Cell Structure and Function

Cell Theory (CED Unit 2)

All living organisms are composed of one or more cells.
The cell is the basic unit of structure and organization in organisms.
All cells arise from pre-existing cells (Virchow, 1855).

Prokaryotic vs Eukaryotic Cells

Feature	Prokaryotic	Eukaryotic
Nucleus	No (nucleoid region)	Yes, membrane-bound
Membrane-bound organelles	No	Yes
DNA	Circular, single	Linear, in chromosomes
Size	0.1 — 5 $\mu$ M	10 — 100 $\mu$ M
Ribosomes	70S (smaller)	80S (larger)
Cell division	Binary fission	Mitosis, meiosis
Examples	Bacteria, Archaea	Plants, animals, fungi, protists

Worked Example: Distinguishing prokaryotic and eukaryotic features.

A student examines a cell under a microscope and observes: no visible nucleus, a cell wall, and Ribosomes. The cell is approximately 2 $\mu$ M in diameter.

Since there is no membrane-bound nucleus, this is a prokaryotic cell. Both prokaryotes and Eukaryotes can have cell walls (plant cell walls are made of cellulose; bacterial cell walls are Made of peptidoglycan), so the presence of a cell wall is not diagnostic. The small size (2 $\mu$ M) Is consistent with a prokaryotic cell (prokaryotes are 0.1—5 $\mu$ M, while eukaryotes are 10—100 $\mu$ M).

The Cell Membrane (CED Unit 2)

Fluid Mosaic Model

The cell membrane is a fluid mosaic of:

Phospholipid bilayer: Amphipathic molecules with hydrophilic heads facing outward and hydrophobic tails facing inward. This creates a selectively permeable barrier.
Proteins: Embedded (integral) or surface (peripheral). Functions include transport, signaling, and enzymatic activity.
Cholesterol: Modulates membrane fluidity. At high temperatures, it restrains movement; at low temperatures, it prevents tight packing.
Carbohydrates: Glycoproteins and glycolipids on the outer surface for cell recognition and signaling.

Why the membrane is described as “fluid mosaic”:

Fluid: The phospholipid bilayer is not rigid. Phospholipids can move laterally within their own layer (lateral diffusion), and some can flip between layers (flip-flop, though this is rare). Proteins also drift within the bilayer. This fluidity allows the membrane to change shape (e.g., during endocytosis) and for membrane components to be redistributed.
Mosaic: The membrane is a patchwork of different molecules (phospholipids, proteins, cholesterol, carbohydrates) of different sizes and functions, like tiles in a mosaic.

Membrane Transport

Type	Direction	Energy Required?	Mediator
Simple diffusion	High to low conc.	No	None
Facilitated diffusion	High to low conc.	No	Channel/carrier protein
Osmosis	High to low water potential	No	Aquaporins
Active transport	Low to high conc.	Yes (ATP)	Pump
Cotransport (secondary)	Low to high conc.	Yes (ion gradient)	Carrier protein
Bulk transport (exocytosis/endocytosis)	Various	Yes (ATP)	Vesicles

Osmosis and Tonicity

Isotonic: Solute concentration equal inside and outside. No net water movement.
Hypertonic: Higher solute concentration outside. Water moves out; cell shrinks (crenation in animal cells, plasmolysis in plant cells).
Hypotonic: Lower solute concentration outside. Water moves in; cell swells (lysis in animal cells, turgor pressure in plant cells).

Worked Example: Predicting the effect of tonicity on cells.

A red blood cell is placed in a 0.5% NaCl solution (hypotonic, since the normal concentration inside A red blood cell is about 0.9% NaCl).

Water moves into the cell by osmosis (from the hypotonic solution into the more concentrated Cytoplasm). The cell swells. Because animal cells have no cell wall, the cell will eventually burst (lysis), releasing its contents into the surrounding solution.

If the same cell were placed in a 2% NaCl solution (hypertonic), water would move out of the cell. The cell would shrink (crenate) as it loses water.

Organelles (CED Unit 2)

Nucleus

Nuclear envelope: Double membrane with nuclear pores.
Chromatin: DNA + histone proteins (condenses into chromosomes during cell division).
Nucleolus: Site of rRNA synthesis and ribosome assembly.

Ribosomes

Site of protein synthesis (translation).
Free ribosomes: In cytoplasm, synthesize proteins for cytoplasmic use.
Bound ribosomes: On rough ER, synthesize proteins for secretion or membrane insertion.
Composed of large and small subunits made of rRNA and proteins.

Endoplasmic Reticulum (ER)

Rough ER: Studded with ribosomes. Protein synthesis, folding, modification. Transport vesicles bud off to the Golgi.
Smooth ER: No ribosomes. Lipid synthesis, detoxification (liver), calcium storage (muscle cells).

Golgi Apparatus

Stack of flattened membranous sacs (cisternae).
Modifies, sorts, and packages proteins and lipids from the ER.
Generates lysosomes, secretory vesicles, and plasma membrane components.
Cis face: Receives vesicles from ER.
Trans face: Ships vesicles to destination.

Worked Example: Tracing a secretory protein.

A pancreatic cell produces insulin. Trace the path of insulin from synthesis to export.

Nucleus: The gene for insulin is transcribed, producing mRNA.
Rough ER: The mRNA is translated by ribosomes on the rough ER. The insulin polypeptide is synthesised and enters the ER lumen, where it begins to fold.
Transport vesicles: Vesicles bud from the ER and carry the insulin to the Golgi apparatus.
Golgi apparatus: The insulin is modified (proinsulin is cleaved to form active insulin), sorted, and packaged into secretory vesicles.
Secretory vesicles: The vesicles move to the plasma membrane, fuse with it (exocytosis), and release insulin into the extracellular fluid.

Lysosomes

Membrane-bound vesicles containing hydrolytic enzymes.
Function in intracellular digestion, autophagy, and apoptosis (programmed cell death).
Internal pH $\approx 5$ (acidic) for optimal enzyme activity.
Defective lysosomes cause storage diseases (e.g., Tay-Sachs disease).

Vacuoles

Central vacuole (plants): Large, stores water, ions, metabolites. Provides turgor pressure.
Contractile vacuole (protists): Pumps out excess water.
Food vacuoles: Formed by phagocytosis.

Mitochondria

Site of cellular respiration (aerobic).
Double membrane: outer membrane (smooth) and inner membrane (folded into cristae).
Matrix: Contains DNA, ribosomes, enzymes for the Krebs cycle.
Intermembrane space: Site of proton gradient for chemiosmosis.
Produce ATP through oxidative phosphorylation.

Chloroplasts (Plants and Algae)

Site of photosynthesis.
Double membrane, with internal thylakoid membranes stacked into grana.
Thylakoid lumen: Site of the light-dependent reactions.
Stroma: Fluid surrounding thylakoids; site of the Calvin cycle.
Contain DNA, ribosomes, and pigments (chlorophyll).

Cytoskeleton

Microfilaments (actin): 7 nm diameter. Cell motility, cytokinesis, muscle contraction.
Intermediate filaments: 10 nm diameter. Structural support, tension-bearing.
Microtubules: 25 nm diameter. Shape, intracellular transport (motor proteins: kinesin, dynein), chromosome movement during cell division.
Centrosome and centrioles: Organize microtubules. Centrioles form the mitotic spindle in animal cells.

Cell Wall (Plants, Fungi, Bacteria)

Plants: Cellulose microfibrils embedded in a matrix of hemicellulose and pectin.
Fungi: Chitin.
Bacteria: Peptidoglycan.
Provides structural support and protection. Freely permeable to small molecules.

Extracellular Matrix (Animal Cells)

Composed of glycoproteins (collagen, fibronectin), proteoglycans, and other proteins.
Provides structural support, cell adhesion, and signaling.
Integrins connect the ECM to the cytoskeleton.

Endosymbiotic Theory (CED Unit 2)

Mitochondria and chloroplasts evolved from free-living prokaryotes that were engulfed by ancestral Eukaryotic cells.

Evidence:

Both have their own circular DNA (similar to bacterial DNA).
Both have their own ribosomes (70S, similar to bacterial ribosomes).
Both reproduce by binary fission (independent of the cell).
Both have double membranes (the inner membrane is the original prokaryotic membrane).
Both are similar in size to prokaryotes.

Cell Signaling (CED Unit 4)

Steps in Cell Signaling

Reception: A signaling molecule (ligand) binds to a receptor protein.

Intracellular receptors: Ligand must cross the membrane (e.g., steroid hormones).
Cell-surface receptors: Ligand binds to the extracellular domain (e.g., GPCRs, receptor tyrosine kinases, ligand-gated ion channels).

Transduction: The signal is relayed and amplified through a signal transduction pathway.

Often involves second messengers (cAMP, $\mathrm{Ca^{2+}$ , $\mathrm{IP_3$ DAG).
Protein kinases phosphorylate target proteins, activating or deactivating them.
Protein phosphatases remove phosphate groups, reversing kinase action.
Cascades amplify the signal (one activated kinase activates many downstream targets).

Response: The signal triggers a cellular response (gene expression, enzyme activation, cytoskeletal rearrangement).

G-Protein Coupled Receptors (GPCRs)

Ligand binds to GPCR.
GPCR activates a G-protein (exchanges GDP for GTP).
Activated G-protein activates an effector enzyme (e.g., adenylyl cyclase).
Effector produces a second messenger (e.g., cAMP from ATP).
Second messenger activates protein kinases in a phosphorylation cascade.

Apoptosis

Programmed cell death, critical for development and homeostasis. Key regulators:

Bcl-2 family: Anti-apoptotic (Bcl-2) and pro-apoptotic (Bax, Bak) proteins.
Caspases: Proteases that cleave cellular proteins during apoptosis.
Signals include DNA damage, external signals (Fas ligand), and internal stress.

Worked Example: The epinephrine signaling pathway.

Epinephrine (ligand) binds to a GPCR on a liver cell.
The GPCR activates a G-protein, which activates adenylyl cyclase.
Adenylyl cyclase converts ATP to cAMP (second messenger).
CAMP activates protein kinase A (PKA).
PKA phosphorylates enzymes that activate glycogen phosphorylase.
Glycogen phosphorylase converts glycogen to glucose-6-phosphate.
Glucose is released into the blood, raising blood glucose levels.

This pathway amplifies the signal: one epinephrine molecule can activate many G-proteins, each of Which produces many cAMP molecules, each of which activates many PKA enzymes.

Receptor Tyrosine Kinases (RTKs)

RTKs are another major class of cell-surface receptors that play important roles in growth and Division signaling.

A signaling molecule (e.g., a growth factor) binds to the extracellular domain of the RTK.
Two RTKs dimerize (come together in pairs).
Each RTK phosphorylates the tyrosine residues on the tail of the other RTK (autophosphorylation).
The activated receptor can now activate intracellular relay proteins, triggering a phosphorylation cascade (often involving the Ras protein and a MAP kinase cascade).
The final response is often the activation of transcription factors that alter gene expression.

Why RTKs are important: Mutations that cause RTKs to be constitutively active (always “on”) are Associated with many cancers. For example, HER2 is an RTK that is overexpressed in some breast Cancers. The drug Herceptin (trastuzumab) targets HER2.

Intracellular Receptors

Steroid hormones (e.g., cortisol, estrogen, testosterone) and thyroid hormones are small and Hydrophobic enough to diffuse directly through the plasma membrane. They bind to intracellular Receptors in the cytoplasm or nucleus.

The hormone diffuses through the plasma membrane.
It binds to a receptor protein, forming a hormone-receptor complex.
The complex acts as a transcription factor, binding to specific DNA sequences (hormone response elements) in the promoter region of target genes.
This activates or represses transcription of specific genes.
The response is slower than cell-surface receptor signaling because it requires changes in gene expression.

Common Pitfalls

Confusing the functions of rough and smooth ER. Rough ER is for protein synthesis; smooth ER is for lipid synthesis and detoxification.
Thinking lysosomes are only for digestion. They also play roles in autophagy and apoptosis.
Confusing osmosis direction. Water moves from hypotonic (low solute) to hypertonic (high solute).
Misidentifying the site of cellular respiration. It occurs in the mitochondria, not the chloroplasts.
Confusing the cis and trans faces of the Golgi. Cis receives from ER; trans ships to destinations.
Thinking all cells have a cell wall. Animal cells do not have cell walls.
Confusing active and passive transport. Active transport requires energy (ATP) and moves against the gradient; passive transport does not require energy and moves down the gradient.
Forgetting the role of the cytoskeleton. Microtubules are for intracellular transport and chromosome movement; microfilaments are for cell motility and cytokinesis.
Confusing integrins and cadherins. Integrins connect cells to the ECM; cadherins connect cells to each other.
Thinking signal transduction always activates a response. Some signals inhibit responses; the outcome depends on the specific pathway and cell type.
Confusing GPCRs and RTKs. GPCRs use G-proteins and second messengers; RTKs dimerize and autophosphorylate, often activating the MAP kinase cascade.
Thinking all second messengers are the same. cAMP, $\mathrm{Ca^{2+}$ , $\mathrm{IP_3$ And DAG have different roles and activate different downstream pathways.
Confusing exocytosis and endocytosis direction. Exocytosis releases materials out of the cell; endocytosis brings materials in.
Forgetting that the cell membrane is selectively permeable, not fully permeable. Only small, nonpolar molecules can diffuse freely; larger or polar molecules need transport proteins.
Misidentifying the roles of the nucleolus. The nucleolus produces rRNA and assembles ribosomal subunits, not mRNA or tRNA.

Practice Questions

Compare and contrast prokaryotic and eukaryotic cells in terms of size, organelles, DNA organization, and ribosomes.
A red blood cell is placed in a hypertonic solution. Describe what happens to the cell and explain why.
Trace the path of a secretory protein from synthesis to export, naming all organelles and transport steps involved.
Explain how the structure of the phospholipid bilayer relates to its function as a selectively permeable barrier.
Describe three pieces of evidence supporting the endosymbiotic theory.
Explain the role of second messengers in signal transduction pathways. Why are they important?
Compare the structure and function of microfilaments, intermediate filaments, and microtubules.
Explain how G-protein coupled receptors transduce an extracellular signal into an intracellular response, using the epinephrine signaling pathway as an example.
A cell has a solute concentration of 0.3 M. It is placed in a 0.1 M solution. Predict the direction of water movement and explain your reasoning.
Describe the structure and function of the extracellular matrix in animal cells. How do integrins connect the ECM to the cytoskeleton?
Explain why cholesterol is important in cell membranes and how it affects membrane fluidity at different temperatures.
Compare phagocytosis, pinocytosis, and receptor-mediated endocytosis in terms of mechanism and the types of substances transported.
Explain how apoptosis differs from necrosis and why apoptosis is important for development.
A plant cell is placed in a hypertonic solution. Describe what happens to the cell and explain why the result is different from what would happen to an animal cell.
Explain the roles of protein kinases and protein phosphatases in signal transduction pathways. How do they work together to regulate cellular responses?
Describe how the structure of a mitochondrion is adapted for its function in ATP production.
A researcher adds a drug that blocks the Na+/K+ pump. Explain the immediate and long-term effects on the cell.
Explain how the nuclear pore regulates the transport of molecules between the nucleus and the cytoplasm.
Compare the structure and function of the smooth ER in liver cells vs. Muscle cells.
Explain the concept of signal amplification in a phosphorylation cascade, using a numerical example.
Explain the mechanism of receptor tyrosine kinase (RTK) signaling and describe how a mutation that causes constitutive RTK activation can lead to cancer.
Compare GPCR signaling and steroid hormone signaling in terms of the location of the receptor, the speed of the response, and the mechanism of action.
Describe how cholera toxin disrupts normal cell signaling and explain the physiological consequences for the patient.
A researcher labels the proteins on the surface of a cell with a fluorescent tag. After endocytosis, the tag is found inside lysosomes. Explain the pathway the tagged proteins took from the cell surface to the lysosomes.
Explain why the Na+/K+ pump is described as an electrogenic pump and discuss its importance for maintaining the resting membrane potential.

Review: Detailed Comparison of Transport Mechanisms

Understanding the nuances of membrane transport is critical. Here is a more detailed analysis of Each mechanism:

Simple diffusion: Small, nonpolar molecules (e.g., $\mathrm{O_2$ , $\mathrm{CO_2$ Steroid Hormones) diffuse directly through the phospholipid bilayer. The rate depends on the concentration Gradient, temperature, and the surface area of the membrane. No energy or transport protein is Required.

Facilitated diffusion: Polar molecules and ions (e.g., glucose, amino acids, $\mathrm{Na^+$ $\mathrm{K^+$ ) cannot cross the hydrophobic interior of the bilayer and require transport proteins. Channel proteins form hydrophilic pores; carrier proteins undergo conformational changes to shuttle Molecules across. Like simple diffusion, facilitated diffusion is passive (no energy required) and Moves substances down their concentration gradient.

Osmosis: The diffusion of water across a selectively permeable membrane. Water moves from a Region of higher water potential (lower solute concentration) to a region of lower water potential (higher solute concentration). Aquaporins (channel proteins specific to water) facilitate rapid Osmosis in cells that need to regulate water movement quickly (e.g., kidney cells).

Active transport: Moves substances against their concentration gradient, requiring energy from ATP hydrolysis. The $\mathrm{Na^+/\mathrm{K^+$ pump is the classic example: it uses one ATP to Pump 3 $\mathrm{Na^+$ out and 2 $\mathrm{K^+$ in against their gradients. This pump is essential For maintaining the resting membrane potential, which is critical for nerve impulse transmission and Muscle contraction.

Cotransport (secondary active transport): Uses the energy stored in an ion gradient (established By primary active transport) to transport another substance against its gradient. For example, the $\mathrm{Na^+$ -glucose cotransporter in the small intestine uses the $\mathrm{Na^+$ gradient (maintained by the $\mathrm{Na^+/\mathrm{K^+$ pump) to transport glucose into the cell against its Concentration gradient.

Bulk transport: Large molecules or particles are transported via vesicles. Endocytosis brings Materials into the cell (phagocytosis for solid particles, pinocytosis for liquids, Receptor-mediated endocytosis for specific ligands). Exocytosis releases materials from the cell (e.g., secretion of hormones or neurotransmitters). Both require ATP.

Worked Example: Comparing the effects of different transport mechanisms on a cell.

A cell is placed in a medium containing 10 mM glucose and 5 mM amino acids. Inside the cell, glucose Is at 2 mM and amino acids are at 10 mM.

Glucose enters the cell by facilitated diffusion (from 10 mM to 2 mM, down the concentration Gradient). No energy is required.

Amino acids exit the cell by facilitated diffusion (from 10 mM to 5 mM, down the concentration Gradient). No energy is required.

If the cell needs to accumulate amino acids to a concentration higher than 5 mM (e.g., for protein Synthesis), it must use active transport (or a cotransporter that uses the $\mathrm{Na^+$ gradient) To move amino acids against their concentration gradient. This requires ATP (directly or Indirectly).

Review: Prokaryotic Cell Structures in Detail

Capsule: A slimy, gelatinous layer outside the cell wall in some bacteria. It protects against Desiccation and helps the bacterium evade the host immune system by making it harder for phagocytes To engulf it.

Pili: Short, hair-like appendages on the surface of many bacteria. They are involved in Attachment to surfaces (including host tissues) and in conjugation (a form of horizontal gene Transfer where a pilus connects two bacterial cells and allows DNA to be transferred).

Flagella: Long, whip-like appendages used for locomotion. They rotate like propellers, powered By a proton gradient across the bacterial membrane (not by ATP directly).

Plasmids: Small, circular DNA molecules separate from the main bacterial chromosome. They often Carry genes for antibiotic resistance and can be transferred between bacteria through conjugation. Plasmids are widely used in genetic engineering as vectors to carry foreign DNA into host cells.

Nucleoid: The region in the cytoplasm where the circular bacterial chromosome is located. Unlike The eukaryotic nucleus, it is not surrounded by a membrane.

Worked Example: Antibiotic resistance and plasmids.

A bacterium carries a plasmid with a gene for beta-lactamase, an enzyme that breaks down penicillin. When penicillin is present, the bacterium survives because it produces beta-lactamase. Through Conjugation, the plasmid can be transferred to other bacteria, spreading resistance even without Exposure to the antibiotic. This is why overuse of antibiotics accelerates the spread of resistance. The plasmid is replicated independently of the main chromosome, so even a single copy confers Resistance.

Review: Plasmolysis and Turgor Pressure

When a plant cell is placed in a hypertonic solution, water leaves the cell by osmosis. The cell Membrane pulls away from the cell wall, a process called plasmolysis. The cell becomes flaccid.

When a plant cell is placed in a hypotonic solution, water enters by osmosis. The cytoplasm swells And presses against the rigid cell wall, creating turgor pressure. The cell is described as Turgid. Turgor pressure provides structural support to non-woody plant tissues. When plants lose Turgor (e.g., during drought), they wilt.

Worked Example: Why plant cells do not burst in hypotonic solutions.

When an animal cell is placed in a hypotonic solution, it swells and may burst (lyse) because there Is no cell wall to constrain expansion. A plant cell, however, has a rigid cellulose cell wall that Exerts an inward pressure (wall pressure) as the cell expands. Water continues to enter until the Turgor pressure equals the osmotic pressure, at which point there is no net water movement. The cell Is turgid but intact. This is why plants rely on turgor pressure for support.

Worked Example: Calculating water potential and predicting osmosis.

A plant cell has a solute potential of $-600$ kPa and a pressure potential of $300$ kPa. The cell is Placed in a solution with a water potential of $-200$ kPa.

Cell water potential: $\psi = \psi_s + \psi_p = -600 + 300 = -300$ kPa.

Since the cell water potential ( $-300$ kPa) is higher (less negative) than the solution water Potential ( $-200$ kPa), water will move from the cell into the solution (from higher to lower water Potential). The cell will lose water and become plasmolysed.

Review: The Endomembrane System

The endomembrane system is a network of membranes and organelles that work together to modify, Package, and transport proteins and lipids. It includes:

Nuclear envelope: Controls transport between nucleus and cytoplasm.
Endoplasmic reticulum: Synthesis (rough ER for proteins, smooth ER for lipids) and initial modification.
Golgi apparatus: Further modification, sorting, and packaging.
Vesicles: Transport between organelles and to the plasma membrane.
Plasma membrane: Final destination for many proteins; site of exocytosis.
Lysosomes: Digestion and recycling of cellular components.

The endomembrane system does not include mitochondria, chloroplasts, or peroxisomes, which are Considered semi-autonomous organelles (they have their own DNA and replicate independently).

Worked Example: Tracing a lysosomal enzyme.

A lysosomal enzyme (a hydrolytic enzyme) is synthesised in the same way as a secretory protein, but Instead of being secreted, it is tagged with a mannose-6-phosphate marker in the Golgi apparatus. This marker is recognised by receptors on the Golgi membrane, and the enzyme is packaged into Vesicles that fuse with lysosomes. Without this tagging system, the enzyme would be secreted from The cell. This demonstrates how the Golgi apparatus sorts proteins to different destinations.

Review: Junctions Between Cells

In multicellular organisms, cells are connected by specialised junctions:

Junction Type	Function	Found In
Tight junctions	Form seals between adjacent cells, preventing leakage	Epithelial cells (intestine, kidney)
Desmosomes	Strong anchoring junctions, like rivets	Skin, heart muscle
Gap junctions	Channels between cells for direct communication	Heart muscle, embryos

Tight junctions prevent substances from passing between cells (forcing them through the cells Themselves, which can regulate transport). Desmosomes provide mechanical strength to tissues under Stress. Gap junctions allow ions and small molecules to pass directly between cells, enabling rapid Coordination (e.g., synchronous contraction of heart muscle cells).

Worked Example: Why gap junctions are essential in cardiac muscle.

Cardiac muscle cells (cardiomyocytes) are connected by gap junctions that form intercalated discs. These gap junctions allow ions (especially $\mathrm{Ca^{2+}$ ) to flow freely between adjacent Cells, so an action potential generated in one cell can spread rapidly to all connected cells. This Ensures that the entire heart muscle contracts as a coordinated unit (a functional syncytium). Without gap junctions, the heart would not beat in a synchronised manner, leading to ineffective Pumping and potential arrhythmias.

Review: Plant Cell Structures in Detail

Plant cells have several structures that are not found in animal cells:

Cell wall: Made of cellulose microfibrils embedded in a matrix of hemicellulose and pectin. Cellulose is a polysaccharide consisting of long chains of $\beta$ -glucose molecules linked by $\beta$ -1,4-glycosidic bonds. The microfibrils are arranged in layers, with each layer running at a Slightly different angle to the one below (cross-laminated structure), giving the wall great tensile Strength. The cell wall is fully permeable to water and dissolved substances.

Middle lamella: A thin layer of pectin that cements adjacent plant cells together. Pectin is a Polysaccharide that can be broken down by enzymes (pectinases) during fruit ripening, which is why Ripe fruits become softer.

Plasmodesmata: Narrow channels through the cell wall that connect the cytoplasm of adjacent Plant cells. They allow the transport of small molecules (sugars, amino acids, ions) and signalling Molecules between cells, facilitating communication and coordination.

Central vacuole: A large, fluid-filled organelle that can occupy up to 90% of the cell volume in Mature plant cells. It is surrounded by a membrane called the tonoplast. Functions include storage Of water, ions, nutrients, and waste products; maintaining turgor pressure; contributing to cell Growth; storing pigments (anthocyanins in flowers); and storing defensive compounds (toxins that Deter herbivores).

Chloroplasts: The site of photosynthesis. Chloroplasts have a double membrane, with an internal System of thylakoid membranes stacked into grana, surrounded by stroma. Like mitochondria, Chloroplasts have their own circular DNA and ribosomes (70S), supporting the endosymbiotic theory.

Peroxisomes: Small organelles that contain oxidative enzymes (e.g., catalase). They break down Fatty acids by beta-oxidation and detoxify harmful by-products of metabolism, such as hydrogen Peroxide ( $\mathrm{H_2\mathrm{O_2$ ), which catalase converts to water and oxygen.

Review: Microscopy Techniques

Light microscopy: Uses visible light and glass lenses. Maximum resolution approximately 200 nm. Can observe living cells. Limited magnification ( up to $\times$ 1500). Staining increases Contrast: methylene blue stains DNA blue; iodine stains starch blue-black.

Electron microscopy: Uses a beam of electrons and electromagnetic lenses. Maximum resolution Approximately 0.2 nm. Much higher magnification (up to $\times$ 2,000,000). Cannot observe living Specimens.

TEM vs SEM:

TEM: Electrons pass through thin sections. Produces 2D images of internal structure.
SEM: Electrons bounce off the surface. Produces 3D images of surface features.

Magnification calculation:

$\mathrm{Magnification = \frac{\mathrm{Image size}{\mathrm{Actual size}$

Worked Example: A mitochondrion measures 8 mm in an electron micrograph at $\times$ 10,000. Actual size $= 8 / 10,000 = 0.0008$ mm $= 0.8$ $\mu$ M. This is within the expected Range (0.5—10 $\mu$ M).

Worked Example: Converting between units for magnification calculations.

A cell appears 4.5 cm wide in a light micrograph. The actual cell width is 30 $\mu$ M.

Convert to the same units: 4.5 cm $= 45$ mm $= 45,000$ $\mu$ M.

Magnification $= 45,000 / 30 = \times 1,500$ .

This is at the limit of light microscopy, which has a maximum useful magnification of approximately $\times$ 1,500 (beyond this, the image becomes blurry due to the resolution limit of approximately 200 nm).

Review: Endocytosis and Exocytosis

Endocytosis: The cell membrane folds inward to form a vesicle, engulfing external material.

Phagocytosis (“cell eating”): Large solid particles are engulfed. The vesicle fuses with a lysosome for digestion.
Pinocytosis (“cell drinking”): Small droplets of extracellular fluid are taken in.
Receptor-mediated endocytosis: Specific molecules bind to receptors, cluster in coated pits, and are internalised in clathrin-coated vesicles.

Exocytosis: Vesicles fuse with the plasma membrane, releasing contents outside the cell. Used For secretion of hormones and neurotransmitters.

Worked Example: How cholera toxin exploits cell signalling.

Cholera toxin binds to receptors on intestinal cells and is taken up by receptor-mediated Endocytosis. Inside, the toxin activates a G-protein that constitutively activates adenylyl cyclase, Producing excessive cAMP. Elevated cAMP activates CFTR chloride channels, causing massive chloride Secretion. Water follows by osmosis, producing severe watery diarrhoea.

Worked Example: LDL cholesterol uptake by receptor-mediated endocytosis.

LDL (low-density lipoprotein) particles carry cholesterol in the blood. LDL receptors on the cell Surface bind LDL particles. The receptor-LDL complex clusters in coated pits and is internalised by Receptor-mediated endocytosis. Inside the cell, the vesicle fuses with an endosome, where the LDL Dissociates from the receptor. The LDL is delivered to lysosomes, where the cholesterol is released. The receptors are recycled back to the cell surface. Mutations in the LDL receptor gene cause Familial hypercholesterolemia, where LDL cannot be taken up efficiently, leading to very high blood Cholesterol and early heart disease.

Review: The Cytoskeleton and Cell Motility

Actin and myosin: In muscle cells, actin and myosin filaments interact to produce contraction. In non-muscle cells, they are involved in cytokinesis (contractile ring), cell crawling, and Phagocytosis.

Microtubule-based transport: Kinesin moves towards the plus end (cell periphery); dynein moves Towards the minus end (centrosome). Both use ATP to power movement, taking steps of approximately 8 Nm per ATP hydrolysed.

Worked Example: Taxol as a chemotherapy drug.

Taxol stabilises microtubules, preventing depolymerisation. During cell division, the mitotic Spindle cannot function, arresting the cell cycle at metaphase. Rapidly dividing cancer cells are Most affected, but normal dividing cells (hair follicles, immune cells) are also impacted, causing Side effects.

Worked Example: Colchicine and its effect on cell division.

Colchicine is another drug that affects microtubules, but in the opposite way to taxol. Colchicine Binds to tubulin and prevents microtubule polymerisation. Without functional microtubules, the Mitotic spindle cannot form, and cells are arrested in prometaphase. Colchicine has been used to Treat gout (by inhibiting neutrophil motility) and in cancer research (to arrest cells at metaphase For chromosome analysis — karyotyping).

Review: Viral Structure and Replication

Viruses are not considered living organisms because they cannot reproduce independently, do not Carry out metabolic processes, and have no cellular structure. However, they have genetic material (DNA or RNA) enclosed in a protein coat (capsid), and some have a lipid envelope derived from the Host cell membrane.

Viral replication cycle (lytic):

Attachment: The virus binds to specific receptors on the host cell surface.
Entry: The virus enters the cell by endocytosis or membrane fusion.
Replication: The viral genetic material is replicated using the host cell’s machinery.
Assembly: New viral particles are assembled from the replicated components.
Release: The host cell lyses, releasing new viruses to infect other cells.

Lysogenic cycle (temperate phages): Some viruses (e.g., bacteriophage lambda) can integrate Their DNA into the host chromosome as a prophage. The prophage is replicated along with the host DNA And is passed to daughter cells during cell division. (e.g., stress), the Prophage can be excised and enter the lytic cycle.

Worked Example: Why antibiotics do not work against viruses.

Antibiotics target structures and processes that are specific to bacteria (e.g., peptidoglycan cell Wall, 70S ribosomes, bacterial enzymes). Viruses do not have these structures; they use the host Cell’s machinery to replicate. Therefore, antibiotics are ineffective against viral infections. Antiviral drugs target viral-specific processes (e.g., reverse transcriptase inhibitors for HIV).

Worked Example: HIV replication and antiretroviral drugs.

HIV is a retrovirus that contains RNA as its genetic material and reverse transcriptase, an enzyme That converts RNA into DNA. The replication cycle involves:

HIV binds to CD4 receptors (and co-receptors CCR5 or CXCR4) on helper T cells.
The virus enters the cell, and reverse transcriptase converts viral RNA into DNA.
The viral DNA integrates into the host chromosome (integrase).
The host cell transcribes the viral DNA into mRNA and new viral RNA.
New viral proteins are synthesised and assembled into new viral particles.
New viruses bud from the host cell membrane.

Antiretroviral drugs target different stages: reverse transcriptase inhibitors (AZT), protease Inhibitors (block viral protein processing), integrase inhibitors (block DNA integration), and entry Inhibitors (block binding to CD4/co-receptors). Combination antiretroviral therapy (cART) uses Multiple drugs to prevent resistance.

Review: Detailed Comparison of Cell Junctions

Feature	Tight Junctions	Desmosomes	Gap Junctions
Structure	Fusion of outer membrane layers	Disc-shaped plaques with intermediate filaments	Protein channels (connexins)
Function	Seal between cells	Mechanical adhesion	Direct communication
What passes	Nothing (seal)	Mechanical stress	Ions, small molecules, signals
Location examples	Intestinal epithelium	Skin, heart muscle	Cardiac muscle, embryonic tissue

Review: Summary Table of Organelle Functions

Organelle	Function	Found In
Nucleus	DNA storage, transcription, ribosome assembly	All eukaryotes
Mitochondria	Aerobic respiration, ATP production	All eukaryotes
Chloroplasts	Photosynthesis	Plants, algae
Rough ER	Protein synthesis, folding, modification	All eukaryotes
Smooth ER	Lipid synthesis, detoxification, Ca $^{2+}$ storage	All eukaryotes
Golgi apparatus	Modification, sorting, packaging of proteins/lipids	All eukaryotes
Lysosomes	Intracellular digestion, autophagy	Animals, some protists
Peroxisomes	Fatty acid oxidation, detoxification of H $_2$ O $_2$	All eukaryotes
Vacuole	Storage, turgor pressure	Plants, protists
Cytoskeleton	Support, movement, intracellular transport	All eukaryotes
Cell wall	Structural support, protection	Plants, fungi, bacteria
Centrioles	Organise microtubules, mitotic spindle	Animals
Plasmodesmata	Intercellular communication in plants	Plants

Practice Problems

Question 1: Predicting the effect of a metabolic inhibitor on a secretory protein

A researcher adds brefeldin A to pancreatic cells. This drug blocks the transport of vesicles from The ER to the Golgi apparatus. Describe the effect on insulin production and explain which Organelles would accumulate the insulin.

Answer

Insulin would be synthesised on ribosomes bound to the rough ER and enter the ER lumen, where it Would begin to fold. However, transport vesicles could not carry insulin from the ER to the Golgi Apparatus. The insulin would accumulate inside the rough ER, causing it to dilate. The Golgi Apparatus would not receive the protein, so no secretory vesicles would form and no insulin would be Exported from the cell. The cell would still produce mRNA and translate the protein, but the Secretory pathway would be blocked at the ER-to-Golgi transport step.

Question 2: Comparing transport mechanisms in different conditions

A cell has an internal $\mathrm{K^+$ concentration of $140 \mathrm{ mM$ and an external $\mathrm{K^+$ concentration of $5 \mathrm{ mM$ . The membrane potential is $-70 \mathrm{ mV$ (inside negative). Predict the direction of $\mathrm{K^+$ movement through (a) a $\mathrm{K^+$ Leak channel and (b) the $\mathrm{Na^+/\mathrm{K^+$ pump, and explain your reasoning.

Answer

(a) Through a $\mathrm{K^+$ leak channel (passive transport): $\mathrm{K^+$ would move out of the Cell. The concentration gradient favours outward movement (140 mM inside vs 5 mM outside). The Electrical gradient also favours outward movement because the inside of the cell is negative, Repelling the positive $\mathrm{K^+$ ions. Both gradients drive $\mathrm{K^+$ out of the cell.

(b) Through the $\mathrm{Na^+/\mathrm{K^+$ pump (active transport): The pump moves $\mathrm{K^+$ Into the cell against its concentration gradient. This requires ATP hydrolysis. The pump Continuously transports $2 \mathrm{ K^+$ in and $3 \mathrm{ Na^+$ out per ATP consumed, Maintaining the resting membrane potential and the concentration gradients.

Question 3: Endosymbiotic theory and antibiotic evidence

Explain how the observation that the antibiotic streptomycin inhibits protein synthesis in both Bacteria and mitochondria, but not in the cytoplasm of eukaryotic cells, provides evidence for the Endosymbiotic theory.

Answer

Streptomycin targets the 70S ribosomes found in prokaryotes. Mitochondria also have 70S ribosomes, While eukaryotic cytoplasmic ribosomes are 80S. The fact that streptomycin inhibits mitochondrial Protein synthesis but not cytoplasmic protein synthesis in eukaryotic cells demonstrates that Mitochondrial ribosomes are prokaryotic in nature. This supports the endosymbiotic theory, which Proposes that mitochondria evolved from free-living prokaryotes that were engulfed by an ancestral Eukaryotic cell. The prokaryotic ribosomes were retained, along with circular DNA, binary fission, And a double membrane.

Question 4: Signal transduction and cholera toxin

Cholera toxin modifies a G-protein so that it cannot hydrolyse GTP to GDP. Explain the downstream Effects on the cAMP pathway in intestinal cells and why this leads to severe diarrhoea.

Answer

Normally, a G-protein is activated when it binds GTP and is inactivated when it hydrolyses GTP to GDP. Cholera toxin prevents GTP hydrolysis, locking the G-protein in its active state. The Constitutively active G-protein continuously activates adenylyl cyclase, which produces excessive CAMP. Elevated cAMP activates protein kinase A (PKA), which phosphorylates and opens CFTR chloride Channels. Massive amounts of $\mathrm{Cl^-$ are secreted into the intestinal lumen. $\mathrm{Na^+$ And water follow by osmosis, producing large volumes of watery diarrhoea. This demonstrates how Disrupting the normal “off” switch in a signaling pathway can have severe physiological Consequences.

Question 5: Water potential and plant cell behaviour

A plant cell has a solute potential of $-800 \mathrm{ kPa$ and a pressure potential of $400 \mathrm{ kPa$ . The cell is placed in a solution with a water potential of $-500 \mathrm{ kPa$ . Calculate the cell’s water potential and predict the direction of water Movement.

Answer

Cell water potential: $\psi = \psi_s + \psi_p = -800 + 400 = -400 \mathrm{ kPa$ .

The cell water potential ( $-400 \mathrm{ kPa$ ) is higher (less negative) than the solution water Potential ( $-500 \mathrm{ kPa$ ). Water moves from higher water potential to lower water potential, So water will move from the cell into the surrounding solution. The cell will lose water, the Pressure potential will decrease, and the cell may become plasmolysed if enough water is lost.

Worked Examples

Example 1: Comparing mitosis and meiosis

Compare mitosis and meiosis in terms of the number of divisions, daughter cells produced, and genetic variation.

Solution:

Feature	Mitosis	Meiosis
Divisions	1	2
Daughter cells	2	4
Chromosome number	Same as parent	Half of parent
Genetic variation	No	Yes (crossing over, independent assortment)
Function	Growth, repair, asexual reproduction	Production of gametes

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