Comprehensive Study Guide: Cell Structure, Membranes, Metabolism, Respiration, and Photosynthesis

Cell Structure and Function

Cell Theory

The Cell Theory is a foundational concept in biology that describes the properties of cells. It consists of three main parts:

• All living things are made of cells. Every organism, from bacteria to plants and animals, is composed of one or more cells.

• The cell is the basic unit of life. Cells are the smallest units that can carry out all life processes.

• All cells come from pre-existing cells. New cells are produced by the division of existing cells.

Prokaryotic vs. Eukaryotic Cells

• Prokaryotic cells (e.g., bacteria, archaea): Lack a nucleus and membrane-bound organelles; DNA is found in the nucleoid region.

• Eukaryotic cells (e.g., plants, animals, fungi, protists): Have a true nucleus and various membrane-bound organelles.

Feature	Prokaryotic	Eukaryotic
Nucleus	No	Yes
Organelles	No	Yes
Size	Small (1-10 μm)	Larger (10-100 μm)
Examples	Bacteria, Archaea	Plants, Animals, Fungi, Protists

Endosymbiotic Theory

The Endosymbiotic Theory explains the origin of mitochondria and chloroplasts. It proposes that these organelles originated as free-living prokaryotes that were engulfed by ancestral eukaryotic cells, forming a symbiotic relationship.

• Evidence: Double membranes, their own DNA, and ribosomes similar to prokaryotes.

Nucleus and Its Components

• Nucleus: Contains genetic material (DNA) and controls cellular activities.

• Nucleolus: Site of ribosomal RNA (rRNA) synthesis and ribosome assembly.

• Nuclear envelope: Double membrane with nuclear pores for transport.

Endomembrane System

• Rough Endoplasmic Reticulum (rER): Smooth Endoplasmic ReticulumS

• tudded with ribosomes; synthesizes and modifies proteins.

• (sER): Lacks ribosomes; synthesizes lipids, detoxifies chemicals.

• Golgi Apparatus: Modifies, sorts, and packages proteins and lipids for transport.

• Protein Pathway: rER → Golgi → Vesicles → Destination (e.g., plasma membrane, lysosome).

Lysosomes, Peroxisomes, and Vacuoles

• Lysosomes: Contain hydrolytic enzymes for digestion of macromolecules.

• Peroxisomes: Break down fatty acids and detoxify harmful substances (produce hydrogen peroxide).

• Vacuoles: Storage organelles; large central vacuole in plants maintains turgor pressure.

Mitochondria and Chloroplasts

• Mitochondria: Site of aerobic respiration; produces ATP.

• Chloroplasts: Site of photosynthesis in plants and algae.

• Both have double membranes and their own DNA.

Cytoskeleton

• Microtubules: Hollow tubes; maintain cell shape, form spindle fibers, and are involved in movement (cilia, flagella).

• Microfilaments: Actin filaments; support cell shape, involved in muscle contraction and cell movement.

• Intermediate Filaments: Provide mechanical support; more stable than microtubules and microfilaments.

Centrioles, Cilia, and Flagella

• Centrioles: Organize microtubules during cell division (animal cells).

• Cilia and Flagella: Structures for cell movement; cilia are short and numerous, flagella are longer and usually singular.

Disease States Related to Cell Structure

• Progeria: Premature aging due to nuclear envelope defects.

• Adrenoleukodystrophy (ALD): Peroxisomal disorder affecting fatty acid breakdown.

• Tay Sachs: Lysosomal storage disease; accumulation of GM2 ganglioside in neurons.

Membrane Structure and Function

Membrane Proteins and Lipid Bilayer

• Integral proteins: Span the lipid bilayer; involved in transport and signaling.

• Peripheral proteins: Loosely attached to the membrane surface.

• P side (Protoplasmic side): Faces the cytoplasm.

• E side (Exoplasmic side): Faces the extracellular space.

Extracellular Matrix (ECM)

• Definition: Network of proteins and carbohydrates outside animal cells providing structural and biochemical support.

• Main Components:

  • Collagen: Provides tensile strength.

  • Proteoglycans: Hydrate and cushion tissues.

  • Fibronectin: Connects ECM to cell surface receptors.

  • Laminin: Influences cell differentiation, migration, and adhesion.

• Disease States:

  • Marfan's Syndrome: Defect in fibrillin.

  • Epidermolysis bullosa (EB): Defect in lamin B3.

  • Osteogenesis imperfecta: Defect in collagen.

Intercellular Junctions

Junction Type	Function	Example	Disease State
Tight Junctions	Seal cells together	Intestinal lining	Celiac disease
Desmosomes	Anchor cells together	Skin epithelium	Epidermolysis bullosa
Gap Junctions	Allow communication	Cardiac muscle	Epilepsy, Charcot-Marie-Tooth

Osmosis and Tonicity

• Osmosis: Diffusion of water across a semipermeable membrane.

• Hypotonic: Solution has lower solute concentration; cell gains water (lysis in animal cells, turgid in plants).

• Hypertonic: Solution has higher solute concentration; cell loses water (crenation in animal cells, plasmolysis in plants).

• Isotonic: Equal solute concentration; no net water movement.

Passive and Active Transport

• Passive Transport: No energy required; includes diffusion, facilitated diffusion (via channels and carriers).

• Active Transport: Requires energy (ATP); moves substances against their concentration gradient.

• Channels vs. Carriers: Channels form pores; carriers undergo conformational changes.

Bulk Transport: Endocytosis

• Phagocytosis: "Cell eating"; uptake of large particles.

• Pinocytosis: "Cell drinking"; uptake of fluids and solutes.

• Receptor-mediated endocytosis: Specific uptake via clathrin-coated pits (e.g., LDL uptake; defect causes familial hypercholesterolemia).

Genetic Basis of Membrane Diseases

• HIV Resistance: Mutation in CCR5 protein prevents viral entry; CCR5 inhibitors block this protein.

• Cystic Fibrosis (CF): Defective CFTR protein impairs chloride transport; drugs like Trikafta improve function.

Electrogenic Pumps and Proton Pump Inhibitors

• Electrogenic pumps: Create voltage across membranes (e.g., Na+/K+ pump, proton pumps).

• Proton Pump Inhibitors (PPIs): Drugs like Prevacid or Nexium block H+/K+ ATPase in stomach lining, reducing acid production.

Metabolism and Enzymes

Energy, Work, and Heat

• Energy: Capacity to do work or produce heat.

• Work: Movement of matter against opposing forces.

• Heat: Energy transfer due to temperature difference.

Exergonic vs. Endergonic Reactions; Catabolic vs. Anabolic

• Exergonic: Release energy; spontaneous ($\Delta G < 0$).

• Endergonic: Require energy input; non-spontaneous ($\Delta G > 0$).

• Catabolic: Break down molecules; release energy.

• Anabolic: Build complex molecules; require energy.

ATP Structure and Function

• ATP (Adenosine Triphosphate): Energy currency of the cell; transfers phosphate groups to drive endergonic reactions.

• ATP Hydrolysis: $\mathrm{ATP} + \mathrm{H}_2\mathrm{O} \rightarrow \mathrm{ADP} + \mathrm{P_i} + \text{energy}$

• Phosphorylated Intermediate: Molecule with a phosphate group attached, making it more reactive.

• ATP Cycle: Continuous regeneration of ATP from ADP and $P_i$.

Enzymes and Their Regulation

• Enzymes: Biological catalysts; lower activation energy ($E_a$) for reactions.

• Induced Fit Model: Enzyme changes shape to fit substrate.

• Enzyme Reaction: $\mathrm{E} + \mathrm{S} \rightarrow \mathrm{E}-\mathrm{S} \rightarrow \mathrm{P} + \mathrm{E}$

• Equilibrium: Forward and reverse reactions occur at the same rate.

• Metabolic Disequilibrium: Cells maintain non-equilibrium to drive metabolism.

Enzyme Regulation

• Competitive Inhibition: Inhibitor binds active site; competes with substrate.

• Non-competitive Inhibition: Inhibitor binds elsewhere; changes enzyme shape.

• Allosteric Regulation: Regulatory molecule binds at a site other than the active site.

• Drug Example: Alli inhibits pancreatic lipase, reducing fat absorption.

Cellular Respiration

Summary Reaction and Redox

• Overall Reaction: $\mathrm{C}_6\mathrm{H}_{12}\mathrm{O}_6 + 6\mathrm{O}_2 \rightarrow 6\mathrm{CO}_2 + 6\mathrm{H}_2\mathrm{O} + \text{energy (ATP)}$

• Oxidation: Loss of electrons (LEO: Lose Electrons = Oxidation).

• Reduction: Gain of electrons (GER: Gain Electrons = Reduction).

Stages of Aerobic Respiration

1. Glycolysis: Cytoplasm; glucose → 2 pyruvate, 2 ATP, 2 NADH.

2. Acetyl CoA Formation: Mitochondrial matrix; pyruvate → acetyl CoA, 2 NADH, 2 CO2.

3. Krebs Cycle (Citric Acid Cycle): Mitochondrial matrix; acetyl CoA → 6 NADH, 2 FADH2, 2 ATP, 4 CO2.

4. Electron Transport Chain (ETC): Inner mitochondrial membrane; produces ~30 ATP.

Key Enzymes in Glycolysis

• Hexokinase (HK): Glucose → Glucose-6-phosphate

• Phosphofructokinase (PFK): Fructose-6-phosphate → Fructose-1,6-bisphosphate

• Phosphoglycerate kinase (PGK): 1,3-Bisphosphoglycerate → 3-Phosphoglycerate

• Pyruvate kinase (PK): Phosphoenolpyruvate → Pyruvate

Energy Yield per Glucose

Stage	NADH	FADH2	ATP	CO2
Glycolysis	2	0	2	0
Acetyl CoA Formation	2	0	0	2
Krebs Cycle	6	2	2	4
ETC	-	-	~30	0

Role of NAD+/NADH and FAD/FADH2

• NAD+ and FAD are electron carriers; they accept electrons during glycolysis and the Krebs cycle, becoming NADH and FADH2, which donate electrons to the ETC.

Disease: Congenital Infantile Lactic Acidosis

• Caused by Pyruvate Dehydrogenase Complex Deficiency; leads to accumulation of lactic acid due to impaired conversion of pyruvate to acetyl CoA.

Key Dehydrogenase Reactions in Krebs Cycle

• Isocitrate Dehydrogenase (oxidative decarboxylation)

• α-Ketoglutarate Dehydrogenase (oxidative decarboxylation)

• Succinate Dehydrogenase

• Malate Dehydrogenase

Oxidative decarboxylation steps: Isocitrate Dehydrogenase, α-Ketoglutarate Dehydrogenase, Pyruvate Dehydrogenase (not in Krebs but related).

Chemiosmosis and ATP Synthase

• Chemiosmosis: Process by which a proton gradient across the inner mitochondrial membrane drives ATP synthesis.

• ATP Synthase Reaction: $4\ \mathrm{H}^+ + 4\ e^- + \mathrm{O}_2 \rightarrow 2\ \mathrm{H}_2\mathrm{O}$

Anaerobic Fermentation

• Lactic Acid Fermentation: Pyruvate → Lactate; regenerates NAD+.

• Alcoholic Fermentation: Pyruvate → Ethanol + CO2; regenerates NAD+.

• Final Electron Acceptors: Organic molecules (not O2).

ATP Production: Substrate-Level vs. Oxidative Phosphorylation

• Substrate-Level Phosphorylation: Direct transfer of phosphate to ADP (glycolysis, Krebs cycle).

• Oxidative Phosphorylation: ATP synthesis powered by the ETC and chemiosmosis.

Photosynthesis

Chloroplast Structure and Light Absorption

• Chloroplast: Contains stroma, thylakoid membranes, thylakoid lumen, and photosystems.

• When a photon is absorbed: Electron in the reaction center is excited to a higher energy state.

Photolysis and Oxygen Evolution

• Photolysis: Splitting of water by light energy in photosystem II; releases O2 into the atmosphere.

Light Reactions vs. Calvin Cycle

Process	Location	Starting Materials	End Products
Light Reactions	Thylakoid membrane	Light, H2O, NADP+, ADP	O2, ATP, NADPH
Calvin Cycle	Stroma	CO2, ATP, NADPH	G3P (sugar), NADP+, ADP

Electron Flow in Photosystems

• Noncyclic Photophosphorylation: Electrons flow from H2O → PSII → PSI → NADP+; produces ATP and NADPH.

• Cyclic Photophosphorylation: Electrons cycle within PSI; produces ATP only.

Proton Gradient and ATP Synthesis

• Light-driven electron transport pumps H+ into the thylakoid lumen, creating a gradient that drives ATP synthase.

Calvin Cycle Phases

• Carbon Fixation: CO2 attached to RuBP by RUBISCO.

• Reduction: ATP and NADPH reduce 3-PGA to G3P.

• Regeneration: RuBP is regenerated for the cycle to continue.

Roles: RUBISCO catalyzes fixation; ATP and NADPH provide energy and reducing power.

C3, C4, and CAM Pathways

• C3 Plants: Use Calvin cycle directly; susceptible to photorespiration.

• C4 Plants: Use PEP carboxylase to fix CO2 in mesophyll cells, then Calvin cycle in bundle sheath cells; reduces photorespiration.

• CAM Plants: Fix CO2 at night; Calvin cycle during the day; adaptation to arid environments.

Laboratory Concepts

Semipermeable Membranes

• Hypotonic: Cell swells; may lyse (animal) or become turgid (plant).

• Hypertonic: Cell shrinks; crenation (animal), plasmolysis (plant).

• Isotonic: No net water movement.

Enzyme Lab

• Factors affecting enzyme activity: pH, substrate concentration, enzyme concentration, inhibitors (e.g., hydroxylamine).

Photosynthesis Lab

• Absorption Spectrum: Shows which wavelengths of light are absorbed by pigments.

• TLC (Thin Layer Chromatography): Separates plant pigments.

• Hill Reaction: Demonstrates light-driven reduction of electron acceptors in isolated chloroplasts.

Additional info: Some explanations and tables were expanded for clarity and completeness based on standard biology curriculum.