General Biology Study Notes: Chemical Context of Life, Water, Carbon, Biological Molecules, and Cell Structure

Chapter 2: The Chemical Context of Life

Concept 2.1: Matter

Matter is anything that takes up space and has mass. All living organisms are composed of matter, which consists of elements and compounds.

• Element: A substance that cannot be broken down by chemical reactions.

• Compound: A substance consisting of two or more elements in a fixed ratio.

• Example: Water (H2O) and sodium chloride (NaCl).

Concept 2.2: Atomic Structure and Properties

The properties of an element depend on the structure of its atoms, which are composed of protons, neutrons, and electrons.

• Atomic Number: Number of protons in the nucleus.

• Mass Number: Sum of protons and neutrons.

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

• Radioactive Isotopes: Decay spontaneously, emitting particles and energy.

Electron Distribution and Chemical Properties

The chemical behavior of an atom is determined by the distribution of electrons in electron shells.

• Valence Electrons: Electrons in the outermost shell.

• Valence Shell: The outermost electron shell.

Concept 2.3: Chemical Bonds

Chemical bonds form when atoms share or transfer valence electrons. The major types are covalent, ionic, and hydrogen bonds.

• Covalent Bond: Sharing of a pair of valence electrons.

• Ionic Bond: Transfer of electrons, resulting in charged ions.

• Hydrogen Bond: Weak bond between a hydrogen atom and an electronegative atom.

Electronegativity and Polar Covalent Bonds

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

• Polar Covalent Bond: Unequal sharing of electrons, causing partial charges.

Chapter 3: Water and Life

Water: The Molecule That Supports Life

Water is essential for life, existing in all three physical states and supporting biological processes.

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

• Hydrogen Bonds: Responsible for water's unique properties.

Concept 3.1: Cohesion and Adhesion

• Cohesion: Water molecules stick together via hydrogen bonds.

• Adhesion: Water molecules stick to other substances.

Concept 3.2: Moderation of Temperature

• High Specific Heat: Water resists temperature changes.

• Evaporative Cooling: Heat is removed as water evaporates.

Concept 3.3: Floating of Ice

• Ice floats because hydrogen bonds keep water molecules apart, making ice less dense than liquid water.

Concept 3.4: Water as a Solvent

• Solution: Homogeneous mixture of substances.

• Solvent: Dissolving agent (water).

• Solute: Substance dissolved.

• Hydrophilic: Affinity for water.

• Hydrophobic: Repels water.

Concept 3.5: Acids, Bases, and pH

• Acid: Increases H+ concentration.

• Base: Reduces H+ concentration.

• pH Scale: $pH = -\log[H^+]$

Chapter 4: Carbon and the Molecular Diversity of Life

Carbon: The Backbone of Life

Carbon's ability to form four covalent bonds makes it the basis for organic molecules.

• Organic Chemistry: Study of carbon compounds.

• Hydrocarbons: Molecules consisting of only carbon and hydrogen.

Concept 4.1: Organic Diversity

• Carbon chains vary in length, branching, double bond position, and ring structure.

Concept 4.2: Functional Groups

• Functional groups are key to molecular function.

Functional Group	Properties
Hydroxyl	Polar, forms hydrogen bonds
Carbonyl	Polar, found in sugars
Carboxyl	Acidic, donates H+
Amino	Basic, accepts H+
Sulfhydryl	Forms disulfide bonds
Phosphate	Contributes negative charge
Methyl	Non-polar

Chapter 5: The Structure and Function of Large Biological Molecules

The Molecules of Life

Biological macromolecules include carbohydrates, lipids, proteins, and nucleic acids.

• Polymer: Long molecule made of repeating units (monomers).

• Dehydration Reaction: Joins monomers by removing water.

• Hydrolysis: Breaks polymers by adding water.

Concept 5.2: Carbohydrates

• Monosaccharides: Simple sugars (e.g., glucose).

• Disaccharides: Two monosaccharides joined by glycosidic linkage.

• Polysaccharides: Polymers of sugars (e.g., starch, cellulose).

Concept 5.3: Lipids

• Fats: Constructed from glycerol and fatty acids.

• Phospholipids: Major component of cell membranes.

• Steroids: Lipids with four fused rings (e.g., cholesterol).

Concept 5.4: Proteins

• Amino Acids: Monomers of proteins, each with an amino and carboxyl group.

• Polypeptide: Polymer of amino acids.

• Protein Structure: Four levels: primary, secondary, tertiary, quaternary.

Level	Description
Primary	Sequence of amino acids
Secondary	Hydrogen bonds form alpha helices and beta sheets
Tertiary	Interactions among R groups
Quaternary	Multiple polypeptide chains

Concept 5.5: Nucleic Acids

• DNA: Double helix, stores genetic information.

• RNA: Single-stranded, involved in protein synthesis.

Chapter 6: A Tour of the Cell

The Fundamental Units of Life

All organisms are made of cells, which are the basic units of life.

• Prokaryotic Cells: No nucleus, DNA in nucleoid, no membrane-bound organelles.

• Eukaryotic Cells: Nucleus, membrane-bound organelles.

Concept 6.2: Internal Membranes

• Compartmentalization allows specialization of cellular functions.

Concept 6.3: Genetic Instructions

• Nucleus: Contains most DNA, surrounded by nuclear envelope.

• Chromosomes: DNA organized into units.

• Ribosomes: Sites of protein synthesis.

Concept 6.4: Endomembrane System

• Endoplasmic Reticulum (ER): Smooth (lipid synthesis) and rough (protein synthesis).

• Golgi Apparatus: Modifies, sorts, and ships proteins.

• Lysosomes: Digestive compartments.

• Vacuoles: Storage and maintenance.

Concept 6.5: Energy Conversion

• Mitochondria: Sites of cellular respiration, produce ATP.

• Chloroplasts: Sites of photosynthesis in plants and algae.

Concept 6.6: Cytoskeleton

• Microtubules: Shape, support, and motility.

• Microfilaments: Actin filaments, cell movement.

• Intermediate Filaments: Support cell shape.

Concept 6.7: Extracellular Components

• Cell Wall: Found in plants, provides protection and structure.

• Extracellular Matrix (ECM): Animal cells, made of glycoproteins.

• Cell Junctions: Tight, desmosomes, and gap junctions coordinate cellular activities.