Key Concepts in the Chemical Context of Life, Water and Life, Carbon Chemistry, Biological Macromolecules, and Cell Structure

Chapter 2: The Chemical Context of Life

Elements, Compounds, and Essential Elements

• Element: A substance that cannot be broken down into other substances by chemical means (e.g., Oxygen, Carbon).

• Compound: A substance consisting of two or more elements combined in a fixed ratio (e.g., H2O).

• Essential elements: Elements required for an organism to survive, grow, and reproduce. About 20–25% of the 92 natural elements are essential for life.

• Trace elements: Elements required by an organism in only minute quantities (e.g., Iron, Iodine).

Elements in Living Matter

• Approximately 96% of living matter is composed of carbon (C), hydrogen (H), oxygen (O), and nitrogen (N).

Atoms and Subatomic Particles

• Atom: The smallest unit of an element that retains the properties of that element.

• Subatomic particles: Protons (positive charge), neutrons (no charge), and electrons (negative charge).

Atomic Number, Mass Number, and Electron Shells

• Atomic number: Number of protons in an atom.

• Mass number: Sum of protons and neutrons in the nucleus.

• Valence electron: Electron in the outermost shell.

• Valence shell: Outermost electron shell of an atom.

Isotopes and Radioactive Isotopes

• Isotopes: Atoms of the same element with different numbers of neutrons.

• Radioactive isotopes: Isotopes that decay spontaneously, giving off particles and energy.

Chemical Bonds

• Covalent bond: Sharing of a pair of valence electrons by two atoms.

• Single bond: Sharing of one pair of electrons ($A - B$).

• Double bond: Sharing of two pairs of electrons ($A = B$).

• Electronegativity: Atom's attraction for electrons in a covalent bond.

• Polar covalent bond: Electrons are shared unequally due to differences in electronegativity.

• Nonpolar covalent bond: Electrons are shared equally.

• Ionic bond: Attraction between oppositely charged ions formed when electrons are transferred from one atom to another.

• Ion: Charged atom or molecule.

• Cation: Positively charged ion.

• Anion: Negatively charged ion.

• Hydrogen bond: Weak attraction between a hydrogen atom and an electronegative atom (often O or N).

• Van der Waals interaction: Weak attractions due to transient local partial charges.

Chemical Reactions and Equilibrium

• Chemical equilibrium: State in which the rate of the forward reaction equals the rate of the reverse reaction.

• Reactants: Starting materials in a chemical reaction.

• Products: Substances formed from a chemical reaction.

Chapter 3: Water and Life

Properties of Water

• Four emergent properties of water that support life:

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

  • Moderation of temperature: Water absorbs and releases heat with little temperature change.

  • Expansion upon freezing: Ice is less dense than liquid water.

  • Versatility as a solvent: Water dissolves many substances.

• Hydrogen bonds are responsible for these properties.

Cohesion, Adhesion, and Surface Tension

• Cohesion: Attraction between water molecules.

• Adhesion: Attraction between water molecules and other substances.

• Surface tension: Measure of how difficult it is to stretch or break the surface of a liquid.

Temperature Moderation

• Water moderates temperature by absorbing heat from warmer air and releasing stored heat to cooler air.

• Specific heat: Amount of heat required to raise 1 g of a substance by 1°C.

• Heat of vaporization: Heat required to convert 1 g of a liquid to gas.

• Evaporative cooling: As liquid evaporates, the surface cools down.

Solutions and Solubility

• Solution: Homogeneous mixture of two or more substances.

• Solvent: Dissolving agent (e.g., water).

• Solute: Substance dissolved in a solvent.

• Aqueous solution: Solution where water is the solvent.

• Hydrophilic: Substance that has an affinity for water.

• Hydrophobic: Substance that repels water.

Acids, Bases, and pH

• Hydrogen ion (H+): Proton released in water.

• Hydroxide ion (OH-): Water molecule that lost a proton.

• Hydronium ion (H3O+): Water molecule with an extra proton.

• Acid: Substance that increases H+ concentration in solution.

• Base: Substance that reduces H+ concentration.

• pH: Measure of H+ concentration; calculated as $pH = -\log_{10}[H^+]$

• As pH increases, [H+] decreases (solution becomes more basic); as pH decreases, [H+] increases (solution becomes more acidic).

• Buffer: Substance that minimizes changes in pH by accepting or donating H+.

Chapter 4: Carbon and the Molecular Diversity of Life

Organic Compounds and Hydrocarbons

• Organic compounds: Compounds containing carbon and hydrogen, often with oxygen, nitrogen, and other elements.

• Hydrocarbons: Organic molecules consisting only of carbon and hydrogen.

Complexity of Organic Molecules

• The ability of carbon to form four covalent bonds leads to a diversity of stable structures (chains, rings, branches).

• Carbon has 4 valence electrons and can form 4 covalent bonds.

Isomers

• Isomers: Compounds with the same molecular formula but different structures and properties.

• Structural isomers: Differ in covalent arrangements of atoms.

• Cis-trans (geometric) isomers: Differ in spatial arrangement around a double bond.

• Enantiomers: Mirror images of each other, differ in spatial arrangement around an asymmetric carbon.

Functional Groups

• Seven functional groups important in the chemistry of life:

  • Hydroxyl (-OH): Alcohols, polar.

  • Carbonyl (C=O): Ketones and aldehydes.

  • Carboxyl (-COOH): Acts as an acid.

  • Amino (-NH2): Acts as a base.

  • Sulfhydryl (-SH): Forms disulfide bonds.

  • Phosphate (-OPO32-): Contributes negative charge.

  • Methyl (-CH3): Affects gene expression.

Energy Source for Cellular Processes

• ATP (adenosine triphosphate) is the primary energy carrier in cells.

Chapter 5: The Structure and Function of Large Biological Molecules

Macromolecules, Polymers, and Monomers

• Macromolecule: Large molecule formed by joining smaller molecules (e.g., proteins, nucleic acids).

• Polymer: Long molecule consisting of many similar building blocks (monomers).

• Monomer: Small building block molecule.

• Enzyme: Protein that acts as a catalyst to speed up chemical reactions.

Dehydration and Hydrolysis Reactions

• Dehydration reaction: Two monomers bond together through the loss of a water molecule.

• Hydrolysis: Polymers are disassembled to monomers by the addition of water.

Carbohydrates

• Carbohydrates: Sugars and polymers of sugars.

• Monosaccharide: Simple sugar (e.g., glucose).

• Disaccharide: Two monosaccharides joined by a glycosidic linkage (e.g., sucrose).

• Polysaccharide: Many monosaccharides joined together (e.g., starch, glycogen, cellulose).

• Starch: Storage polysaccharide in plants; composed of glucose monomers.

• Glycogen: Storage polysaccharide in animals.

• Cellulose: Structural polysaccharide in plant cell walls; differs from starch in glycosidic linkages.

Lipids

• Lipids: Hydrophobic molecules, including fats, phospholipids, and steroids.

• Glycerol: Three-carbon alcohol; backbone of fats.

• Fatty acid: Long hydrocarbon chain with a carboxyl group.

• Triglyceride: Three fatty acids linked to glycerol.

• Phospholipid: Two fatty acids and a phosphate group attached to glycerol; major component of cell membranes.

• Saturated fatty acid: No double bonds; solid at room temperature.

• Unsaturated fatty acid: One or more double bonds; liquid at room temperature.

Proteins

• Proteins: Polymers of amino acids; perform many functions (enzymes, structure, transport, etc.).

• Amino acid: Organic molecule with amino and carboxyl groups.

• Four levels of protein structure:

  • Primary: Sequence of amino acids.

  • Secondary: Coils and folds (alpha helix, beta sheet) due to hydrogen bonds.

  • Tertiary: Overall 3D shape due to interactions among R groups.

  • Quaternary: Association of multiple polypeptides.

Nucleic Acids

• Nucleic acids: Polymers of nucleotides (DNA and RNA).

• Nucleotide: Nitrogenous base, pentose sugar, and phosphate group.

• Nucleoside: Nitrogenous base and sugar (no phosphate).

• DNA: Deoxyribonucleic acid; stores genetic information.

• RNA: Ribonucleic acid; involved in protein synthesis.

• Nitrogenous bases in DNA: Adenine (A), Thymine (T), Cytosine (C), Guanine (G).

• Two families: Pyrimidines (C, T, U) and Purines (A, G).

• DNA structure: Double helix with complementary base pairing (A-T, C-G).

Chapter 6: A Tour of the Cell

Microscopy

• Types of microscopes:

  • Light microscope (LM): Uses visible light; lower resolution.

  • Electron microscope (EM): Uses electron beams; higher resolution.

Prokaryotic vs. Eukaryotic Cells

• Prokaryotic cells: No nucleus or membrane-bound organelles; DNA in nucleoid region (e.g., bacteria, archaea).

• Eukaryotic cells: Have nucleus and membrane-bound organelles (e.g., plants, animals, fungi, protists).

Organelles and Their Functions

• Organelle: Specialized structure within a cell with a specific function.

• Nucleus: Contains genetic material (DNA).

• Ribosomes: Synthesize proteins.

• Rough ER: Protein synthesis and modification; has ribosomes.

• Smooth ER: Lipid synthesis, detoxification.

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

• Lysosomes: Digestive organelles; break down macromolecules.

• Vacuoles: Storage and structural support (large central vacuole in plants).

• Plasma/cell membrane: Selective barrier; regulates passage of substances.

• Mitochondria: Site of cellular respiration; produces ATP.

• Chloroplasts: Site of photosynthesis in plants and algae.

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

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

• Cell wall: Rigid structure outside plasma membrane (plants, fungi, some protists).

Chromosomes and Chromatin

• Chromosome: DNA molecule with associated proteins; carries genetic information.

• Chromatin: Complex of DNA and proteins in the nucleus; condenses to form chromosomes during cell division.

Endomembrane System

• Includes nuclear envelope, ER, Golgi apparatus, lysosomes, vacuoles, and plasma membrane; involved in synthesis, transport, and metabolism of cellular products.

Cell Junctions

• Structures that connect cells together and facilitate communication.

• Types include tight junctions, desmosomes, and gap junctions (animals); plasmodesmata (plants).

Animal vs. Plant Cells

Feature	Animal Cell	Plant Cell
Cell Wall	No	Yes
Chloroplasts	No	Yes
Central Vacuole	No (small vacuoles)	Yes (large)
Lysosomes	Yes	Rare

Example: Plant cells have a rigid cell wall and chloroplasts for photosynthesis, while animal cells do not.