General Biology Study Notes: Chapters 2–8 (Atoms, Molecules, Cells, Energy, Photosynthesis, and Cell Division)

Chapter 2: The Chemical Basis of Life

Atomic Structure and Elements

• Atoms are the basic units of matter, composed of protons (positive charge), neutrons (neutral), and electrons (negative charge).

• Atomic number is defined by the number of protons in an atom.

• Isotopes are atoms of the same element with different numbers of neutrons.

Chemical Bonds and Molecules

• Ionic bonds: Formed when electrons are transferred from one atom to another, resulting in oppositely charged ions (e.g., NaCl).

• Covalent bonds: Formed when atoms share electrons (e.g., H2, O2).

• Polar covalent bonds: Unequal sharing of electrons, leading to partial charges (e.g., H2O).

• Hydrogen bonds: Weak attractions between a hydrogen atom in one molecule and an electronegative atom in another (important in water and DNA structure).

Properties of Water

• Polarity: Water is a polar molecule, leading to hydrogen bonding.

• Cohesion: Water molecules stick together due to hydrogen bonds.

• Adhesion: Water molecules stick to other substances.

• Surface tension: The measure of how difficult it is to break the surface of a liquid.

• Capillary action: Movement of water up narrow tubes against gravity due to cohesion and adhesion.

• Specific heat: Water has a high specific heat, meaning it resists temperature changes.

• Density: Ice is less dense than liquid water due to hydrogen bonding, allowing ice to float.

Acids, Bases, and pH

• Acids release H+ ions in solution; bases accept H+ or release OH- ions.

• pH scale: Measures the concentration of H+ ions; lower pH = more acidic, higher pH = more basic.

Salts

• Formed from the neutralization of acids and bases.

Example:

• NaOH (base) + HCl (acid) → NaCl (salt) + H2O (water)

Additional info:

• Water’s unique properties are essential for life, including its role as a solvent, temperature buffer, and medium for chemical reactions.

Chapter 3: The Molecules of Cells

Organic Molecules and Functional Groups

• Organic molecules contain carbon and hydrogen; carbon forms four covalent bonds, allowing for diverse structures.

• Functional groups are specific groups of atoms that confer characteristic properties (e.g., hydroxyl, carboxyl, amino, phosphate).

Macromolecules: Carbohydrates, Lipids, Proteins, Nucleic Acids

• Carbohydrates: Sugars and polymers of sugars; main energy source (e.g., glucose, starch, cellulose).

• Lipids: Hydrophobic molecules including fats, phospholipids, and steroids; important for energy storage and membrane structure.

• Proteins: Polymers of amino acids; functions include catalysis (enzymes), structure, transport, and signaling.

• Nucleic acids: DNA and RNA; store and transmit genetic information.

Protein Structure

• Primary structure: Sequence of amino acids.

• Secondary structure: Alpha helices and beta sheets formed by hydrogen bonding.

• Tertiary structure: Overall 3D shape due to side chain interactions.

• Quaternary structure: Association of multiple polypeptide chains.

Enzymes

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

• Enzyme activity can be affected by temperature, pH, and inhibitors.

Nucleic Acids

• DNA: Double-stranded, contains deoxyribose sugar, bases A, T, C, G.

• RNA: Single-stranded, contains ribose sugar, bases A, U, C, G.

Additional info:

• Mutations in DNA can affect protein structure and function, leading to genetic disorders.

Chapter 4: A Tour of the Cell

Prokaryotic vs. Eukaryotic Cells

• Prokaryotic cells: Lack a nucleus and membrane-bound organelles; include bacteria and archaea.

• Eukaryotic cells: Have a nucleus and membrane-bound organelles; include plants, animals, fungi, and protists.

Cell Organelles and Their Functions

• Nucleus: Contains genetic material (DNA); controls cell activities.

• 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 for transport.

• Lysosomes: Contain digestive enzymes; break down waste.

• Mitochondria: Site of cellular respiration; produces ATP.

• Chloroplasts: Site of photosynthesis in plant cells.

• Cell membrane: Regulates movement of substances in and out of the cell.

• Cell wall: Provides structure and support in plant, fungal, and some prokaryotic cells.

Microscopy

• Light microscopes use light and lenses to magnify images.

• Electron microscopes (SEM, TEM) use beams of electrons for higher resolution imaging.

Surface Area to Volume Ratio

• Cells are small to maximize surface area relative to volume, increasing efficiency of material exchange.

Additional info:

• Specialized structures in eukaryotic cells allow compartmentalization of functions, increasing cellular efficiency.

Chapter 5: The Working Cell

Thermodynamics and Cellular Energy

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

• Second Law of Thermodynamics: Energy transformations increase entropy (disorder).

• Cells use energy from food to power cellular work, often using ATP as the energy currency.

Enzymes and Metabolism

• Enzymes lower activation energy, speeding up reactions.

• Metabolic pathways are sequences of enzyme-catalyzed reactions.

Cell Membrane Structure and Function

• Fluid Mosaic Model: Describes the cell membrane as a flexible bilayer of phospholipids with embedded proteins.

• Phospholipids: Have hydrophilic heads and hydrophobic tails, forming a bilayer.

• Membrane proteins function in transport, signaling, and cell recognition.

Transport Across Membranes

• Passive transport: Diffusion and facilitated diffusion; movement down concentration gradients without energy input.

• Osmosis: Diffusion of water across a selectively permeable membrane.

• Active transport: Movement against concentration gradients, requiring energy (ATP).

• Endocytosis and exocytosis: Bulk transport of materials into and out of cells via vesicles.

Example:

• Na+/K+ pump actively transports sodium and potassium ions across the membrane.

Chapter 6: How Cells Harvest Chemical Energy

Aerobic Cellular Respiration

• Cells extract energy from glucose in the presence of oxygen to produce ATP.

• Overall equation:

$C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + ATP$

• Occurs in three main stages: glycolysis, citric acid cycle (Krebs cycle), and oxidative phosphorylation (electron transport chain and chemiosmosis).

• ATP yield: About 32 ATP per glucose molecule.

Anaerobic Respiration and Fermentation

• Occurs without oxygen; glycolysis followed by fermentation (lactic acid or alcoholic).

• Lactic acid fermentation: Occurs in muscles; produces lactic acid.

• Alcoholic fermentation: Occurs in yeast; produces ethanol and CO2.

Additional info:

• Respiration provides energy for all cellular activities and is essential for life.

Chapter 7: Photosynthesis: Using Light to Make Food

Overview of Photosynthesis

• Photosynthesis converts solar energy into chemical energy, producing glucose and oxygen.

• Overall equation:

$6CO_2 + 6H_2O + \text{Light Energy} \rightarrow C_6H_{12}O_6 + 6O_2$

• Occurs in chloroplasts of plants and algae.

Light-Dependent and Light-Independent Reactions

• Light-dependent reactions: Capture light energy to produce ATP and NADPH; occur in thylakoid membranes.

• Calvin Cycle (light-independent reactions): Use ATP and NADPH to fix CO2 into glucose; occur in the stroma.

Adaptations and Environmental Factors

• C3, C4, and CAM plants: Different strategies for carbon fixation adapted to various environments.

• Stomata: Openings in leaves that regulate gas exchange and water loss.

Additional info:

• Photosynthesis is the foundation of most food chains and supports life on Earth by producing oxygen.

Chapter 8: The Cellular Basis of Reproduction and Inheritance

Cell Division and the Cell Cycle

• Cell division is essential for growth, repair, and reproduction.

• Cell cycle: Series of stages (G1, S, G2, M) that cells go through during division.

• Mitosis: Division of the nucleus, producing two genetically identical daughter cells.

• Cytokinesis: Division of the cytoplasm.

Chromosomes and Genetic Information

• Chromosomes: Structures made of DNA and proteins; carry genetic information.

• Homologous chromosomes: Pairs of chromosomes with the same genes but possibly different alleles.

• Sister chromatids: Identical copies of a chromosome joined together.

Regulation of the Cell Cycle

• Checkpoints ensure proper division; failure can lead to uncontrolled cell growth (cancer).

Meiosis and Genetic Variation

• Meiosis: Cell division that produces gametes (sperm and eggs) with half the chromosome number.

• Increases genetic variation through independent assortment and crossing over.

Genetic Disorders and Chromosome Abnormalities

• Non-disjunction can lead to abnormal chromosome numbers (e.g., Down syndrome, Turner syndrome).

Additional info:

• Genetic variation is essential for evolution and adaptation in populations.