Cell Structure

Microscopes and Cell Size

Microscopy is essential for studying cell structure and function. Different types of microscopes provide varying levels of detail and allow observation of living or nonliving specimens.

• Light Microscope: Views living cells; resolution ~200 nm.

• Transmission Electron Microscope (TEM): Reveals internal details in thin sections; uses nonliving specimens.

• Scanning Electron Microscope (SEM): Shows surface detail; nonliving specimens.

• Fluorescence Microscopy: Locates labeled molecules within cells.

• Magnification: Enlarges images; Resolution: Distinguishes nearby points.

All cells share basic features: plasma membrane, cytosol, DNA, and ribosomes.

• Prokaryotes: No membrane-bound nucleus; DNA in nucleoid; includes Bacteria and Archaea.

• Eukaryotes: Membrane-bound nucleus and organelles.

Cell size and shape affect surface area-to-volume ratio, impacting exchange rates and metabolic demand.

• Surface Area (SA):

• Volume (V):

• SA:V Ratio:

• Doubling side length halves SA:V ratio.

Organelles and Protein Export

Eukaryotic cells contain specialized organelles for distinct functions. Both plant and animal cells share many organelles, but some are unique.

• Nucleus: Stores DNA; nucleolus assembles ribosomal subunits.

• Ribosomes: Translate mRNA into protein.

• Rough ER: Folds/processes secreted and membrane proteins.

• Smooth ER: Synthesizes lipids, detoxifies, stores Ca2+.

• Golgi Apparatus: Modifies and sorts proteins.

• Mitochondria: Generate most ATP via aerobic respiration.

• Peroxisomes: Oxidize molecules, break down H2O2.

• Vesicles: Transport cargo.

• Plant-specific: Cellulose wall, large central vacuole (turgor, storage, digestion), chloroplasts.

• Animal-specific: Lysosomes (acidic digestion), centrosomes with centrioles.

Protein export pathway:

1. Ribosome at rough ER

2. ER

3. Vesicle

4. Cis Golgi

5. Trans Golgi

6. Secretory vesicle

7. Plasma membrane

8. Exocytosis

Endomembrane system: Nuclear envelope, ER, Golgi, vesicles/endosomes, lysosomes, vacuoles, plasma membrane. Mitochondria, chloroplasts, peroxisomes, and ribosomes are outside this system.

Cytoskeletal Fibers and Cell Junctions

The cytoskeleton provides structural support and facilitates movement.

• Actin Microfilaments: Contraction (with myosin), cell crawling, cleavage furrow.

• Intermediate Filaments: Tensile strength, nuclear lamina, desmosome attachment.

• Tubulin Microtubules: Transport tracks, mitotic spindle, cilia/flagella (9+2 arrangement).

Cell junctions connect cells and regulate communication:

• Tight Junctions: Seal leakage between animal cells.

• Desmosomes: Anchor cells against mechanical stress.

• Gap Junctions: Allow ions/small molecules to pass between animal cells.

• Plasmodesmata: Channels between plant cells through cell walls.

Membrane Structure and Function

Fluid Mosaic Model and Membrane Fluidity

Biological membranes are dynamic structures composed of lipids and proteins.

• Mosaic: Diverse proteins and lipids form a dynamic membrane.

• Amphipathic: Molecules have hydrophilic and hydrophobic regions.

• Phospholipids: Heads face water; tails face inward.

• Permeability: Small nonpolar molecules (O2, CO2) cross easily; ions and polar solutes require proteins.

Factors affecting fluidity:

• Higher temperature, more cis-unsaturated tails, shorter tails = more fluid.

• Lower temperature, more saturated tails, longer tails = less fluid.

• Cholesterol: Buffers fluidity; restrains motion when warm, prevents tight packing when cool.

Membrane proteins:

• Integral: Embedded; transmembrane proteins span bilayer.

• Peripheral: Attached to membrane surface.

• Channel: Selective pore, sometimes gated.

• Carrier: Binds solute, changes shape; can be passive or active.

Transport Direction and Energy

Membranes regulate transport based on direction and energy requirements.

Ion direction combines concentration and electrical gradients. Carrier saturation leads to a plateau in transport rate.

Tonicity and Bulk Transport

Tonicity compares solute concentration outside and inside the cell, affecting water movement.

• Hypotonic: Water enters; animal cells swell/lyse, plant cells become turgid.

• Hypertonic: Water exits; animal cells shrink, plant cells may plasmolyze.

• Isotonic: No sustained net water movement; plant cells often flaccid.

Bulk transport mechanisms:

• Exocytosis: Vesicle fuses with membrane, releases cargo.

• Phagocytosis: Engulfs particles/cells.

• Pinocytosis: Takes up fluid.

• Receptor-mediated endocytosis: Selectively concentrates bound ligands.

Metabolism and Enzymes

Key Terms and Concepts

Metabolism includes all chemical reactions in cells, divided into catabolic and anabolic pathways.

• Catabolic: Breakdown, releases energy.

• Anabolic: Building, requires energy.

• Kinetic Energy: Energy of motion.

• Potential Energy: Stored energy.

• Open System: Exchanges matter and energy.

• Closed System: Exchanges energy, not matter.

• Isolated System: Exchanges neither.

• Exergonic: ; spontaneous.

• Endergonic: ; requires energy input.

• Activation Energy: Barrier to reaction.

Thermodynamics and ATP

Cells obey the laws of thermodynamics and use ATP as the main energy currency.

• First Law: Energy is conserved.

• Second Law: Spontaneous processes increase total entropy.

• Cells build local order by importing resources and exporting waste/heat.

• ATP hydrolysis:

• Coupled reactions: Net must be negative for favorability.

Enzyme Function and Regulation

Enzymes are biological catalysts that speed up reactions by lowering activation energy.

• Active site: Substrate-binding/catalytic region.

• Induced fit: Binding changes enzyme shape.

• Enzymes do not change or equilibrium position.

• Temperature and pH affect enzyme activity.

Regulation mechanisms:

• Competitive Inhibitor: Competes at active site; reversible with more substrate.

• Allosteric Regulator: Binds elsewhere; can inhibit or activate.

• Noncompetitive Inhibitor: Lowers maximum rate; cannot be overcome with substrate.

• Irreversible Inhibitor: Permanently inactivates enzyme.

• Cofactor: Nonprotein helper; inorganic (e.g., Mg2+) or organic (e.g., NAD+).

• Cooperativity: Binding at one subunit affects others.

• Negative Feedback: Product inhibits early pathway step.

Cellular Respiration and Fermentation

Redox Reactions and Stages

Cellular respiration extracts energy from glucose via redox reactions in four main stages.

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• NAD+ is reduced to NADH, which carries electrons.

Typical aerobic total: 30-32 ATP per glucose.

Proton Gradient and Oxygen

Electron transport chain (ETC) and chemiosmosis generate most ATP.

• NADH/FADH2 donate electrons; energy pumps H+ from matrix to intermembrane space.

• O2 is the final electron acceptor; water forms.

• ATP synthase: H+ returns to matrix, driving .

• Substrate-level phosphorylation: Direct phosphate transfer to ADP.

• Oxidative phosphorylation: ETC establishes gradient; chemiosmosis powers ATP synthase.

Fermentation and Regulation

Fermentation allows glycolysis to continue in the absence of oxygen by regenerating NAD+.

• Net 2 ATP per glucose from glycolysis; fermentation adds none.

• Lactate fermentation: Pyruvate → lactate (no CO2).

• Alcohol fermentation: Pyruvate → acetaldehyde + CO2 → ethanol.

• Facultative anaerobe: Grows with or without O2.

• Obligate anaerobe: Cannot grow in O2.

• Anaerobic respiration uses ETC with non-O2 acceptor; fermentation uses no ETC.

• High ATP/citrate slows glycolysis; AMP promotes it.

Photosynthesis

Locations and Electron Flow

Photosynthesis occurs in chloroplasts, with light reactions in thylakoid membranes and the Calvin cycle in the stroma.

• Light Reactions: Use light and H2O; produce ATP, NADPH, O2.

• Released O2 comes from water.

• Calvin Cycle: Uses CO2, ATP, NADPH; produces net G3P.

Linear electron flow:

• H2O → PSII P680 → ETC → PSI P700 → NADP+ (becomes NADPH).

• Water splitting replaces PSII electrons and releases O2.

• H+ accumulates in lumen; returns to stroma through ATP synthase.

Contrast: Mitochondria pump H+ from matrix to intermembrane space; chloroplasts pump H+ into lumen.

Linear vs. Cyclic Electron Flow

Cyclic flow supplements ATP relative to NADPH demand. Respiratory ETC final acceptor: O2. Photosynthetic final acceptor: NADP+.

Calvin Cycle Accounting

• Fixation: Rubisco joins CO2 to RuBP; splits into 3-PGA.

• Reduction: ATP/NADPH convert 3-PGA to G3P.

• Regeneration: Most G3P rebuilds RuBP using ATP.

• 3 CO2 → 1 net G3P: requires 9 ATP + 6 NADPH.

• 6 CO2 → 2 net G3P: 18 ATP + 12 NADPH.

• G3P is the direct net product.

Photorespiration and Adaptations

• Rubisco + CO2: Carbon fixation.

• Rubisco + O2: Photorespiration; wastes resources, loses fixed carbon.

• Hot/dry conditions: Stomatal closure lowers CO2, increases oxygenation risk.

• C4 Plants: Spatial separation; PEP-carboxylase in mesophyll, CO2 release near rubisco in bundle sheath (e.g., maize).

• CAM Plants: Temporal separation; stomata open at night, stored acids release CO2 by day (e.g., cacti).

• Both reduce photorespiration and use Calvin cycle.

Cell Communication

Signal Delivery and Stages

Cells communicate via chemical signals, which are delivered through various mechanisms.

• Paracrine: Local diffusion to nearby cells.

• Synaptic: Neuron releases transmitter across synapse.

• Endocrine: Hormone travels in blood to distant targets.

• Only cells with appropriate receptors respond.

Three stages of signaling:

1. Reception: Ligand activates receptor.

2. Transduction: Intracellular relay.

3. Response: Change in enzyme activity, gene expression, movement, secretion, growth, or survival.

Three Receptor Types

Second Messengers

• cAMP route: GPCR → G protein → adenylyl cyclase → ATP converted to cAMP → protein kinase A → response.

• IP3/Ca2+ route: Phospholipase C cleaves PIP2 → IP3 + DAG. IP3 opens ER Ca2+ channels → cytosolic Ca2+ rises → calcium-sensitive proteins respond.

• DAG stays in membrane; Ca2+ can activate proteins via calmodulin.

• Ligand = first messenger; cAMP, IP3, Ca2+ = second messengers.

• Kinase: Adds phosphate; Phosphatase: Removes phosphate.

• Phosphorylation can activate or inhibit targets.

• Amplification: One activated molecule stimulates many downstream targets.

• Termination: GTP hydrolysis, ligand removal, cAMP degradation, dephosphorylation, Ca2+ pumping.

Apoptosis

Apoptosis is regulated programmed cell death, essential for development and homeostasis.

• Caspases dismantle cell; DNA fragments; membrane-bound pieces are cleared.

• Removes damaged/unnecessary cells; limits inflammation compared to uncontrolled rupture.

• Failure can allow dangerous cells to survive.

Example: A drug disrupts microtubules, vesicle delivery declines because microtubule transport tracks fail, affecting secretion but not protein synthesis.

Additional info: These notes expand brief points into full academic explanations, add definitions, and provide context for exam preparation.