Cells

Cells

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Board Coverage AQA Paper 1 | Edexcel A Paper 1 | OCR (A) Paper 1 | CIE Paper 2

1. Cell Theory and Microscopy

1.1 Cell Theory

The cell theory, developed by Schleiden and Schwann (1838--1839) and later refined by Virchow, states:

1. All living organisms are composed of one or more cells.
2. The cell is the basic unit of structure and organisation in organisms.
3. All cells arise from pre-existing cells (biogenesis).

1.2 Microscopy

Light microscopy uses visible light ($\lambda \approx 400$--$700\ \mathrm{nm}$) focused through glass lenses. The maximum resolving power of a light microscope is limited by diffraction:

$d = \frac◆LB◆0.61\lambda◆RB◆◆LB◆n\sin\theta◆RB◆$

where $d$ is the minimum resolvable distance, $\lambda$ is the wavelength, $n$ is the refractive index of the medium, and $\theta$ is the half-angle of the cone of light. For light microscopy, $d \approx 200\ \mathrm{nm}$, giving a maximum useful magnification of approximately $\times 1500$.

Electron microscopy uses a beam of electrons ($\lambda \approx 0.005\ \mathrm{nm}$) instead of light, giving a resolving power of approximately $0.2\ \mathrm{nm}$ and effective magnifications up to $\times 2000000$.

Feature	Light Microscope	Electron Microscope
Resolution	$\approx 200\ \mathrm{nm}$	$\approx 0.2\ \mathrm{nm}$
Magnification	Up to $\times 1500$	Up to $\times 2000000$
Specimen	Living or dead	Dead only (vacuum required)
Contrast	Staining (dyes)	Heavy metal staining
Cost	Low	High

Transmission electron microscopy (TEM): electrons pass through thin sections; produces 2D images of internal ultrastructure.

Scanning electron microscopy (SEM): electrons are scattered from the surface; produces 3D images of surface features.

Magnification is defined as:

$\mathrm{Magnification} = \frac◆LB◆\mathrm{Image\ size}◆RB◆◆LB◆\mathrm{Actual\ size}◆RB◆$

Laser scanning confocal microscopy uses laser light and pinhole apertures to eliminate out-of-focus light, producing sharp optical sections through thick specimens. This allows 3D reconstruction without the need for physical sectioning.

warning

Common Pitfall Students often confuse magnification with resolution. Magnification is how much larger the image appears; resolution is the ability to distinguish two closely spaced objects as separate. Increasing magnification without increasing resolution produces a larger but blurry image -- no additional detail is revealed.

1.3 Cell Fractionation

Cell fractionation is the process of breaking open cells and separating organelles by differential centrifugation:

1. Homogenisation: cells are broken open in an isotonic, buffered, ice-cold solution. The isotonic condition prevents osmotic lysis or shrinkage; the cold temperature reduces enzyme activity that would degrade organelles; the buffer maintains pH.
2. Filtration: the homogenate is filtered through a gauze to remove debris.
3. Differential centrifugation: the filtrate is centrifuged at increasing speeds. At each step, the heaviest (densest) organelles form a pellet at the bottom of the tube:

Centrifugation Speed	Pellet	Supernatant Contains
Low ($1000\ \mathrm{g}$, 10 min)	Nuclei	All other organelles
Medium ($10000\ \mathrm{g}$, 20 min)	Mitochondria, lysosomes	Lighter organelles
High ($100000\ \mathrm{g}$, 60 min)	Ribosomes, microsomes (ER fragments)	Cytosol

2. Prokaryotic and Eukaryotic Cells

2.1 Fundamental Distinctions

All cells fall into one of two categories based on whether they possess a membrane-bound nucleus.

Definition. A prokaryotic cell lacks a membrane-bound nucleus and membrane-bound organelles. Its DNA is a single circular molecule located in the nucleoid region. Prokaryotes include bacteria and archaea.

Definition. A eukaryotic cell possesses a membrane-bound nucleus and membrane-bound organelles. Its DNA is organised into linear chromosomes within the nucleus. Eukaryotes include animals, plants, fungi, and protists.

Feature	Prokaryote	Eukaryote
Nucleus	Absent (nucleoid region)	Present, with nuclear envelope
DNA	Circular, naked; no histones	Linear, associated with histones
Ribosomes	$70\mathrm{S}$ ($50\mathrm{S} + 30\mathrm{S}$)	$80\mathrm{S}$ ($60\mathrm{S} + 40\mathrm{S}$)
Membrane-bound organelles	Absent	Present (mitochondria, ER, Golgi, etc.)
Cell wall	Peptidoglycan (bacteria)	Cellulose (plants) or chitin (fungi)
Size	Typically $1$--$5\ \mu\mathrm{m}$	Typically $10$--$100\ \mu\mathrm{m}$
Reproduction	Binary fission (asexual)	Mitosis, meiosis
Flagella	Simple, rotating	Complex, $9 + 2$ microtubule arrangement

warning

Common Pitfall The "S" in ribosome sizes (70S, 80S) stands for Svedberg units, which measure sedimentation rate during centrifugation -- not molecular weight. Svedberg units are not additive: $50\mathrm{S} + 30\mathrm{S} = 70\mathrm{S}$ is a coincidence of sedimentation rates, not molecular masses.

2.2 Prokaryotic Cell Structure

Prokaryotic cells possess several structures not found in eukaryotes:

• Capsule (slime layer): a protective polysaccharide layer outside the cell wall; aids adhesion and protects against phagocytosis.
• Plasmid: small, circular, extra-chromosomal DNA that can carry genes for antibiotic resistance (R-plasmids). Plasmids replicate independently of the main chromosome and can be transferred between bacteria by conjugation.
• Pilus (plural: pili): protein filaments that attach bacteria to surfaces or to other cells. Sex pili are used in conjugation to transfer plasmids.
• Flagellum (plural: flagella): a rigid, rotating filament driven by a proton motor at the base, used for locomotion.

Prokaryotic cells also share some structures with eukaryotes:

• Cell membrane (phospholipid bilayer): controls exchange of substances.
• Cytoplasm: site of metabolic reactions; contains ribosomes and plasmids.
• Mesosomes: infoldings of the cell membrane -- thought to be artefacts of fixation rather than genuine structures (not examined on most boards).

3. Eukaryotic Cell Organelles

3.1 The Nucleus

The nucleus is the largest organelle ($d \approx 5$--$10\ \mu\mathrm{m}$), enclosed by a nuclear envelope consisting of two phospholipid bilayers. The envelope is perforated by nuclear pores (diameter $\approx 9\ \mathrm{nm}$) that allow selective transport of mRNA, tRNA, and proteins between the nucleus and cytoplasm. Transport through nuclear pores is regulated and requires energy.

The nucleus contains:

• Chromatin: DNA loosely associated with histone proteins; condenses into visible chromosomes during cell division.
• Nucleolus: a dense region within the nucleus where rRNA is transcribed and ribosome subunits are assembled. The nucleolus is not membrane-bound.

3.2 Mitochondria

Mitochondria ($d \approx 1$--$10\ \mu\mathrm{m}$, length up to $7\ \mu\mathrm{m}$) are the site of aerobic respiration, specifically the Krebs cycle (matrix) and oxidative phosphorylation (inner membrane/cristae). They have:

• Outer membrane: permeable to small molecules.
• Inner membrane: highly folded into cristae to increase surface area for the electron transport chain and ATP synthase. Impermeable to most ions.
• Matrix: contains the mitochondrial DNA (circular), $70\mathrm{S}$ ribosomes, enzymes for the Krebs cycle, and the link reaction.

The presence of circular DNA and $70\mathrm{S}$ ribosomes is strong evidence for the endosymbiotic theory: mitochondria were once free-living prokaryotes that were engulfed by a larger cell.

3.3 Endoplasmic Reticulum

The endoplasmic reticulum (ER) is a network of membrane-bound flattened sacs (cisternae) continuous with the nuclear envelope.

• Rough ER (RER): studded with $80\mathrm{S}$ ribosomes on its outer surface. Functions in protein synthesis and folding (especially proteins destined for secretion or for the plasma membrane). Proteins enter the ER lumen where they fold and may be glycosylated.
• Smooth ER (SER): lacks ribosomes. Functions in lipid synthesis, steroid hormone synthesis, detoxification (liver cells have abundant SER), and calcium ion storage.

3.4 Golgi Apparatus

The Golgi apparatus consists of stacked, flattened cisternae with vesicles at the periphery. It receives proteins from the RER via transport vesicles, then modifies, sorts, and packages them:

1. Cis face (receiving side): vesicles fuse with the Golgi, releasing their contents.
2. Modification: proteins may be glycosylated (sugar groups added), phosphorylated, or cleaved.
3. Trans face (shipping side): modified proteins are packaged into secretory vesicles for transport to the plasma membrane (exocytosis), lysosomes, or other destinations.

3.5 Lysosomes

Lysosomes are membrane-bound vesicles ($d \approx 0.1$--$1.0\ \mu\mathrm{m}$) containing hydrolytic enzymes (lipases, proteases, nucleases) optimised for pH $\approx 5$. They function in:

• Phagocytosis: engulfing and digesting pathogens (in phagocytes).
• Autophagy: breaking down worn-out organelles.
• Apoptosis: programmed cell death.

warning

Common Pitfall Plant cells do have lysosomes, though they are sometimes called vacuoles with hydrolytic activity. However, plant cells also have a large permanent vacuole, which is a distinct structure with different functions (turgor, storage, waste isolation).

3.6 Other Organelles

• Ribosomes: $80\mathrm{S}$ in cytoplasm, $70\mathrm{S}$ in mitochondria and chloroplasts. Sites of translation.
• Centrioles: cylindrical structures of $9$ triplets of microtubules, found in animal cells (absent in most plant cells). Form the centrosome and organise the spindle during mitosis.
• Chloroplasts (plants only): double-membraned organelles containing thylakoids (site of the light-dependent reactions) and stroma (site of the light-independent reactions/Calvin cycle). Contain circular DNA and $70\mathrm{S}$ ribosomes.

3.7 Plant Cells: Additional Structures

Plant cells possess structures absent from animal cells:

• Cell wall: made of cellulose microfibrils embedded in a matrix of hemicellulose and pectin. Provides mechanical support, prevents osmotic lysis, and determines cell shape. Fully permeable.
• Middle lamella: pectin-rich layer between adjacent cell walls, cementing cells together.
• Permanent vacuole: a large, central, membrane-bound (tonoplast) compartment containing cell sap (a solution of sugars, amino acids, salts, pigments). Functions in turgor maintenance, storage, and waste isolation.
• Plasmodesmata: channels through the cell wall that allow cytoplasmic communication between adjacent plant cells.

4. Viruses

4.1 Structure

Viruses are acellular -- they are not cells and do not possess cytoplasm, ribosomes, or cell membranes. A virion (virus particle) consists of:

1. Genetic material: either DNA or RNA (never both), single-stranded or double-stranded.
2. Protein coat (capsid): made of capsomere subunits; protects the genetic material and aids attachment to host cells.
3. Envelope (in some viruses): a phospholipid bilayer derived from the host cell membrane, with viral glycoproteins embedded.

4.2 Replication

Viruses are obligate intracellular parasites -- they cannot replicate independently. They must invade a host cell and hijack its metabolic machinery. The basic stages are:

1. Attachment: the virus binds to specific receptor proteins on the host cell surface.
2. Injection/entry: the viral genome enters the host cell (by endocytosis or fusion).
3. Replication: the viral genome is replicated using the host's enzymes and nucleotides.
4. Synthesis: viral proteins are synthesised on the host's ribosomes.
5. Assembly: new virions are assembled from the components.
6. Release: virions leave the host cell by lysis (killing the cell) or budding (enveloped viruses).

Viruses are not considered living organisms because they do not carry out respiration, nutrition, excretion, growth, or response to stimuli independently.

5. Cell Membranes

5.1 The Fluid Mosaic Model

The fluid mosaic model (Singer and Nicolson, 1972) describes the cell membrane as:

• Fluid: phospholipid molecules move laterally within the bilayer; their movement is constrained by hydrophobic interactions but is rapid and continuous. Cholesterol reduces fluidity at high temperatures and prevents crystallisation at low temperatures.
• Mosaic: proteins are embedded in or attached to the bilayer, creating a pattern of different molecules.

5.2 Membrane Components

Component	Location	Function
Phospholipids	Bilayer	Form the basic structure; partially permeable barrier
Cholesterol	Interspersed between phospholipids	Regulates membrane fluidity and stability
Intrinsic (transmembrane) proteins	Span the bilayer	Transport proteins (channels, carriers); receptors
Extrinsic (peripheral) proteins	On one surface only	Enzymes; cell signalling; cytoskeleton attachment
Glycoproteins	Extrinsic, with carbohydrate chains	Cell recognition; antigenic markers
Glycolipids	Phospholipid with carbohydrate chain	Cell recognition; tissue compatibility

5.3 Membrane Transport

Simple diffusion: passive movement of small, non-polar molecules (O$_2$, CO$_2$) down their concentration gradient through the phospholipid bilayer. Rate depends on: surface area, concentration gradient, temperature, distance.

Facilitated diffusion: passive movement of larger or polar molecules (glucose, amino acids, ions) through transmembrane proteins. Two types:

• Channel proteins: water-filled pores selective for specific ions ($\mathrm{Na^+}$, $\mathrm{K^+}$, $\mathrm{Cl^-}$). May be gated (voltage-gated or ligand-gated).
• Carrier proteins: undergo conformational change to shuttle molecules across the membrane.

Osmosis: the net movement of water molecules across a partially permeable membrane from a region of higher water potential to a region of lower water potential.

$\Psi = \Psi_s + \Psi_p$

where $\Psi$ is water potential, $\Psi_s$ is solute potential (always negative), and $\Psi_p$ is pressure potential.

Active transport: the movement of molecules against their concentration gradient, requiring energy from ATP hydrolysis. Carried out by carrier proteins that act as pumps (e.g., the $\mathrm{Na^+/K^+}$ ATPase pump, which moves $3\ \mathrm{Na^+}$ out and $2\ \mathrm{K^+}$ in per ATP hydrolysed).

Co-transport (secondary active transport): uses the concentration gradient of one molecule (typically $\mathrm{Na^+}$) established by primary active transport to drive the transport of another molecule against its gradient. This is the mechanism by which glucose is absorbed in the ileum.

5.4 Factors Affecting Membrane Permeability

• Temperature: increasing temperature increases kinetic energy, making the membrane more fluid and more permeable. Above a critical temperature, proteins denature and the membrane may become fully permeable.
• Solvents: organic solvents (ethanol, acetone) dissolve the lipid bilayer, increasing permeability.
• pH: extreme pH denatures membrane proteins.

6. Cell Division

6.1 Mitosis

Mitosis produces two genetically identical daughter cells with the same diploid ($2n$) chromosome number as the parent cell. It occurs in somatic (body) cells for growth, repair, and asexual reproduction.

Phases:

1. Prophase: chromatin condenses into visible chromosomes (each consisting of two sister chromatids joined at the centromere). The nucleolus disappears. Centrioles move to opposite poles and the spindle forms.
2. Metaphase: chromosomes align at the metaphase plate (cell equator) attached to spindle fibres by their centromeres.
3. Anaphase: centromeres divide; sister chromatids are pulled to opposite poles by the spindle, now called chromosomes. The cell elongates.
4. Telophase: chromosomes decondense; the nuclear envelope reforms; the nucleolus reappears. Cytokinesis (division of the cytoplasm) follows.

warning

warning Replication occurs during the S phase of interphase, before mitosis begins. By the time mitosis starts, each chromosome already consists of two identical sister chromatids.

6.2 The Cell Cycle

The cell cycle consists of:

• Interphase ($G_1$, $S$, $G_2$): cell growth and DNA replication. This accounts for approximately 90% of the cycle.
• Mitosis ($M$ phase): nuclear division.
• Cytokinesis: cytoplasmic division.

Regulation is by cyclins and cyclin-dependent kinases (CDKs). Cyclin concentration rises and falls cyclically; when cyclin binds to CDK, the complex triggers the next stage of the cell cycle. Mutations in genes regulating the cell cycle (proto-oncogenes and tumour suppressor genes) can lead to uncontrolled division (cancer).

7. Quantitative Microscopy and Magnification

7.1 Working with Magnification

Microscopy calculations appear frequently in examinations. The fundamental relationship is:

$\mathrm{Magnification} = \frac◆LB◆\mathrm{Image\ size}◆RB◆◆LB◆\mathrm{Actual\ size}◆RB◆$

This can be rearranged to find any one variable when the other two are known. Units must be consistent -- convert all measurements to the same unit (typically $\mu\mathrm{m}$) before calculating.

Conversion factors:

$1\ \mathrm{mm} = 1000\ \mu\mathrm{m}, \quad 1\ \mu\mathrm{m} = 1000\ \mathrm{nm}, \quad 1\ \mathrm{nm} = 1000\ \mathrm{pm}$

Worked Example 1. A cell is observed under a microscope with a magnification of $\times 400$. The image of the cell measures $4.8\ \mathrm{mm}$ across. Calculate the actual diameter of the cell.

$\mathrm{Actual\ size} = \frac◆LB◆\mathrm{Image\ size}◆RB◆◆LB◆\mathrm{Magnification}◆RB◆ = \frac◆LB◆4.8\ \mathrm{mm}◆RB◆◆LB◆400◆RB◆ = 0.012\ \mathrm{mm} = 12\ \mu\mathrm{m}$

Worked Example 2. A mitochondrion has an actual length of $5\ \mu\mathrm{m}$. If an electron micrograph is taken at a magnification of $\times 50000$, what will be the length of the mitochondrion in the image?

$\mathrm{Image\ size} = 5\ \mu\mathrm{m} \times 50000 = 250000\ \mu\mathrm{m} = 250\ \mathrm{mm} = 25\ \mathrm{cm}$

7.2 Scale Bars

A scale bar on a micrograph provides a direct conversion between image distance and actual distance. If a scale bar of length $2\ \mathrm{cm}$ on the image represents $10\ \mu\mathrm{m}$ in reality, then any measurement on the image is converted by multiplying by $\frac◆LB◆10\ \mu\mathrm{m}◆RB◆◆LB◆2\ \mathrm{cm}◆RB◆ = 5\ \mu\mathrm{m\ cm^{-1}}$.

Worked Example 3. A micrograph shows a scale bar labelled $5\ \mu\mathrm{m}$ that measures $20\ \mathrm{mm}$ on the printed image. A cell on the same image measures $48\ \mathrm{mm}$ across. Calculate the actual cell diameter.

Scale factor $= \frac◆LB◆5\ \mu\mathrm{m}◆RB◆◆LB◆20\ \mathrm{mm}◆RB◆ = \frac◆LB◆5000\ \mathrm{nm}◆RB◆◆LB◆20\ \mathrm{mm}◆RB◆ = 250\ \mathrm{nm\ mm^{-1}}$.

Cell diameter $= 48\ \mathrm{mm} \times 250\ \mathrm{nm\ mm^{-1}} = 12000\ \mathrm{nm} = 12\ \mu\mathrm{m}$.

7.3 Calculating Actual Size from Electron Micrographs

When working with TEM or SEM images, the magnification is often stated on the micrograph. To calculate actual size from the image:

1. Measure the dimension of interest on the printed image (in mm).
2. Apply the magnification formula.

Worked Example 4. A TEM image is labelled $\times 200000$. A ribosome on the image measures $0.25\ \mathrm{mm}$ in diameter. Calculate the actual diameter.

$\mathrm{Actual\ diameter} = \frac◆LB◆0.25 \times 10^{-3}\ \mathrm{m}◆RB◆◆LB◆200000◆RB◆ = 1.25 \times 10^{-9}\ \mathrm{m} = 1.25\ \mathrm{nm}$

This is consistent with the expected diameter of a ribosome ($\approx 20\ \mathrm{nm}$) only if the measurement is of a sub-component. If the full ribosome is being measured, the student should recheck the image measurement. This highlights the importance of sanity-checking answers against known biological dimensions.

warning

Common Pitfall Students frequently forget to convert units before applying the magnification formula. Always convert both image size and actual size to the same unit. A common error is to leave the answer in mm when the question asks for $\mu\mathrm{m}$. Write down the conversion explicitly to avoid losing marks.

8. Endocytosis and Exocytosis

8.1 Mechanism of Endocytosis

Endocytosis is the process by which cells engulf substances by folding the membrane inward to form a vesicle. It is an active process requiring ATP. Two main types are distinguished by the size of the vesicle formed:

Phagocytosis ("cell eating"): the cell membrane extends pseudopodia around a solid particle (e.g., a bacterium or dead cell), enclosing it in a large phagocytic vacuole ($d \approx 1$--$5\ \mu\mathrm{m}$). This vacuole then fuses with a lysosome, whose hydrolytic enzymes digest the contents. Phagocytosis is carried out by specialised cells: neutrophils and macrophages in mammals.

Pinocytosis ("cell drinking"): the cell membrane invaginates to form small vesicles ($d \approx 0.1\ \mu\mathrm{m}$) that take in droplets of extracellular fluid. This is a non-specific process that all cells can perform.

Receptor-mediated endocytosis: a specific form of pinocytosis in which receptor proteins on the cell surface bind specific ligand molecules (e.g., cholesterol-bound LDL, iron-bound transferrin). The receptor-ligand complexes cluster in clathrin-coated pits, which invaginate to form clathrin-coated vesicles. The clathrin coat is then removed and the vesicle fuses with an endosome, where the ligand is released. This mechanism allows cells to concentrate specific molecules from the extracellular fluid with high selectivity.

8.2 Mechanism of Exocytosis

Exocytosis is the reverse process: intracellular vesicles fuse with the plasma membrane, releasing their contents to the extracellular space. This requires:

1. Vesicle transport: vesicles are moved along microtubules by motor proteins (kinesin and dynein) using ATP.
2. Docking: vesicles are brought to the plasma membrane and dock at specific sites.
3. Fusion: SNARE proteins on the vesicle (v-SNAREs) and on the plasma membrane (t-SNAREs) bind together, pulling the membranes into close apposition. Calcium ions ($\mathrm{Ca^{2+}}$) trigger the final fusion step.

Exocytosis is essential for secretion of hormones, neurotransmitters, digestive enzymes, and mucus, as well as for insertion of new membrane proteins and lipids into the plasma membrane.

warning

Common Pitfall Students often state that endocytosis and exocytosis are forms of diffusion. They are not. Both are active processes requiring ATP. They involve bulk transport of large quantities of material in membrane-bound vesicles, which is fundamentally different from the passive movement of individual molecules through the bilayer.

9. Osmosis and Water Potential Calculations

9.1 Quantifying Water Potential

Water potential ($\Psi$) is measured in pressure units (kilopascals, $\mathrm{kPa}$). Pure water at standard temperature and pressure has a water potential of $0\ \mathrm{kPa}$. The addition of solutes lowers water potential (makes it more negative):

$\Psi = \Psi_s + \Psi_p$

where $\Psi_s$ (solute potential, also called osmotic potential) is always zero or negative, and $\Psi_p$ (pressure potential) is positive in turgid plant cells and zero in animal cells and flaccid plant cells.

9.2 Worked Examples

Worked Example 1. A plant cell is placed in a solution with water potential $\Psi_{\mathrm{solution}} = -400\ \mathrm{kPa}$. The cell has a solute potential $\Psi_s = -700\ \mathrm{kPa}$ and a pressure potential $\Psi_p = +300\ \mathrm{kPa}$. Determine the direction of net water movement.

$\Psi_{\mathrm{cell}} = \Psi_s + \Psi_p = -700 + 300 = -400\ \mathrm{kPa}$

Since $\Psi_{\mathrm{cell}} = \Psi_{\mathrm{solution}} = -400\ \mathrm{kPa}$, there is no net water movement. The cell is in equilibrium with the external solution.

Worked Example 2. A plant cell with $\Psi_s = -900\ \mathrm{kPa}$ and $\Psi_p = +450\ \mathrm{kPa}$ is placed in pure water ($\Psi = 0\ \mathrm{kPa}$). Describe what happens.

$\Psi_{\mathrm{cell}} = -900 + 450 = -450\ \mathrm{kPa}$

Water moves from pure water ($0\ \mathrm{kPa}$) into the cell ($-450\ \mathrm{kPa}$) down the water potential gradient. As water enters, the pressure potential increases (the cell becomes more turgid). Equilibrium is reached when $\Psi_{\mathrm{cell}} = 0\ \mathrm{kPa}$, i.e., when $\Psi_p = +900\ \mathrm{kPa}$.

Worked Example 3. A red blood cell (which has no cell wall and therefore $\Psi_p = 0$) is placed in a solution with $\Psi = -300\ \mathrm{kPa}$. The red blood cell has $\Psi_s = -300\ \mathrm{kPa}$. What happens?

$\Psi_{\mathrm{cell}} = -300 + 0 = -300\ \mathrm{kPa}$

No net water movement -- the solution is isotonic. If the solution had $\Psi = -100\ \mathrm{kPa}$ (hypotonic), water would enter the cell, causing it to swell and potentially burst (haemolysis). If the solution had $\Psi = -500\ \mathrm{kPa}$ (hypertonic), water would leave, causing the cell to shrink (crenation).

9.3 Osmosis in Plant Cells: Plasmolysis

When a plant cell is placed in a hypertonic solution (more negative water potential than the cell), water leaves by osmosis. The protoplast (the living part of the cell inside the cell wall) shrinks and pulls away from the cell wall. This is plasmolysis. The point at which the protoplast just begins to pull away is the incipient plasmolysis point, at which $\Psi_p = 0$ and $\Psi_{\mathrm{cell}} = \Psi_s$.

Plasmolysis is reversible if the cell is returned to a hypotonic solution before permanent damage occurs.

warning

Common Pitfall Students often write that plant cells "burst" in hypotonic solutions. They do not -- the rigid cell wall exerts an inward pressure (wall pressure) that opposes further water entry once turgidity is reached. Only animal cells (which lack cell walls) burst in hypotonic solutions.

10. The Cell Cycle in Detail

10.1 Checkpoint Control

The cell cycle has three major checkpoints where the progression is assessed before the cycle is allowed to proceed:

Checkpoint	Location	What is Assessed
$\mathrm{G_1/S}$	Late $\mathrm{G_1}$	Cell size, nutrient availability, DNA damage
$\mathrm{G_2/M}$	Late $\mathrm{G_2}$	DNA replication complete and accurate
M (spindle assembly)	Metaphase	All chromosomes attached to spindle fibres

At each checkpoint, cyclin-CDK complexes phosphorylate target proteins that either promote or inhibit progression. If damage is detected, the checkpoint arrests the cycle to allow repair. If repair fails, apoptosis (programmed cell death) may be triggered.

10.2 Cyclins and CDKs

Cyclins are a family of regulatory proteins whose concentration fluctuates cyclically. Different cyclins act at different stages:

• Cyclin D: rises in response to growth factor signalling; activates CDK4/6 to phosphorylate Rb protein, releasing E2F transcription factor and allowing transition past $\mathrm{G_1/S}$.
• Cyclin E: peaks at the $\mathrm{G_1/S}$ boundary; activates CDK2 for S phase entry.
• Cyclin A: rises during S phase and $\mathrm{G_2}$; activates CDK2 for DNA replication.
• Cyclin B: peaks during $\mathrm{G_2}$ and M phase; activates CDK1 (also called CDC2) for mitotic entry.

A cyclin-CDK complex is only active when both components are present. Cyclin concentration is regulated by synthesis (transcription and translation) and degradation (ubiquitin-proteasome pathway). This ensures that CDK activity is strictly periodic.

10.3 Proto-oncogenes and Tumour Suppressor Genes

Mutations in two classes of genes disrupt cell cycle regulation:

Proto-oncogenes code for proteins that promote cell division (e.g., growth factors, growth factor receptors, signal transduction proteins, cyclins). A mutation that causes overexpression or constitutive activation converts a proto-oncogene into an oncogene, driving uncontrolled proliferation. For example, the ras proto-oncogene codes for a GTPase involved in signal transduction; a mutation that locks RAS in its active (GTP-bound) state causes continuous signalling to divide.

Tumour suppressor genes code for proteins that inhibit cell division or promote apoptosis. The most well-known is TP53 (p53), which halts the cell cycle at $\mathrm{G_1}$ when DNA damage is detected, allowing repair. If damage is irreparable, p53 triggers apoptosis. Mutations in TP53 are found in approximately 50% of all human cancers.

Cancer requires mutations in multiple genes: typically activation of one or more oncogenes plus inactivation of two or more tumour suppressor genes (Knudson's two-hit hypothesis).

warning

Common Pitfall Students often state that "one mutation causes cancer." Cancer is a multistep process requiring the accumulation of several mutations in genes regulating the cell cycle, DNA repair, and apoptosis. A single mutation in a proto-oncogene or tumour suppressor gene is necessary but not sufficient for malignancy.

11. Meiosis: Overview and Comparison with Mitosis

11.1 Key Differences

Feature	Mitosis	Meiosis
Divisions	One	Two
Daughter cells	2, genetically identical ($2n$)	4, genetically distinct ($n$)
Synapsis/crossing over	Absent	Present (prophase I)
Homologous pairing	Absent	Present (bivalents at metaphase I)
Metaphase alignment	Individual chromosomes at equator	Bivalents at equator
Anaphase	Sister chromatids separate	Homologous chromosomes separate (Meiosis I)
Function	Growth, repair, asexual reproduction	Production of gametes for sexual reproduction

For a detailed treatment of meiosis with genetic cross analysis, see Genetics and DNA.

11.2 The Significance of Meiosis

Meiosis is essential for sexual reproduction because it:

1. Halves the chromosome number ($2n \to n$) so that fertilisation ($n + n$) restores the diploid number.
2. Generates genetic variation through crossing over (prophase I) and independent assortment (metaphase I), which are the raw material for natural selection.
3. Prevents chromosome doubling with each generation, which would make cells non-viable.

12. Specialised Cells

12.1 Examples of Cell Specialisation

Cell specialisation (differentiation) is the process by which cells become adapted to perform specific functions. All specialised cells develop from unspecialised stem cells through differential gene expression.

Specialised Cell	Adaptations	Function
Red blood cell	Biconcave disc shape; no nucleus; no mitochondria; contains haemoglobin	$\mathrm{O_2}$ transport
Sperm cell	Flagellum for swimming; many mitochondria; acrosome with digestive enzymes	Fertilisation
Root hair cell (plant)	Elongated projection; large surface area; thin wall	Mineral ion absorption
Palisade mesophyll cell	Elongated; many chloroplasts near upper surface; thin walls	Photosynthesis
Guard cell	Kidney-shaped; unevenly thickened walls; chloroplasts	Stomatal aperture control
Neurone	Long axon; dendrites; myelin sheath; synaptic terminals	Transmission of nerve impulses
Phagocyte (white blood)	Flexible membrane; lysosomes; lobed nucleus	Engulfing pathogens
Squamous epithelial cell	Very thin and flat; smooth surface	Gas exchange surface

12.2 Stem Cells

Stem cells are undifferentiated cells with the capacity to divide and differentiate into specialised cell types.

• Totipotent: can differentiate into any cell type, including extra-embryonic tissues. The zygote and early morula (up to the 8-cell stage in humans) are totipotent.
• Pluripotent: can differentiate into any cell type except extra-embryonic tissues. Embryonic stem cells (from the inner cell mass of the blastocyst) are pluripotent.
• Multipotent: can differentiate into a limited range of cell types within a given tissue. Adult stem cells (e.g., haematopoietic stem cells in bone marrow, which produce all blood cell types) are multipotent.
• Unipotent: can only produce one cell type, but retain the capacity for self-renewal.

Therapeutic uses: stem cells can be used to replace damaged tissues (e.g., spinal cord injury, Parkinson's disease, type 1 diabetes, burns). Bone marrow transplants use haematopoietic stem cells to repopulate the blood cell lineages after chemotherapy. Induced pluripotent stem cells (iPSCs) are adult cells reprogrammed to a pluripotent state by introducing transcription factors (Oct4, Sox2, Klf4, c-Myc), offering an ethically uncontroversial alternative to embryonic stem cells.

warning

Common Pitfall Students often conflate pluripotent and totipotent stem cells. Totipotent cells can form a complete organism including placenta and umbilical cord; pluripotent cells can form all body cell types but not extra-embryonic tissues. Only the zygote and very early embryonic cells are totipotent.

Practice Problems

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Problem 1

Describe the process of cell fractionation and explain why each step must be carried out under specific conditions (cold, buffered, isotonic).

Answer. Cell fractionation involves three steps. (1) Homogenisation: cells are placed in a cold, buffered, isotonic solution and broken open (e.g., with a blender or ultrasonication). The solution must be cold to reduce the activity of enzymes that would degrade organelles; buffered to maintain a constant pH, since enzyme activity is pH-dependent; and isotonic to prevent osmotic lysis (in a hypotonic solution) or shrinkage (in a hypertonic solution) of organelles. (2) Filtration: the homogenate is passed through a gauze to remove unbroken cells and large debris. (3) Differential centrifugation: the filtrate is centrifuged at progressively higher speeds. At each speed, the densest remaining organelles sediment into a pellet, which is removed. The supernatant is then centrifuged at a higher speed to pellet the next densest organelles, and so on. This separates organelles by size and density.

If you get this wrong, revise: Cell Fractionation

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Problem 2

Explain three ways in which the structure of mitochondria is related to their function in aerobic respiration.

Answer. (1) The inner membrane is folded into cristae, greatly increasing the surface area available for the electron transport chain and ATP synthase enzymes, maximising ATP production. (2) The matrix contains the enzymes for the Krebs cycle and the link reaction, concentrating the reactants and products of these pathways to increase reaction rates. (3) The outer membrane is permeable to small molecules (pyruvate, $\mathrm{NADH}$), allowing substrates from the cytoplasm to enter the mitochondrion. Additionally, the presence of circular DNA and $70\mathrm{S}$ ribosomes supports the endosymbiotic theory, explaining how mitochondria retained their own genetic machinery.

If you get this wrong, revise: Mitochondria

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Problem 3

Compare and contrast prokaryotic and eukaryotic cells. In your answer, refer to DNA structure, ribosomes, and cell walls.

Answer. Prokaryotic cells are typically smaller ($1$--$5\ \mu\mathrm{m}$) than eukaryotic cells ($10$--$100\ \mu\mathrm{m}$). Prokaryotic DNA is a single circular molecule located free in the cytoplasm (nucleoid), not associated with histone proteins. Eukaryotic DNA is linear, organised into chromosomes within a membrane-bound nucleus, and associated with histone proteins. Prokaryotic ribosomes are $70\mathrm{S}$ (composed of $50\mathrm{S}$ and $30\mathrm{S}$ subunits), whereas eukaryotic ribosomes are $80\mathrm{S}$ (composed of $60\mathrm{S}$ and $40\mathrm{S}$ subunits). Prokaryotic cell walls contain peptidoglycan; eukaryotic cell walls (in plants) contain cellulose, and fungal cell walls contain chitin. Both types have a phospholipid cell membrane and cytoplasm, but only eukaryotes possess membrane-bound organelles (mitochondria, ER, Golgi).

If you get this wrong, revise: Prokaryotic and Eukaryotic Cells

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Problem 4

Describe the roles of the Golgi apparatus in protein processing and transport. Why would a cell that secretes large amounts of protein (e.g., a pancreatic acinar cell) have an exceptionally large Golgi apparatus?

Answer. The Golgi apparatus receives transport vesicles from the RER containing newly synthesised proteins. It modifies these proteins by adding carbohydrate groups (glycosylation), phosphate groups, or lipid groups, and may cleave the protein into its active form. It then sorts the modified proteins and packages them into secretory vesicles, which bud from the trans face and move to the plasma membrane for exocytosis. A pancreatic acinar cell secretes large quantities of digestive enzymes, so it requires an extensive RER for protein synthesis and a correspondingly large Golgi apparatus for the modification, sorting, and packaging of these proteins into secretory vesicles. The size of an organelle generally reflects the cell's functional demands.

If you get this wrong, revise: Golgi Apparatus

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Problem 5

Explain the fluid mosaic model of cell membranes. How does cholesterol affect membrane fluidity at high and low temperatures?

Answer. The fluid mosaic model describes the cell membrane as a bilayer of phospholipid molecules in which proteins are embedded (intrinsic/transmembrane proteins) or attached to the surface (extrinsic/peripheral proteins). The bilayer is "fluid" because individual phospholipid molecules can move laterally within their own monolayer by diffusion, and "mosaic" because the various components create a heterogeneous pattern. Cholesterol is a small, hydrophobic molecule interspersed between phospholipid tails. At high temperatures, it restricts the movement of phospholipids, reducing fluidity and making the membrane less permeable. At low temperatures, it prevents phospholipid tails from packing too closely and crystallising, maintaining some fluidity. Cholesterol therefore buffers membrane fluidity, keeping it within an optimal range.

If you get this wrong, revise: The Fluid Mosaic Model

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Problem 6

Are viruses living organisms? Justify your answer with reference to the characteristics of life and the structure and behaviour of viruses.

Answer. Viruses are not considered living organisms. They possess genetic material (DNA or RNA) and can evolve through mutation and natural selection, but they lack the other characteristics of life. They do not carry out respiration, nutrition, or excretion independently. They have no metabolism of their own and cannot synthesise proteins or generate ATP without a host cell. They do not grow or develop. They cannot reproduce independently -- they require a host cell's ribosomes, enzymes, and nucleotides to replicate. Their acellular structure (no cytoplasm, no cell membrane, no ribosomes) further distinguishes them from cells. While they are obligate intracellular parasites that can cause disease, they are more accurately described as infectious agents rather than living organisms.

If you get this wrong, revise: Viruses

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Problem 7

An electron micrograph shows a mitochondrion. The scale bar indicates that $1\ \mathrm{mm}$ on the image represents $0.2\ \mu\mathrm{m}$ in reality. The mitochondrion measures $6.5\ \mathrm{mm}$ in length on the image. (a) Calculate the actual length. (b) If the magnification of the micrograph was $\times 25000$, what is the expected image length, and does it match?

Answer. (a) Actual length $= 6.5\ \mathrm{mm} \times 0.2\ \mu\mathrm{m\ mm^{-1}} = 1.3\ \mu\mathrm{m}$.

(b) Expected image length $= 1.3\ \mu\mathrm{m} \times 25000 = 32500\ \mu\mathrm{m} = 32.5\ \mathrm{mm}$.

The actual measurement on the image ($6.5\ \mathrm{mm}$) does not match the expected image length ($32.5\ \mathrm{mm}$) for the stated magnification. This indicates either the scale bar is not at the same magnification as the image, or the stated magnification is incorrect. This discrepancy highlights the importance of using scale bars (which are always at the same magnification as the image) rather than stated magnification values for calculations.

If you get this wrong, revise: Quantitative Microscopy and Magnification

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Problem 8

Describe the role of ATP in the following cellular processes: (a) active transport, (b) exocytosis, (c) DNA replication. For each, explain what the energy from ATP hydrolysis is used for.

Answer. (a) Active transport: carrier proteins (pumps) use ATP to change conformation, moving molecules against their concentration gradient. For example, the $\mathrm{Na^+/K^+}$ ATPase hydrolyses one ATP to move $3\ \mathrm{Na^+}$ out and $2\ \mathrm{K^+}$ in against their gradients. The energy from ATP is used to induce the conformational change in the pump protein.

(b) Exocytosis: vesicles are transported along microtubules by motor proteins (kinesin) that hydrolyse ATP to "walk" along the microtubule. ATP is also required for SNARE-mediated fusion of the vesicle with the plasma membrane. The energy drives the mechanical movement and the membrane rearrangement.

(c) DNA replication: helicase unwinds the double helix by breaking hydrogen bonds (energy-consuming). DNA polymerase catalyses phosphodiester bond formation between nucleotides, using energy from the nucleotide triphosphates (dNTPs have high-energy phosphate bonds). The energy released when two phosphate groups are cleaved from each dNTP provides the energy for the phosphodiester bond.

If you get this wrong, revise: Cell Membranes and DNA Replication

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Problem 9

A plant cell with $\Psi_s = -850\ \mathrm{kPa}$ is placed in a solution of sucrose with concentration $0.35\ \mathrm{mol\ dm^{-3}}$ at $20\ ^\circ\mathrm{C}$. (a) Calculate the water potential of the external solution. (b) Determine the direction of net water movement. (c) Calculate the pressure potential at equilibrium.

Answer. (a) $\Psi_{\mathrm{solution}} = -iCRT = -1 \times 350 \times 8.314 \times 293 = -852605\ \mathrm{Pa} \approx -853\ \mathrm{kPa}$.

(b) Initially, $\Psi_p = 0$ (the cell is placed in the solution and has not yet adjusted), so $\Psi_{\mathrm{cell}} = \Psi_s + \Psi_p = -850\ \mathrm{kPa}$.

Since $\Psi_{\mathrm{solution}} = -853\ \mathrm{kPa} < \Psi_{\mathrm{cell}} = -850\ \mathrm{kPa}$, water moves out of the cell (from higher to lower water potential).

(c) As water leaves, the cell loses turgor. At equilibrium, $\Psi_{\mathrm{cell}} = \Psi_{\mathrm{solution}} = -853\ \mathrm{kPa}$:

$-850 + \Psi_p = -853$, so $\Psi_p = -3\ \mathrm{kPa}$.

A negative $\Psi_p$ means the protoplast is pulling away from the cell wall (incipient plasmolysis or full plasmolysis, depending on the cell wall). The cell is plasmolysed.

If you get this wrong, revise: Osmosis and Water Potential Calculations

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13. The Cytoskeleton

13.1 Components

The cytoskeleton is a network of protein fibres that provides structural support, enables movement, and organises intracellular transport.

Component	Diameter	Protein	Structure	Function
Microfilaments (actin filaments)	$\approx 7\ \mathrm{nm}$	Actin	Two intertwined helical chains	Cell shape changes, cell division (cleavage furrow), muscle contraction
Intermediate filaments	$\approx 10\ \mathrm{nm}$	Keratin, vimentin, lamin	Rope-like fibres of intertwined subunits	Mechanical strength (nuclear lamina, hair, nails)
Microtubules	$\approx 25\ \mathrm{nm}$	Tubulin ($\alpha$ and $\beta$)	Hollow cylinders of 13 protofilaments	Chromosome movement (spindle fibres), intracellular transport (tracks for motor proteins), cilia and flagella

13.2 Motor Proteins

Motor proteins move along cytoskeletal filaments, carrying cargo (vesicles, organelles, chromosomes):

Motor Protein	Track	Direction	Energy Source	Function
Kinesin	Microtubules	Towards (+) end (away from centrosome)	ATP	Transport of vesicles and organelles towards cell periphery
Dynein	Microtubules	Towards (-) end (towards centrosome)	ATP	Retrograde transport; movement of cilia and flagella
Myosin	Microfilaments (actin)	Towards (+) end	ATP	Muscle contraction; cytokinesis; cytoplasmic streaming

13.3 Cilia and Flagella

Cilia are short, hair-like projections ($\approx 10\ \mu\mathrm{m}$ long, $0.2\ \mu\mathrm{m}$ diameter) that beat in coordinated waves. They are found on epithelial cells lining the respiratory tract (moving mucus and trapped particles away from the lungs) and in the Fallopian tubes (moving the ovum towards the uterus).

Flagella are longer ($\approx 50$--$200\ \mu\mathrm{m}$) and typically occur singly (e.g., sperm tail).

Both have the same 9+2 arrangement of microtubules: 9 pairs of fused microtubules (doublets) form an outer ring, surrounding a central pair of single microtubules. Dynein arms between the outer doublets use ATP to slide the doublets past each other, causing the cilium or flagellum to bend.

Primary ciliary dyskinesia (Kartagener syndrome) is caused by defective dynein arms, resulting in immotile cilia. Symptoms include chronic respiratory infections (mucus not cleared), male infertility (immotile sperm), and situs inversus (organs on the wrong side of the body, because cilia are needed to establish left-right asymmetry during embryonic development).

14. The Endomembrane System

14.1 Overview

The endomembrane system is a network of organelles that work together to synthesise, modify, package, and transport proteins and lipids:

$\text{Rough ER} \to \text{Vesicles} \to \text{Golgi apparatus} \to \text{Secretory vesicles} \to \text{Cell membrane}$

14.2 The Golgi Apparatus in Detail

The Golgi apparatus consists of flattened membrane-bound sacs (cisternae) stacked on top of each other, with a cis face (receiving side, near the ER) and a trans face (shipping side, near the cell membrane).

Functions:

1. Protein modification: adding carbohydrate groups (glycosylation) to form glycoproteins. This occurs in a specific sequence: oligosaccharide chains are trimmed and extended as the protein moves through the Golgi cisternae.
2. Lipid modification: adding carbohydrates to lipids to form glycolipids.
3. Proteolytic processing: cleaving pro-proteins into their active forms (e.g., proinsulin $\to$ insulin + C-peptide).
4. Sorting and packaging: directing modified proteins to their correct destinations:
   • Default pathway: proteins without a specific sorting signal are transported to the cell membrane in secretory vesicles and released by exocytosis.
   • Lysosomal pathway: proteins tagged with mannose-6-phosphate are directed to lysosomes.
   • Plasma membrane pathway: transmembrane proteins are incorporated into the membrane.

14.3 Lysosomal Storage Diseases

Lysosomes contain approximately 60 different hydrolytic enzymes (lipases, proteases, nucleases, glycosidases) that function optimally at pH $\approx 5.0$ (maintained by a $\mathrm{H^+}$-ATPase pump in the lysosomal membrane).

Lysosomal storage diseases result from inherited deficiencies in individual lysosomal enzymes, causing substrates to accumulate:

Disease	Deficient Enzyme	Accumulating Substance	Symptoms
Tay-Sachs disease	Hexosaminidase A	$\mathrm{GM_2}$ ganglioside	Progressive neurodegeneration, blindness, death by age 4
Gaucher disease	Glucocerebrosidase	Glucocerebroside	Enlarged liver and spleen, bone pain, anaemia
Niemann-Pick disease	Sphingomyelinase	Sphingomyelin	Hepatosplenomegaly, neurological deterioration

15. Cell Division: Detailed Mechanisms

15.1 Regulation of the Cell Cycle

The cell cycle is regulated by cyclins and cyclin-dependent kinases (CDKs):

Cyclin	CDK Partner	Phase Controlled	Function
Cyclin D	CDK4/6	G1 $\to$ S	Phosphorylates Rb protein, releasing E2F transcription factor to initiate S phase
Cyclin E	CDK2	G1/S transition	Initiates DNA replication
Cyclin A	CDK2	S phase	Maintains S phase progression
Cyclin B	CDK1 (CDC2)	G2 $\to$ M	Triggers entry into mitosis (MPF = maturation-promoting factor)

Cyclin concentrations fluctuate throughout the cell cycle (synthesised and degraded at specific points), while CDKs are present at relatively constant levels. The cyclin-CDK complex is only active when both components are present.

15.2 Checkpoints

Three major checkpoints ensure the cell cycle proceeds correctly:

1. G1 checkpoint (restriction point): checks cell size, nutrient availability, growth signals, and DNA damage. If conditions are not met, the cell enters $\mathrm{G_0}$ (quiescence). This is the most important checkpoint in mammalian cells.
2. G2 checkpoint: checks that DNA replication is complete and that there is no DNA damage. If DNA damage is detected, p53 (a tumour suppressor protein) halts the cycle and activates DNA repair enzymes.
3. M checkpoint (spindle assembly checkpoint): checks that all chromosomes are correctly attached to spindle fibres at the metaphase plate. If any chromosome is unattached, anaphase is delayed.

15.3 Apoptosis

Apoptosis (programmed cell death) is an orderly, controlled process that eliminates damaged, infected, or unnecessary cells without causing inflammation (unlike necrosis, which is uncontrolled cell death that triggers inflammation).

Mechanism:

1. Internal signals: DNA damage activates p53, which upregulates pro-apoptotic proteins (Bax, Bak) that form pores in the mitochondrial outer membrane.
2. Cytochrome c release from mitochondria into the cytoplasm.
3. Cytochrome c binds to Apaf-1, forming the apoptosome, which activates caspase-9 (initiator caspase).
4. Caspase-9 activates effector caspases (caspase-3, -7), which cleave target proteins:
   • Activate nucleases that fragment DNA into ladders of $\approx 200\ \mathrm{bp}$ multiples.
   • Degrade cytoskeletal proteins.
   • Cause membrane blebbing.
5. The cell breaks into apoptotic bodies, which are phagocytosed by macrophages.

External signals: death ligands (e.g., FasL on cytotoxic T cells) bind to death receptors (e.g., Fas) on the target cell, activating caspase-8 directly (extrinsic pathway).

Failure of apoptosis contributes to cancer (cells that should die continue to divide) and autoimmune diseases.

16. Prokaryotic Cell Biology in Depth

16.1 Bacterial Cell Wall Structure

Bacterial cell walls are made of peptidoglycan (murein), a polymer consisting of:

• Glycan chains: alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) residues linked by $\beta$-1,4-glycosidic bonds.
• Peptide cross-links: short peptide chains (tetrapeptides) attached to NAM, cross-linked by a peptide bridge. This provides structural strength.

Gram-positive bacteria (e.g., Staphylococcus aureus) have a thick peptidoglycan layer ($20$--$80\ \mathrm{nm}$) containing teichoic acids. They retain the crystal violet stain in the Gram stain.

Gram-negative bacteria (e.g., Escherichia coli) have a thin peptidoglycan layer ($2$--$10\ \mathrm{nm}$) between the inner and outer membranes. The outer membrane contains lipopolysaccharide (LPS), which is an endotoxin. They do not retain crystal violet and stain pink/red with safranin.

16.2 Antibiotic Mechanisms Targeting Cell Walls

Antibiotic	Target	Mechanism
Penicillin	Transpeptidase (cross-linking enzyme)	Binds to transpeptidase active site, preventing peptide cross-linking. Cell wall becomes weak; cell lyses due to osmotic pressure.
Vancomycin	D-alanyl-D-alanine terminus of peptide side chains	Binds to D-Ala-D-Ala, blocking transpeptidase access.
Bacitracin	Dephosphorylation of bactoprenol	Prevents recycling of the lipid carrier needed for peptidoglycan synthesis.

Penicillin resistance can arise through:

• $\beta$-lactamase production: an enzyme that hydrolyses the $\beta$-lactam ring of penicillin, inactivating it.
• Altered penicillin-binding proteins (PBPs) with reduced affinity for penicillin (e.g., MRSA -- methicillin-resistant S. aureus).
• Reduced permeability of the outer membrane (in Gram-negative bacteria).

warning

Common Pitfall Students often state that "penicillin kills bacteria by breaking down the cell wall." Penicillin does not break down existing peptidoglycan. It prevents the formation of new cross-links during cell wall synthesis. The cell wall weakens because it cannot be repaired or expanded, and the bacterium lyses due to the inward osmotic pressure (water entering by osmosis).

18. Viruses: Structure, Replication, and Defence

18.1 Viral Structure

Viruses are not cells. They are obligate intracellular parasites that consist of:

Component	Description	Function
Nucleic acid	Either DNA or RNA (never both); single-stranded or double-stranded; linear or circular	Carries genetic information
Capsid	Protein coat made of capsomeres (protein subunits) arranged with icosahedral, helical, or complex symmetry	Protects the nucleic acid; mediates attachment to host cell
Envelope (some viruses)	Phospholipid bilayer derived from the host cell membrane during budding	Helps the virus enter host cells; contains viral glycoproteins for receptor binding

18.2 Viral Replication Cycle (Generalised)

1. Attachment: viral surface proteins bind to specific receptors on the host cell surface (this determines host specificity).
2. Entry: the virus (or its genome) enters the host cell by endocytosis or membrane fusion.
3. Uncoating: the viral capsid is removed, releasing the viral genome.
4. Replication: the viral genome is replicated using the host cell's machinery (some viruses provide their own polymerases).
5. Synthesis: viral proteins are synthesised using the host cell's ribosomes.
6. Assembly: new viral particles are assembled from the newly synthesised components.
7. Release: new virions leave the host cell by budding (enveloped viruses) or cell lysis (non-enveloped viruses).

18.3 HIV: A Case Study

Human Immunodeficiency Virus (HIV) is a retrovirus (RNA virus that reverse-transcribes its genome into DNA):

Step	Description
1. Attachment	gp120 glycoprotein on HIV binds to CD4 receptor and CCR5/CXCR4 co-receptor on T helper cells
2. Fusion and entry	Viral envelope fuses with the host cell membrane
3. Reverse transcription	Viral RNA is converted to DNA by reverse transcriptase (this enzyme has no proofreading activity, so mutations occur frequently -- contributing to the virus's ability to evade the immune system)
4. Integration	Viral DNA is integrated into the host cell's genome by integrase, forming a provirus
5. Transcription	Host RNA polymerase II transcribes the proviral DNA into viral mRNA and genomic RNA
6. Translation	Viral proteins (gag, pol, env) are synthesised
7. Assembly	New viral particles are assembled at the host cell membrane
8. Budding	New virions bud from the host cell, acquiring an envelope

Why HIV is difficult to cure:

• The provirus is integrated into the host genome and can remain latent (inactive) for years, invisible to the immune system and to antiviral drugs.
• Reverse transcriptase has no proofreading activity, so the virus mutates rapidly, generating many variants that can escape immune detection and drug treatment.
• The virus targets T helper cells, which are essential for coordinating the immune response. Destroying T helper cells weakens the entire immune system.

18.4 Antiviral Drugs

Drug	Target	Mechanism
AZT (zidovudine)	Reverse transcriptase	Nucleoside analogue: incorporated into viral DNA by reverse transcriptase, causing chain termination (DNA synthesis stops)
Protease inhibitors (e.g., ritonavir)	HIV protease	Prevents cleavage of viral polyproteins into functional proteins
Reverse transcriptase inhibitors (non-nucleoside)	Reverse transcriptase	Bind to reverse transcriptase at a site other than the active site, causing conformational changes that inactivate the enzyme
Neuraminidase inhibitors (oseltamivir/Tamiflu)	Influenza neuraminidase	Prevents release of new influenza virions from infected cells
Aciclovir	Viral DNA polymerase (herpes viruses)	Nucleoside analogue; activated by viral thymidine kinase (selectively toxic to virus-infected cells); incorporated into viral DNA, causing chain termination

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tip

Diagnostic Test

17. Cell Membrane Transport: Advanced Topics

17.1 Facilitated Diffusion vs Active Transport

Feature	Facilitated Diffusion	Active Transport
Energy required	No (passive)	Yes (ATP or electrochemical gradient)
Direction	Down concentration gradient	Against concentration gradient
Carrier proteins	Channel proteins and carrier proteins	Carrier proteins (pumps) only
Saturability	Yes (limited number of transporters)	Yes
Specificity	Specific to particular molecules	Highly specific
Examples	Glucose transport via GLUT4 in muscle cells	$\mathrm{Na^+/K^+}$ ATPase; $\mathrm{Ca^{2+}}$ ATPase; sodium-glucose co-transporter (SGLT1)

17.2 Co-Transport (Secondary Active Transport)

Secondary active transport uses the energy stored in an ion gradient (established by primary active transport) to drive the transport of another molecule against its concentration gradient.

Example: sodium-glucose co-transport (SGLT1) in the ileum.

1. The $\mathrm{Na^+/K^+}$ ATPase (primary active transport) pumps $\mathrm{Na^+}$ out of the cell, maintaining a low intracellular $\mathrm{Na^+}$ concentration and a steep $\mathrm{Na^+}$ gradient.
2. The SGLT1 co-transporter uses the energy released by $\mathrm{Na^+}$ flowing down its gradient into the cell to simultaneously transport glucose against its concentration gradient into the cell.
3. The stoichiometry is 2 $\mathrm{Na^+}$: 1 glucose.
4. Glucose exits the cell on the other side (blood side) via GLUT2 (facilitated diffusion).

17.3 The Sodium-Potassium Pump

The $\mathrm{Na^+/K^+}$ ATPase maintains the resting membrane potential and the concentration gradients of $\mathrm{Na^+}$ and $\mathrm{K^+}$:

$\text{ATP} + 3\mathrm{Na^+}_{\text{in}} + 2\mathrm{K^+}_{\text{out}} \to \text{ADP} + \mathrm{P_i} + 3\mathrm{Na^+}_{\text{out}} + 2\mathrm{K^+}_{\text{in}}$

• Pumps 3 $\mathrm{Na^+}$ out and 2 $\mathrm{K^+}$ in per ATP hydrolysed.
• Electrogenic: the unequal exchange (3:2) creates a net outward current, contributing to the negative resting membrane potential (approximately $-70\ \mathrm{mV}$).
• Accounts for approximately 30--40% of the resting ATP consumption of a typical animal cell.
• Inhibited by ouabain (a cardiac glycoside derived from the foxglove plant, Digitalis purpurea). At therapeutic doses, partial inhibition increases intracellular $\mathrm{Na^+}$, which slows the $\mathrm{Na^+/Ca^{2+}}$ exchanger, increasing intracellular $\mathrm{Ca^{2+}}$ and strengthening heart muscle contraction (used to treat heart failure).

18. The Cell Cycle: Regulation and Checkpoints

18.1 Phases of the Cell Cycle

Phase	Description	Key Events
G1 (Gap 1)	Cell growth and normal metabolism	Organelles duplicate; protein synthesis; cell grows to approximately double its original size
S (Synthesis)	DNA replication	Each chromosome is replicated to form two sister chromatids; centrosome duplicates
G2 (Gap 2)	Preparation for mitosis	Continued protein synthesis; synthesis of microtubules for spindle formation
M (Mitosis)	Nuclear division	Prophase, metaphase, anaphase, telophase; followed by cytokinesis
G0 (quiescence)	Cells that have left the cell cycle	Not actively dividing; may re-enter the cycle (e.g., liver cells) or remain permanently in G0 (e.g., neurons)

18.2 Control of the Cell Cycle: Checkpoints

There are three major checkpoints:

1. G1 checkpoint (restriction point, R): checks cell size, nutrient availability, growth factors, and DNA damage. If conditions are favourable, the cell commits to division. If DNA is damaged, p53 (a tumour suppressor protein) activates p21, which inhibits cyclin-dependent kinases (CDKs), arresting the cell cycle. If the damage is irreparable, p53 triggers apoptosis.

2. G2 checkpoint: checks that DNA replication is complete and that there are no errors. If DNA is damaged or replication is incomplete, the cell cycle is arrested until the problem is resolved.

3. M checkpoint (spindle assembly checkpoint): checks that all chromosomes are attached to the spindle fibres and correctly aligned at the metaphase plate. If any chromosome is not properly attached, anaphase is delayed (preventing non-disjunction).

18.3 Cyclins and CDKs

Progression through the cell cycle is controlled by cyclins (proteins whose concentration fluctuates during the cell cycle) and cyclin-dependent kinases (CDKs) (enzymes that phosphorylate target proteins).

Cyclin	CDK Partner	Peak Concentration	Function
Cyclin D	CDK4/6	G1	Drives cell past the G1 restriction point
Cyclin E	CDK2	G1/S transition	Initiates DNA replication
Cyclin A	CDK2	S phase	Drives DNA replication
Cyclin B	CDK1 (CDC2)	G2/M transition	Triggers entry into mitosis

When a cyclin binds to its CDK partner, the complex phosphorylates specific target proteins, activating or inhibiting them to drive the next phase of the cell cycle.

18.4 Cancer and the Cell Cycle

Cancer is a disease of the cell cycle. Mutations in genes that regulate the cell cycle can lead to uncontrolled cell division:

Gene Type	Normal Function	Effect of Mutation
Proto-oncogene	Stimulates cell division when appropriate (e.g., growth factor receptors, signalling proteins)	Becomes an oncogene: constitutively active, promoting uncontrolled division (e.g., RAS mutations in 25% of cancers)
Tumour suppressor gene	Inhibits cell division; promotes DNA repair; promotes apoptosis (e.g., p53, Rb)	Loss of function: cell cycle checkpoints fail, allowing damaged cells to divide
DNA repair gene	Repairs DNA damage (e.g., BRCA1, BRCA2)	Loss of function: mutations accumulate more rapidly

Tumour formation: a single mutation is usually insufficient to cause cancer. Multiple mutations are required (the "multi-hit hypothesis"). For example, colon cancer typically requires mutations in at least 5--6 genes (APC, KRAS, p53, SMAD4, etc.) over many years.

18.5 Apoptosis: Programmed Cell Death

Apoptosis is a tightly regulated process of programmed cell death that:

• Removes damaged, infected, or unnecessary cells.
• Prevents the release of intracellular contents (which could cause inflammation, unlike necrosis).
• Is essential for development (e.g., removal of webbing between fingers during embryonic development; removal of autoreactive T cells in the thymus).

Mechanism:

1. Initiation: triggered by internal signals (DNA damage, oxidative stress) via the intrinsic pathway (involves mitochondria, cytochrome c release, caspase-9 activation) or external signals (death ligands such as FasL binding to death receptors) via the extrinsic pathway (involves caspase-8 activation).
2. Execution: initiator caspases activate effector caspases (caspase-3, -6, -7), which cleave target proteins, including:
   • Nuclear lamins (breakdown of the nuclear envelope).
   • Cytoskeletal proteins (cell shrinks and rounds up).
   • PARP (prevents DNA repair).
3. Cell dismantling: the cell breaks into apoptotic bodies (membrane-bound fragments containing intact organelles and DNA fragments).
4. Phagocytosis: apoptotic bodies are phagocytosed by macrophages (they display "eat me" signals such as phosphatidylserine on the outer leaflet of the plasma membrane).

19. Prokaryotic Cells: Detailed Structure

19.1 Bacterial Cell Wall

Feature	Gram-Positive Bacteria	Gram-Negative Bacteria
Peptidoglycan layer	Thick (many layers)	Thin (1--2 layers)
Teichoic acids	Present (linked to peptidoglycan)	Absent
Outer membrane	Absent	Present (lipopolysaccharide, LPS)
Periplasmic space	Narrow or absent	Present (between inner and outer membranes)
Lipopolysaccharide (LPS)	Absent	Present (endotoxin; can cause fever, shock)
Gram stain result	Purple (retains crystal violet)	Pink/red (does not retain crystal violet; takes up safranin)
Examples	Staphylococcus, Streptococcus, Bacillus, Clostridium	E. coli, Salmonella, Pseudomonas, Neisseria

How antibiotics target the cell wall:

• Penicillin: inhibits transpeptidase (penicillin-binding protein), which cross-links peptidoglycan strands. Weakens the cell wall, causing lysis (by osmosis) in growing bacteria.
• Vancomycin: binds to D-alanyl-D-alanine terminus of peptidoglycan precursors, blocking cross-linking.
• Bacitracin: interferes with peptidoglycan synthesis by blocking the recycling of bactoprenol (a lipid carrier).

19.2 Bacterial Growth Curve

When bacteria are grown in a closed batch culture:

Phase	Description	Growth Rate	Why
Lag phase	Bacteria adapt to new conditions; synthesise enzymes	Zero	Cells are not yet dividing; preparing for growth
Exponential (log) phase	Rapid division; population doubles at constant rate	Maximum	Nutrients are abundant; no limiting factors
Stationary phase	Growth rate equals death rate; population is stable	Zero	Nutrients are depleted; toxic waste products accumulate
Decline (death) phase	Death rate exceeds growth rate	Negative	Nutrient exhaustion; accumulation of toxic waste; pH change

Calculating the mean division time:

During exponential phase, if the population doubles from $10^4$ to $10^8$ in 6.6 hours:

Number of divisions $= \log_2\left(\frac{10^8}{10^4}\right) = \log_2(10^4) \approx 13.3$ divisions.

Mean division time $= \frac◆LB◆6.6 \times 60◆RB◆◆LB◆13.3◆RB◆ \approx 30$ minutes.

19.3 Bacterial Genetic Exchange

Method	Mechanism	What is Transferred	Significance
Conjugation	Direct contact via sex pilus (F pilus); plasmid DNA is copied and transferred	Plasmid DNA (can carry antibiotic resistance genes, e.g., R plasmid)	Major route of antibiotic resistance spread; requires F+ (donor) and F- (recipient) cells
Transformation	Uptake of free DNA from the environment; requires competence	Linear DNA fragments	Griffith's experiment (1928): demonstrated transformation in S. pneumoniae; basis of recombinant DNA technology
Transduction	Bacteriophage (virus) transfers bacterial DNA during infection	Bacterial DNA (can be any part of the genome)	Can transfer any gene, including toxin genes (e.g., diphtheria toxin, cholera toxin)

20. Microscopy: Advanced Techniques

20.1 Resolution and Magnification

$\text{Resolution} = \frac◆LB◆0.61\lambda◆RB◆◆LB◆n\sin\theta◆RB◆$

Where $\lambda$ = wavelength of light/electrons; $n$ = refractive index of the medium; $\theta$ = half-angle of the cone of light entering the objective.

Microscope Type	Resolution	Maximum Magnification	Specimen Requirements
Light microscope	$\approx 200\ \mathrm{nm}$	$\approx 1,500\times$	Thin section; may be stained; can be living
Transmission electron microscope (TEM)	$\approx 0.2\ \mathrm{nm}$	$\approx 1,000,000\times$	Very thin section (50--100 nm); fixed; stained with heavy metals; dead
Scanning electron microscope (SEM)	$\approx 5\ \mathrm{nm}$	$\approx 200,000\times$	Surface features; coated with metal (gold); dead

20.2 Cell Fractionation and Ultracentrifugation

Cell fractionation separates organelles by size and density:

1. Homogenisation: cells are broken open (e.g., by blender, homogeniser) in cold, isotonic buffer (cold to reduce enzyme activity; isotonic to prevent organelle damage by osmosis).
2. Filtration: the homogenate is filtered through a muslin cloth to remove debris and unbroken cells.
3. Differential centrifugation: the filtrate is centrifuged at increasing speeds:

Centrifugation Speed	Force ($\times g$)	Pellet Contains
Low speed (1,000 $g$, 10 min)	Low	Nuclei (largest organelles)
Medium speed (10,000 $g$, 20 min)	Medium	Mitochondria, lysosomes, peroxisomes
High speed (100,000 $g$, 60 min)	High	Ribosomes, microsomes (ER fragments), small vesicles
Very high speed (300,000 $g$, 2 hrs)	Very high	Ribosomal subunits, viruses

21. Eukaryotic Cell Specialisation

21.1 Examples of Specialised Cells

Cell Type	Specialisation	Adaptations	Function
Red blood cell (erythrocyte)	Gas transport	Biconcave disc (increases surface area:volume ratio for gas exchange); no nucleus (more room for haemoglobin); no mitochondria (no $\mathrm{O_2}$ consumed); flexible membrane (squeezes through narrow capillaries, diameter $\approx 7\ \mu\mathrm{m}$)	Transport $\mathrm{O_2}$ (bound to haemoglobin) and $\mathrm{CO_2}$
Sperm cell	Fertilisation	Many mitochondria (ATP for tail movement); acrosome (contains digestive enzymes to penetrate egg); streamlined head; long flagellum for swimming; haploid nucleus	Deliver genetic material to egg
Egg cell (ovum)	Fertilisation; early development	Large (contains nutrient reserves); haploid nucleus; zona pellucida (protective layer); cortical granules (prevent polyspermy after fertilisation)	Receives sperm; provides nutrients for early embryo
Neutrophil	Phagocytosis	Multi-lobed nucleus (flexible, can squeeze through tissues); many lysosomes (contain hydrolytic enzymes to digest pathogens)	Engulf and destroy pathogens
Squamous epithelial cell	Diffusion	Very flat and thin (short diffusion distance); closely packed	Line surfaces where diffusion occurs (alveoli, blood vessels, Bowman's capsule)
Ciliated epithelial cell	Moving mucus	Cilia on apical surface (beat in coordinated motion to move mucus); many mitochondria (ATP for ciliary beating); goblet cells (produce mucus)	Line trachea, bronchi, oviducts
Root hair cell	Water and mineral uptake	Elongated projection (root hair) greatly increases surface area; thin cell wall for short diffusion distance; many mitochondria (ATP for active transport); high concentration of carrier proteins	Absorb water and minerals from soil
Palisade mesophyll cell	Photosynthesis	Elongated and packed with chloroplasts (near top of leaf for maximum light); thin cell walls; large vacuole (pushes chloroplasts to periphery)	Main site of photosynthesis in leaves

21.2 Stem Cells

Type	Source	Potency	Can Differentiate Into
Totipotent	Early embryo (up to 8-cell stage)	Can form any cell type, including extra-embryonic tissues (placenta)	All cell types
Pluripotent	Embryonic stem cells (inner cell mass of blastocyst)	Can form any cell type except extra-embryonic tissues	All cell types of the organism
Multipotent	Adult stem cells (bone marrow, umbilical cord blood)	Can form a limited range of cell types	Blood cells, bone, cartilage, fat (mesenchymal stem cells)
Unipotent	Some adult stem cells	Can form only one cell type	Hepatocytes (liver stem cells); satellite cells (muscle)

Therapeutic uses of stem cells:

• Bone marrow transplants: treating leukaemia (cancer of white blood cells). High-dose chemotherapy destroys the patient's bone marrow; donor stem cells are infused to reconstitute the immune system.
• Skin grafts: using cultured epidermal stem cells to treat severe burns.
• Corneal repair: limbal stem cell transplants to restore the corneal epithelium.
• Research: iPSCs (induced pluripotent stem cells) used for disease modelling, drug testing, and potential regenerative therapies.

Ethical issues:

• Embryonic stem cells require destruction of embryos (ethical concerns about the moral status of the embryo).
• Adult stem cells are less controversial but have more limited differentiation potential.
• iPSCs avoid the destruction of embryos but may carry epigenetic memory of their cell of origin.

22. Cell Communication: Gap Junctions and Plasmodesmata

22.1 Gap Junctions (Animal Cells)

Gap junctions are channels that directly connect the cytoplasm of adjacent animal cells:

• Composed of connexin proteins arranged in a ring (connexon) in the plasma membrane of each cell.
• Allow the passage of ions ($\mathrm{Ca^{2+}}$, $\mathrm{K^+}$), small molecules (cAMP, $\mathrm{IP_3}$, glucose, amino acids), and electrical signals (action potentials) between cells.
• Diameter of each channel: approximately 1.5 nm.
• Functions: electrical coupling between cardiac muscle cells (allows coordinated contraction); spread of calcium waves; metabolic coupling (sharing nutrients); communication between neurons in the retina.

22.2 Plasmodesmata (Plant Cells)

Plasmodesmata are channels that connect adjacent plant cells through the cell wall:

• Each plasmodesma contains a desmotubule (narrow tube of endoplasmic reticulum).
• The space between the desmotubule and the plasma membrane (cytoplasmic sleeve) allows the passage of molecules.
• Allow the passage of ions, sugars, amino acids, mRNA, and some proteins between cells.
• Can be gated (regulated) to control the size of molecules that pass through.
• Functions: transport of photosynthates (sucrose) between cells; spread of signalling molecules (including plant viruses); developmental signalling.

22.3 Cell Adhesion Molecules

Type	Description	Function
Cadherins	Calcium-dependent transmembrane proteins	Cell-cell adhesion; tissue formation; maintaining tissue integrity
Integrins	Transmembrane proteins that link the extracellular matrix to the cytoskeleton	Cell-ECM adhesion; cell signalling; migration
Selectins	Carbohydrate-binding transmembrane proteins	Mediate temporary cell-cell adhesion (e.g., leukocyte rolling on blood vessel walls during inflammation)
Immunoglobulin superfamily (IgCAMs)	Transmembrane proteins with immunoglobulin domains	Cell-cell adhesion in the nervous system (e.g., NCAM, involved in axon guidance)

22.4 The Extracellular Matrix (ECM)

The ECM is a complex network of proteins and polysaccharides secreted by cells:

Component	Description	Function
Collagen	Most abundant ECM protein; forms strong fibres	Tensile strength; structural framework
Elastin	Elastic protein that can stretch and recoil	Elasticity in tissues that undergo stretching (blood vessels, lungs, skin)
Fibronectin	Glycoprotein that connects cells to the ECM	Cell adhesion; cell migration; wound healing
Proteoglycans	Core protein + glycosaminoglycan (GAG) chains	Hydration and resistance to compression (e.g., cartilage); regulate growth factor activity
Hyaluronic acid	Large GAG; not attached to a core protein	Lubrication in joints; hydration; space-filling

23. The Cytoskeleton

23.1 Components of the Cytoskeleton

Component	Protein	Diameter	Structure	Functions
Microfilaments (actin filaments)	Actin	$\approx 7\ \mathrm{nm}$	Two intertwined actin chains	Cell shape; cell movement (pseudopodia, cleavage furrow); muscle contraction (thin filaments)
Intermediate filaments	Keratin, vimentin, lamin, desmin	$\approx 10\ \mathrm{nm}$	Fibrous proteins wound into ropes	Mechanical strength; structural support; nuclear lamina
Microtubules	Tubulin ($\alpha$ and $\beta$)	$\approx 25\ \mathrm{nm}$	13 protofilaments of tubulin dimers in a hollow cylinder	Chromosome movement during mitosis; intracellular transport (motor proteins); structural support; cilia and flagella

23.2 Motor Proteins

Motor Protein	Moves Along	Direction	Energy Source	Function
Kinesin	Microtubules	Towards the plus end (away from the centrosome)	ATP hydrolysis	Transport of vesicles and organelles towards the cell periphery
Dynein	Microtubules	Towards the minus end (towards the centrosome)	ATP hydrolysis	Retrograde transport (vesicles towards cell body); beating of cilia and flagella
Myosin	Actin filaments	Towards the plus end	ATP hydrolysis	Muscle contraction; cytokinesis; cell crawling

23.3 Cilia and Flagella

Cilia and flagella are extensions of the cell membrane supported by microtubules arranged in a "9 + 2" pattern (9 pairs of microtubules surrounding a central pair):

Feature	Cilia	Flagella
Length	Short (5--10 $\mu\mathrm{m}$)	Long (up to 200 $\mu\mathrm{m}$)
Number per cell	Many	Usually 1 or 2
Movement	Coordinated beating (metachronal rhythm)	Undulating (wave-like)
Function	Move mucus over epithelial surfaces (respiratory tract, oviducts); move egg along oviduct	Sperm motility
"9+2" arrangement	Yes	Yes
ATP source	Dynein arms between microtubule pairs	Dynein arms

Primary ciliary dyskinesia: a genetic disorder caused by defective dynein arms, resulting in immotile cilia. Symptoms: chronic respiratory infections (mucus not cleared), male infertility (immotile sperm), situs inversus (organs on the wrong side of the body, because nodal cilia cannot direct left-right asymmetry during development).

---

tip

Diagnostic Test Ready to test your understanding of Cells? The diagnostic test contains the hardest questions within the A-Level specification for this topic, each with a full worked solution.

Unit tests probe edge cases and common misconceptions. Integration tests combine Cells with other biology topics to test synthesis under exam conditions.

See Diagnostic Guide for instructions on self-marking and building a personal test matrix.

24. Viruses: Structure and Replication

24.1 Virus Structure

Viruses are not cells. They are obligate intracellular parasites consisting of:

Component	Description
Genetic material	Either DNA or RNA (single-stranded or double-stranded; linear or circular) -- never both
Protein coat (capsid)	Made of capsomeres (protein subunits); protects the genome; determines host cell specificity
Envelope (some viruses)	Lipid bilayer derived from the host cell membrane during budding; contains viral glycoproteins (e.g., gp120/gp41 in HIV; haemagglutinin in influenza)

Viruses are not considered living because they:

• Do not have a cell membrane, cytoplasm, or ribosomes.
• Cannot carry out metabolic reactions independently.
• Cannot reproduce without a host cell.
• Do not respond to stimuli.
• Do not grow.

24.2 Virus Replication Cycle (Generalised)

1. Attachment: the virus binds to specific receptors on the host cell surface (this determines host range and tissue tropism).
2. Entry: the virus enters the cell (by fusion with the membrane, endocytosis, or injection of nucleic acid).
3. Uncoating: the viral genome is released from the capsid inside the cell.
4. Replication: the viral genome is replicated using host or viral enzymes.
5. Synthesis: viral proteins are synthesised using host ribosomes.
6. Assembly: new viral particles are assembled from the synthesized components.
7. Release: new virions leave the cell (by lysis or budding). Budding (enveloped viruses) does not immediately kill the host cell; lysis (non-enveloped viruses) destroys the host cell.

24.3 Bacteriophages

Bacteriophages (phages) are viruses that infect bacteria:

Phage Type	Example	Replication Strategy
Lytic phage	T4 phage	Lytic cycle: phage attaches, injects DNA, hijacks host machinery to produce new phages, lyses the cell to release progeny (approx. 200 per infected cell)
Lysogenic phage	Lambda phage	Lysogenic cycle: phage DNA integrates into the bacterial chromosome as a prophage; the prophage is replicated along with the bacterial DNA; under stress (e.g., UV light), the prophage excises and enters the lytic cycle

Lysogenic conversion: when a prophage carries genes that change the phenotype of the host bacterium. For example, the cholera toxin gene in Vibrio cholerae is carried by a prophage (CTX$\phi$); Corynebacterium diphtheriae only produces diphtheria toxin when infected by the $\beta$-phage.

25. Prokaryotic vs Eukaryotic Cells: Summary Comparison

Feature	Prokaryotic Cell	Eukaryotic Cell
Size	1--5 $\mu\mathrm{m}$	10--100 $\mu\mathrm{m}$
Nucleus	No true nucleus; nucleoid region	True nucleus with nuclear envelope (double membrane with nuclear pores)
DNA	Circular; not associated with histones	Linear chromosomes; associated with histones (chromatin)
Membrane-bound organelles	None	Mitochondria, ER, Golgi, lysosomes, etc.
Ribosomes	70S (30S + 50S subunits)	80S (40S + 60S subunits)
Cell wall	Present in bacteria (peptidoglycan); absent in archaea	Present in plants (cellulose), fungi (chitin); absent in animals
Flagella	Simple, rotating (single protein, flagellin)	Complex, "9+2" microtubule arrangement
Reproduction	Binary fission (asexual)	Mitosis and meiosis (asexual and sexual)
Cell division	No spindle; no mitosis	Spindle fibres; mitosis
Metabolic diversity	Extremely diverse (anaerobic, aerobic, chemoautotrophic, photoautotrophic)	Mostly aerobic (obligate); some anaerobic (yeast, muscle)
Internal membranes	Mesosomes (infoldings of cell membrane)	Extensive (ER, Golgi, mitochondria, vesicles)
Cytoplasm	No cytoskeleton (in most bacteria)	Complex cytoskeleton (microfilaments, microtubules, intermediate filaments)
Gene organisation	Operons; no introns (in most)	Individual genes; introns and exons; split genes
Time to replicate	20--30 minutes (E. coli)	8--24 hours (human cell in culture)

26. Practical Skills: Using a Microscope

26.1 Calculating Magnification

$\text{Magnification} = \frac◆LB◆\text{size of image}◆RB◆◆LB◆\text{size of object}◆RB◆$

Example: a cell is observed through a microscope at 400x magnification. The cell measures $4\ \mathrm{mm}$ on the micrograph. What is the actual size?

$\text{Actual size} = \frac◆LB◆\text{image size}◆RB◆◆LB◆\text{magnification}◆RB◆ = \frac◆LB◆4\ \mathrm{mm}◆RB◆◆LB◆400◆RB◆ = 0.01\ \mathrm{mm} = 10\ \mu\mathrm{m}$

26.2 Preparing a Temporary Mount

1. Place a drop of water on a clean microscope slide.
2. Place the specimen on the drop (thinly section or single layer).
3. Add a coverslip at an angle to avoid trapping air bubbles.
4. Stain if necessary (e.g., iodine for starch; methylene blue for animal cells).

26.3 Calculating Mitotic Index

The mitotic index is the percentage of cells in a population that are undergoing mitosis at a given time:

$\text{Mitotic index} = \frac◆LB◆\text{number of cells in mitosis}◆RB◆◆LB◆\text{total number of cells observed}◆RB◆ \times 100$

Example: In a sample of 200 cells, 12 are in prophase, 8 in metaphase, 4 in anaphase, and 6 in telophase.

Cells in mitosis $= 12 + 8 + 4 + 6 = 30$.

Mitotic index $= \frac{30}{200} \times 100 = 15\%$.

A high mitotic index indicates rapid cell division (e.g., in cancerous tissue or meristems). A low mitotic index indicates slow division or quiescence.

27. The Cell Surface Membrane: Fluid Mosaic Model in Detail

27.1 Membrane Components

Component	Structure	Function
Phospholipids	Hydrophilic phosphate head, hydrophobic fatty acid tails; form bilayer	Form the basic structure; selectively permeable barrier
Cholesterol	Small, amphipathic molecule interspersed between phospholipids	Reduces membrane fluidity at high temperatures; prevents freezing at low temperatures; maintains membrane stability
Intrinsic (transmembrane) proteins	Span the entire bilayer; hydrophobic regions interact with lipid tails	Channel proteins (facilitated diffusion); carrier proteins (active transport and facilitated diffusion); receptors
Extrinsic (peripheral) proteins	On inner or outer surface; attached by ionic bonds or to intrinsic proteins	Enzymes; cell signalling; cytoskeleton attachment
Glycoproteins	Proteins with carbohydrate chains	Cell recognition (e.g., ABO blood group antigens); receptors; cell-cell adhesion
Glycolipids	Lipids with carbohydrate chains	Cell recognition; cell-cell signalling; tissue compatibility
Cholesterol	See above	See above

27.2 Factors Affecting Membrane Fluidity

Factor	Effect	Explanation
Temperature (increase)	Increases fluidity	More kinetic energy; phospholipids move more; membrane becomes more permeable
Temperature (decrease)	Decreases fluidity	Less kinetic energy; phospholipids pack more tightly; membrane becomes less permeable
Saturated fatty acids	Decreases fluidity	Straight tails pack tightly together
Unsaturated fatty acids (cis double bonds)	Increases fluidity	Kinked tails prevent tight packing
Cholesterol	Buffers fluidity changes	Reduces fluidity at high temperature; increases fluidity at low temperature

28. Prokaryotic Cells: Detailed Structure

28.1 Components of a Prokaryotic Cell

Component	Description	Function
Cell wall	Made of peptidoglycan (murein); not cellulose or chitin	Provides shape; prevents osmotic lysis
Plasma membrane	Phospholipid bilayer (no cholesterol, unlike eukaryotes)	Selective permeability; site of respiration (no mitochondria); site of photosynthesis (in cyanobacteria, on thylakoids)
Cytoplasm	No membrane-bound organelles; no endoplasmic reticulum; no Golgi	Contains ribosomes (70S), plasmids, and metabolic enzymes
Ribosomes	70S (30S + 50S subunits); smaller than eukaryotic 80S	Protein synthesis
Nucleoid	Region of cytoplasm containing a single, circular DNA molecule (not enclosed in a nuclear envelope)	Contains the chromosome (genetic material)
Plasmids	Small, circular, extrachromosomal DNA molecules	Often carry antibiotic resistance genes; can be transferred between bacteria (conjugation)
Flagellum (plural: flagella)	Rotating filament (driven by proton motor at base)	Propulsion (swimming)
Pili (fimbriae)	Short, hair-like protein appendages	Attachment to surfaces; conjugation (sex pili transfer plasmids between bacteria)
Capsule (slime layer)	Polysaccharide or polypeptide layer outside the cell wall	Protection from phagocytosis; adhesion to surfaces; prevents desiccation
Mesosome	Infolding of the plasma membrane	May be involved in DNA replication and cell division (controversial; may be an artefact of electron microscopy preparation)

28.2 Gram Staining

Step	What Happens	Result for Gram-Positive	Result for Gram-Negative
1. Crystal violet	Purple dye enters all cells	Purple	Purple
2. Iodine (mordant)	Forms crystal violet-iodine complex	Purple (trapped in thick peptidoglycan)	Purple
3. Alcohol/acetone (decolouriser)	Dissolves outer membrane (Gram-negative); dehydrates peptidoglycan (Gram-positive)	Remains purple (thick peptidoglycan retains dye)	Becomes colourless (dye washed out)
4. Safranin (counterstain)	Red dye stains decolourised cells	Purple (safranin has no visible effect)	Pink/red (safranin stains the cell)

Feature	Gram-Positive	Gram-Negative
Peptidoglycan layer	Thick (20--80 nm)	Thin (2--7 nm)
Outer membrane	Absent	Present (lipopolysaccharide layer)
Periplasmic space	Absent	Present
Teichoic acids	Present (in peptidoglycan)	Absent
Examples	Staphylococcus, Streptococcus, Bacillus	E. coli, Salmonella, Pseudomonas

29. Viruses: Structure and Replication

29.1 General Virus Structure

Component	Description
Genetic material	Either DNA or RNA (never both); single-stranded or double-stranded; linear or circular
Capsid	Protein coat that protects the genetic material; made of capsomeres (protein subunits)
Envelope (some viruses)	Lipid bilayer derived from the host cell membrane during budding; contains viral glycoproteins
Attachment proteins	Project from the capsid or envelope; bind to specific receptors on the host cell surface

29.2 Examples of Viruses

Virus	Genetic Material	Envelope?	Host Cell	Disease
HIV	ssRNA (+ sense)	Yes	CD4+ T cells, macrophages	AIDS
Influenza virus	ssRNA (- sense, segmented)	Yes	Respiratory epithelial cells	Influenza (flu)
SARS-CoV-2	ssRNA (+ sense)	Yes	Respiratory epithelial cells (ACE2 receptor)	COVID-19
Tobacco mosaic virus (TMV)	ssRNA (+ sense)	No	Plant cells (leaf mesophyll)	Tobacco mosaic disease
Bacteriophage $\lambda$	dsDNA	No (tail)	E. coli bacteria	Bacterial lysis
Adenovirus	dsDNA	No	Respiratory epithelial cells	Common cold, conjunctivitis
Herpes simplex virus (HSV)	dsDNA	Yes	Nerve cells (latent infection in ganglia)	Cold sores, genital herpes

29.3 Why Viruses Are Not Alive

Characteristic of Life	Do Viruses Show It?	Explanation
Cellular organisation	No	Acellular (no cytoplasm, no ribosomes, no cell membrane)
Metabolism	No	No independent metabolism; rely entirely on host cell machinery
Reproduction	No (not independently)	Can only replicate inside a living host cell
Response to stimuli	No	No homeostatic mechanisms
Growth	No	Assembled from pre-formed components; do not grow

30. Stem Cells

30.1 Types of Stem Cells

Type	Source	Potency	Can Differentiate Into
Totipotent	Zygote; early embryo (up to 4-cell stage)	Can form ANY cell type AND extra-embryonic tissues (placenta)	All cell types + placental tissue
Pluripotent	Embryonic stem cells (ESCs) from the inner cell mass of the blastocyst (5--7 days)	Can form ANY cell type but NOT extra-embryonic tissues	All 220+ cell types in the body
Multipotent	Adult stem cells (bone marrow, umbilical cord blood, adipose tissue)	Can form a limited range of cell types within one tissue type	Bone marrow: RBCs, WBCs, platelets; Neural stem cells: neurons, astrocytes, oligodendrocytes
Unipotent	Some adult stem cells	Can form only ONE cell type	Satellite cells (muscle stem cells) $\to$ skeletal muscle cells only

30.2 Sources of Stem Cells

Source	Advantages	Disadvantages
Embryonic stem cells (ESCs)	Pluripotent; unlimited self-renewal; can differentiate into any cell type	Ethical controversy (destruction of embryo); risk of teratoma formation; immune rejection
Adult stem cells	No ethical issues; patient's own cells = no immune rejection; lower tumour risk	Limited potency; fewer in number; harder to isolate and culture
Induced pluripotent stem cells (iPSCs)	Pluripotent; patient's own cells (no immune rejection); no embryo destruction	Risk of mutations from reprogramming; may not be fully equivalent to ESCs; expensive
Umbilical cord blood	Rich in haematopoietic stem cells; painless collection; lower immune rejection	Limited volume; only haematopoietic stem cells (not pluripotent)

30.3 Therapeutic Uses of Stem Cells

Application	Stem Cell Type	Current Status
Bone marrow transplant (leukaemia)	Haematopoietic stem cells from bone marrow or cord blood	Well-established treatment
Skin grafts (burns)	Epidermal stem cells from patient's own skin	Routine in specialist centres
Corneal repair (limbal stem cell deficiency)	Limbal stem cells from healthy eye or cultured	Available; good outcomes
Spinal cord injury	Neural stem cells or mesenchymal stem cells	Clinical trials ongoing
Parkinson's disease	Dopaminergic neurons derived from ESCs or iPSCs	Clinical trials; promising early results
Type 1 diabetes	Pancreatic $\beta$ cells derived from stem cells	Research stage; clinical trials planned

31. The Cytoskeleton

31.1 Components of the Cytoskeleton

Component	Protein	Diameter	Structure	Function
Microfilaments (actin filaments)	Actin (globular G-actin polymerises to filamentous F-actin)	~7 nm	Two helical chains of actin subunits twisted together	Cell movement (amoeboid movement, cytokinesis); cell shape; microvilli
Intermediate filaments	Various (keratin, vimentin, lamin, desmin, neurofilaments)	~10 nm	Rope-like fibres (more stable than microfilaments)	Mechanical strength; structural support; anchors organelles; nuclear lamina
Microtubules	Tubulin ($\alpha$-tubulin + $\beta$-tubulin dimers)	~25 nm	Hollow tubes of 13 protofilaments (tubulin dimers)	Cell shape; intracellular transport (motor proteins: kinesin and dynein walk along microtubules); spindle fibres in mitosis/meiosis; cilia and flagella

31.2 Motor Proteins

Motor Protein	Direction of Movement	Cargo	Role
Kinesin	Moves towards the (+) end of microtubules (away from the centrosome)	Vesicles, organelles, mRNA	Anterograde transport (e.g., moving neurotransmitter vesicles down the axon)
Dynein	Moves towards the (-) end of microtubules (towards the centrosome)	Vesicles, organelles	Retrograde transport; drives beating of cilia and flagella
Myosin	Moves along actin filaments	Vesicles, organelles	Muscle contraction; cytokinesis; cell crawling

32. The Endoplasmic Reticulum and Golgi Apparatus

32.1 Rough Endoplasmic Reticulum (RER)

Feature	Description
Appearance	Flattened sacs (cisternae) studded with ribosomes on the cytoplasmic surface
Function	Synthesis of proteins destined for secretion, the plasma membrane, or lysosomes; proteins enter the RER lumen during synthesis
Transport	Vesicles bud off from the RER and carry proteins to the Golgi apparatus
Location	Near the nucleus (continuous with the nuclear envelope)

32.2 Smooth Endoplasmic Reticulum (SER)

Feature	Description
Appearance	Tubular network; no ribosomes
Functions	Lipid and steroid synthesis (e.g., cholesterol, steroid hormones); carbohydrate metabolism; detoxification (in liver cells, SER contains enzymes that break down drugs, alcohol, and other toxins); calcium storage (in muscle cells, SER is called sarcoplasmic reticulum)
Location	Throughout the cytoplasm

32.3 Golgi Apparatus

Feature	Description
Appearance	Stack of flattened membrane-bound sacs (cisternae) with vesicles budding off at the edges
Functions	Modifies proteins (glycosylation: adding carbohydrate groups); sorts proteins into different vesicles; packages proteins into secretory vesicles for exocytosis; forms lysosomes
Direction	Vesicles arrive from the RER at the cis face (receiving side); modified proteins leave from the trans face (shipping side)
Transport	Secretory vesicles carry proteins to the plasma membrane (exocytosis) or to lysosomes

33. The Extracellular Matrix (ECM)

33.1 Components of the ECM

Component	Description	Function
Collagen	Most abundant protein in the body; forms strong fibres	Provides tensile strength (resists stretching); major component of connective tissue (tendons, skin, bone)
Elastin	Elastic protein that can stretch and recoil	Provides elasticity (e.g., in arterial walls, lungs, skin)
Fibronectin	Glycoprotein that connects cells to the ECM	Links integrins (cell surface receptors) to collagen and other ECM components; involved in cell adhesion and migration
Proteoglycans	Protein core with long chains of GAGs (glycosaminoglycans, e.g., chondroitin sulfate, heparan sulfate)	Fill the spaces between cells; resist compression (especially in cartilage); bind growth factors and signalling molecules
Hyaluronic acid	Large GAG (not attached to a protein core)	Lubricates joints; provides hydration and turgor to tissues; component of the vitreous humour of the eye

33.2 Functions of the ECM

Function	Description
Structural support	Provides a scaffold for tissues; determines tissue architecture
Cell signalling	ECM components bind to cell surface receptors (integrins); activate intracellular signalling pathways; influence gene expression, cell division, and differentiation
Cell adhesion	Cells attach to the ECM via integrins; provides anchorage
Filtration	Basement membrane (specialised ECM) filters blood in the glomerulus (kidney)
Wound healing	ECM provides a framework for tissue repair; fibroblasts deposit new collagen during scar formation

34. Apoptosis: Programmed Cell Death

34.1 What Is Apoptosis?

Apoptosis is an orderly, genetically programmed process of cell death that occurs during normal development and tissue homeostasis.

34.2 Process of Apoptosis

Step	Description
1. Signal	Cell receives a signal to undergo apoptosis (internal signal: DNA damage detected by p53 protein; external signal: death signals from immune cells)
2. Enzyme activation	Caspases (cysteine proteases) are activated (initiator caspases $\to$ executioner caspases)
3. Cell shrinkage	Cell loses water; becomes smaller; cytoskeleton breaks down
4. Chromatin condensation	DNA is cut into fragments by endonucleases (DNA laddering on gel electrophoresis)
5. Membrane blebbing	The plasma membrane forms irregular blebs (outward bulges)
6. Apoptotic body formation	The cell fragments into membrane-bound apoptotic bodies
7. Phagocytosis	Apoptotic bodies are engulfed and digested by neighbouring cells or macrophages (no inflammatory response because cell contents are not released)

34.3 Apoptosis vs Necrosis

Feature	Apoptosis	Necrosis
Cause	Genetically programmed; physiological or mild stress	Uncontrolled cell death; caused by severe injury, toxin, or hypoxia
Process	Orderly; energy-dependent (requires ATP)	Disorderly; energy-independent
Membrane integrity	Maintained until late; apoptotic bodies form	Lost early; cell contents leak out
Inflammation	No inflammation (cell contents are contained)	Inflammation occurs (cell contents released; attracts immune cells)
DNA fragmentation	Organised (laddering pattern)	Random (smear pattern)
Role	Essential for development; removes damaged or unwanted cells	Pathological; harmful to surrounding tissue

34.4 Examples of Apoptosis

Example	Why Apoptosis Is Needed
Embryonic development	Tissue remodelling (e.g., separation of fingers and toes by apoptosis of webbing tissue)
Immune system	Removal of self-reactive T cells in the thymus (negative selection); removal of surplus B cells after infection
Skin	Shedding of dead skin cells from the epidermis
Menstrual cycle	Breakdown of the endometrium if implantation does not occur
DNA damage	If DNA damage is too severe to repair, p53 triggers apoptosis (prevents cancer)

35. Microscopy

35.1 Types of Microscopy

Type	Resolution	Magnification	Specimen Preparation	What Can Be Seen
Light microscope	~200 nm	Up to ~1500x	Staining (e.g., methylene blue, iodine, eosin); sectioning	Cell structure (nucleus, chloroplasts, cell walls); living specimens (with special techniques)
Transmission electron microscope (TEM)	~0.1 nm	Up to ~1,000,000x	Specimen fixed, dehydrated, embedded in resin; ultra-thin sections (~100 nm); stained with heavy metals (uranium, lead)	Internal ultrastructure (organelles, membranes, ribosomes); very high resolution
Scanning electron microscope (SEM)	~10 nm	Up to ~100,000x	Specimen fixed, dehydrated; coated with gold/palladium	3D surface detail (external features of cells, pollen grains, insects); not internal structure
Laser scanning confocal microscopy	~200 nm	Up to ~1000x	Fluorescent staining; optical sectioning (no physical sectioning needed)	3D images of fluorescently labelled structures inside living cells

35.2 Magnification and Scale

$\text{Magnification} = \frac◆LB◆\text{Image size}◆RB◆◆LB◆\text{Actual size}◆RB◆$

$\text{Actual size} = \frac◆LB◆\text{Image size}◆RB◆◆LB◆\text{Magnification}◆RB◆$

Unit	Symbol	Conversion
Metre	m	--
Millimetre	mm	$10^{-3}$ m
Micrometre	$\mu$m	$10^{-6}$ m
Nanometre	nm	$10^{-9}$ m

36. Cell Division: Mitosis in Detail

36.1 The Four Stages of Mitosis

Stage	What Happens
Prophase	Chromosomes condense (become visible as two sister chromatids joined at the centromere); nuclear envelope begins to break down; nucleolus disappears; centrioles move to opposite poles; spindle fibres begin to form
Metaphase	Chromosomes line up at the metaphase plate (equator of the cell); spindle fibres attach to centromeres; chromosomes are at their most condensed (best stage to observe chromosomes under a microscope)
Anaphase	Centromeres divide; sister chromatids are pulled to opposite poles by the spindle fibres (shortening of microtubules); chromosomes are now individual chromatids (V-shaped)
Telophase	Chromatids arrive at the poles; they decondense (become chromatin again); nuclear envelope reforms around each set of chromosomes; nucleolus reappears; cytokinesis (cytoplasmic division) begins

36.2 Cytokinesis

Feature	Animal Cells	Plant Cells
Mechanism	Cleavage furrow: contractile ring of actin and myosin pinches the cell in two from the outside	Cell plate: vesicles from the Golgi apparatus fuse at the equator; form a new cell wall (middle lamella) between the two daughter cells
Result	Two identical daughter cells	Two identical daughter cells with new cell walls

37. Eukaryotic Cell Structure Summary

37.1 Organelle Functions Quick Reference

Organelle	Function
Nucleus	Contains genetic material (DNA); controls cell activities via gene expression
Nucleolus	rRNA synthesis; ribosome assembly
Rough ER	Protein synthesis (for secretion, membrane, lysosomes)
Smooth ER	Lipid synthesis; detoxification; calcium storage
Golgi apparatus	Protein modification, sorting, packaging
Mitochondria	Aerobic respiration; ATP production
Chloroplasts (plants only)	Photosynthesis
Ribosomes	Protein synthesis (80S in cytoplasm; 70S in mitochondria/chloroplasts)
Lysosomes	Intracellular digestion; contain hydrolytic enzymes
Centrioles	Organise spindle fibres during cell division; form basal bodies of cilia
Cytoskeleton	Cell shape; movement; intracellular transport
Cell membrane	Selective barrier; cell signalling; cell recognition
Cell wall (plants, fungi)	Structural support; prevents osmotic lysis
Vacuole (plants)	Storage (water, ions, pigments); maintains turgor pressure
Peroxisomes	Breakdown of fatty acids ($\beta$-oxidation); detoxification of hydrogen peroxide

38. Prokaryotic vs Eukaryotic Cells: Summary Comparison

Feature	Prokaryotic Cell	Eukaryotic Cell
Size	1--10 $\mu$m	10--100 $\mu$m
Nucleus	No true nucleus (nucleoid region)	True nucleus with nuclear envelope and nucleolus
DNA	Single, circular chromosome; no histones	Multiple linear chromosomes; associated with histones
Ribosomes	70S (smaller)	80S (larger)
Membrane-bound organelles	None	Many (mitochondria, ER, Golgi, lysosomes, etc.)
Cell wall	Present (peptidoglycan in bacteria)	In plants (cellulose) and fungi (chitin); absent in animals
Plasma membrane	Present; no cholesterol	Present; contains cholesterol
Cytoskeleton	Simple (no microtubules, no intermediate filaments)	Complex (microtubules, microfilaments, intermediate filaments)
Reproduction	Binary fission (asexual)	Mitosis and meiosis; also meiosis (sexual reproduction)
Flagella	Simple, rotating (9+2 microtubule arrangement, but different protein composition)	Complex, 9+2 microtubule arrangement; beating motion
Plasmids	Present	Absent (in most eukaryotes)
Metabolic diversity	Very high (chemolithoautotrophs, photoautotrophs, heterotrophs)	Lower (mainly heterotrophic; some photoautotrophic)

39. Specialised Plant Cells

39.1 Palisade Mesophyll vs Spongy Mesophyll

Feature	Palisade Mesophyll	Spongy Mesophyll
Position	Upper layers of the mesophyll (near the upper epidermis)	Lower layers of the mesophyll (near the lower epidermis)
Cell shape	Columnar; elongated; tightly packed	Loosely packed; many air spaces (large intercellular air spaces)
Chloroplast density	Very high (many chloroplasts per cell)	Fewer chloroplasts per cell
Primary function	Photosynthesis (light harvesting)	Gas exchange (air spaces allow $\mathrm{CO_2}$ to reach palisade cells; $\mathrm{O_2}$ to diffuse out)

39.2 Other Specialised Plant Cells

Cell Type	Location	Function
Root hair cell	Root epidermis (just behind the tip)	Increases surface area for mineral ion and water absorption from soil
Guard cell	Epidermis (flanking stomata)	Controls opening and closing of stomata (regulates gas exchange and transpiration)
Xylem vessel element	Xylem	Dead, hollow cells forming tubes for water transport
Companion cell	Phloem (adjacent to sieve tube elements)	Loads sucrose into sieve tubes via active transport; provides metabolic support
Sclerenchyma (fibres)	Scattered in vascular bundles; also in stems	Lignified, dead cells that provide mechanical strength and support
Collenchyma	Below the epidermis in young stems	Living cells with unevenly thickened cellulose cell walls; provides flexible support to young growing stems

40. Cell Fractionation

40.1 Principles

Cell fractionation is the process of breaking open cells and separating the organelles by differential centrifugation.

Step	Description
1. Homogenisation	Cells are placed in a cold, isotonic buffer solution and homogenised (blended) to break the plasma membrane while leaving organelles intact
2. Cold temperature	Reduces enzyme activity; prevents organelle damage by proteases
3. Isotonic buffer	Prevents organelles from bursting (if too dilute) or shrinking (if too concentrated) by osmosis
4. Buffered pH	Maintains a constant pH; prevents enzyme denaturation and organelle damage
5. Filtration	Homogenate is filtered through gauze to remove debris (unbroken cells, connective tissue)
6. Differential centrifugation	Organelles are separated by spinning at increasing speeds; heavier/larger organelles sediment first

40.2 Centrifugation Steps

Centrifuge Speed	Time	Organelle Sedimented	Supernatant Contains
Low speed (~1000 g)	10 min	Nuclei	Mitochondria, lysosomes, microsomes, ribosomes (in solution)
Medium speed (~10,000 g)	20 min	Mitochondria, lysosomes	Microsomes (ER fragments), ribosomes (in solution)
High speed (~100,000 g)	60 min	Microsomes (rough ER, smooth ER), ribosomes	Soluble cytoplasm (enzymes, metabolites)

41. Mitosis in Detail

41.1 Interphase (Preparation for Division)

Phase	Key Events
G1 (Gap 1)	Cell grows; organelles duplicate; proteins are synthesised
S (Synthesis)	DNA replication occurs (each chromosome is copied to form two sister chromatids joined at the centromere)
G2 (Gap 2)	Cell continues to grow; synthesises proteins needed for mitosis (e.g., tubulin for spindle fibres)

41.2 Prophase

Event	Description
Chromatin condensation	DNA coils and supercoils; chromosomes become visible as two sister chromatids joined at the centromere
Spindle formation	Centrioles (in animal cells) move to opposite poles; spindle fibres (microtubules) form from the centrioles and extend across the cell
Nuclear envelope	Breaks down and disappears
Nucleolus	Disappears

41.3 Metaphase

Event	Description
Alignment	Chromosomes line up at the metaphase plate (equator of the cell)
Attachment	Spindle fibres attach to the centromere of each chromosome via the kinetochore
Checkpoint	The spindle assembly checkpoint ensures all chromosomes are correctly attached before anaphase begins

41.4 Anaphase and Telophase

Phase	Events
Anaphase	Sister chromatids are pulled apart to opposite poles by the spindle fibres (shortening of spindle fibres); the centromere divides first; each chromatid is now an independent chromosome
Telophase	Chromosomes arrive at the poles and begin to decondense (uncoil back into chromatin); the nuclear envelope reforms around each set of chromosomes; the nucleolus reappears
Cytokinesis	The cytoplasm divides: in animal cells, the cell membrane is pulled inwards by a contractile ring of actin filaments (cleavage furrow); in plant cells, a cell plate forms from vesicles containing cell wall material at the equator; the cell plate grows outwards to divide the cell into two daughter cells

41.5 The Significance of Mitosis

Significance	Description
Growth	Produces new cells for tissue growth (e.g., bone elongation at the epiphyseal plate)
Repair	Replaces damaged or dead cells (e.g., skin cells, liver cells after injury)
Asexual reproduction	Produces genetically identical offspring in organisms that reproduce asexually (e.g., binary fission in bacteria, budding in yeast, runners in strawberry plants)
Genetic continuity	Produces daughter cells that are genetically identical to the parent cell (same chromosome number and same alleles)

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