Chapter 2: The Chemistry of Life – Foundations for Anatomy & Physiology

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The Chemistry of Life

Introduction: The Role of Chemistry in Anatomy & Physiology

Chemistry forms the foundation of all biological processes in the human body. Understanding the chemical level of organization is essential for comprehending the structure and function of cells, tissues, and organs in anatomy and physiology.

Chemical Level of Organization: The most basic structural level, involving atoms and molecules.
Example: Bones are strong due to minerals and the protein collagen, both of which are chemicals.
Importance: All physiological processes are based on chemical interactions.

Atoms and Elements

Definitions and Basic Concepts

Matter: Anything that has mass and occupies space.
Chemistry: The study of matter and its interactions.
Atom: The smallest unit of matter that retains its original properties.
Element: A substance composed of one or more identical atoms; cannot be broken down into simpler substances by chemical means.

Atoms and Atomic Structure

Subatomic Particles

Protons (p+): Positively charged particles located in the atomic nucleus.
Neutrons (n0): Uncharged particles, slightly larger than protons, also in the nucleus.
Electrons (e-): Negatively charged, tiny particles that orbit the nucleus in electron shells.

Atomic Neutrality and Electron Shells

Atoms are electrically neutral because the number of protons equals the number of electrons.
The number of neutrons may vary, resulting in different isotopes.
Most atomic mass comes from protons and neutrons.
Electron Shells:
- 1st shell: holds up to 2 electrons
- 2nd shell: holds up to 8 electrons
- 3rd shell: holds up to 18 electrons (but is stable with 8)

Example: Carbon Atom

6 protons, 6 neutrons, 6 electrons

Elements in the Human Body

Major, Mineral, and Trace Elements

Major Elements (96% of body mass):
- Oxygen (O): 65%
- Carbon (C): 18%
- Hydrogen (H): 10%
- Nitrogen (N): 3%
Mineral Elements (<4%): Sodium (Na), Potassium (K), Calcium (Ca), Chloride (Cl), Magnesium (Mg), Phosphorus (P), Sulfur (S)
Trace Elements: Iron (Fe), Copper (Cu), Iodine (I), Zinc (Zn), and others

Isotopes and Radioactivity

Definitions and Applications

Mass Number: Total number of protons and neutrons in the nucleus.
Isotope: Atoms with the same number of protons but different numbers of neutrons.
Radioisotopes: Unstable isotopes that emit energy (radiation); used in nuclear medicine.

Example: Hydrogen Isotopes

Hydrogen-1: 0 neutrons
Deuterium (Hydrogen-2): 1 neutron
Tritium (Hydrogen-3): 2 neutrons

Matter Combined: Mixtures and Chemical Bonds

Mixtures

Mixture: Physical combination of atoms; can be separated physically.
Molecule: Chemical combination of atoms; can only be separated by chemical means.

Types of Mixtures

Suspensions: Liquid with large solid particles that settle out (e.g., blood cells in plasma).
Colloids: Liquid with small, non-settling particles (e.g., milk).
Solutions: One substance dissolves in another (e.g., salt water).

Chemical Bonds

Types of Chemical Bonds

Ionic Bonds: Electrons are transferred from a metal to a nonmetal, forming charged ions (cations and anions) that attract each other.
Covalent Bonds: Electrons are shared between two nonmetals; can be single, double, or triple bonds.
Polar Covalent Bonds: Electrons are shared unequally, creating partial charges (e.g., water).
Nonpolar Covalent Bonds: Electrons are shared equally (e.g., O2, N2).
Hydrogen Bonds: Weak attractions between partially positive and negative regions of polar molecules (important in water and DNA structure).

Chemical Notation and Reactions

Chemical Equations

Reactants: Substances that undergo change (left side).
Products: Substances produced (right side).
Reversible Reactions: Indicated by double arrows ().
Irreversible Reactions: Indicated by a single arrow ().

Energy and Chemical Reactions

Types of Energy

Potential Energy: Stored energy (e.g., chemical bonds).
Kinetic Energy: Energy of motion.
Chemical Energy: Energy stored in chemical bonds.
Electrical Energy: Movement of charged particles.
Mechanical Energy: Direct transfer between objects.

Types of Chemical Reactions

Catabolic (Decomposition) Reactions: Break down larger molecules into smaller ones; generally exergonic.
- Example:
Exchange Reactions: Atoms or electrons are exchanged; includes oxidation-reduction (redox) reactions.
- Example:
Anabolic (Synthesis) Reactions: Build new molecules; generally endergonic.
- Example:

Enzymes and Reaction Rates

Enzyme Function

Enzymes: Biological catalysts that speed up chemical reactions by lowering activation energy ().
Highly specific for substrates and reactions.
Not permanently altered or consumed in the reaction.
Work via an "induced fit" mechanism: enzyme changes shape to fit the substrate.

Factors Affecting Reaction Rates

Concentration of reactants
Temperature
Properties of reactants (size, phase)
Presence of catalysts (enzymes)

Enzyme Deficiencies

Tay-Sachs Disease: Deficiency of hexosaminidase; leads to fatal accumulation of lipids in brain cells.
Severe Combined Immunodeficiency Syndrome (SCID): Often due to adenosine deaminase deficiency; results in almost no immune function.
Phenylketonuria (PKU): Deficiency of phenylalanine hydroxylase; can cause intellectual disability if untreated.

Inorganic Compounds: Water, Acids, Bases, and Salts

Water

Makes up 50-65% of body mass.
Absorbs and carries heat, cushions and lubricates tissues, and is the body's primary solvent.
Dissolves hydrophilic (polar) substances but not hydrophobic (nonpolar) substances.

Acids, Bases, and pH

Acids: Proton (H+) donors; increase H+ concentration in water.
Bases: Proton acceptors; decrease H+ concentration.
pH Scale: Measures hydrogen ion concentration;
pH 7 is neutral; below 7 is acidic; above 7 is basic.
Buffers: Resist changes in pH; major buffer in blood is the carbonic acid–bicarbonate system.

Salts and Electrolytes

Salt: Compound formed from a metal cation and nonmetal anion (e.g., NaCl).
Electrolytes: Ions in solution that conduct electricity; essential for nerve and muscle function.

Organic Compounds

Hydrocarbons, Monomers, and Polymers

Hydrocarbons: Chains or rings of carbon and hydrogen; backbone of organic molecules.
Monomers: Single subunits (e.g., glucose, amino acids, nucleotides).
Polymers: Chains of monomers (e.g., starch, proteins, DNA).
Dehydration Synthesis: Links monomers by removing water.
Hydrolysis: Breaks polymers by adding water.

Carbohydrates

Composed of C, H, and O in a 1:2:1 ratio; polar and hydrophilic.
Monosaccharides: Simple sugars (e.g., glucose, fructose, ribose).
Disaccharides: Two monosaccharides joined (e.g., sucrose, lactose).
Polysaccharides: Long chains (e.g., starch in plants, glycogen in animals).
Glycoproteins and Glycolipids: Carbohydrates covalently bonded to proteins or lipids; important for cell recognition.

Lipids

Composed mostly of C and H; nonpolar and hydrophobic.
Fatty Acids: Hydrocarbon chains with a carboxylic acid group.
Saturated: No double bonds; solid at room temperature.
Monounsaturated: One double bond; liquid at room temperature.
Polyunsaturated: Two or more double bonds; liquid at room temperature.
Triglycerides: Three fatty acids linked to glycerol; energy storage.
Phospholipids: Glycerol, two fatty acids, and a phosphate group; amphiphilic; main component of cell membranes.
Steroids: Four-ring structure; includes cholesterol, bile acids, and hormones.

Proteins

Composed of C, H, O, N, and sometimes S; can be polar or nonpolar.
Amino Acids: 21 types; central carbon, amino group, carboxyl group, and R group.
Peptide Bonds: Covalent bonds linking amino acids.
Levels of Structure:
- Primary: Amino acid sequence
- Secondary: Alpha helix and beta sheet (hydrogen bonds)
- Tertiary: 3D folding (R group interactions)
- Quaternary: Multiple polypeptide chains
Denaturation: Loss of structure and function due to heat, pH, or chemicals.

Nucleic Acids

Composed of C, H, O, N, P; includes DNA and RNA.
Nucleotides: Monomers with a nitrogenous base, five-carbon sugar, and phosphate group.
Pyrimidines: Cytosine, Thymine, Uracil
Purines: Adenine, Guanine
ATP (Adenosine Triphosphate): Main energy currency of the cell.
DNA: Double helix; deoxyribose sugar; bases A, T, C, G; stores genetic information.
RNA: Single strand; ribose sugar; bases A, U, C, G; involved in protein synthesis.

Summary Table: Major Organic Compounds

Class	Monomer	Main Elements	Functions	Examples
Carbohydrates	Monosaccharide	C, H, O	Energy, structure, cell recognition	Glucose, glycogen, starch
Lipids	Fatty acid	C, H, O (few O)	Energy storage, membranes, hormones	Triglycerides, phospholipids, cholesterol
Proteins	Amino acid	C, H, O, N (sometimes S)	Structure, enzymes, signaling, defense	Enzymes, antibodies, hemoglobin
Nucleic Acids	Nucleotide	C, H, O, N, P	Genetic information, energy (ATP)	DNA, RNA, ATP