Chapter 2: Chemical Basis of Anatomy & Physiology

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Chapter 2 Learning Outcomes

Describe components of an atom, including subatomic particles and how atomic structure affects interactions between atoms.
Compare and contrast the ways in which atoms combine to form chemical bonds.
Distinguish among the major types of chemical reactions important for physiology.
Describe the crucial role of enzymes in metabolism.
Distinguish between inorganic and organic compounds.
Explain how the chemical properties of water make life possible.
Explain what pH is, how it relates to acids and bases, and the function of buffers.
Describe monomers and polymers, and the importance of functional groups in organic compounds.
Discuss the structures and functions of carbohydrates, lipids, proteins, nucleic acids, and high-energy compounds.

Introduction to Chemistry in Anatomy & Physiology

What is Chemistry?

Chemistry is the science that deals with the structure of matter, including the composition and properties of substances and how they interact.

Structure of atoms forms the basic chemical building blocks.
Atoms combine to form increasingly complex structures, both living and non-living.

What is Matter?

Matter is anything that takes up space and has mass. All matter is made up of atoms.

Atoms combine to form molecules with different characteristics.
Chemical characteristics of molecules determine physiology at molecular and cellular levels.

Atomic Structure

Subatomic Particles

Atoms are composed of three main subatomic particles:

Protons: Positive charge, 1 mass unit, located in the atomic nucleus.
Neutrons: Neutral charge, 1 mass unit, located in the atomic nucleus.
Electrons: Negative charge, very low mass, found in the electron cloud surrounding the nucleus.

The electron cloud is a spherical area containing electrons. The electron shell is a 2D representation of the electron cloud, showing energy levels.

Atomic number: Number of protons in the nucleus.
Atomic mass / Mass number: Number of protons plus neutrons.

Elements and Isotopes

Elements

An element is a pure substance composed only of one kind of atom. Elements are organized in the periodic table.

The atomic number determines chemical properties.
Mass number is the sum of protons and neutrons.

Isotopes

Isotopes are versions of elements based on mass number. Radioisotopes have radioactive nuclei and decay, giving off energy as radioactivity.

Decay rate is expressed as half-life.

Principal Elements in the Human Body

The human body is composed of several principal elements, each with specific physiological roles.

Element	Percentage of Total Body Weight	Significance
Oxygen (O)	65.0	Component of water and other compounds; essential for respiration.
Carbon (C)	18.6	Found in all organic molecules.
Hydrogen (H)	9.7	Component of water and most other compounds in the body.
Nitrogen (N)	3.2	Found in proteins, nucleic acids, and other organic compounds.
Calcium (Ca)	1.8	Important for bones, teeth, membrane function, nerve impulses, muscle contraction, and blood clotting.
Phosphorus (P)	1.0	Found in bones and teeth, nucleic acids, and high-energy compounds.
Potassium (K)	0.4	Important for membrane function, nerve impulses, and muscle contraction.
Sodium (Na)	0.2	Important for blood volume, membrane function, nerve impulses, and muscle contraction.
Chlorine (Cl)	0.2	Important for blood volume, membrane function, and water absorption.
Magnesium (Mg)	0.06	Cofactor for many enzymes.
Sulfur (S)	0.04	Found in many proteins.
Iron (Fe)	0.007	Essential for oxygen transport and energy capture.
Iodine (I)	0.0002	Component of hormones of the thyroid gland.
Trace elements	various	Some function as cofactors; many are poorly understood.

Electron Shells and Chemical Bonding

Electron Shells

Electrons occupy energy levels called shells. The outermost shell is the valence shell, which determines bonding properties.

Lower shells fill first (up to 2 electrons).
Atoms are most stable when their valence shell is full.

Chemical Bonds

Chemical bonds form molecules and compounds by sharing, gaining, or losing electrons to fill the valence shell.

Ionic bonds: Transfer of electrons from one atom to another, forming ions (cations and anions).
Covalent bonds: Sharing of electrons between atoms. Can be non-polar (equal sharing) or polar (unequal sharing).
Hydrogen bonds: Weak attractions between polar molecules, important for water properties and biological molecules.

Chemical Reactions and Metabolism

Chemical Reactions

Chemical reactions involve the formation or breaking of chemical bonds. Reactants are the starting materials; products are the result.

Decomposition (catabolism): Breaks chemical bonds ().
Synthesis (anabolism): Forms chemical bonds ().

Energy in Chemical Reactions

Kinetic energy: Energy of motion.
Potential energy: Stored energy, often in chemical bonds.
Law of Conservation of Energy: Energy cannot be created or destroyed, only transformed.

Enzymes

Enzymes are protein catalysts that lower the activation energy required for chemical reactions, making metabolism possible.

Enzymes are not changed or used up in reactions.
They exhibit specificity, saturation limits, and regulation by cellular chemicals.

Inorganic vs. Organic Compounds

Organic Compounds

Contain both carbon and hydrogen.
Include carbohydrates, proteins, lipids, and nucleic acids.

Inorganic Compounds

Do not contain both carbon and hydrogen.
Include water, oxygen, carbon dioxide, acids, bases, and salts.

Properties of Water

Water is essential for life and makes up about two-thirds of body weight.

Solvent: Dissolves many substances, forming solutions.
Reactivity: Participates in chemical reactions.
High heat capacity: Absorbs and retains heat.
Lubrication: Moistens and reduces friction.

Aqueous Solutions

Dissociation: Many inorganic compounds split into ions in water.
Electrolytes: Ions that conduct electricity in solution; imbalances can disrupt body functions.
Hydrophilic: Water-loving, includes ions and polar molecules.
Hydrophobic: Water-fearing, includes nonpolar molecules like fats and oils.

pH, Acids, Bases, and Buffers

pH Scale

pH is the negative logarithm of the hydrogen ion concentration ().

Neutral pH: 7.0 (pure water).
Acidic pH: Less than 7.0 (high concentration).
Basic (alkaline) pH: Greater than 7.0 (low concentration).
Human blood pH: 7.35–7.45.

Acids, Bases, and Buffers

Acids: Release hydrogen ions ().
Bases: Remove hydrogen ions, often by releasing hydroxide ions ().
Buffers: Stabilize pH by neutralizing strong acids or bases; often involve a weak acid and its related salt.
Carbonic acid-bicarbonate buffer system is crucial in human physiology.

Monomers, Polymers, and Functional Groups

Macromolecules are made of monomer subunits joined to form polymers. Functional groups determine chemical properties.

Monomers: Small, repeating units (e.g., glucose, amino acids).
Polymers: Chains of monomers (e.g., starch, proteins).
Functional groups: Specific groups of atoms that confer chemical reactivity (e.g., hydroxyl, carboxyl, amino).

Carbohydrates

Carbohydrates contain carbon, hydrogen, and oxygen in a 1:2:1 ratio. They are a primary energy source.

Monosaccharides: Simple sugars (glucose, fructose, galactose).
Disaccharides: Two monosaccharides joined (sucrose, maltose).
Polysaccharides: Polymers of many sugars (glycogen, starch, cellulose).

Lipids

Lipids are hydrophobic molecules made mostly of carbon and hydrogen. They include fats, oils, and waxes.

Fatty acids: Long chains of C and H with a carboxyl group; can be saturated (no double bonds) or unsaturated (one or more double bonds).
Eicosanoids: Derived from arachidonic acid; include leukotrienes (immune system) and prostaglandins (local hormones).
Glycerides: Fatty acids attached to glycerol; mono-, di-, and triglycerides (energy source, insulation, protection).
Steroids: Four-ringed carbon structures (cholesterol, sex hormones, corticosteroids).
Phospholipids and glycolipids: Diglyceride attached to a phosphate group (phospholipid) or sugar (glycolipid); have hydrophilic heads and hydrophobic tails; key components of cell membranes.

Proteins

Proteins are the most abundant and important organic molecules, composed of amino acids (monomers).

Support: Structural proteins.
Movement: Contractile proteins.
Transport: Carrier proteins.
Buffering: Regulation of pH.
Metabolic regulation: Enzymes.
Coordination and control: Hormones.
Defense: Antibodies.

Structure of Amino Acids

Central carbon atom
Hydrogen atom
Amino group (–NH2)
Carboxyl group (–COOH)
Variable side chain (R group)

Protein Structure Levels

Primary: Sequence of amino acids.
Secondary: Hydrogen bonds form spirals or pleats.
Tertiary: Coiling and folding into 3D shape.
Quaternary: Interaction of multiple polypeptide chains.

Enzymes

Lower activation energy for reactions.
Not changed or used up in reactions.
Denatured by high temperature, chemicals, or pH changes.
Substrates bind to active site; enzymes exhibit specificity, saturation limits, and regulation.

Nucleic Acids

Nucleic acids are large organic molecules that store and process genetic information.

DNA (deoxyribonucleic acid): Determines inherited characteristics, directs protein synthesis, controls enzyme production and metabolism.
RNA (ribonucleic acid): Controls intermediate steps in protein synthesis.
Nucleotide: Monomer unit, consists of a pentose sugar, phosphate group, and nitrogenous base (A, G, T, C, U).

DNA Structure

Double helix of paired nucleotide chains.
Hydrogen bonds between complementary bases: Adenine (A)–Thymine (T), Cytosine (C)–Guanine (G).

RNA Structure

Single chain of nucleotides.
Types: Messenger RNA (mRNA), Transfer RNA (tRNA), Ribosomal RNA (rRNA).
Uracil (U) replaces thymine (T).

High-Energy Compounds

High-energy compounds store and transfer energy within cells, primarily through phosphate bonds.

Phosphorylation: Addition of a phosphate group to another molecule, producing a high-energy bond.
Adenosine monophosphate (AMP): Nucleotide with one phosphate.
Adenosine diphosphate (ADP): Two phosphate groups.
Adenosine triphosphate (ATP): Three phosphate groups; main energy currency of the cell.
ATPase: Enzyme that catalyzes conversion of ATP to ADP.