Chapter 12: The Endomembrane System and Peroxisomes

Structure and Function of the Rough Endoplasmic Reticulum (RER)

The Rough Endoplasmic Reticulum (RER) is a key organelle involved in protein synthesis and processing within eukaryotic cells.

• Structure: Extension of the outer nuclear membrane, composed of interconnected cisternae (flattened membrane sacs) with a lumen (cisternal space). Ribosomes are attached to its surface, giving it a 'rough' appearance.

• Function: Synthesis of proteins, folding and assembly into their 3D structure, and packaging into membrane transport vesicles for delivery to other cellular locations.

• Example: Secretory proteins and membrane proteins are synthesized on the RER.

Structure and Function of the Smooth Endoplasmic Reticulum (SER)

The Smooth Endoplasmic Reticulum (SER) is involved in lipid metabolism and detoxification.

• Structure: Interconnected membrane tubules lacking ribosomes.

• Function: Synthesis of lipids (phospholipids, cholesterol), detoxification of drugs and poisons, and storage of calcium ions (Ca2+).

• Example: SER is abundant in liver cells for detoxification and in muscle cells for Ca2+ storage.

Golgi Apparatus: Structure and Function

The Golgi apparatus is the central organelle for processing and sorting proteins and lipids.

• Structure: Stacks of flattened membrane sacs with distinct cis (receiving) and trans (shipping) faces.

• Function: Processing, modification (e.g., glycosylation), sorting, and packaging of proteins and lipids for vesicular transport.

• Example: Addition of signal sequences (tags) for delivery to specific cellular destinations.

Structure and Functions of Lysosomes

Lysosomes are membrane-bound organelles responsible for digestion and recycling within the cell.

• Origin: Formed by fusion of endosomes (from endocytosis) and Golgi-derived vesicles containing hydrolytic enzymes.

• Function: Digestion and recycling of external materials (heterophagy) and internal materials (autophagy).

• Lysosomal Diseases: Caused by enzyme deficiencies, leading to accumulation of undigested proteins.

Exocytosis and Endocytosis

Cells transport materials via vesicles in processes called exocytosis and endocytosis.

• Exocytosis: Secretory vesicles fuse with the plasma membrane to release contents outside the cell.

• Endocytosis: Receptor-mediated, clathrin-coated pits form endosomes to internalize materials.

• Vesicle Transport: Vesicles move along the cytoskeleton using motor proteins.

Membrane Vesicle Transport

Vesicle transport involves coordination between the ER, Golgi apparatus, lysosomes, plasma membrane, and other organelles.

• Key Point: Ensures proper distribution and delivery of proteins, lipids, and other molecules within the cell.

Peroxisomes: Structure and Function

Peroxisomes are small organelles involved in oxidative reactions and defense against reactive oxygen species.

• Function: Contain high concentrations of peroxides and catalase, which converts peroxides to water.

• Defense: Enzymes neutralize reactive oxygen species, protecting the cell from oxidative damage.

Chapter 13: Cytoskeleton

Three Cytoskeletal Systems

The cytoskeleton provides structural support, facilitates movement, and organizes cellular components.

• Actin Filaments (Microfilaments): Composed of actin subunits; involved in cell shape, movement, and muscle contraction.

• Microtubules: Composed of tubulin subunits; provide tracks for vesicle transport, form mitotic spindle, and maintain cell shape.

• Intermediate Filaments: Composed of various proteins (e.g., keratin, vimentin); provide mechanical strength and structural integrity.

• Examples: Actin in muscle cells, microtubules in neurons, intermediate filaments in epithelial cells.

Molecular Basis of Cytoskeletal Dynamics

Cytoskeletal filaments undergo energy-dependent assembly and disassembly.

• Actin Filaments: Polymerize and depolymerize using ATP hydrolysis.

• Microtubules: Polymerize and depolymerize using GTP hydrolysis.

• Dynamic Instability: Allows rapid reorganization of the cytoskeleton.

Motor Proteins and Directionality

Motor proteins move along cytoskeletal tracks, transporting vesicles and organelles.

• Kinesin: Moves toward the plus end of microtubules (anterograde transport).

• Dynein: Moves toward the minus end of microtubules (retrograde transport).

• Myosin: Moves along actin filaments, involved in muscle contraction and vesicle transport.

• ATP-Driven: Movement is powered by ATP hydrolysis.

• Example: Vesicle transport in the endomembrane system relies on motor proteins.

Chapter 5: Bioenergetics: The Flow of Energy in the Cell

First Law of Thermodynamics in Cells

The first law states that energy cannot be created or destroyed, only transformed.

• Energy Sources: Phototrophic (light) and chemotrophic (chemical) organisms.

• Carbon Sources: Autotrophic (CO2) and heterotrophic (organic compounds).

• Transformation: Cells convert energy from the environment into usable forms (e.g., ATP).

• Example: Photosynthesis transforms light energy into chemical energy.

Second Law of Thermodynamics and Free Energy

The second law states that entropy (disorder) increases in spontaneous processes.

• Free Energy (G): Portion of internal energy available to do work.

• Cellular Work: Cells use free energy for mechanical, transport, and synthetic work.

• Catabolic Processes: Oxidation, energy release, exergonic ().

• Anabolic Processes: Reduction, synthesis, energy requirement, endergonic ().

Steady State and Coupling Reactions

Cells maintain a steady state and couple endergonic and exergonic reactions to obey the second law.

• Coupling: Endergonic reactions are driven by exergonic reactions (e.g., ATP hydrolysis).

• Example: Synthesis of macromolecules is coupled to ATP hydrolysis.

Chapter 9: Chemotrophic Energy Metabolism I – Glycolysis and Fermentation

Metabolic Pathways: Anabolic vs. Catabolic

Metabolic pathways are sequences of enzymatic reactions in cells.

• Anabolic Pathways: Build complex molecules, require energy.

• Catabolic Pathways: Break down molecules, release energy.

• Cellular Respiration: Includes anaerobic (glycolysis, fermentation) and aerobic (glycolysis, citric acid cycle, electron transport chain) processes.

ATP: The Energy Currency

ATP stores and transfers energy within cells.

• High Potential Energy: Due to unstable phosphate bonds.

• Hydrolysis: Highly exergonic, releases energy for cellular work.

• Equation:

Role of Coenzymes

Coenzymes participate in metabolic reactions.

• ATP: Carries energy.

• NADH, FADH2: Carry electrons (reducing power).

• Shared: Used by multiple enzymes in different pathways.

Logic of Glycolysis

Glycolysis is the anaerobic breakdown of glucose to pyruvate, generating ATP and NADH.

• Phase I: Preparation and cleavage (6C glucose split into 2 x 3C).

• Phase II: Oxidation and synthesis of NADH.

• Phase III: Pyruvate formation and ATP generation.

• Substrate-Level Phosphorylation: Exergonic hydrolysis of high-energy metabolites couples with endergonic ATP synthesis.

• Energy Gain: 2 ATP + 2 NADH per glucose.

Regulation of Glycolysis

Glycolysis is regulated by key enzymes and energy charge.

• Key Enzymes: Hexokinase, phosphofructokinase-1, pyruvate kinase.

• Regulation: Inhibitors/activators and ATP/AMP ratio (energy charge).

Fermentation

Fermentation regenerates NAD+ in the absence of oxygen.

• Lactic Acid Fermentation: Occurs in oxygen-deprived muscle cells.

• Ethanol Fermentation: Occurs in yeast.

Gluconeogenesis

Gluconeogenesis is the anabolic pathway for glucose synthesis.

• Not a Simple Reverse: Bypass steps are needed due to irreversible reactions in glycolysis.

• Reciprocal Regulation: Glycolysis and gluconeogenesis are regulated by ATP, ADP/AMP, and F-2,6-bisP.

• Purpose: Prevents futile cycles and ensures efficient energy use.

Chapter 10: Chemotrophic Metabolism II – Citric Acid Cycle and Oxidative Phosphorylation

Mitochondria: Structure and Function

The mitochondria are the site of aerobic respiration and ATP synthesis.

• Origin: Endosymbiotic theory; mitochondria evolved from ancestral prokaryotes.

• Structure: Outer membrane, inner membrane (with cristae), intermembrane space, matrix.

• Compartmentalization: Different metabolic processes occur in specific compartments.

Preparation Step: Pyruvate Dehydrogenase (PDH)

PDH converts pyruvate to acetyl-CoA, linking glycolysis to the citric acid cycle.

• Oxidative Decarboxylation: 3C pyruvate → 2C acetyl-CoA + CO2 + NADH.

Logic of the Citric Acid Cycle

The citric acid cycle oxidizes acetyl-CoA, generating NADH, FADH2, and ATP/GTP.

• First Half: Two steps of oxidative decarboxylation (6C → 4C + 2CO2, energy gain: 2 NADH).

• Substrate-Level Phosphorylation: Succinyl-CoA releases energy to synthesize ATP or GTP.

• Second Half: Regeneration of oxaloacetate (4C), with two oxidations (FADH2 and NADH).

• Energy Gain: Per pyruvate: 1 ATP (or GTP), 4 NADH, 1 FADH2; per glucose: double these values.

Regulation of the Citric Acid Cycle

Regulation occurs at entry and at key steps producing NADH.

• PDH Regulation: Phosphorylation-dephosphorylation and allosteric regulation.

• Amphibolic Nature: The cycle is both catabolic and anabolic, providing intermediates for biosynthesis.

Electron Transport Chain (ETC) Organization

The ETC is a series of protein complexes in the inner mitochondrial membrane.

• Cristae: Increase surface area for ETC and ATP synthesis.

• Electron Flow: NADH → Complex I → Complex III → Complex IV → O2; FADH2 → Complex II → Complex III → Complex IV → O2.

• Complex II: Functions in both the citric acid cycle and ETC.

Coupling Electron Transport to ATP Synthesis

Electron transport drives proton pumping, creating a gradient used for ATP synthesis.

• Proton Gradient: Protons are pumped across the inner membrane, creating electrochemical potential.

• ATP Synthase (Complex V): Uses proton flow to synthesize ATP from ADP and Pi.

• Energy Transformation: Chemical energy → electrochemical potential → kinetic energy → chemical energy (ATP).

• Equation:

Chapter 11: Photosynthesis

Photosynthesis: Key Terms and Concepts

Photosynthesis is the process by which light energy is converted into chemical energy in plants, algae, and some bacteria.

• Key Terms: Photosystem II (PSII), Photosystem I (PSI), chlorophyll, ATP, NADPH, Calvin Cycle.

Harvesting Light Energy

Light energy is absorbed by chlorophyll in PSII and PSI, driving the synthesis of ATP and NADPH.

• PSII: Contains chlorophyll P680 (absorbs at 680 nm).

• PSI: Contains chlorophyll P700 (absorbs at 700 nm).

• Energy Use: Light energy is used to generate ATP and NADPH for carbon fixation.

Oxygen Generation in PSII

PSII splits water molecules, releasing oxygen as a byproduct.

• Importance: Oxygen production sustains aerobic life in the biosphere.

The Calvin Cycle

The Calvin Cycle assimilates fully oxidized carbon (CO2) into carbohydrates.

• Process: Uses ATP and NADPH to reduce CO2 and synthesize sugars.

• Equation: