Molecular and Cellular Biology: Exam 2 Study Guide

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 in eukaryotic cells, involved in protein synthesis and processing.

• Structure: The RER is an extension of the outer nuclear membrane, composed of interconnected cisternae (flattened membrane sacs). Its internal space is called the lumen or cisternal space.

• Ribosomes: Ribosomes are attached to the cytosolic surface, giving the RER its 'rough' appearance.

• Function: The RER is responsible for the synthesis of proteins destined for secretion, membrane insertion, or lysosomal targeting. It also facilitates protein folding, 3D assembly, and packaging into transport vesicles.

• Example: Secretory proteins such as insulin are synthesized in the RER.

Structure and Function of the Smooth Endoplasmic Reticulum (SER)

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

• Structure: Composed of interconnected membrane tubules.

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

• Example: Liver cells have abundant SER for detoxification.

Golgi Apparatus: Structure and Function

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

• Structure: Stacks of flattened membrane sacs called cisternae, with distinct cis (entry) and trans (exit) faces.

• Function: Modifies, sorts, and packages proteins and lipids for transport. Modifications include glycosylation and addition of signal sequences for targeting.

• Example: Glycoproteins are formed by glycosylation in the Golgi.

Lysosomes: Structure and Function

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 of external materials (heterophagy) and internal cell components (autophagy).

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

• Example: Tay-Sachs disease is a lysosomal storage disorder.

Membrane Vesicle Transport

Cells use vesicles for transport between organelles and the plasma membrane.

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

• Endocytosis: Receptor-mediated endocytosis involves clathrin-coated pits forming endosomes.

• Vesicle Movement: Vesicles travel along the cytoskeleton using motor proteins.

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 enzyme, which converts peroxides to water.

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

• Example: Peroxisomes are abundant in liver cells for detoxification.

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: Tubulin subunits; provide tracks for vesicle transport, form mitotic spindle, and maintain cell shape.

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

• Example: Actin in muscle cells, microtubules in neurons, keratin in epithelial cells.

Cytoskeletal Dynamics

Cytoskeletal filaments undergo energy-dependent assembly and disassembly, allowing rapid reorganization.

• Actin and Microtubules: Polymerize and depolymerize using ATP (actin) or GTP (microtubules).

• Dynamic Instability: Microtubules alternate between growth and shrinkage.

• Equation: $\text{ATP} + \text{Actin monomer} \rightarrow \text{Actin filament} + \text{ADP}$

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 (retrograde transport).

• Myosin: Moves along actin filaments.

• ATP-driven: Motor proteins use ATP hydrolysis for movement.

• Example: Vesicle transport from ER to Golgi uses kinesin.

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 one form to another (e.g., light to chemical).

• Example: Photosynthesis transforms light energy into chemical energy.

Second Law of Thermodynamics and Free Energy

The second law states that entropy increases in spontaneous processes; cells use free energy to do work.

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

• Equation: $\Delta G = \Delta H - T\Delta S$

• Catabolic: Exergonic, energy-releasing, $\Delta G < 0$

• Anabolic: Endergonic, energy-requiring, $\Delta G > 0$

Cellular Work and Energy Coupling

Cells perform mechanical, transport, and synthetic work using free energy.

• Steady State: Cells maintain non-equilibrium by coupling exergonic and endergonic reactions.

• Example: ATP hydrolysis drives endergonic processes.

Chapter 9: Chemotrophic Energy Metabolism I – Glycolysis and Fermentation

Metabolic Pathways: Anabolic vs. Catabolic

Metabolism consists of interconnected pathways for energy production and biosynthesis.

• Anabolic: Build complex molecules, require energy.

• Catabolic: Break down molecules, release energy.

• Cellular Respiration: Anaerobic (glycolysis, fermentation) and aerobic (glycolysis, citric acid cycle, ETC).

ATP: The Energy Currency

ATP stores and transfers energy within cells.

• High Potential Energy: Due to repulsion between phosphate groups.

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

• Equation: $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i + \text{Energy}$

Coenzymes in Metabolism

Coenzymes participate in enzymatic reactions and transfer energy or electrons.

• ATP: Energy carrier.

• NADH, FADH2: Electron carriers (reducing power).

Glycolysis: Overview and Phases

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 NADH synthesis.

• Phase III: Pyruvate formation and ATP generation.

• Substrate-level Phosphorylation: Direct transfer of phosphate to ADP.

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

Regulation of Glycolysis

Glycolysis is tightly regulated by key enzymes and energy charge.

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

• Regulation: Inhibitors/activators and ATP/AMP ratio.

Fermentation

Fermentation regenerates NAD+ in the absence of oxygen.

• Lactic Acid: Forms in oxygen-deprived muscle cells.

• Ethanol: Forms in yeast.

Gluconeogenesis

Gluconeogenesis synthesizes glucose from non-carbohydrate precursors.

• 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.

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

Mitochondria: Structure and Function

The mitochondria are the site of aerobic respiration, with distinct compartments for metabolic processes.

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

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

• Function: Citric acid cycle and oxidative phosphorylation occur in the matrix and inner membrane.

Pyruvate Dehydrogenase and Acetyl-CoA Formation

Pyruvate is converted to Acetyl-CoA before entering the citric acid cycle.

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

• Equation: $\text{Pyruvate} + \text{NAD}^+ + \text{CoA} \rightarrow \text{Acetyl-CoA} + \text{CO}_2 + \text{NADH}$

Citric Acid Cycle: Logic and Steps

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

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

• Substrate-level Phosphorylation: Succinyl-CoA → Succinate releases energy for ATP/GTP synthesis.

• 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 and Amphibolic Nature

The citric acid cycle is regulated at key steps and serves both catabolic and anabolic functions.

• Regulation: Entry (PDH), allosteric regulation of NADH-producing enzymes.

• Amphibolic: Provides intermediates for biosynthesis.

Electron Transport Chain (ETC) Organization

The ETC is a series of complexes in the inner mitochondrial membrane that transfer electrons and pump protons.

• Chemical Logic: Electrons from NADH and FADH2 flow through complexes I-IV to oxygen.

• Complex II: Succinate dehydrogenase; links citric acid cycle and ETC.

• Entry/Exit: NADH enters at Complex I, FADH2 at Complex II; electrons exit at Complex IV (reduce O2).

Coupling Electron Transport to ATP Synthesis

Electron transport is coupled to proton pumping, creating a gradient used by ATP synthase (Complex V).

• Proton Gradient: Drives ATP synthesis via chemiosmosis.

• ATP Synthase: Converts electrochemical potential energy to chemical energy in ATP.

• Energy Transformation: Chemical (citric acid cycle) → electrochemical (proton gradient) → kinetic (H+ flow) → chemical (ATP).

• Equation: $\text{ADP} + \text{P}_i \rightarrow \text{ATP}$

Chapter 11: Photosynthesis

Photosynthesis: Key Terms and Concepts

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

• Definition: Conversion of CO2 and H2O into glucose and O2 using light energy.

• Equation: $6\text{CO}_2 + 6\text{H}_2\text{O} + \text{light energy} \rightarrow \text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2$

Light Harvesting in PSII and PSI

Photosystems II (PSII) and I (PSI) absorb light and drive electron transport for ATP and NADPH synthesis.

• 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.

Oxygen Generation and the Calvin Cycle

PSII splits water, releasing oxygen, while the Calvin Cycle assimilates CO2 into carbohydrates.

• Oxygen: PSII is essential for oxygen production in the biosphere.

• Calvin Cycle: Reduces fully oxidized carbon in CO2 to form carbohydrates.

• Example: Rubisco catalyzes CO2 fixation in the Calvin Cycle.

Cytoskeletal System	Subunit	Primary Function	Example
Actin Filaments	Actin	Cell shape, movement, muscle contraction	Muscle cells
Microtubules	Tubulin	Vesicle transport, mitotic spindle, cell shape	Neurons
Intermediate Filaments	Keratin, vimentin, etc.	Mechanical strength, structural integrity	Epithelial cells