The Chemistry of Life: Foundations for Anatomy & Physiology

Ch. 2 The Chemistry of Life

Atoms: The Smallest Unit of Matter

All matter is composed of atoms, which are the fundamental building blocks of chemical elements. Atoms combine to form all substances, both living and nonliving.

• Matter: Anything that occupies space and has mass (e.g., organisms, rocks, water).

• Chemical Element: A pure substance made of only one type of atom.

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

Atomic Structure: Atoms are composed of three subatomic particles:

• Protons: Positively charged, located in the nucleus, mass = 1 AMU.

• Neutrons: No charge, located in the nucleus, mass = 1 AMU.

• Electrons: Negatively charged, orbit the nucleus, mass ≈ 0 AMU.

Subatomic Particle	Electric Charge	Atomic Mass Unit (AMU)	Location
Proton	+1	1	Nucleus
Neutron	0	1	Nucleus
Electron	-1	0	Electron shell

Elements of Life and Atomic Properties

Only a small subset of elements are essential for life, with the majority of living mass composed of Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur (CHNOPS).

• Atomic Number: Number of protons in the nucleus; defines the element.

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

• Atomic Mass: Weighted average mass of all isotopes of an element.

Electron Orbitals and Energy Shells

Electrons occupy energy shells (orbitals) around the nucleus. The arrangement of electrons determines chemical reactivity.

• Shells closer to the nucleus are lower in energy; distant shells are higher in energy.

• Valence Electrons: Electrons in the outermost shell, important for bonding.

• 1st shell holds up to 2 electrons; 2nd shell up to 8 electrons.

The Octet Rule

Atoms are most stable when their valence shell is full (usually 8 electrons, except for the first shell which is full at 2).

• Atoms with incomplete valence shells are more reactive.

• Atoms gain, lose, or share electrons to achieve a full valence shell.

Isotopes

Isotopes are atoms of the same element with different numbers of neutrons, resulting in different mass numbers but identical chemical properties.

• Example: Carbon-12, Carbon-13, and Carbon-14 all have 6 protons but differ in neutrons.

• Radioactive Isotopes: Unstable isotopes that decay, emitting radiation.

Isotope	Protons	Neutrons	Electrons
Carbon-12	6	6	6
Carbon-13	6	7	6
Carbon-14	6	8	6

Chemical Bonds

Chemical bonds are attractive forces that hold atoms together in molecules and compounds.

• Molecule: Two or more atoms chemically bonded (e.g., O2).

• Compound: Molecule composed of two or more different elements (e.g., H2O).

• Intramolecular Bonds: Bonds within a molecule.

• Intermolecular Bonds: Bonds between molecules.

Covalent Bonds

Covalent bonds involve the sharing of electron pairs between atoms. They are the strongest type of chemical bond in biological molecules.

• Nonpolar Covalent Bonds: Equal sharing of electrons (e.g., O2).

• Polar Covalent Bonds: Unequal sharing of electrons, resulting in partial charges (e.g., H2O).

• Electronegativity: The tendency of an atom to attract electrons in a bond.

Noncovalent Bonds

Noncovalent bonds do not involve sharing electrons. They include ionic bonds, hydrogen bonds, and van der Waals interactions.

• Ionic Bonds: Attraction between oppositely charged ions (cations and anions).

• Hydrogen Bonds: Weak attraction between a hydrogen atom and an electronegative atom (F, O, N).

• Van der Waals Forces: Weak, transient attractions between molecules.

Water: Structure and Properties

Water is a polar molecule with unique properties essential for life, largely due to its ability to form hydrogen bonds.

• Cohesion: Water molecules stick to each other.

• Adhesion: Water molecules stick to other substances.

• Surface Tension: Difficulty of breaking the surface of water due to cohesion.

• High Specific Heat: Water resists temperature changes, helping maintain homeostasis.

• High Heat of Vaporization: Large amount of energy required for water to evaporate.

• Density: Ice is less dense than liquid water, allowing it to float.

• Universal Solvent: Water dissolves many substances due to its polarity.

Acids, Bases, and pH

The concentration of hydrogen ions (H+) in solution determines acidity or basicity, measured by the pH scale.

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

• Base: Substance that decreases H+ concentration (often by releasing OH-).

• pH Scale: Ranges from 0 (acidic) to 14 (basic), with 7 being neutral.

• Buffers: Substances that minimize changes in pH by accepting or donating H+.

Carbon and Organic Molecules

Carbon is the backbone of organic molecules, capable of forming four covalent bonds and a variety of structures (chains, rings, branches).

• Organic Molecules: Contain carbon and hydrogen, often with oxygen, nitrogen, phosphorus, or sulfur.

• Hydrocarbons: Molecules made only of carbon and hydrogen.

• Functional Groups: Specific groups of atoms that confer chemical reactivity (e.g., hydroxyl, carboxyl, amino, phosphate).

Biomolecules: Monomers and Polymers

Biomolecules are essential organic molecules in living organisms, classified into four main types: carbohydrates, proteins, nucleic acids, and lipids.

• Monomers: Small building blocks (e.g., monosaccharides, amino acids, nucleotides).

• Polymers: Long chains of monomers (e.g., polysaccharides, polypeptides, nucleic acids).

• Dehydration Synthesis: Links monomers by removing water to form polymers.

• Hydrolysis: Breaks polymers into monomers by adding water.

Carbohydrates

Carbohydrates are hydrated carbon molecules, serving as energy sources and structural components.

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

• Disaccharides: Two monosaccharides linked together (e.g., maltose).

• Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen, cellulose).

• Glycosidic Bonds: Covalent bonds linking monosaccharides.

• Functions: Energy storage (starch in plants, glycogen in animals), structural support (cellulose, chitin).

Proteins

Proteins are polymers of amino acids, performing a vast array of functions in cells.

• Amino Acids: Monomers with a central carbon, amino group, carboxyl group, and variable R-group.

• Peptide Bonds: Covalent bonds linking amino acids.

• Levels of Structure:

  • Primary: Sequence of amino acids.

  • Secondary: Alpha-helices and beta-sheets (hydrogen bonding).

  • Tertiary: 3D folding of a single polypeptide.

  • Quaternary: Association of multiple polypeptides.

• Denaturation: Loss of protein structure (and function) due to environmental changes.

• Chaperone Proteins: Assist in proper folding or refolding of proteins.

Nucleic Acids

Nucleic acids store and transmit genetic information. They are polymers of nucleotides.

• Nucleotide: Composed of a phosphate group, pentose sugar (ribose or deoxyribose), and nitrogenous base.

• DNA: Double helix, stores genetic information, bases: A, T, C, G.

• RNA: Single-stranded, involved in protein synthesis, bases: A, U, C, G.

• Phosphodiester Bonds: Link nucleotides in a chain.

Lipids

Lipids are hydrophobic molecules, diverse in structure and function, and do not form true polymers.

• Fats (Triglycerides): Glycerol + 3 fatty acids (energy storage).

• Phospholipids: Glycerol + 2 fatty acids + phosphate group (major component of cell membranes, amphipathic).

• Steroids: Four fused carbon rings (e.g., cholesterol).

• Waxes: Fatty acids bound to long-chain alcohols (protection, water loss prevention).

Energy and Thermodynamics

Energy is the capacity to do work. Biological systems obey the laws of thermodynamics.

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

• Kinetic Energy: Energy of motion.

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

• Second Law: Energy transformations increase entropy (disorder); some energy is lost as heat.

Chemical Reactions and Enzymes

Chemical reactions involve making or breaking bonds. Enzymes are biological catalysts that speed up reactions by lowering activation energy.

• Reactants: Starting materials.

• Products: Resulting materials.

• Endergonic Reactions: Require energy input.

• Exergonic Reactions: Release energy.

• ATP: Main energy currency of the cell; hydrolysis releases energy for cellular work.

• Enzyme-Substrate Complex: Temporary association during catalysis.

• Cofactors and Coenzymes: Non-protein helpers for enzyme function.

• Enzyme Inhibition: Competitive (active site) or noncompetitive (allosteric site) inhibition regulates enzyme activity.

*Additional info: This summary expands on the provided notes with academic context, definitions, and examples to ensure completeness and clarity for college-level study.*