Chapter 7: Inside the Cell

Introduction

This chapter explores the fundamental characteristics shared by all known life forms, focusing on the structure and function of cells. It distinguishes between the two major types of cells—prokaryotic and eukaryotic—and introduces the concept of cellular compartmentalization and specialization.

• Cell: The basic structural and functional unit of all living organisms.

• Prokaryotes: Organisms whose cells lack a nucleus (e.g., Bacteria and Archaea).

• Eukaryotes: Organisms whose cells contain a nucleus and other membrane-bound organelles (e.g., plants, animals, fungi, protists).

7.1 Bacterial and Archaeal Cell Structures and Their Functions

• Prokaryotic cells organize their genetic material in a single, circular chromosome located in a region called the nucleoid.

• Chromosomes contain DNA, which encodes genes.

• Prokaryotes may also have small, circular DNA molecules called plasmids.

• Photosynthetic prokaryotes have internal membrane complexes for photosynthesis (e.g., Cyanobacteria).

• Ribosomes synthesize proteins and are found in both prokaryotes and eukaryotes.

• Other structures: cell wall, plasma membrane, flagella (for movement), and storage granules.

7.2 Eukaryotic Cell Structures and Their Functions

• Eukaryotic cells are compartmentalized into organelles, each with specialized functions:

  • Nucleus: Contains genetic material (DNA) and is the site of RNA synthesis.

  • Ribosomes: Sites of protein synthesis.

  • Endoplasmic Reticulum (ER): Rough ER synthesizes proteins; Smooth ER synthesizes lipids.

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

  • Lysosomes: Contain digestive enzymes for breaking down macromolecules.

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

  • Mitochondria: Sites of cellular respiration and ATP production.

  • Chloroplasts: Sites of photosynthesis in plant cells.

  • Cytoskeleton: Network of protein filaments for cell shape, movement, and transport.

7.3 Putting the Parts into a Whole

• Multicellular organisms have specialized cells with distinct structures and functions.

• Cellular compartmentalization allows for efficient and regulated biochemical processes.

7.4 Cell Systems in Nucleated Transport

• Transport of materials into and out of the nucleus involves nuclear pores and nuclear transport proteins.

• Regulation of gene expression and communication between the nucleus and cytoplasm is essential for cell function.

7.5 Cell Systems II: The Endomembrane System Manufactures, Ships, and Recycles Cargo

• The endomembrane system includes the nuclear envelope, ER, Golgi apparatus, lysosomes, and vesicles.

• Responsible for the synthesis, modification, transport, and recycling of cellular materials.

7.6 Cell Systems III: The Dynamic Cytoskeleton

• The cytoskeleton is composed of microfilaments (actin), intermediate filaments, and microtubules.

• Functions include cell movement, division, structural support, and intracellular transport.

• Specialized cytoskeletal structures are found in muscle contraction, cilia, and flagella.

Chapter 8: Energy and Enzymes

Introduction

This chapter examines how cells obtain and use energy, focusing on the role of enzymes in catalyzing biochemical reactions.

8.1 What Happens to Energy in Chemical Reactions?

• Potential energy: Stored energy due to position or structure.

• Kinetic energy: Energy of motion.

• Energy transformations occur in all living cells, often involving the transfer of electrons (redox reactions).

• Energy is stored in chemical bonds; breaking and forming bonds involves energy changes.

• Enthalpy (H): Total energy in a molecule.

• Gibbs free energy (G): Energy available to do work. The change in free energy () determines if a reaction is spontaneous.

• Where is the change in enthalpy, is temperature in Kelvin, and is the change in entropy.

8.2 Nonspontaneous Reactions May Be Driven Using Chemical Energy

• Cells couple exergonic (energy-releasing) and endergonic (energy-consuming) reactions to drive necessary processes.

• ATP (adenosine triphosphate) is the primary energy currency of the cell.

• Phosphorylation (adding a phosphate group) can activate or deactivate molecules.

8.3 How Enzymes Work

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

• They are highly specific for their substrates.

• Enzyme activity can be regulated by inhibitors, activators, and environmental conditions (pH, temperature).

• Enzymes are not consumed in the reactions they catalyze.

8.4 What Factors Affect Enzyme Function?

• Enzyme function is affected by temperature, pH, substrate concentration, and the presence of inhibitors or activators.

• Enzymes are optimized for particular environments.

8.5 Enzymes Can Work Together in Metabolic Pathways

• Metabolic pathways are series of enzyme-catalyzed reactions.

• Catabolic pathways: Break down molecules to release energy.

• Anabolic pathways: Build complex molecules from simpler ones, requiring energy.

Chapter 9: Cellular Respiration & Fermentation

Introduction

This chapter describes how cells harvest energy from organic molecules, primarily glucose, to produce ATP through cellular respiration and fermentation.

9.1 An Overview of Cellular Respiration

• Cellular respiration: The process by which cells convert biochemical energy from nutrients into ATP, releasing waste products.

• Overall equation for aerobic respiration:

• Major stages: Glycolysis, Pyruvate processing, Citric acid cycle, Electron transport chain & chemiosmosis.

9.2 Glycolysis: Oxidizing Glucose to Pyruvate

• Occurs in the cytosol; glucose is split into two molecules of pyruvate.

• Net gain: 2 ATP and 2 NADH per glucose molecule.

• Does not require oxygen (anaerobic process).

9.3 Processing Pyruvate to Acetyl CoA

• Pyruvate is transported into the mitochondria (in eukaryotes).

• Each pyruvate is converted to acetyl CoA, producing NADH and releasing CO2.

9.4 The Citric Acid Cycle: Oxidizing Acetyl CoA to CO2

• Also known as the Krebs cycle or TCA cycle.

• Occurs in the mitochondrial matrix.

• Each acetyl CoA is oxidized, producing 3 NADH, 1 FADH2, 1 ATP (or GTP), and 2 CO2 per cycle.

• Cycle turns twice per glucose molecule.

9.5 Electron Transport and Chemiosmosis: Building a Proton Gradient to Produce ATP

• Electron transport chain (ETC) is located in the inner mitochondrial membrane.

• Electrons from NADH and FADH2 are transferred through protein complexes, releasing energy used to pump protons (H+) into the intermembrane space.

• This creates a proton gradient, which drives ATP synthesis via ATP synthase (chemiosmosis).

• Oxygen is the final electron acceptor, forming water.

9.6 Fermentation

• Occurs when oxygen is not available.

• Allows glycolysis to continue by regenerating NAD+ from NADH.

• Produces less ATP than aerobic respiration.

• Types: Lactic acid fermentation (in animals), alcoholic fermentation (in yeast and some bacteria).

Table: Comparison of Aerobic Respiration and Fermentation

Additional info:

• Some prokaryotes can use alternative electron acceptors in respiration (e.g., nitrate, sulfate).

• Cellular respiration is a highly regulated process, with feedback mechanisms controlling the rate of ATP production.