Chapter 7 – Inside the Cell

Overview of Cell Structure

This chapter explores the structural and functional differences between prokaryotic and eukaryotic cells, the roles of various organelles, and the mechanisms of intracellular transport and cytoskeletal dynamics.

• Prokaryotic Cells: Simpler cells lacking a nucleus and most organelles. Includes Bacteria and Archaea.

• Eukaryotic Cells: More complex, with membrane-bound organelles and a defined nucleus. Includes plants, animals, fungi, and protists.

Prokaryotic Cell Components

• Cell Wall: Rigid structure providing support and protection.

• Plasma Membrane: Phospholipid bilayer controlling entry and exit of substances.

• Cytoplasm: Gel-like substance containing cellular components.

• Nucleoid: Region containing the circular DNA chromosome.

• Plasmids: Small, circular DNA molecules with additional genes.

• Ribosomes: Sites of protein synthesis.

• Fimbriae: Hair-like structures for attachment.

• Flagella: Tail-like structures for movement.

Example: Escherichia coli uses flagella for motility and fimbriae to adhere to surfaces.

Eukaryotic Cell Components and Compartmentalization

• Nucleus: Contains DNA; surrounded by the nuclear envelope with nuclear pores for transport.

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

• Endoplasmic Reticulum (ER):

  • Rough ER (RER): Studded with ribosomes; synthesizes proteins.

  • Smooth ER: Lacks ribosomes; synthesizes lipids and detoxifies chemicals.

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

• Lysosomes: Contain digestive enzymes for autophagy and recycling.

• Peroxisomes: Break down fatty acids and detoxify harmful substances.

• Mitochondria: Site of cellular respiration; contains its own DNA (mtDNA).

• Chloroplasts (plants/algae): Site of photosynthesis; contains thylakoids, grana, and stroma.

• Vacuole (plants): Storage and maintenance of cell turgor.

• Cytoskeleton: Network of protein filaments (actin filaments, intermediate filaments, microtubules) for structure and movement.

Benefits of Compartmentalization: Increases efficiency by separating incompatible reactions and localizing processes.

Transport Mechanisms

• Nuclear Envelope Transport: Proteins with nuclear localization signals ("zip codes") are imported via nuclear pore complexes.

• Endomembrane System: Proteins synthesized in the RER are transported to the Golgi, then to lysosomes, plasma membrane, or secretion via vesicles.

• Endocytosis: Uptake of materials via vesicle formation (includes phagocytosis and receptor-mediated endocytosis).

• Exocytosis: Export of materials by vesicle fusion with the plasma membrane.

• Autophagy: Recycling of cellular components via lysosomes.

Cytoskeleton and Motility

• Actin Filaments (Microfilaments): Provide cell shape and enable movement (e.g., muscle contraction).

• Intermediate Filaments: Provide mechanical strength (e.g., nuclear lamins).

• Microtubules: Hollow tubes for organelle movement and cell division; form cilia and flagella.

• Motor Proteins: (e.g., kinesin, dynein, myosin) move along cytoskeletal filaments to transport cargo.

• Cilia and Flagella: Microtubule-based structures for movement; cilia are short and numerous, flagella are longer and fewer.

Example: Sperm cells use flagella for motility; respiratory tract cells use cilia to move mucus.

Chapter 8 – Energy and Enzymes

Energy in Biological Systems

This chapter examines how cells transform energy, the role of enzymes in catalyzing reactions, and the regulation of metabolic pathways.

• Kinetic Energy: Energy of motion.

• Potential Energy: Stored energy (e.g., in chemical bonds).

• First Law of Thermodynamics: Energy cannot be created or destroyed, only transformed.

• Second Law of Thermodynamics: Entropy (disorder) increases in spontaneous processes.

Gibbs Free Energy and Reaction Spontaneity

• Gibbs Free Energy (G): Determines if a reaction is spontaneous.

• Equation:

• Exergonic: ; releases energy; spontaneous.

• Endergonic: ; requires energy input; nonspontaneous.

Enzymes and Catalysis

• Enzymes: Biological catalysts that lower activation energy and increase reaction rates.

• Active Site: Region where substrate binds and reaction occurs.

• Induced Fit: Enzyme changes shape to fit substrate upon binding.

• Activation Energy (): Energy required to start a reaction.

• Enzyme Helpers:

  • Cofactors: Inorganic ions (e.g., Mg2+, Fe2+).

  • Coenzymes: Organic molecules (e.g., NAD+, FAD).

  • Prosthetic Groups: Non-amino acid groups tightly bound to enzymes.

Regulation of Enzyme Activity

• Competitive Inhibition: Inhibitor binds active site, blocking substrate.

• Allosteric Regulation: Molecule binds elsewhere, changing enzyme shape and activity.

• Covalent Modification: Chemical changes (e.g., phosphorylation) alter enzyme activity.

• Feedback Inhibition: End product of a pathway inhibits an earlier step.

• Environmental Factors: Temperature and pH affect enzyme structure and function.

Metabolic Pathways

• Catabolic Pathways: Break down molecules, releasing energy (e.g., cellular respiration).

• Anabolic Pathways: Build complex molecules, requiring energy (e.g., protein synthesis).

• Energetic Coupling: Exergonic reactions drive endergonic reactions (often via ATP hydrolysis or redox reactions).

Example: ATP hydrolysis () releases energy to drive cellular work.

Chapter 9 – Cellular Respiration and Fermentation

Overview of Cellular Respiration

Cellular respiration is a series of metabolic pathways that convert glucose into ATP, the cell's main energy currency. It includes glycolysis, pyruvate processing, the citric acid cycle, and oxidative phosphorylation.

Four Stages of Cellular Respiration

1. Glycolysis: Occurs in the cytosol; breaks glucose into two pyruvate molecules.

   • Inputs: Glucose, 2 ATP, 2 NAD+

   • Outputs: 2 Pyruvate, 4 ATP (net 2 ATP), 2 NADH

   • Phases: Energy investment and energy payoff.

2. Pyruvate Processing: In mitochondrial matrix; pyruvate converted to acetyl CoA.

   • Inputs: 2 Pyruvate, 2 NAD+, 2 CoA

   • Outputs: 2 Acetyl CoA, 2 NADH, 2 CO2

3. Citric Acid Cycle (TCA/Krebs Cycle): In mitochondrial matrix; completes glucose oxidation.

   • Inputs: 2 Acetyl CoA, 6 NAD+, 2 FAD, 2 ADP

   • Outputs: 4 CO2, 6 NADH, 2 FADH2, 2 ATP

4. Electron Transport Chain (ETC) and Oxidative Phosphorylation: Inner mitochondrial membrane; uses NADH and FADH2 to generate ATP.

   • Inputs: 10 NADH, 2 FADH2, O2

   • Outputs: ~26-28 ATP, H2O

Fermentation

• Occurs when O2 is absent.

• Lactic Acid Fermentation: Pyruvate reduced to lactate (e.g., in muscle cells).

• Alcohol Fermentation: Pyruvate converted to ethanol and CO2 (e.g., in yeast).

• ATP Yield: Fermentation produces much less ATP than cellular respiration.

Comparison Table: Cellular Respiration vs. Fermentation

Chapter 10 – Photosynthesis

Overview of Photosynthesis

Photosynthesis is the process by which autotrophs convert light energy into chemical energy, producing organic molecules and oxygen from carbon dioxide and water.

Light Reactions and the Calvin Cycle

• Light-Capturing Reactions: Occur in thylakoid membranes; convert light energy to ATP and NADPH.

• Calvin Cycle: Occurs in the stroma; uses ATP and NADPH to fix CO2 into sugars.

Pigments and Light Absorption

• Chlorophylls: Main pigments absorbing blue and red light.

• Carotenoids: Accessory pigments absorbing other wavelengths and protecting chlorophyll.

• Antenna Complex: Array of pigments that funnel energy to the reaction center.

Photosystems and Electron Flow

• Photosystem II: Splits water, releases O2, and generates ATP via photophosphorylation.

• Photosystem I: Produces NADPH.

• Z Scheme: Describes the flow of electrons from water through PSII and PSI to NADP+.

• Noncyclic Electron Flow: Both ATP and NADPH produced.

• Cyclic Electron Flow: Only ATP produced; electrons cycle back to PSI.

Carbon Fixation Pathways

• C3 Pathway: Most plants; CO2 fixed directly by rubisco.

• C4 Pathway: Spatial separation of initial CO2 fixation and Calvin cycle; reduces photorespiration.

• CAM Pathway: Temporal separation; CO2 fixed at night, Calvin cycle during day.

• Photorespiration: Rubisco binds O2 instead of CO2, reducing efficiency.

Phases of the Calvin Cycle

1. Carbon Fixation: CO2 attached to RuBP by rubisco.

2. Reduction: ATP and NADPH used to convert 3-PGA to G3P.

3. Regeneration: RuBP regenerated from G3P using ATP.

Example: G3P can be used to synthesize glucose, starch, or other organic molecules.

Summary Table: C3, C4, and CAM Pathways