale fitted into the microscope eyepiece. Has arbitrary units
(e.g., 100 divisions).

• Stage Micrometer: A slide with an accurately drawn scale (e.g., 1 mm divided into 100
units, so each unit = 0.01 mm or 10 µm).

• Calibration: The eyepiece graticule is calibrated using the stage micrometer at each
magnification. Align the scales and determine the actual length corresponding to one
eyepiece unit (epu).

• Measurement: Measure the specimen in epu using the eyepiece graticule. Convert epu
to actual units (µm or mm) using the calibration factor for that magnification.

• Scale Bars: A line drawn on a diagram or micrograph representing a known actual length
(e.g., 10 µm). Calculate magnification using M = Measured length of scale bar
Actual length it represents .

3
1.3 Eukaryotic Cell Structure

Eukaryotic cells have a membrane-bound nucleus and other membrane-bound organelles. Exam-
ples: plant cells, animal cells, fungal cells, protoctists.

Common Organelles (Animal and Plant Cells)

• Cell Surface Membrane (Plasma Membrane): (≈ 7 nm thick) Partially permeable

phospholipid bilayer with embedded proteins, cholesterol (animals), glycoproteins, glycol-
ipids. Controls entry/exit of substances. (Details in Topic 4).
• Nucleus: Largest organelle, contains chromosomes (DNA + histone proteins = chro-
matin). Controls cell activities via gene expression. Surrounded by a nuclear envelope
(double membrane) perforated by nuclear pores (allow passage of mRNA, tRNA, ribo-
somes, proteins, ATP, etc.). Contains one or more nucleoli (singular: nucleolus) involved
in ribosome synthesis.
• Cytoplasm: The material between the nucleus and cell surface membrane, including the
cytosol (aqueous component) and organelles.
• Mitochondrion (plural: mitochondria): (≈ 1 µm diameter) Site of aerobic respiration,
producing ATP. Surrounded by a double membrane (envelope). Inner membrane folded
into cristae (increase surface area). Central fluid-filled space is the matrix. Contains 70S
ribosomes and circular DNA.
• Ribosomes: Site of protein synthesis (translation). Small organelles (≈ 25 nm). Made
of ribosomal RNA (rRNA) and protein. Eukaryotic cytoplasm has 80S ribosomes. Mito-
chondria and chloroplasts have 70S ribosomes. Can be free in cytoplasm or attached to
RER.
• Endoplasmic Reticulum (ER): Network of flattened sacs (cisternae) continuous with
the outer nuclear membrane.
– Rough ER (RER): Studded with ribosomes. Modifies and transports proteins syn-
thesized on the attached ribosomes (e.g., folding, adding carbohydrate chains).
– Smooth ER (SER): Lacks ribosomes. Involved in lipid and steroid synthesis, detox-
ification (liver), storage of calcium ions (muscle).
• Golgi Apparatus (Golgi Body/Complex): Stack of flattened, membrane-bound sacs
(cisternae). Modifies, sorts, and packages proteins and lipids received from the ER into
vesicles for secretion or delivery to other organelles. Forms lysosomes. Synthesises glyco-
proteins.
• Lysosomes: Simple spherical sacs containing hydrolytic (digestive) enzymes. Break down
unwanted structures, old organelles, or material taken in by endocytosis. Involved in
apoptosis (programmed cell death). (More common in animal cells; plant vacuole may
have lysosomal function).

Structures Primarily in Animal Cells

• Centrioles: Pair of short cylinders, arranged at right angles near the nucleus in the
centrosome. Made of microtubules (9 triplets). Involved in spindle formation during

4
 nuclear division (though their exact role is debated, especially as plants lack them but still
form spindles). Form basal bodies of cilia/flagella.

• Cilia (singular: cilium) / Flagella (singular: flagellum): Hair-like extensions from the cell
surface. Used for locomotion or moving fluids. Contain microtubules in a ’9+2’ arrange-
ment. Cilia are shorter and more numerous than flagella.

• Microvilli: Finger-like extensions of the cell surface membrane. Increase surface area for
absorption (e.g., in gut lining, kidney tubules).

Structures Primarily in Plant Cells

• Cell Wall: Rigid outer layer outside the cell surface membrane. Provides structural sup-
port and protection, prevents bursting due to osmosis. Freely permeable. Made primarily
of cellulose (a polysaccharide). May be reinforced with lignin in some cells (e.g., xylem).

• Chloroplasts: (≈ 3 µm to 10 µm diameter) Site of photosynthesis. Surrounded by a double

membrane (envelope). Contain internal membranes called thylakoids, stacked into grana
(singular: granum). Thylakoids contain chlorophyll and other photosynthetic pigments.
Fluid-filled space is the stroma, containing enzymes for the light-independent stage, 70S
ribosomes, and circular DNA. Starch grains may be present.

• Large Permanent Vacuole: Large, fluid-filled sac occupying a significant volume of

mature plant cells. Contains cell sap (solution of sugars, salts, pigments, etc.). Surrounded
by a membrane called the tonoplast. Maintains turgor pressure against the cell wall,
provides support, stores substances.

• Plasmodesmata (singular: plasmodesma): Fine strands of cytoplasm connecting adjacent

plant cells through pores in their cell walls. Allow communication and transport between
cells (forming the symplast pathway).

Diagrams (TikZ representations)

Lysosome
to.
Mi Cell Membrane
RER Nucleus
Golgi
Cytoplasm

Figure 1: Simplified Animal Cell

5
 Cell Wall
Cell Membrane
Chloro.

Vacuole
Nucleus

Mito.

Figure 2: Simplified Plant Cell

Comparison of Animal and Plant Cells

• Present in both: Cell surface membrane, nucleus, cytoplasm, mitochondria, ribosomes,

ER, Golgi apparatus.

• Animal only (typically): Centrioles, cilia/flagella (common), lysosomes (common), mi-

crovilli (specialised cells), small temporary vacuoles.

• Plant only (typically): Cell wall (cellulose), chloroplasts (photosynthetic parts), large
permanent central vacuole, tonoplast, plasmodesmata.

• Shape: Animal cells often irregular/rounded; Plant cells more fixed/regular shape due to
cell wall.

1.4 Prokaryotic Cell Structure (Bacteria)

Prokaryotic cells lack a membrane-bound nucleus and other membrane-bound organelles. Ex-
amples: Bacteria, Archaea.

Key Features of a Typical Bacterium

• Unicellular.

• Size: Generally 1 µm to 5 µm diameter (much smaller than eukaryotes).

• Cell Wall: Present in most. Made of peptidoglycan (murein), not cellulose. Provides
support and prevents osmotic lysis.

• Cell Surface Membrane: Phospholipid bilayer, similar function to eukaryotes. May be

infolded (mesosomes - function debated, possibly artefact; or photosynthetic membranes
in cyanobacteria).

• Cytoplasm: Contains ribosomes, enzymes, etc. No membrane-bound organelles (no mi-

tochondria, ER, Golgi, chloroplasts, lysosomes).

• Genetic Material: Single, circular chromosome located in a region called the nucleoid
(not enclosed by a membrane). DNA is ’naked’ (not associated with histone proteins).

6
 • Plasmids: Small, circular DNA molecules separate from the main chromosome. Often
carry genes for antibiotic resistance or other ’extra’ functions. Can be transferred between
bacteria.

• Ribosomes: 70S type (smaller than eukaryotic 80S ribosomes). Site of protein synthesis.

• Flagellum (plural: flagella): (Present in some) Simpler structure than eukaryotic flagella.
Used for motility. Rotates like a propeller. Made of flagellin protein.

• Pili (singular: pilus): (Present in some) Fine protein rods used for attachment to surfaces
or other cells (e.g., during conjugation for plasmid transfer).

• Capsule/Slime Layer: (Present in some) Extra protective layer outside the cell wall.
Often polysaccharide-based. Protects against dehydration, phagocytosis, antibiotics.

Comparison of Prokaryotic and Eukaryotic Cells

Feature Prokaryotic Cell (e.g., Bacterium) Eukaryotic Cell (e.g., Animal/P

Nucleus Absent (nucleoid region) Present (membrane-bound)
DNA Circular, naked Linear, associated with histones
Plasmids Often present Absent (except some yeasts)
Membrane-bound organelles Absent Present (mitochondria, ER, Golgi, et
Ribosomes 70S 80S (cytoplasm/RER), 70S (mito/ch
Cell Wall Peptidoglycan (most) Cellulose (plants), Chitin (fungi), Ab
Average Size ≈ 1 µm to 5 µm ≈ 10 µm to 100 µm
Cell Division Binary fission Mitosis/Meiosis

Table 1: Comparison of Prokaryotic and Eukaryotic Cells

1.5 Viruses

• Acellular: Not made of cells. Do not fit standard cell theory.

• Obligate intracellular parasites: Can only reproduce inside living host cells, using the host’s
metabolic machinery.

• Structure:

– Genetic material: DNA or RNA (can be single or double-stranded). Forms the core.
– Capsid: Protective protein coat surrounding the genetic material. Composed of
protein subunits called capsomeres.
– Envelope: (Present in some, e.g., HIV, influenza virus) Outer lipid bilayer derived
from the host cell membrane, often with embedded viral glycoproteins (spikes).

• Size: Very small (≈ 20 nm to 300 nm). Only visible with electron microscope.

• Lack metabolism, ribosomes, cytoplasm, organelles.

• Specificity: Often infect only specific types of host cells due to interactions between viral
surface proteins and host cell receptors.

7
1.6 The Role of ATP

• Adenosine Triphosphate (ATP) is the universal energy currency in all cells.

• Cells use energy released from the hydrolysis of ATP to ADP + Pi (inorganic phosphate)
to power energy-requiring processes (e.g., active transport, muscle contraction, synthesis
of macromolecules). (Details in Topic 12).

• ATP is generated primarily through respiration (in mitochondria) and photosynthesis (in
chloroplasts).

8
2 Biological Molecules

Focuses on the structure and function of key organic molecules essential for life, based on the
versatile element carbon. Water’s properties are also crucial.

2.1 Testing for Biological Molecules

Reducing Sugars (e.g., glucose, fructose, maltose)

• Benedict’s Test:

1. Add Benedict’s reagent (alkaline copper(II) sulfate - blue) to the sample.

2. Heat in a water bath (≈ 80 ◦ C).
3. Positive result: Colour change from blue → green → yellow → orange → brick-red
precipitate (copper(I) oxide). The final colour depends on the concentration.
4. Negative result: Solution remains blue.

• Semi-quantitative test: By comparing the final colour to known standards or timing

the first colour change, an estimate of concentration can be made (requires standardised
conditions - volume, temperature, time).

Non-reducing Sugars (e.g., sucrose)

1. Perform Benedict’s test. If negative (remains blue), proceed.

2. Take a fresh sample, add dilute hydrochloric acid (HCl).

3. Heat in a water bath (hydrolyses glycosidic bond, breaking sucrose into glucose and fruc-
tose).

4. Neutralise the acid by adding sodium hydrogencarbonate solution (or similar alkali) care-
fully until effervescence stops. Check pH.

5. Perform Benedict’s test again.

6. Positive result for non-reducing sugar: Colour change (green to brick-red) occurs after
hydrolysis and neutralisation.

Starch

• Iodine Test:

1. Add iodine solution (iodine dissolved in potassium iodide solution - yellow/brown) to

the sample.
2. Positive result: Colour change to blue-black.
3. Negative result: Solution remains yellow/brown.

9
Lipids

• Emulsion Test:

1. Add ethanol to the sample, shake well to dissolve any lipid.

2. Pour the ethanol solution into a separate test tube containing water.
3. Positive result: A cloudy white emulsion forms.
4. Negative result: Solution remains clear.

Proteins

• Biuret Test:

1. Add Biuret reagent (sodium hydroxide + copper(II) sulfate) to the sample. (Or add
NaOH first, then a few drops of copper sulfate solution).
2. Positive result: Colour change from blue to purple/lilac. Detects peptide bonds.
3. Negative result: Solution remains blue.

2.2 Carbohydrates and Lipids

Monomers, Polymers, Macromolecules

• Monomer: A relatively simple molecule used as a basic building block for a polymer (e.g.,
monosaccharide, amino acid, nucleotide).

• Polymer: A giant molecule made from many similar repeating subunits (monomers) joined
together by covalent bonds in a chain (e.g., polysaccharide, polypeptide, polynucleotide).

• Macromolecule: A very large organic molecule (e.g., polysaccharide, protein, nucleic

acid). Polymers are macromolecules.

• Condensation Reaction: Joins two molecules together with the formation of a chemical
bond (e.g., glycosidic, ester, peptide) and the release of a water molecule. Used to build
polymers.

• Hydrolysis Reaction: Breaks a chemical bond between two molecules using a water
molecule. Used to break down polymers into monomers.

Carbohydrates

General formula Cx (H2 O)y . Contain C, H, O.

Monosaccharides:

• Simple sugars, single sugar unit. General formula (CH2 O)n . Soluble, sweet.

• Examples:

10
 – Trioses (3C): e.g., glyceraldehyde (intermediate in respiration/photosynthesis).
– Pentoses (5C): e.g., Ribose (in RNA, ATP), Deoxyribose (in DNA).
– Hexoses (6C): e.g., Glucose, Fructose, Galactose. Formula C6 H12 O6 .
• Glucose: Main respiratory substrate. Exists in chain and ring forms. Ring form is more
stable.
– α-glucose: -OH group on Carbon 1 points below the ring plane.
– β-glucose: -OH group on Carbon 1 points above the ring plane.
– These are isomers.
• All monosaccharides are reducing sugars. Fructose and Galactose are isomers of Glucose.

OH OH

OH OH

O O
α-glucose β-glucose

Figure 3: Ring forms of α-glucose and β-glucose (simplified representation).

Disaccharides:

• Two monosaccharides joined by a glycosidic bond formed via a condensation reaction

(releasing H2 O). Formula C12 H22 O11 . Soluble, sweet.
• Examples:
– Maltose = α-glucose + α-glucose (reducing sugar)
– Sucrose = α-glucose + fructose (non-reducing sugar)
– Lactose = glucose + galactose (reducing sugar)
• Glycosidic bond is named based on the carbons involved (e.g., α-1,4 glycosidic bond in
maltose).
• Broken down by hydrolysis (addition of H2 O).

O
OH OH
O
Condensation
+
OH OH Hydrolysis + H2 O
OH OOH
H
O O
α-glucose α-glucose Maltose
O

Figure 4: Formation of an α-1,4 glycosidic bond in maltose.

11
Polysaccharides:

• Polymers of monosaccharides (usually glucose) joined by glycosidic bonds. Large molecules

(macromolecules). Often insoluble.

• Starch: Energy storage in plants. Mixture of two polysaccharides:

– Amylose: Unbranched chain of α-glucose units joined by α-1,4 glycosidic bonds.

Coils into a helix.
– Amylopectin: Branched chain of α-glucose. Mainly α-1,4 bonds, but also α-1,6
bonds forming branches.

Starch is compact (helical/branched structure) and insoluble (doesn’t affect water poten-
tial). Easily hydrolysed to glucose when needed.

• Glycogen: Energy storage in animals (liver, muscles). Similar structure to amylopectin

but more highly branched (α-1,4 and α-1,6 bonds). Compact, insoluble. Rapidly hydrol-
ysed to glucose.

• Cellulose: Structural component of plant cell walls. Polymer of β-glucose joined by

β-1,4 glycosidic bonds. Alternate glucose units are inverted by 180°. Forms long, straight,
unbranched chains. Chains lie parallel, linked by many hydrogen bonds to form strong
microfibrils and then fibres. Provides high tensile strength to cell walls.

Lipids

Contain C, H, O (less O than carbohydrates). Insoluble in water (hydrophobic), soluble in

organic solvents (e.g., ethanol).

Triglycerides:

• Fats (solid at room temp) and oils (liquid at room temp).

• Formed by condensation reaction between one glycerol molecule and three fatty acid
molecules.

• Glycerol: An alcohol with three -OH groups.

• Fatty Acids: Long hydrocarbon chain (tail) with a carboxyl group (-COOH) head.

– Saturated: No C=C double bonds in the hydrocarbon tail. Straight chains pack
closely. Usually solid fats (e.g., animal fats).
– Unsaturated: One or more C=C double bonds in the tail. Double bonds cause
’kinks’, preventing close packing. Usually liquid oils (e.g., plant oils). Monounsatu-
rated (one C=C), Polyunsaturated (many C=C).

• Ester Bond: Formed between -COOH group of fatty acid and -OH group of glycerol via
condensation (releasing H2 O). Three ester bonds per triglyceride.

• Functions: Energy storage (release more energy per gram than carbohydrates due to
higher proportion of C-H bonds), insulation, buoyancy, protection of organs, source of
metabolic water (when oxidised).

12
 • Non-polar and Hydrophobic: Due to long hydrocarbon tails.

Condensation
R-COOH + HO-CH2 - R-COO-CH2 - + H2 O
Fatty Acid Glycerol (part) Hydrolysis
Ester Bond (part)

Figure 5: Formation of an ester bond (simplified).

Phospholipids:

• Similar to triglycerides, but one fatty acid is replaced by a phosphate group (PO3−
4 ).

• Structure: Glycerol + 2 Fatty Acids + Phosphate group.

• Amphipathic: Have both hydrophilic and hydrophobic parts.

– Hydrophilic Head: Phosphate group (negatively charged) and glycerol. Polar.

Attracted to water.
– Hydrophobic Tails: Two fatty acid hydrocarbon chains. Non-polar. Repelled by
water.

• Form bilayers in aqueous environments - the basis of cell membranes. Heads face outwards
into water, tails face inwards away from water. (Details in Topic 4).

2.3 Proteins

Polymers of amino acids. Contain C, H, O, N, often S.

Amino Acids

• Monomers of proteins. 20 common types found in organisms.

• General Structure: Central carbon atom bonded to:

– Amino group (-NH2 )

– Carboxyl group (-COOH)
– Hydrogen atom (-H)
– R group (side chain): Varies between different amino acids, determining their
properties (e.g., polar, non-polar, acidic, basic).

Peptide Bonds

• Amino acids join via condensation reactions.

• -COOH group of one amino acid reacts with -NH2 group of another.

• Forms a peptide bond (-CO-NH-) and releases H2 O.

13
 • Two amino acids = dipeptide. Many amino acids = polypeptide.

• Polypeptide chain has an N-terminus (free -NH2 group) and a C-terminus (free -COOH
group).

• Broken by hydrolysis.

Levels of Protein Structure

• Primary Structure: The sequence of amino acids in the polypeptide chain. Determined
by the gene. Covalent peptide bonds.

• Secondary Structure: Regular coiling or folding of the polypeptide chain due to hydrogen
bonds between -CO- and -NH- groups of the peptide backbone.

– α-helix: Coiled structure.

– β-pleated sheet: Folded, sheet-like structure (can be parallel or anti-parallel).

• Tertiary Structure: Further folding of the polypeptide chain into a specific 3D shape.
Determined by interactions between R groups:

– Hydrogen bonds: Between polar R groups.

– Ionic bonds: Between charged R groups (acidic and basic).
– Disulfide bonds (bridges): Strong covalent bonds (-S-S-) between sulfur atoms of
two cysteine R groups.
– Hydrophobic interactions: Non-polar R groups cluster together in the interior,
away from water.

• Quaternary Structure: (Found in some proteins) Association of two or more polypeptide

chains (subunits). Also involves interactions between R groups, and may include non-
protein prosthetic groups (e.g., haem in haemoglobin).

Globular and Fibrous Proteins

• Globular Proteins: Polypeptide chains folded into compact, roughly spherical shapes.
Generally soluble (hydrophilic R groups on outside). Often have metabolic/physiological
roles. Examples:

– Haemoglobin: Oxygen transport in red blood cells. Quaternary structure (2 α-

globin, 2 β-globin chains). Each chain contains a haem prosthetic group with an iron
ion (Fe2+ ) that binds oxygen. Globular shape and solubility essential for transport in
blood.
– Enzymes (e.g., catalase, amylase - Topic 3).
– Hormones (e.g., insulin).
– Antibodies (Topic 11).

• Fibrous Proteins: Long, parallel polypeptide chains with little tertiary/quaternary fold-
ing. Chains linked by cross-bridges. Insoluble. Have structural roles. Examples:

14
 – Collagen: Main structural protein in connective tissue (skin, tendons, bone). Qua-
ternary structure: three polypeptide chains wound into a triple helix. High tensile
strength. Glycine common (small R group allows close packing). Cross-links between
molecules form strong fibrils.
– Keratin (hair, nails).
– Elastin (elastic fibres).

2.4 Water

Essential for life. Unique properties due to its polarity and hydrogen bonding.

Structure and Hydrogen Bonding

• H2 O molecule is polar: Oxygen atom is slightly negative (δ − ), hydrogen atoms are slightly
positive (δ + ).

• Hydrogen Bonds: Weak electrostatic attraction between δ + H of one water molecule and
δ − O of another.

• Each water molecule can form H-bonds with up to four others. Creates a cohesive network.

Properties and Roles

• Solvent Action: Excellent solvent for polar molecules and ions (hydrophilic substances)
due to its polarity. Water molecules surround and separate solute particles. Medium for
metabolic reactions and transport (e.g., blood plasma, xylem/phloem sap).

• High Specific Heat Capacity: Requires a large amount of energy to raise the tempera-
ture of water. Hydrogen bonds restrict movement of molecules, absorbing energy. Stabilises
temperatures within cells and organisms, and in aquatic environments.

• High Latent Heat of Vaporisation: Requires a large amount of energy to convert liquid
water to water vapour (gas). Hydrogen bonds must be broken. Evaporation (e.g., sweating,
transpiration) has a significant cooling effect.

• Cohesion: Attraction between water molecules due to H-bonds. Creates surface tension
and allows water to move in continuous columns (e.g., in xylem).

• Adhesion: Attraction between water molecules and other polar surfaces (e.g., cellulose in
xylem walls). Helps water move up xylem.

• Density: Ice is less dense than liquid water (H-bonds hold molecules further apart in
crystal lattice). Ice floats, insulating water below.

• Transparency: Allows light to penetrate for aquatic photosynthesis.

15
3 Enzymes

Biological catalysts, essential for life. Mostly globular proteins.

3.1 Mode of Action of Enzymes

• Catalyst: Speeds up a chemical reaction without being used up itself.

• Enzyme: Biological catalyst, usually a protein.

• Intracellular Enzymes: Catalyse reactions inside cells (e.g., enzymes for respiration).

• Extracellular Enzymes: Secreted by cells to catalyse reactions outside cells (e.g., diges-
tive enzymes).

• Active Site: Specific 3D region on the enzyme molecule where the substrate binds. Com-
plementary shape to the substrate. Formed by a few amino acids from the polypeptide
chain(s).

• Substrate: The molecule(s) upon which an enzyme acts.

• Enzyme-Substrate Complex: Temporary complex formed when the substrate binds to

the active site.

• Mechanism:

1. Substrate collides with and binds to the active site.

2. Binding induces a slight change in the enzyme’s shape (induced fit) for optimal
binding and catalysis. (Supersedes simpler lock-and-key hypothesis where fit was
assumed perfect initially).
3. Enzyme lowers the activation energy of the reaction (energy required to start the
reaction) by holding substrate(s) in a way that facilitates bond breaking/formation.
4. Substrate is converted into product(s).
5. Product(s) detach from the active site.
6. Enzyme is unchanged and free to bind another substrate molecule.

• Specificity: Each enzyme typically catalyses only one type of reaction involving specific
substrates, due to the precise complementary shape of the active site and substrate.

Lock-and-Key

Substrate
Enzyme E-S Complex

Induced-Fit

Substrate
Enzyme E-S Complex

Figure 6: Models of enzyme action.

16
Measuring Reaction Rates

• Rate can be measured by:

– Rate of formation of product (e.g., volume of oxygen produced by catalase acting on

hydrogen peroxide).
– Rate of disappearance of substrate (e.g., time taken for starch to disappear when
acted on by amylase, tested with iodine).

• Initial Rate: The rate of reaction at the very beginning (time = 0), when substrate
concentration is highest. Usually the fastest rate. Determined from the steepest gradient
of a progress curve (product formed or substrate used vs. time).

• Colorimeter: Can be used to measure reaction progress if there is a colour change

(e.g., disappearance of starch-iodine colour, formation of coloured product). Measures
absorbance of light.

3.2 Factors Affecting Enzyme Action

Temperature

• Low temperatures: Enzyme and substrate molecules have low kinetic energy. Fewer
collisions, less energy per collision. Low reaction rate.

• Increasing temperature: Molecules gain kinetic energy, move faster. More frequent
collisions between enzyme and substrate. More collisions have sufficient energy (activation
energy). Reaction rate increases.

• Optimum Temperature: The temperature at which the enzyme shows maximum activ-
ity. For most human enzymes, ≈ 37 ◦ C to 40 ◦ C.

• High temperatures (above optimum): Increased vibration of enzyme molecule breaks

weak bonds (hydrogen, ionic). Tertiary structure changes, active site loses its specific
shape. Enzyme is denatured. Substrate no longer fits. Reaction rate decreases rapidly.
Denaturation is usually irreversible.

pH

• pH affects the ionisation of R groups (especially acidic -COOH and basic -NH2 ) in the
enzyme, particularly those forming the active site.

• Optimum pH: The pH at which the enzyme shows maximum activity. Specific for each
enzyme (e.g., pepsin pH ≈ 2, trypsin pH ≈ 8, most intracellular enzymes pH ≈ 7).

• Changes from optimum pH: Alteration in charges of R groups disrupts ionic bonds that
maintain the enzyme’s tertiary structure. Active site shape changes. Substrate binding is
less efficient. Extreme pH changes cause irreversible denaturation.

• Buffer solutions are used in experiments to maintain a constant pH.

17
 Rate Rate
Optimum Optimum

Temperature (◦ C) pH

Figure 7: Effect of temperature and pH on enzyme activity.

Enzyme Concentration

• If substrate concentration is high (not limiting), the initial reaction rate is directly propor-
tional to the enzyme concentration.

• More enzyme molecules = more active sites available = faster rate.

Substrate Concentration

• At low substrate concentrations, the reaction rate is proportional to substrate concentra-

tion. More substrate = more collisions with active sites.

• At high substrate concentrations, the enzyme active sites become saturated with substrate.
The enzyme is working at its maximum rate (Vmax ). Further increases in substrate con-
centration do not increase the rate, as substrate molecules are ’queuing’ for an active site.
Enzyme concentration becomes the limiting factor.

Michaelis-Menten Constant (Km )

• Vmax : Maximum rate of reaction when enzyme is saturated with substrate.

• Km (Michaelis-Menten constant): The substrate concentration at which the reaction rate

is half of Vmax ( 21 Vmax ).

• Km is a measure of the enzyme’s affinity for its substrate.

• Low Km = High affinity (enzyme binds substrate effectively even at low concentrations).

• High Km = Low affinity (enzyme requires high substrate concentrations to work effi-
ciently).

• Km allows comparison of the efficiency/affinity of different enzymes or the same enzyme

with different substrates.

Inhibitor Concentration

• Inhibitors: Substances that reduce the rate of enzyme activity.

• Reversible Inhibitors: Bind temporarily to the enzyme.

18
 – Competitive Inhibitors: Similar shape to the substrate. Compete with the sub-
strate for the active site. Bind to the active site, blocking substrate entry. Inhibition
is reduced by increasing substrate concentration (substrate ’outcompetes’ inhibitor).
Effect: Increases Km (lower affinity), Vmax remains unchanged (can be reached at
very high substrate concentrations).
– Non-competitive Inhibitors: Bind to a site on the enzyme other than the active
site (allosteric site). Binding changes the tertiary structure of the enzyme, including
the active site shape, so substrate cannot bind effectively. Inhibition is not affected by
substrate concentration. Effect: Km remains unchanged (affinity of remaining active
enzymes is the same), Vmax is reduced (fewer enzyme molecules are functional).

• Irreversible Inhibitors: Bind permanently to the enzyme, often covalently, destroying

its activity (e.g., heavy metal ions, some nerve gases).

Rate Rate
Vmax
No Inhibitor Vmax (no inhib.)
No Inhibitor
Vmax (inhib.)
+ Comp. Inhib.
+ Non-comp. Inhib.

Competitive [S] Non-competitive [S]

Figure 8: Effect of inhibitors on enzyme kinetics.

3.3 Immobilised Enzymes

• Immobilised Enzymes: Enzymes that are physically attached to an inert material or

trapped within a matrix (e.g., alginate beads, porous glass).

• Method (example): Mix enzyme solution with sodium alginate solution. Drop mixture
into calcium chloride solution. Calcium ions cause alginate to form insoluble calcium
alginate beads, trapping the enzyme inside.

• Advantages:

– Enzyme can be easily recovered and reused, reducing costs.

– Product is not contaminated with the enzyme.
– Immobilised enzymes are often more stable to changes in temperature and pH than
free enzymes.
– Reactions can be controlled more easily (e.g., by passing substrate through a column
of immobilised enzyme).

• Disadvantage: Immobilisation process may reduce enzyme activity slightly. Substrate

access to enzyme may be restricted.

• Example Application: Use of immobilised lactase to produce lactose-free milk. Milk is

passed over beads containing lactase; lactose is hydrolysed to glucose and galactose.

19
4 Cell Membranes and Transport

Cell membranes control the passage of substances and play roles in cell signalling and recognition.

4.1 Fluid Mosaic Membranes

The Fluid Mosaic Model

• Proposed by Singer and Nicolson (1972). Describes membrane structure.

• Fluid: Phospholipids and proteins can move laterally within their own layer. Membrane is
not rigid. Fluidity depends on fatty acid saturation (more unsaturated = more fluid), tail
length (shorter = more fluid), temperature (higher = more fluid), and cholesterol content.

• Mosaic: Diverse proteins are embedded or attached to the phospholipid bilayer, creating
a pattern like a mosaic.

• Phospholipid Bilayer: Basic structure. Formed due to hydrophobic interactions between

fatty acid tails (facing inwards) and hydrophilic interactions between phosphate heads
(facing outwards into aqueous environment). Acts as a barrier to water-soluble substances.

• Proteins:

– Integral proteins: Span the entire membrane (transmembrane) or are partly em-
bedded. Have hydrophobic regions within the bilayer and hydrophilic regions exposed
to the aqueous environment.
– Peripheral proteins: Attached to the surface (inner or outer) of the membrane,
often bound to integral proteins.

• Cholesterol: (Mainly animal cells) Steroid lipid. Fits between phospholipid molecules.
Regulates fluidity: reduces fluidity at moderate temperatures by restricting phospholipid
movement; prevents solidification at low temperatures by disrupting packing. Also reduces
permeability to small water-soluble molecules and ions. Increases mechanical stability.

• Glycolipids and Glycoproteins: Lipids or proteins with short, branching carbohydrate

chains attached. Found on the outer surface of the cell membrane, forming the glycocalyx.
Roles in cell recognition (e.g., ABO blood group antigens), cell adhesion, and as receptors
for signalling molecules.

Extracellular space
Glycoprotein Glycolipid

Integral
Cholesterol

Peripheral

Cytoplasm

Figure 9: Fluid Mosaic Model of the cell membrane.

20
Roles of Membrane Components

• Phospholipids: Form basic bilayer structure; barrier to water-soluble substances; allow

passage of lipid-soluble substances.
• Cholesterol: Regulates fluidity and stability; reduces permeability to ions/polar molecules.
• Proteins:
– Transport (Channel and Carrier proteins - see 4.2).
– Enzymes (e.g., embedded in mitochondrial inner membrane).
– Receptors for cell signalling (e.g., hormone receptors).
– Cell recognition / Antigens (Glycoproteins).
– Cell adhesion.
– Attachment to cytoskeleton.
• Glycolipids/Glycoproteins: Cell recognition, cell adhesion, receptors.

Cell Signalling

Communication between cells, often over long distances.

• Main Stages:
1. Secretion: Specific chemical signal (ligand, e.g., hormone) released from signalling
cell.
2. Transport: Ligand travels to target cell (e.g., via bloodstream).
3. Reception: Ligand binds to specific receptor protein on the target cell surface (or
inside cell if ligand is lipid-soluble). Binding is highly specific.
4. Transduction: Binding triggers a change in the receptor, initiating a cascade of
events inside the target cell (often involving second messengers like cAMP, or phos-
phorylation cascades). Signal is amplified.
5. Response: Cascade leads to a specific cellular response (e.g., enzyme activation, gene
transcription, secretion).

4.2 Movement Into and Out of Cells

Passive Transport (No ATP required)

Movement down a concentration or electrochemical gradient.

Simple Diffusion:

• Net movement of small, non-polar molecules (e.g., O2 , CO2 ) or small polar molecules (like
water, slowly) across the phospholipid bilayer from a region of higher concentration to
lower concentration.
• Rate depends on: concentration gradient steepness, temperature, surface area, diffusion
distance, size/nature of molecule.

21
Facilitated Diffusion:

• Net movement of specific ions or polar molecules (e.g., glucose, amino acids) across the
membrane down their concentration gradient, assisted by transport proteins.

• Channel Proteins: Form water-filled pores. Often specific for one type of ion. Can be
gated (open/close in response to stimuli, e.g., voltage-gated channels in neurones). Faster
than carrier proteins.

• Carrier Proteins: Bind to specific solute, change shape (conformation), and release solute
on the other side. Slower, can become saturated.

Osmosis:

• Net movement of water molecules from a region of higher water potential to a region of
lower water potential across a partially permeable membrane.

• Water Potential (ψ): Measure of the tendency of water to move. Pure water has ψ = 0
kPa (highest value). Adding solute lowers (makes more negative) the water potential.
Increasing pressure increases (makes less negative) the water potential.

• Effects on Cells:

– Animal Cells:
∗ In hypotonic solution (higher ψ outside): Water enters, cell swells and bursts
(lysis).
∗ In isotonic solution (same ψ): No net water movement.
∗ In hypertonic solution (lower ψ outside): Water leaves, cell shrinks (crenation).
– Plant Cells:
∗ In hypotonic solution: Water enters, vacuole swells, protoplast pushes against cell
wall. Cell becomes turgid. Cell wall prevents bursting. Turgor pressure increases
internal ψ.
∗ In isotonic solution: No net water movement. Cell is flaccid.
∗ In hypertonic solution: Water leaves, vacuole shrinks, protoplast pulls away from
cell wall (plasmolysis). Cell is plasmolysed.

• Knowledge of solute potential and pressure potential is not required for AS.

Active Transport (Requires ATP)

Movement against a concentration or electrochemical gradient.

• Requires specific carrier proteins (often called pumps).

• Energy from ATP hydrolysis causes the carrier protein to change shape, moving the solute
across the membrane against its gradient.

• Examples: Sodium-potassium pump (Na+ /K+ pump) in animal cells, proton pumps in
phloem loading.

22
Bulk Transport (Requires ATP)

Movement of large quantities of material across the membrane.

Endocytosis:

• Movement of material into the cell. Cell surface membrane invaginates, engulfs material,
and pinches off to form a vesicle inside the cytoplasm.

• Phagocytosis (’cell eating’): Engulfing large solid particles (e.g., bacteria by phagocytes).
Forms phagocytic vacuole (phagosome).

• Pinocytosis (’cell drinking’): Engulfing external fluid containing dissolved substances.

Forms small vesicles.

Exocytosis:

• Movement of material out of the cell. Vesicles (e.g., from Golgi) containing the material
move to the cell surface membrane, fuse with it, and release contents outside.

• Examples: Secretion of hormones, neurotransmitters, digestive enzymes; release of waste

products.

Surface Area to Volume Ratio

• As an object (e.g., cell, organism) increases in size, its volume increases faster than its
surface area.
Surface Area
• Ratio = . This ratio decreases as size increases.
Volume
• Calculation for simple shapes (e.g., cube of side length L): SA = 6L2 , Vol = L3 , Ratio =
6/L.

• Implications: Larger cells have a relatively smaller surface area for exchange processes
(diffusion, osmosis, active transport) compared to their metabolic needs (volume). This
limits cell size. Adaptations to increase SA:V ratio include folding (microvilli, cristae),
flattened shapes, or specialised transport systems in larger organisms.

• Investigating effect of SA:V ratio on diffusion using agar blocks of different sizes containing
indicator, placed in acid. Time how long it takes for acid to diffuse to the centre (indicated
by colour change).

23
5 The Mitotic Cell Cycle

Describes how eukaryotic cells replicate through a regulated cycle of growth and division, ensuring
genetic continuity.

5.1 Replication and Division of Nuclei and Cells

Chromosome Structure

(Structure just before mitosis)

• Composed of DNA tightly coiled around histone proteins. DNA + histones = chro-
matin.

• Consists of two identical sister chromatids joined at the centromere.

• Each chromatid contains one identical DNA molecule, produced during S phase.

• Telomeres: Protective caps of repetitive, non-coding DNA sequences at the ends of

chromosomes. Prevent loss of genes during replication and prevent chromosomes fusing.
Shorten with each division in most somatic cells.

The Mitotic Cell Cycle

Sequence of events between one cell division and the next.

• Interphase: Longest phase. Cell grows, performs normal functions, and prepares for
division.

– G1 (Gap 1): Cell growth, protein synthesis, organelle duplication.

– S (Synthesis): DNA replication occurs. Each chromosome becomes two sister chro-
matids.
– G2 (Gap 2): Further growth, protein synthesis (e.g., tubulin for spindle), check for
DNA errors, ATP synthesis.

• M Phase (Mitotic Phase): Nuclear division (mitosis) followed by cytoplasmic division

(cytokinesis).

– Mitosis: Produces two genetically identical daughter nuclei. Divided into Prophase,
Metaphase, Anaphase, Telophase.
– Cytokinesis: Division of the cytoplasm to form two separate daughter cells.

Importance of Mitosis

Produces genetically identical daughter cells for:

• Growth of multicellular organisms (from zygote).

24
 • Repair of damaged tissues (replacing dead or damaged cells).

• Asexual reproduction (producing genetically identical offspring from one parent, e.g.,
budding in Hydra, vegetative propagation in plants).

Role of Telomeres

• Protect ends of chromosomes from degradation and fusion.

• DNA polymerase cannot replicate the very ends of linear chromosomes. Telomeres act as
a buffer of non-coding DNA, so essential genes are not lost during replication.

• Telomeres shorten with each cell division. Eventually, they become critically short, sig-
nalling the cell to stop dividing (senescence) or undergo apoptosis.

• Enzyme telomerase can lengthen telomeres (active in stem cells, germ cells, cancer cells).

Stem Cells

• Undifferentiated or partially differentiated cells that can divide by mitosis indefinitely.

• When they divide, they can produce more stem cells or differentiate into specialised cell
types.

• Role in cell replacement and tissue repair throughout life (e.g., skin, gut lining, blood
cells produced from bone marrow stem cells).

• Potency varies: Totipotent (zygote - any cell type + placenta), Pluripotent (embryonic
stem cells - any cell type except placenta), Multipotent (adult stem cells - limited range of
cell types).

Cancer

• Result of uncontrolled cell division (mitosis).

• Caused by mutations in genes that regulate the cell cycle (e.g., proto-oncogenes, tumour
suppressor genes).

• Cancer cells divide repeatedly, forming a mass called a tumour.

• Benign tumours: Remain localised.

• Malignant tumours: Invade surrounding tissues and can spread (metastasise) to form sec-
ondary tumours elsewhere.

5.2 Chromosome Behaviour in Mitosis

Mitosis ensures each daughter nucleus receives an identical set of chromosomes.

25
Stages of Mitosis

• Prophase:

– Chromatin condenses and coils, becoming visible as chromosomes (each with two sister
chromatids).
– Nuclear envelope breaks down.
– Nucleolus disappears.
– Centrioles (animal cells) move to opposite poles and organise microtubule formation
into a spindle.

• Metaphase:

– Chromosomes line up along the equator (metaphase plate) of the spindle.

– Spindle fibres (microtubules) attach to the centromere of each chromosome (specifi-
cally, to kinetochores).

• Anaphase:

– Centromeres divide.
– Sister chromatids separate, becoming individual chromosomes.
– Spindle fibres shorten, pulling the chromosomes towards opposite poles of the cell,
centromere first.

• Telophase:

– Chromosomes arrive at the poles and start to decondense (uncoil) back into chromatin.
– Spindle fibres break down.
– Nuclear envelope reforms around each set of chromosomes.
– Nucleolus reappears in each nucleus.

Cytokinesis

• Division of the cytoplasm, usually occurs concurrently with telophase.

• Animal cells: Cell surface membrane constricts around the equator (cleavage furrow
forms), eventually pinching the cell into two.

• Plant cells: Vesicles from Golgi apparatus align along the equator, fuse to form a cell
plate. Cell plate develops into a new cell wall, separating the two daughter cells.

Identifying Stages

Ability to recognise stages from diagrams, photomicrographs, and microscope slides (e.g., root tip
squash). Key features: visibility and arrangement of chromosomes, presence/absence of nuclear
envelope, spindle formation/disappearance.

26
Prophase Metaphase Anaphase Telophase

Figure 10: Simplified stages of mitosis.

27
6 Nucleic Acids and Protein Synthesis

Focuses on the structure of DNA and RNA, their replication, and their roles in storing genetic
information and synthesising proteins.

6.1 Structure of Nucleic Acids and Replication of DNA

Nucleotide Structure

• Monomers of nucleic acids.

• Composed of three parts:

1. Pentose Sugar: A 5-carbon sugar.

– Deoxyribose in DNA.
– Ribose in RNA (has one more -OH group than deoxyribose).
2. Phosphate Group: (−PO3−
4 ) Acidic part.
3. Nitrogenous Base: Contains nitrogen, has ring structure(s).

• ATP (Adenosine Triphosphate): A phosphorylated nucleotide. Structure: Adenine +

Ribose + 3 Phosphate groups. Energy currency (see Topic 12). Not a monomer for nucleic
acids in this form, but related.

Nitrogenous Bases

• Purines: Double-ring structure.

– Adenine (A)
– Guanine (G)

• Pyrimidines: Single-ring structure.

– Cytosine (C)
– Thymine (T) - Found only in DNA.
– Uracil (U) - Found only in RNA (replaces Thymine).

DNA Structure

• Deoxyribonucleic Acid. Stores genetic information.

• Double Helix: Two polynucleotide strands coiled around each other.

• Antiparallel Strands: The two strands run in opposite directions (one runs 5’ to 3’, the
other runs 3’ to 5’). The numbers refer to the carbon atoms on the deoxyribose sugar.

• Sugar-Phosphate Backbone: Alternating deoxyribose sugars and phosphate groups

linked by covalent phosphodiester bonds. Phosphate links Carbon 5’ of one sugar to
Carbon 3’ of the next. Backbone is on the outside of the helix.

28
 • Nitrogenous Bases: Paired in the centre of the helix. Held together by hydrogen bonds.

• Complementary Base Pairing: Specific pairing rules:

– Adenine (A) always pairs with Thymine (T) via two hydrogen bonds (A ≃ T ).

– Guanine (G) always pairs with Cytosine (C) via three hydrogen bonds (G ≡ C).

A purine always pairs with a pyrimidine, keeping the helix width constant. The sequence
of bases on one strand determines the sequence on the other.

3’ 5’
G C

A T

C G

T A

G C

A T
5’ 3’

Figure 11: Simplified representation of DNA double helix showing antiparallel strands and base
pairing.

RNA Structure

• Ribonucleic Acid. Involved in protein synthesis.

• Single Polynucleotide Strand (usually).

• Sugar is Ribose.

• Base Uracil (U) replaces Thymine (T). Base pairing: A=U, GC.

• Types:

– Messenger RNA (mRNA): Carries genetic code from DNA in nucleus to ribosomes
in cytoplasm. Linear strand.
– Transfer RNA (tRNA): Carries specific amino acids to the ribosome during trans-
lation. Folded ’cloverleaf’ structure with an anticodon loop and an amino acid at-
tachment site.
– Ribosomal RNA (rRNA): Component of ribosomes, along with protein. Catalytic
role in peptide bond formation.

DNA Replication

• Process of copying DNA. Occurs during S phase of interphase.

• Semi-conservative Replication: Each new DNA molecule consists of one original (par-
ent) strand and one newly synthesised strand.

29
 • Steps:

1. Unwinding: Enzyme DNA helicase unwinds the double helix and breaks hydrogen
bonds between bases, separating the two strands.
2. Template: Each separated strand acts as a template for the synthesis of a new
complementary strand.
3. Synthesis: Enzyme DNA Polymerase moves along each template strand, adding
free DNA nucleotides (dNTPs) according to complementary base pairing rules (A with
T, G with C).
4. Directionality: DNA Polymerase can only add nucleotides to the 3’ end of a growing
strand. Synthesis occurs in the 5’ to 3’ direction.
5. Leading Strand: Synthesised continuously in the 5’ to 3’ direction, following the
movement of the replication fork. Template strand runs 3’ to 5’.
6. Lagging Strand: Synthesised discontinuously in short fragments (Okazaki frag-
ments) in the 5’ to 3’ direction, away from the replication fork. Template strand
runs 5’ to 3’. Requires multiple RNA primers.
7. Joining: Enzyme DNA Ligase joins the Okazaki fragments together by forming
phosphodiester bonds in the sugar-phosphate backbone. RNA primers are removed
and replaced with DNA.

• Result: Two identical DNA double helices are produced from one original molecule.

6.2 Protein Synthesis

Process of using genetic information in DNA to produce proteins. Two main stages: transcription
and translation.

The Genetic Code

• The sequence of bases in DNA determines the sequence of amino acids in a polypeptide.

• Gene: A sequence of nucleotides in DNA that codes for a polypeptide (or functional RNA).

• Triplet Code: Three consecutive bases (codon in mRNA, triplet in DNA) specify one
amino acid.

• Universal: The same codons code for the same amino acids in almost all organisms.

• Degenerate (Redundant): Most amino acids are coded for by more than one codon.

• Non-overlapping: Each base is read only once as part of a single codon.

• Start and Stop Codons: Specific codons signal the start (e.g., AUG - methionine) and
end of translation.

Transcription

• Synthesis of mRNA from a DNA template. Occurs in the nucleus (eukaryotes).

30
 • Enzyme RNA Polymerase binds to the promoter region of a gene.

• DNA strands unwind and separate locally.

• One strand acts as the template strand (transcribed strand). The other is the non-
template or non-transcribed strand.

• RNA Polymerase moves along the template strand, synthesising a complementary mRNA
strand using free RNA nucleotides (ATP, UTP, CTP, GTP). Base pairing rules: A with U,
T with A, G with C, C with G. mRNA is built in the 5’ to 3’ direction.

• Transcription stops when RNA polymerase reaches a terminator sequence.

• mRNA Processing (Eukaryotes): The initial RNA transcript (primary transcript)

is modified before leaving the nucleus.

– Splicing: Non-coding sequences (introns) are removed. Coding sequences (exons)

are joined together.
– Addition of a 5’ cap and a 3’ poly-A tail (protect mRNA and aid ribosome binding).

• Mature mRNA moves out of the nucleus through nuclear pores into the cytoplasm.

Translation

• Synthesis of a polypeptide from the mRNA sequence. Occurs at ribosomes in the cyto-
plasm.

• Ribosome: Binds to mRNA and moves along it, reading codons. Provides sites for tRNA
binding and catalyses peptide bond formation.

• tRNA: Each tRNA molecule carries a specific amino acid and has an anticodon - three
bases complementary to an mRNA codon.

• Steps:

1. Initiation: Ribosome binds to mRNA at the start codon (usually AUG). tRNA with
complementary anticodon (UAC) carrying methionine binds.
2. Elongation: Ribosome moves along mRNA one codon at a time (5’ to 3’). Correct
tRNA with complementary anticodon binds to the next codon in the ribosome’s A-
site. Peptide bond forms between the amino acid on the new tRNA and the growing
polypeptide chain held by the tRNA in the P-site. Ribosome translocates; empty
tRNA leaves from E-site. Process repeats.
3. Termination: Ribosome reaches a stop codon on mRNA. Release factor binds.
Polypeptide chain is released. Ribosome dissociates from mRNA.

• Polypeptide chain folds into its specific 3D structure (secondary, tertiary, possibly qua-
ternary) to become a functional protein. May undergo further modification (e.g., in
ER/Golgi).

31
Gene Mutations

• A change in the sequence of base pairs in a DNA molecule. May result in an altered
polypeptide.

• Types:

– Substitution: One base is replaced by another.

∗ Silent mutation: New codon codes for the same amino acid (due to degenerate
code). No effect on polypeptide.
∗ Missense mutation: New codon codes for a different amino acid. Effect depends on
the role of that amino acid in protein structure/function (e.g., sickle cell anaemia
- Glu to Val).
∗ Nonsense mutation: New codon is a stop codon. Results in a truncated, usually
non-functional polypeptide.
– Deletion: One or more bases are removed.
– Insertion: One or more bases are added.

• Frameshift Mutation: Deletions or insertions (unless in multiples of three) shift the

reading frame of codons from the point of mutation onwards. Usually leads to a completely
altered amino acid sequence and often a premature stop codon, resulting in a non-functional
protein. More severe than substitutions.

32
7 Transport in Plants

Plants require transport systems to move water, mineral ions, and organic solutes between dif-
ferent parts.

7.1 Structure of Transport Tissues

Two main transport tissues in vascular bundles: xylem and phloem.

Distribution in Herbaceous Dicotyledons

(Ability to draw plan diagrams required)

• Stem: Vascular bundles arranged in a ring towards the outside. Xylem is towards the in-
side, phloem towards the outside. Cambium (meristematic tissue) may be present between
xylem and phloem. Central region is pith, outer region is cortex.

• Root: Central vascular tissue (vascular cylinder). Xylem often forms a central star/core
shape. Phloem located in the gaps between the arms of the xylem star. Surrounded by
endodermis and pericycle. Outer region is cortex.

• Leaf : Vascular bundles (veins) scattered throughout the mesophyll. Xylem typically lo-
cated on the upper side (towards adaxial surface), phloem on the lower side (towards
abaxial surface).

Xylem Structure and Function

• Transports water and dissolved mineral ions from roots to leaves; provides structural sup-
port.

• Composed of several cell types, main conducting cells are xylem vessel elements:

– Dead cells (empty lumen, no protoplast) - reduces resistance to water flow.

– Form continuous, hollow tubes (xylem vessels) by joining end-to-end with loss of
end walls.
– Cell walls thickened with lignin (a hard, waterproof polymer). Provides strength
to withstand tension (negative pressure) and prevents collapse. Lignification pattern
varies (e.g., spiral, annular, pitted).
– Pits: Non-lignified areas in the walls allowing lateral movement of water between
vessels or to surrounding tissues.

• Also contains parenchyma (living cells for storage) and fibres (lignified cells for support).

Phloem Structure and Function

• Transports organic solutes (mainly sucrose, also amino acids, hormones) - called assimi-
lates - from source to sink. This is translocation.

33
 • Main conducting cells are sieve tube elements:

– Living cells, but highly modified: very little cytoplasm (thin peripheral layer), no
nucleus, no large vacuole, few organelles - reduces resistance to flow.
– Joined end-to-end to form sieve tubes.
– End walls are perforated by pores, forming sieve plates. Allow passage of sap be-
tween elements.

• Each sieve tube element is closely associated with a companion cell:

– Living cell with dense cytoplasm, large nucleus, many mitochondria, many ribosomes.
Metabolically very active.
– Connected to its sieve tube element by numerous plasmodesmata.
– Provides metabolic support to the sieve tube element (which lacks nucleus/ribosomes).
Plays a crucial role in loading sucrose into the sieve tube element (using ATP).

• Also contains parenchyma and fibres.

7.2 Transport Mechanisms

Water Transport (Soil to Air)

• Absorption at Root Hairs: Water moves from soil (high ψ) into root hair cells (lower
ψ) by osmosis.

• Movement Across Root Cortex: Water moves towards the central xylem down a water
potential gradient via two pathways:

– Apoplast Pathway: Movement through interconnected cell walls (made of cellulose

fibres) and intercellular spaces. Water does not enter cytoplasm. Main pathway across
the cortex.
– Symplast Pathway: Movement from cytoplasm to cytoplasm via plasmodesmata.
Water enters root hair cytoplasm by osmosis, then moves cell-to-cell.

• Role of Endodermis: Inner boundary of cortex. Cells have a waterproof band, the Cas-
parian strip (impregnated with suberin), in their radial and transverse walls. Blocks the
apoplast pathway, forcing water entering the xylem to pass through the partially perme-
able cell surface membrane and cytoplasm of endodermal cells. Allows plant to control ion
uptake into xylem.

• Movement into Xylem: Water moves from endodermal cells into xylem vessels down
the water potential gradient.

• Movement up the Xylem (Cohesion-Tension Theory):

– Transpiration: Evaporation of water vapour from surfaces inside the leaf (mainly
mesophyll cell walls) into air spaces, followed by diffusion out through stomata down
a water vapour potential gradient. Creates low ψ in mesophyll cells.
– Water Potential Gradient: Transpiration creates tension (negative pressure) in
the xylem, pulling water up from the roots. A continuous water potential gradient
exists from soil → root → stem → leaf → air.

34
 – Cohesion: Attraction between water molecules due to hydrogen bonds. Maintains
continuous columns of water in the narrow xylem vessels.
– Adhesion: Attraction between water molecules and the polar lignified/cellulose walls
of the xylem vessels. Helps counteract gravity and maintain water column.
– Water moves up the xylem by mass flow under tension.

Translocation of Assimilates (Source to Sink)

• Movement of organic solutes (e.g., sucrose, amino acids) in phloem sieve tubes.

• Source: Site of production or storage release (e.g., photosynthesising leaves, storage organs
like tubers releasing sugars).

• Sink: Site of utilisation or storage (e.g., growing roots, fruits, seeds, storage organs).

• Mass Flow Hypothesis (Pressure Flow Hypothesis):

1. Phloem Loading (at Source): Sucrose actively transported from source cells into
companion cells, then into sieve tube elements. Requires ATP. Mechanism often
involves:
– Proton pumps (H+ -ATPase) in companion cell membrane actively pump H+
ions out of the companion cell into surrounding tissue using ATP.
– High H+ concentration outside creates a proton gradient.
– H+ ions flow back into companion cell down their gradient via cotransporter
proteins, bringing sucrose molecules with them (secondary active transport).
– Sucrose diffuses from companion cell into sieve tube element via plasmodesmata.
2. Water Potential Lowered: High sucrose concentration in sieve tube element lowers
its water potential (ψ).
3. Water Entry: Water moves by osmosis from surrounding tissues (mainly xylem)
into the sieve tube element, increasing the hydrostatic pressure.
4. Mass Flow: High hydrostatic pressure at the source and lower hydrostatic pressure at
the sink (where sucrose is removed) creates a pressure gradient. Water and dissolved
solutes (phloem sap) flow down this gradient from source to sink through the sieve
tubes.
5. Phloem Unloading (at Sink): Sucrose is removed from sieve tube elements by sur-
rounding sink cells (often actively transported out). This increases the water potential
in the sieve tube.
6. Water Exit: Water moves by osmosis out of the sieve tube element into surrounding
tissues (e.g., xylem), reducing the hydrostatic pressure at the sink.

Adaptations of Xerophytes

Plants adapted to reduce water loss by transpiration in dry environments. Examples: Marram
grass, Cacti.

• Reduced leaf surface area (e.g., needles, spines instead of broad leaves).

• Thick waxy cuticle (reduces evaporation from epidermis).

35
• Sunken stomata (located in pits or grooves, traps moist air, reduces water potential gradi-
ent).

• Hairs on epidermis (trap moist air).

• Rolled leaves (encloses lower epidermis with stomata in a humid microenvironment, e.g.,
Marram grass).

• Reduced number of stomata.

• Deep/extensive root systems.

• Succulent tissues (store water).

36
8 Transport in Mammals

Complex, active animals require efficient transport systems for nutrients, gases, waste products,
and heat.

8.1 The Circulatory System

• Closed Double Circulation: Blood passes through the heart twice for each complete
circuit of the body. Blood remains within vessels.

– Pulmonary Circulation: Heart → Lungs → Heart.

– Systemic Circulation: Heart → Rest of Body → Heart.

• Components: Heart (pump), Blood (transport medium), Blood Vessels (tubes).

Blood Vessels

• Arteries: Carry blood away from the heart. Thick, muscular, elastic walls to withstand
high pressure and maintain blood flow (elastic recoil smooths pulses). Narrow lumen rela-
tive to wall thickness. Divide into smaller arterioles.

– Elastic Arteries (e.g., Aorta, Pulmonary Artery): Large amount of elastic tissue in
walls to stretch and recoil.
– Muscular Arteries: More smooth muscle, less elastic tissue. Control blood flow to
different regions via vasoconstriction/vasodilation.

• Arterioles: Small arteries connecting arteries to capillaries. Significant smooth muscle

content allows regulation of blood flow into capillary beds. Major site of peripheral resis-
tance, influencing blood pressure.

• Capillaries: Smallest vessels (≈ 7 µm diameter). Site of exchange between blood and

tissues. Walls are one cell thick (squamous endothelium) on a basement membrane -
provides short diffusion distance. Form extensive networks (capillary beds) providing
large surface area. Narrow lumen forces red blood cells to pass single file, slowing flow and
maximising exchange. Permeable walls (small gaps between endothelial cells).

• Venules: Small veins collecting blood from capillaries.

• Veins: Carry blood towards the heart. Thinner, less muscular/elastic walls than arteries
(blood pressure is much lower). Wider lumen than arteries. Contain semilunar valves
to prevent backflow of blood, especially in limbs (assisted by skeletal muscle pump).

Lumen Lumen

Artery Capillary Vein

Figure 12: Simplified comparison of blood vessel structure (relative lumen/wall size).

37
Blood Components

• Plasma: Liquid matrix (≈ 55

– Plasma Proteins (e.g., albumin, fibrinogen, globulins/antibodies): Maintain os-

motic potential, involved in blood clotting, transport, immunity. Too large to easily
leave capillaries.

• Blood Cells (≈ 45

– Red Blood Cells (Erythrocytes): Transport oxygen. Biconcave disc shape (large
SA:V ratio). No nucleus or mitochondria when mature (maximises space for haemoglobin).
Flexible (can squeeze through capillaries). Contain haemoglobin.
– White Blood Cells (Leukocytes): Involved in immune defence. Various types:
∗ Phagocytes: Engulf pathogens (Neutrophils - lobed nucleus, granular cyto-
plasm; Monocytes - largest, kidney-shaped nucleus, become macrophages in
tissues).
∗ Lymphocytes: Specific immunity (B-lymphocytes - produce antibodies; T-
lymphocytes - T-helper and T-killer cells). Large round nucleus, little cyto-
plasm. (Details in Topic 11).
– Platelets (Thrombocytes): Cell fragments involved in blood clotting.

Tissue Fluid

• Fluid surrounding body cells. Formed from blood plasma leaking out of capillaries.

• Formation: At arteriole end of capillary bed, high hydrostatic pressure (blood pressure)
forces plasma fluid out through gaps between endothelial cells. Proteins and cells remain
in blood. This outward pressure is greater than the inward osmotic pull due to plasma
proteins. Net movement out.

• Composition: Similar to plasma but with very few plasma proteins. Contains dissolved
nutrients (glucose, O2 , ions) for cells and waste products (CO2 , urea) from cells.

• Return: At venule end of capillary bed, blood pressure is lower. Water potential inside
capillary is lower than tissue fluid (due to plasma proteins). Water moves back into capillary
by osmosis. Some tissue fluid drains into lymphatic system.

• Function: Medium for exchange of substances between blood and cells.

8.2 Transport of Oxygen and Carbon Dioxide

Oxygen Transport

• Mainly transported by haemoglobin (Hb) within red blood cells.

• Hb is a globular protein with quaternary structure (2α, 2β chains), each containing an

iron(Fe2+ ) haem group.

• Each Fe2+ can reversibly bind one O2 molecule. Hb + 4O2 ⇌ Hb(O2 )4 (Oxyhaemoglobin).

38
 • Oxygen Dissociation Curve: S-shaped (sigmoid) graph showing percentage saturation
of Hb with O2 against partial pressure of oxygen (pO2 ).
– Loading (Lungs): High pO2 . Hb has high affinity for O2 , becomes almost fully
saturated (≈ 97
– Unloading (Respiring Tissues): Low pO2 . Hb has lower affinity for O2 , releases
O2 readily.
– Sigmoid Shape: Due to cooperative binding. Binding of first O2 molecule causes
conformational change in Hb, increasing affinity for subsequent O2 molecules. Makes
loading/unloading efficient over physiological pO2 range.
• Bohr Shift (Bohr Effect): Dissociation curve shifts to the right in the presence of high
partial pressure of carbon dioxide (pCO2 ) / high H+ concentration (low pH).
– CO2 dissolves, forms carbonic acid (H2 CO3 ), dissociates releasing H+ .
– H+ ions bind to Hb, altering its conformation and reducing its affinity for O2 .
– Hb releases O2 more readily at any given pO2 .
– Significance: In actively respiring tissues, pCO2 is high, enhancing O2 unloading
where it is most needed. In lungs, pCO2 is low, enhancing O2 loading.

Carbon Dioxide Transport

Transported in three forms:

1. Dissolved in Plasma (≈ 5
2. As Hydrogencarbonate Ions (HCO−
3 ) in Plasma (≈ 85

• CO2 diffuses from tissues into red blood cells.

• Enzyme carbonic anhydrase catalyses: CO2 + H2 O ⇌ H2 CO3 (carbonic acid).
• H2 CO3 dissociates: H2 CO3 ⇌ H+ + HCO−
3.
• HCO−
3 ions diffuse out of red blood cell into plasma.
• Chloride Shift: To maintain electrical neutrality, chloride ions (Cl− ) diffuse from
plasma into red blood cell as HCO−
3 leaves.
• H+ ions buffered by binding to haemoglobin (forming haemoglobinic acid, HHb),
preventing large pH drop and contributing to Bohr shift.
• In lungs, low pCO2 reverses these reactions: HCO− 3 enters red cell (Cl
− leaves),

combines with H+ (released from Hb as it binds O2 ), forms H2 CO3 , breaks down

(carbonic anhydrase) to CO2 + H2 O. CO2 diffuses into alveoli.
3. Bound to Haemoglobin (Carbaminohaemoglobin) (≈ 10
• CO2 binds directly to terminal amino groups on Hb protein chains (not to haem
group). Hb + CO2 ⇌ HbCO2 .
• Binding is reversible, favoured by low pO2 and high pCO2 (tissues), reversed in lungs.

8.3 The Heart

Muscular pump driving blood circulation.

39
Structure

• Four Chambers: Right Atrium, Right Ventricle, Left Atrium, Left Ventricle.

• Septum: Muscular wall separating right and left sides.

• Walls: Made of cardiac muscle. Ventricle walls are thicker than atrial walls (pump blood
further). Left ventricle wall is thickest (pumps blood to entire body systemically).

• Valves: Ensure one-way blood flow.

– Atrioventricular (AV) Valves: Between atria and ventricles. Tricuspid (right),

Bicuspid/Mitral (left). Prevent backflow into atria when ventricles contract. Attached
to papillary muscles by tendons (heart strings/chordae tendineae) to prevent inversion.
– Semilunar Valves: Between ventricles and arteries. Pulmonary valve (right ventricle
to pulmonary artery), Aortic valve (left ventricle to aorta). Prevent backflow into
ventricles when ventricles relax.

• Major Blood Vessels:

– Vena Cava (Superior and Inferior): Bring deoxygenated blood from body to right
atrium.
– Pulmonary Artery: Takes deoxygenated blood from right ventricle to lungs.
– Pulmonary Veins: Bring oxygenated blood from lungs to left atrium.
– Aorta: Takes oxygenated blood from left ventricle to rest of body.
– Coronary Arteries: Branch off aorta, supply heart muscle itself with oxygenated blood.

The Cardiac Cycle

Sequence of events during one heartbeat (≈ 0.8 seconds at rest).

1. Atrial Systole (≈ 0.1s): Atria contract. Pressure increases in atria, forcing remaining
blood through open AV valves into relaxed ventricles. Semilunar valves closed.

2. Ventricular Systole (≈ 0.3s): Ventricles contract. Pressure rises rapidly in ventricles.

AV valves close (first heart sound, ’lub’). Pressure exceeds arterial pressure, semilunar
valves open. Blood ejected into aorta and pulmonary artery. Atria relax (atrial diastole)
and start refilling.

3. Diastole (≈ 0.4s): Ventricles relax. Pressure falls in ventricles. Semilunar valves close
(second heart sound, ’dub’) as arterial pressure exceeds ventricular pressure, preventing
backflow. Pressure in ventricles falls below atrial pressure, AV valves open. Ventricles
start passively filling with blood from atria.

Pressure changes in atria, ventricles, and arteries drive blood flow and valve action.

Control of Heartbeat

• Cardiac muscle is myogenic (contracts rhythmically without nerve stimulation).

40
• Intrinsic control system coordinates contractions:

1. Sinoatrial Node (SAN): Pacemaker. Located in right atrium wall. Initiates exci-
tation wave spontaneously at regular intervals (≈ 70 times/min at rest).
2. Excitation spreads across atrial walls, causing atrial systole.
3. Wave reaches Atrioventricular Node (AVN): Located in septum near AV valves.
Delays impulse slightly (≈ 0.1s) allowing atria to finish contracting before ventricles
start.
4. AVN transmits excitation down specialized conducting fibres called the Purkyne
tissue (Bundle of His) in the septum.
5. Purkyne tissue carries excitation to the apex (base) of the heart and then up through
ventricle walls.
6. Ventricles contract from the apex upwards, squeezing blood efficiently into arteries.

• Nervous and hormonal control (not required for AS) can modify the intrinsic heart rate
(e.g., during exercise or stress).

41
9 Gas Exchange

Focuses on the structure and function of the mammalian gas exchange system (lungs).

9.1 The Gas Exchange System

Structure

Pathway of air: Nose/Mouth → Pharynx → Larynx → Trachea → Bronchi (singular: bronchus)

→ Bronchioles → Terminal Bronchioles → Respiratory Bronchioles → Alveolar Ducts → Alve-
oli (singular: alveolus).

• Lungs: Located in thoracic cavity, protected by rib cage, separated from abdomen by
diaphragm. Surrounded by pleural membranes.
• Trachea (Windpipe): Tube carrying air to bronchi. Supported by C-shaped rings of
cartilage (prevent collapse, allow flexibility). Lined with ciliated epithelium and goblet
cells.
• Bronchi: Two main branches off trachea, one to each lung. Similar structure to trachea
but narrower, cartilage forms irregular blocks/plates.
• Bronchioles: Finer branching tubes off bronchi. Walls contain smooth muscle, lack car-
tilage. Diameter can be adjusted by muscle contraction/relaxation. Terminal bronchioles
are narrowest airways without alveoli.
• Alveoli: Tiny air sacs (≈ 250 µm diameter) where gas exchange occurs. Walls are one
cell thick (squamous epithelium). Rich capillary network surrounds each alveolus. Surface
covered by thin film of moisture. Contain elastic fibres. Collectively provide huge surface
area (≈ 70 m2 ).

Distribution and Function of Tissues

• Cartilage (Trachea, Bronchi): Provides support, keeps larger airways open. C-shape in
trachea allows oesophagus expansion. Absent in bronchioles.
• Ciliated Epithelium (Trachea, Bronchi, larger Bronchioles): Cilia beat rhythmically to
move mucus layer upwards towards pharynx (mucociliary escalator). Traps pathogens and
particles.
• Goblet Cells (Scattered within ciliated epithelium): Secrete mucus (made of mucin
glycoproteins) which traps particles and pathogens. Fewer in smaller airways.
• Smooth Muscle (Trachea, Bronchi, Bronchioles): Allows adjustment of airway diameter,
controlling airflow resistance (especially in bronchioles). Relaxes during exercise, constricts
in response to irritants.
• Elastic Fibres (Throughout airways and alveoli): Allow stretch during inhalation and
elastic recoil during exhalation (helps force air out, especially from alveoli).
• Squamous Epithelium (Alveoli walls, Capillary endothelium): Extremely thin (one cell
thick) providing very short diffusion pathway for gases.

42
Gas Exchange Mechanism

• Occurs between air in alveoli and blood in surrounding capillaries by diffusion down partial
pressure gradients.

• Oxygen: Higher pO2 in alveolar air than in capillary blood. O2 dissolves in moisture
film, diffuses across alveolar epithelium and capillary endothelium into blood, binds to
haemoglobin.

• Carbon Dioxide: Higher pCO2 in capillary blood than in alveolar air. CO2 diffuses
from blood (mainly from HCO− 3 conversion in red cells) across capillary endothelium and
alveolar epithelium into alveolar air.

• Maintaining Gradients:

– Ventilation (breathing) constantly replaces alveolar air, maintaining high pO2 and low
pCO2 .
– Continuous blood flow through capillaries transports O2 away and brings CO2 , main-
taining low pO2 and high pCO2 in blood arriving at alveoli.

• Adaptations for Efficient Exchange: Large surface area (alveoli), short diffusion dis-
tance (thin walls), steep concentration/partial pressure gradients (maintained by ventila-
tion and blood flow).

Maintaining Health

• Mucus: Traps pathogens and particles. Produced by goblet cells and mucous glands.

• Cilia: Beat to move mucus up and out of airways (swallowed or coughed out).

• Macrophages: Phagocytose particles/pathogens reaching alveoli.

43
10 Infectious Diseases

Diseases caused by pathogens that can be transmitted between hosts.

10.1 Infectious Diseases

• Pathogen: A disease-causing microorganism (e.g., bacterium, virus, fungus, protoctist).

• Infectious Disease: A disease caused by a pathogen.
• Transmissible: Can be passed from one host to another.
• Transmission Methods: Direct contact, airborne droplets, water, food, vectors (e.g.,
insects), body fluids.

Specific Diseases

• Cholera:
– Pathogen: Bacterium Vibrio cholerae.
– Transmission: Contaminated water or food (faecal-oral route).
– Site/Effect: Bacteria colonise small intestine wall, produce toxin (choleragen). Toxin
disrupts ion transport in epithelial cells, causing massive loss of chloride ions and
water into lumen → severe watery diarrhoea, dehydration.
– Prevention/Control: Clean water supply, sewage treatment, hygiene, vaccination (lim-
ited effectiveness). Treatment: Oral rehydration therapy (ORT).
• Malaria:
– Pathogen: Protoctist Plasmodium (P. falciparum, P. vivax, P. ovale, P. malariae).
– Transmission: Vector - female Anopheles mosquito. Bites infected person, ingests
gametocytes. Sexual reproduction in mosquito. Infective stages (sporozoites) injected
into new host during blood meal. Can also be transmitted via blood transfusion,
shared needles, across placenta.
– Site/Effect: Sporozoites travel to liver, multiply. Merozoites released, invade red blood
cells, multiply asexually. Red cells burst, releasing more merozoites and toxins →
cycles of fever, chills, anaemia. P. falciparum can block capillaries (cerebral malaria).
– Prevention/Control: Reduce mosquito numbers (drain swamps, insecticides), avoid
bites (nets, repellents), prophylactic drugs. Treatment: Antimalarial drugs (e.g.,
chloroquine, artemisinin combinations). Resistance is a major problem.
• Tuberculosis (TB):
– Pathogen: Bacteria Mycobacterium tuberculosis (mainly), M. bovis (from cattle).
– Transmission: Airborne droplets (coughing, sneezing) from person with active pul-
monary TB. M. bovis via unpasteurised milk/undercooked meat.
– Site/Effect: Bacteria inhaled, infect lungs. Immune system often walls off bacteria in
tubercles (latent TB). Can reactivate later (active TB), especially if immune system
weakened. Bacteria destroy lung tissue. Can spread to other organs. Symptoms:
persistent cough, coughing blood, fever, weight loss.

44
 – Prevention/Control: BCG vaccination (variable effectiveness), contact tracing, isola-
tion of infectious cases, pasteurisation of milk, cattle testing. Treatment: Long course
(6+ months) of multiple antibiotics. Drug resistance (MDR-TB, XDR-TB) is a major
problem.
• HIV/AIDS:
– Pathogen: Human Immunodeficiency Virus (HIV) - a retrovirus.
– Transmission: Direct exchange of body fluids (blood, semen, vaginal fluids, breast
milk). Main routes: unprotected sexual intercourse, sharing contaminated needles,
mother-to-child (pregnancy, birth, breastfeeding), contaminated blood transfusions.
– Site/Effect: HIV infects and destroys T-helper lymphocytes. Gradual decline in im-
mune system function. Leads to Acquired Immunodeficiency Syndrome (AIDS) -
susceptibility to opportunistic infections (e.g., TB, pneumonia) and certain cancers.
– Prevention/Control: Education (safe sex, no needle sharing), screening of blood do-
nations, antiretroviral drugs for HIV+ pregnant women, barrier contraception (con-
doms). Treatment: Antiretroviral therapy (ART) - combination of drugs slows viral
replication, does not cure. No vaccine currently available.

Factors in Prevention and Control

Consider biological, social, and economic factors for each disease (e.g., poverty, sanitation, edu-
cation, healthcare access, drug resistance, vector control challenges, stigma).

10.2 Antibiotics

• Chemicals that kill or inhibit the growth of bacteria. Originally derived from microorgan-
isms (e.g., fungi like Penicillium), now many are synthetic or semi-synthetic.
• Mechanism of Penicillin: Inhibits enzymes involved in synthesising cross-links in bacte-
rial peptidoglycan cell walls. Weakens wall, cell bursts due to osmotic water entry (bacte-
ricidal, especially effective against Gram-positive bacteria). Only works when bacteria are
actively growing and making new cell walls.
• Why Antibiotics Don’t Affect Viruses: Viruses have no cell wall, metabolism, or
ribosomes of their own. They use host cell machinery. Antibiotics target bacterial-specific
structures or processes.
• Antibiotic Resistance:
– Bacteria evolve resistance through random mutation.
– Widespread use/misuse of antibiotics creates strong selection pressure, favouring re-
sistant strains. Sensitive bacteria are killed, resistant ones survive and multiply.
– Resistance genes often located on plasmids, easily transferred between bacteria (even
different species) via conjugation.
– Consequences: Infections become harder/impossible to treat, increased healthcare
costs, need for new antibiotics.
– Reducing Impact: Use antibiotics only when necessary (not for viral infections),
complete full course, good hygiene, reduce use in agriculture, develop new antibi-
otics/alternatives.

45
11 Immunity

The body’s defence mechanisms against pathogens and foreign substances.

11.1 The Immune System

Phagocytosis

• Non-specific engulfment and destruction of pathogens by phagocytes.

• Neutrophils: First responders. Move out of blood to site of infection (chemotaxis). Engulf
bacteria, kill using enzymes from lysosomes. Short-lived, form pus.

• Macrophages: Develop from monocytes. Larger, longer-lived. Engulf pathogens, cell

debris. Act as Antigen-Presenting Cells (APCs) - display antigens from destroyed
pathogens on their surface to activate lymphocytes.

Antigens

• Molecules (usually proteins or glycoproteins on cell surfaces) recognised as foreign by the

immune system, triggering an immune response.

• Self Antigens: Molecules on the surface of the body’s own cells. Immune system normally
tolerant to these.

• Non-self Antigens: Molecules on pathogens or foreign cells/materials. Stimulate immune

response.

Lymphocytes and the Immune Response

Specific defence involving B- and T-lymphocytes.

Primary Immune Response: (First encounter with a specific antigen)

1. Antigen Presentation: Macrophage engulfs pathogen, processes it, and presents non-self
antigens on its surface bound to MHC molecules.

2. Activation of T-helper cells: Specific T-helper cell with complementary T-cell receptor
binds to the presented antigen on the APC. APC releases cytokines, activating the T-helper
cell.

3. Clonal Selection and Expansion of T-helper cells: Activated T-helper cell divides
rapidly by mitosis to form a clone of identical cells (including active T-helper cells and
memory T-helper cells).

4. Activation of B-cells: Specific B-cell with complementary B-cell receptor binds to the
antigen (either free or on pathogen). T-helper cell from the same clone binds to the B-cell
(presenting the same antigen) and releases cytokines, activating the B-cell.

46
 5. Clonal Selection and Expansion of B-cells: Activated B-cell divides rapidly by mitosis
to form a clone of identical cells.

6. Differentiation: B-cells differentiate into:

• Plasma Cells: Short-lived, produce and secrete large quantities of specific antibodies.
• Memory B-cells: Long-lived, remain in circulation for secondary response.

7. Activation of T-killer cells: T-helper cells also release cytokines that activate specific
T-killer cells which recognise antigens presented on infected body cells. Activated T-killer
cells divide (clonal expansion) and differentiate into active T-killer cells and memory T-
killer cells. Active T-killer cells destroy infected body cells.

Secondary Immune Response: (Subsequent encounter with the same antigen)

• Memory Cells (B and T) recognise the antigen immediately.

• Rapid clonal expansion and differentiation into plasma cells and active T-killer cells.

• Faster, stronger, and longer-lasting response than primary response.

• Pathogen usually eliminated before symptoms develop. Basis of long-term immunity.

11.2 Antibodies and Vaccination

Antibody Structure and Function

• Globular glycoproteins (immunoglobulins).

• Structure: Typically Y-shaped molecule with 4 polypeptide chains (2 identical heavy, 2

identical light) linked by disulfide bonds.

– Constant Region: Same amino acid sequence within a class of antibodies. Binds to
receptors on phagocytes or activates complement system.
– Variable Region: Specific amino acid sequence at the tips of the ’Y’ arms. Forms the
antigen-binding site. Shape is complementary to a specific antigen. Each antibody
molecule has two identical antigen-binding sites.
– Hinge Region: Flexible region allowing arms to move.

• Functions:

– Neutralisation (e.g., binding to toxins or viral attachment sites).

– Agglutination (clumping pathogens together, making phagocytosis easier).
– Opsonisation (coating pathogens to enhance phagocytosis - constant region binds to
phagocyte receptors).
– Activation of complement system (leads to lysis of pathogens).

47
 Variable Region Variable Region

Hinge

Constant Region

Figure 13: Simplified structure of an antibody (IgG).

Monoclonal Antibodies (Mabs)

• Antibodies produced by a single clone of B-cells (plasma cells or hybridomas), all identical
and specific to one antigen epitope.

• Hybridoma Method:

1. Mouse injected with specific antigen.

2. Mouse produces plasma cells secreting the desired antibody.
3. Plasma cells extracted from mouse spleen.
4. Plasma cells fused with immortal myeloma (cancer) cells to create hybridoma cells.
5. Hybridomas cultured and screened to select those producing the desired antibody.
6. Selected hybridomas cloned to produce large quantities of Mabs.

• Uses:

– Diagnosis: Detecting presence of specific antigens or antibodies (e.g., pregnancy

tests, ELISA tests for pathogens/hormones, cancer detection). Mabs can be labelled
(e.g., with enzymes, fluorescent markers).
– Treatment: Targeting specific cells (e.g., cancer cells) or molecules. Mabs can deliver
drugs/radiation directly to cancer cells, or block growth factor receptors, or trigger
immune system to attack cancer cells (e.g., Herceptin for breast cancer). Can also be
used to treat autoimmune diseases.

Types of Immunity

• Active Immunity: Immune system is activated, produces own antibodies and memory
cells. Long-lasting protection.

– Natural Active: Acquired through infection with pathogen.

– Artificial Active: Acquired through vaccination (exposure to antigens).

• Passive Immunity: Individual receives pre-formed antibodies from another source. No

immune response activated, no memory cells produced. Short-term, temporary protection.

– Natural Passive: Antibodies pass from mother to fetus across placenta or to infant
in breast milk.

48
 – Artificial Passive: Injection of antibodies (e.g., antitoxins for tetanus/diphtheria,
antivenom).

Vaccination

• Introduction of antigens (from dead/attenuated pathogens, toxins, or subunits) into the

body to induce artificial active immunity.

• Stimulates a primary immune response without causing the disease.

• Memory cells are produced, providing long-term protection. A subsequent infection triggers
a rapid and strong secondary response.

• Vaccination Programmes: Aim to immunise a large proportion of the population to

control/eradicate infectious diseases. Relies on achieving herd immunity.

• Herd Immunity: When a high percentage of the population is immune (usually through
vaccination), it is difficult for the pathogen to spread, protecting non-immunised individu-
als. Threshold percentage varies depending on the disease’s infectivity.

49