Chapter 2: Basic Chemistry – Matter, Energy, and Biochemistry

Basic Chemistry

Matter and Energy

Understanding matter and energy is fundamental to the study of anatomy and physiology. Matter is anything that occupies space and has mass, while energy is the ability to do work.

• States of Matter:

  • Solid: Definite shape and volume.

  • Liquid: Definite volume; takes the shape of its container.

  • Gas: Neither definite shape nor volume.

• Physical Changes: Do not alter the basic nature of a substance (e.g., changes in state).

• Chemical Changes: Alter the chemical composition of a substance.

• Energy: Has no mass and does not take up space.

  • Kinetic Energy: Energy in action, doing work.

  • Potential Energy: Stored energy, inactive.

• Forms of Energy:

  • Chemical: Stored in chemical bonds.

  • Electrical: Movement of charged particles.

  • Mechanical: Directly involved in moving matter.

  • Radiant: Travels in waves (electromagnetic spectrum).

• Energy Conversion: ATP traps chemical energy from food in its bonds.

Composition of Matter

Elements are the fundamental units of matter. The human body is primarily composed of four elements: oxygen, carbon, hydrogen, and nitrogen.

• Elements: Listed in the periodic table; each has a unique atomic symbol.

• Atoms: Building blocks of elements; differ from one another.

The Basic Atomic Subparticles

• Protons (P+): Positively charged.

• Neutrons (n0): Neutral, uncharged.

• Electrons (e-): Negatively charged.

• Atoms are electrically neutral: Number of protons equals number of electrons.

• Ions: Atoms that have lost or gained electrons.

Models of the Atom

• Planetary Model: Protons and neutrons in nucleus; electrons orbit around.

• Orbital Model: Electrons depicted as a cloud outside the nucleus.

• Electrons: Determine chemical behavior and bonding properties.

Identifying Elements

• Atomic Number: Number of protons; unique to each element.

• Atomic Mass Number: Sum of protons and neutrons.

• Atomic Weight: Approximate mass of the most abundant isotope.

Isotopes and Radioactivity

• Isotopes: Same number of protons/electrons, different number of neutrons.

• Radioisotopes: Unstable, undergo spontaneous decay (radioactivity).

• Applications: Used to tag and trace biological molecules.

Molecules and Compounds

• Molecule: Two or more atoms of the same element combined chemically.

• Compound: Two or more atoms of different elements combined chemically.

• Chemical Equation Example:

  • $\text{H} + \text{H} \rightarrow \text{H}_2$

  • $4\text{H} + \text{C} \rightarrow \text{CH}_4$

Chemical Bonds and Reactions

Role of Electrons

Electrons occupy energy levels called shells. The outermost shell (valence shell) determines chemical bonding.

• Shell Capacities:

  • Shell 1: 2 electrons

  • Shell 2: 8 electrons

  • Shell 3: 18 electrons

• Rule of Eights: Atoms are stable with 8 electrons in the valence shell (except shell 1).

• Reactive Elements: Atoms with less than 8 electrons in the valence shell will gain, lose, or share electrons.

Types of Chemical Bonds

• Ionic Bonds: Electrons are transferred from one atom to another.

  • Anion: Negative charge (gains electron).

  • Cation: Positive charge (loses electron).

• Covalent Bonds: Electrons are shared between atoms.

  • Single: One pair shared.

  • Double: Two pairs shared.

  • Nonpolar: Electrons shared equally (e.g., carbon dioxide).

  • Polar: Electrons shared unequally (e.g., water).

• Hydrogen Bonds: Weak bonds; hydrogen attracted to negative portion of polar molecule. Important for water surface tension and protein structure.

Patterns of Chemical Reactions

• Synthesis Reaction: $\text{A} + \text{B} \rightarrow \text{AB}$ (anabolic, energy absorbed).

• Decomposition Reaction: $\text{AB} \rightarrow \text{A} + \text{B}$ (catabolic, energy released).

• Exchange Reaction: $\text{AB} + \text{C} \rightarrow \text{AC} + \text{B}$ or $\text{AB} + \text{CD} \rightarrow \text{AD} + \text{CB}$ (simultaneous synthesis and decomposition).

• Reversible Reactions: Indicated by double arrows; direction depends on arrow length.

Biochemistry: The Chemical Composition of Living Matter

Inorganic Compounds

• Water: Most abundant; vital properties include high heat capacity, polarity/solvent properties, chemical reactivity, and cushioning.

• High Heat Capacity: Absorbs/releases heat, stabilizes body temperature.

• Polarity/Solvent Properties: Universal solvent; forms solutions and colloids.

• Chemical Reactivity: Hydrolysis reactions (e.g., digestion).

• Cushioning: Protects organs (e.g., cerebrospinal fluid, amniotic fluid).

• Salts: Ionic compounds; dissociate into ions; vital for nerve impulses.

• Electrolytes: Conduct electrical currents.

• Acids: Release H+ ions; proton donors; strong acids ionize completely.

• Bases: Release OH- ions; proton acceptors.

• Neutralization Reaction: Acid + base → water + salt.

  • $\text{NaOH} + \text{HCl} \rightarrow \text{H}_2\text{O} + \text{NaCl}$

• pH: Measures H+ concentration; scale 0–14; 7 is neutral.

  • Acidic: pH < 7 (more H+)

  • Basic: pH > 7 (fewer H+)

  • Each unit change = tenfold change in H+ concentration.

• Buffers: Regulate pH changes.

Organic Compounds

• Contain carbon; large, covalent molecules.

• Polymers: Chainlike molecules made of repeating units (monomers).

• Dehydration Synthesis: Joins monomers by removing water.

• Hydrolysis: Breaks polymers into monomers by adding water.

Carbohydrates

• Contain: Carbon, hydrogen, oxygen.

• Types:

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

  • Disaccharides: Two simple sugars joined (e.g., sucrose, lactose).

  • Polysaccharides: Long chains; storage (e.g., starch, glycogen).

Lipids

• Contain: Carbon, hydrogen, oxygen (C and H outnumber O).

• Types:

  • Triglycerides: Fat deposits; energy storage; made of glycerol and fatty acids.

  • Saturated Fats: Single bonds; solid at room temperature.

  • Unsaturated Fats: Double bonds; liquid at room temperature; heart healthy.

  • Trans Fats: Hydrogenated oils; increase heart disease risk.

  • Omega-3 Fatty Acids: Found in fish and plants; decrease heart disease risk.

  • Phospholipids: Two fatty acid chains (hydrophobic) and a charged head (hydrophilic); form cell membranes.

  • Steroids: Four interlocking rings; include cholesterol, bile salts, vitamin D, hormones.

Proteins

• Contain: Carbon, oxygen, hydrogen, nitrogen, sometimes sulfur.

• Functions: Construction materials, enzymes, hormones, antibodies.

• Built from: Amino acids (contain amine group NH2, acid group COOH, and variable R-group).

• Structure:

  • Primary: Amino acid sequence.

  • Secondary: Twisting/bending (alpha helix, beta-pleated sheet).

  • Tertiary: Compact, globular structure.

  • Quaternary: Combination of polypeptide chains.

• Types:

  • Fibrous (structural): Collagen, keratin; stable.

  • Globular (functional): Antibodies, hormones, enzymes; can be denatured.

• Enzymes: Biological catalysts; increase reaction rates; bind substrates at active site; names end in -ase (e.g., hydrolase, oxidase).

Nucleic Acids

• Form genes; composed of carbon, oxygen, hydrogen, nitrogen, phosphorus.

• Built from: Nucleotides (nitrogenous base, pentose sugar, phosphate group).

• Bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T), Uracil (U).

• DNA: Double-stranded helix; deoxyribose sugar; bases A, T, C, G; found in nucleus; replicates before cell division.

• RNA: Single-stranded; ribose sugar; bases A, U, C, G; three types: messenger, transfer, ribosomal.

Adenosine Triphosphate (ATP)

• Structure: Ribose sugar, adenine base, three phosphate groups.

• Function: Chemical energy for cells; energy released by breaking phosphate bond.

• ADP: Accumulates as ATP is used; ATP replenished by oxidation of food fuels.

Summary Table: Types of Chemical Bonds

Bond Type	Mechanism	Example	Strength
Ionic	Transfer of electrons	NaCl	Moderate
Covalent (Nonpolar)	Equal sharing of electrons	O2, CO2	Strong
Covalent (Polar)	Unequal sharing of electrons	H2O	Strong
Hydrogen	Attraction between H and negative portion of polar molecule	Between water molecules	Weak

Example: ATP Hydrolysis

ATP hydrolysis releases energy for cellular work:

• $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i + \text{energy}$

Additional info: The notes have been expanded to include definitions, examples, and a summary table for chemical bonds. Equations are provided in LaTeX format as required.