Ch. 2 The Chemistry of Life: Structured Study Notes for Anatomy & Physiology

Atoms: The Smallest Unit of Matter

Definition and Structure of Matter

All physical substances are composed of matter, which takes up space and has mass. Matter is made up of chemical elements, and each element consists of atoms—the smallest unit of an element and of matter itself.

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

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

• Atom: The smallest unit of an element, forming both living and nonliving matter.

Atomic Structure and Subatomic Particles

Atoms are composed of three main subatomic particles, each with distinct properties:

• Proton: Positively charged, mass of 1 atomic mass unit (AMU), located in the nucleus.

• Neutron: No charge, mass of 1 AMU, located in the nucleus.

• Electron: Negatively charged, almost no mass, found in electron shells orbiting the nucleus.

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

Examples of Atomic Structure

Carbon atoms are commonly used to illustrate atomic structure, showing protons and neutrons in the nucleus and electrons in surrounding shells.

Elements of Life and Atomic Properties

Elements Essential for Life

Only a small subset of elements are found in living organisms. The periodic table arranges all known elements based on their chemical properties. The majority of biological mass is composed of Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur (CHNOPS).

Atomic Number, Mass Number, and Atomic Mass

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

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

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

Electron Orbitals, Energy Shells, and the Octet Rule

Electron Orbitals and Energy Shells

Electrons occupy three-dimensional regions called orbitals, visualized as energy shells. Shells closer to the nucleus are lower in energy, while distant shells are higher in energy. The outermost shell contains valence electrons, which determine chemical reactivity.

• 1st shell: up to 2 electrons

• 2nd shell: up to 8 electrons

The Octet Rule

Atoms are most stable when their valence shells are fully occupied, typically with 8 electrons (except for hydrogen and helium).

Isotopes and Atomic Mass

Definition and Examples of Isotopes

Isotopes are atoms of the same element with different numbers of neutrons, resulting in different mass numbers but the same atomic number.

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

Chemical Bonding

Types of Chemical Bonds

Chemical bonds are attractive forces holding atoms together in molecules and compounds. Bonds can be intramolecular (within a molecule) or intermolecular (between molecules).

• Molecule: Substance containing two or more chemically bound atoms (e.g., O2).

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

Covalent Bonds

Covalent bonds involve the sharing of electrons between atoms. There are two main types:

• Nonpolar Covalent: Equal sharing of electrons (similar electronegativities).

• Polar Covalent: Unequal sharing of electrons (different electronegativities), resulting in partial charges (δ).

Noncovalent Bonds: Ionic, Hydrogen, and Van der Waals

Ionic Bonding

Ionic bonds are formed by electrical attractions between oppositely charged ions (cations and anions), resulting from the transfer of electrons.

• Anion: Negatively charged ion (gains electron).

• Cation: Positively charged ion (loses electron).

Hydrogen Bonding

Hydrogen bonds are weak interactions between a highly electronegative atom (F, O, or N) and a hydrogen atom. They are crucial for the properties of water and the structure of macromolecules.

Properties of Water

Cohesion, Adhesion, and Surface Tension

Water molecules exhibit cohesion (stick to each other) and adhesion (stick to other substances), resulting in high surface tension.

Density of Water and Ice

Liquid water is more densely packed than solid ice, which forms a lattice structure with stable hydrogen bonds. This causes ice to float and allows aquatic life to survive beneath frozen surfaces.

Thermal Properties: Specific Heat and Heat of Vaporization

• Specific Heat: Amount of heat required to raise/lower 1 gram of a substance by 1°C.

• Heat of Vaporization: Amount of heat required to convert 1 gram of liquid to gas.

Water as a Universal Solvent

Water dissolves many substances due to its polarity, forming aqueous solutions. Hydrophilic substances dissolve easily, while hydrophobic substances do not.

Acids, Bases, and the pH Scale

Acids and Bases

• Acid: Increases concentration of H+ ions in solution.

• Base: Decreases concentration of H+ ions, often by increasing OH- ions.

pH Scale

pH measures the concentration of H+ ions in solution, ranging from 0 (acidic) to 14 (basic). Neutral pH is 7.

Buffers

Buffers resist changes in pH by donating or accepting H+ ions, helping organisms maintain homeostasis.

Carbon and Biomolecules

Carbon as a Building Block

Carbon forms four covalent bonds, allowing for diverse molecular structures. Organic molecules contain carbon and hydrogen, and may include functional groups that confer specific properties.

Functional Groups

• Common functional groups: hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), phosphate (-PO4), methyl (-CH3), sulfhydryl (-SH).

Biomolecules: Carbohydrates, Proteins, Nucleic Acids, and Lipids

Monomers and Polymers

• Monomer: Small building block molecule.

• Polymer: Long chain of monomers linked by covalent bonds.

• Dehydration Synthesis: Forms polymers by removing water.

• Hydrolysis: Breaks polymers into monomers by adding water.

Carbohydrates

• Monosaccharide: Single sugar unit (e.g., glucose).

• Disaccharide: Two covalently linked monosaccharides.

• Polysaccharide: More than 20 linked monosaccharides (e.g., starch, glycogen, cellulose).

• Functions: Structural support and energy storage.

Proteins

• Amino Acid: Monomer of proteins.

• Peptide Bond: Covalent bond linking amino acids.

• Structure Levels: Primary, secondary, tertiary, quaternary.

• Denaturation: Loss of protein function due to environmental changes.

• Chaperone Proteins: Assist in protein folding.

Nucleic Acids

• Nucleotide: Monomer of nucleic acids (DNA, RNA).

• Phosphodiester Bond: Covalent bond linking nucleotides.

• DNA: Double helix, stores genetic information.

• RNA: Single strand, involved in protein synthesis.

Lipids

• Hydrophobic: Insoluble in water.

• Fatty Acids: Saturated (single bonds, solid) or unsaturated (double bonds, liquid).

• Triglycerides: Three fatty acids linked to glycerol.

• Phospholipids: Major component of cell membranes, amphipathic.

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

• Waxes: Protective, prevent water loss.

Energy and Thermodynamics

Potential vs. Kinetic Energy

• Potential Energy: Stored energy available to do work.

• Kinetic Energy: Energy of motion.

Laws of Thermodynamics

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

• Second Law: Energy conversions are not 100% efficient; some energy is lost as heat, increasing entropy.

Chemical Reactions and ATP

Chemical Reactions

• Reactants: Starting materials.

• Products: Resulting materials.

• Endergonic: Requires energy input.

• Exergonic: Releases energy.

ATP: Cellular Energy Currency

• ATP: Adenosine triphosphate, stores and releases energy for cellular work.

• Hydrolysis: Releases energy by breaking phosphate bonds.

• Energy Coupling: ATP hydrolysis powers endergonic reactions.

• Phosphorylation: Transfer of phosphate group to another molecule.

Enzymes: Biological Catalysts

Enzyme Function and Activity

• Enzyme: Catalyzes chemical reactions without being consumed.

• Substrate: Reactant in an enzyme-catalyzed reaction.

• Activation Energy (EA): Minimum energy required to start a reaction.

• Enzyme-Substrate Complex: Temporary binding of substrate to enzyme's active site.

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

Enzyme Inhibition

• Competitive Inhibitor: Competes for active site.

• Noncompetitive Inhibitor: Binds to allosteric site, changing enzyme shape.

Key Equations and Concepts

• Mass Number: $\text{Mass Number} = \text{Number of Protons} + \text{Number of Neutrons}$

• Atomic Mass (Weighted Average): $\text{Atomic Mass} = \sum (\text{Isotope Mass} \times \text{Fractional Abundance})$

• pH: $\text{pH} = -\log_{10}[\text{H}^+]$

Additional info: Academic context and explanations have been expanded for clarity and completeness. Only images directly relevant to the explanation have been included.