The Chemical Level of Organization: Foundations for Anatomy & Physiology

The Chemical Level of Organization

Introduction to Chemistry in Anatomy & Physiology

Chemistry is the science that studies the structure of matter, which is anything that occupies space and has mass. Understanding the chemical level is essential for grasping how physiological processes occur in the human body.

Atoms and Atomic Structure

Subatomic Particles and Atomic Structure

• Atom: The smallest stable unit of matter, composed of protons (positively charged), neutrons (neutral), and electrons (negatively charged).

• Protons and neutrons are located in the nucleus, while electrons orbit in the electron cloud.

• Atomic number: Number of protons in an atom, unique to each element.

• Electron shell: A representation of the electron cloud, showing energy levels where electrons reside.

Elements and Isotopes

• Element: Pure substance made of one type of atom; cannot be broken down by ordinary means.

• There are 92 naturally occurring elements; the human body contains 13 main and 14 trace elements.

• Isotopes: Atoms of the same element with different numbers of neutrons; some are radioactive (radioisotopes) and decay over time (half-life).

Atomic Mass, Atomic Weight, and Moles

• Atomic mass: Actual mass of an atom (protons + neutrons + electrons).

• Atomic weight: Average mass of all isotopes of an element.

• Mole (mol): Quantity containing Avogadro’s number ($6.023 \times 10^{23}$) of atoms; relates atomic weight to grams.

Electron Shells and Chemical Properties

• Electrons occupy energy levels (shells) around the nucleus.

• The first shell holds up to 2 electrons; subsequent shells hold up to 8 electrons each.

• The outermost shell is the valence shell; its electron count determines chemical reactivity.

• Atoms with incomplete valence shells are reactive.

Molecules and Compounds

Formation and Types of Chemical Bonds

• Molecule: Two or more atoms joined by shared electrons.

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

• Chemical bonds: Hold atoms together; include ionic, covalent, and hydrogen bonds.

Chemical Notation

• Symbols and formulas represent atoms, molecules, and reactions.

Ionic Bonds

• Formed by the transfer of electrons from one atom (donor) to another (acceptor), creating ions.

• Cation: Positively charged ion (lost electrons).

• Anion: Negatively charged ion (gained electrons).

• Oppositely charged ions attract, forming ionic compounds (e.g., NaCl).

Covalent Bonds

• Formed when atoms share electrons.

• Single, double, or triple covalent bonds depend on the number of shared electron pairs.

• Nonpolar covalent bonds: Equal sharing of electrons.

• Polar covalent bonds: Unequal sharing, resulting in partial charges (e.g., water molecules).

Hydrogen Bonds

• Weak attractions between the partial positive charge of hydrogen and the partial negative charge of another atom (O, N, or F).

• Responsible for water’s high surface tension and important in stabilizing large molecules like DNA.

States of Matter

• Solid: Definite shape and volume.

• Liquid: Definite volume, no fixed shape.

• Gas: No definite shape or volume.

Chemical Reactions

Types and Energy Considerations

• Chemical reaction: Formation or breaking of chemical bonds, converting reactants to products.

• Metabolism: All chemical reactions in the body.

• Energy: The capacity to do work; can be kinetic (motion) or potential (stored).

• Energy transformations are not 100% efficient; some energy is lost as heat.

Major Types of Chemical Reactions

• Decomposition (Catabolism): Breaks molecules into smaller fragments; releases energy. Example: Hydrolysis.

• Synthesis (Anabolism): Assembles larger molecules from smaller ones; requires energy. Example: Dehydration synthesis.

• Exchange: Rearrangement of components between molecules.

• Reversible: Can proceed in both directions; equilibrium is reached when forward and reverse rates are equal.

Enzymes and Metabolism

Role of Enzymes

• Enzymes: Biological catalysts that lower activation energy, increasing reaction rates without being consumed.

• Each step in a metabolic pathway is catalyzed by a specific enzyme.

• Exergonic reactions: Release more energy than required to start.

• Endergonic reactions: Absorb more energy than they release.

Inorganic and Organic Compounds

Definitions and Examples

• Inorganic compounds: Do not contain carbon-hydrogen bonds as primary structure (e.g., water, salts, acids, bases).

• Organic compounds: Contain carbon-hydrogen bonds (e.g., carbohydrates, proteins, lipids, nucleic acids).

• Nutrients: Essential substances from food.

• Metabolites: Substances involved in metabolism.

Properties of Water

Importance and Properties

• Water is the most abundant and essential compound in the body, making up about two-thirds of body weight.

• Universal solvent: Dissolves many substances, forming solutions.

• Reactivity: Participates in chemical reactions (hydrolysis, dehydration synthesis).

• High heat capacity: Absorbs and retains heat, stabilizing body temperature.

• Lubrication: Reduces friction between surfaces.

Electrolytes and Body Fluids

• Electrolytes: Inorganic substances that dissociate into ions in solution, conducting electricity.

• Electrolyte balance is critical for physiological function.

Hydrophilic and Hydrophobic Compounds

• Hydrophilic: Readily interact with water (ions, polar molecules).

• Hydrophobic: Do not interact with water (nonpolar molecules, fats, oils).

Colloids and Suspensions

• Colloid: Solution with large molecules dispersed (e.g., plasma).

• Suspension: Large particles settle out if undisturbed (e.g., whole blood).

pH and Homeostasis

pH Scale and Its Importance

• pH: Negative logarithm of hydrogen ion concentration ($pH = -\log_{10}[H^+]$).

• Neutral pH (7.0): Equal H+ and OH- ions (pure water).

• Acidic pH (<7): Higher H+ concentration.

• Basic (alkaline) pH (>7): Lower H+ concentration.

• Human blood pH: 7.35–7.45.

Acids, Bases, Salts, and Buffers

Definitions and Physiological Roles

• Acid: Proton donor; increases H+ in solution (e.g., HCl).

• Base: Proton acceptor; decreases H+ in solution (e.g., NaOH).

• Salt: Ionic compound that dissociates into ions other than H+ or OH-.

• Buffer: Stabilizes pH by neutralizing acids or bases; important buffer system: carbonic acid–bicarbonate.

Monomers, Polymers, and Functional Groups

Macromolecules and Functional Groups

• Monomers: Small, identical subunits that join to form polymers via dehydration synthesis.

• Polymers: Large molecules made of monomers; broken down by hydrolysis.

• Functional groups: Specific groupings of atoms that influence properties and reactivity of organic molecules (e.g., amino, carboxyl, hydroxyl, phosphate).

Carbohydrates

Structure and Function

• Organic macromolecules with C, H, and O in a 1:2:1 ratio.

• Primary energy source for the body.

• Types: Monosaccharides (simple sugars), Disaccharides, Polysaccharides.

Monosaccharides

• Simple sugars (3–7 carbons); hydrophilic.

• Glucose is the main metabolic fuel; fructose is an isomer found in fruit.

Disaccharides and Polysaccharides

• Disaccharides: Two monosaccharides joined by dehydration synthesis (e.g., sucrose); broken down by hydrolysis.

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

Lipids

Structure and Function

• Organic macromolecules with C and H (1:2 ratio), little O; mainly hydrophobic.

• Functions: Energy storage, structural components, chemical messengers.

• Types: Fatty acids, eicosanoids, glycerides, steroids, phospholipids, glycolipids.

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 response) and prostaglandins (local signaling).

Glycerides

• Fatty acids attached to glycerol; mono-, di-, and triglycerides (energy storage, insulation, protection).

Steroids

• Four-ring structure; includes cholesterol (membranes), sex hormones, corticosteroids, bile salts.

Phospholipids and Glycolipids

• Phospholipids: Diglyceride + phosphate + nonlipid group; glycolipids: diglyceride + carbohydrate.

• Both have hydrophilic heads and hydrophobic tails; form micelles in water; key in cell membranes.

Proteins

Structure and Function

• Most abundant and vital organic molecules; composed of C, H, O, N.

• Monomers: Amino acids (20 types), each with a central carbon, hydrogen, amino group, carboxyl group, and R group.

• Functions: Support, movement, transport, buffering, metabolic regulation (enzymes), coordination, defense.

Peptide Bonds and Protein Structure

• Peptide bond: Links amino acids via dehydration synthesis.

• Levels of structure: Primary (sequence), secondary (alpha helix/beta sheet), tertiary (3D folding), quaternary (multiple polypeptides).

Protein Types and Enzyme Function

• Globular proteins: Compact, soluble, functional (e.g., enzymes).

• Fibrous proteins: Extended, insoluble, structural (e.g., collagen).

• Enzymes have specificity, saturation limits, and regulation; require cofactors (ions or coenzymes) for activity.

• Denaturation (loss of structure) leads to loss of function.

Glycoproteins and Proteoglycans

• Glycoproteins: Proteins with carbohydrate groups (e.g., enzymes, antibodies, hormones).

• Proteoglycans: Large polysaccharides linked by polypeptides; increase viscosity of tissue fluids.

Nucleic Acids

Structure and Function

• Composed of C, H, O, N, P; store and process genetic information.

• Types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

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

DNA and RNA

• DNA: Double helix of complementary strands (A-T, C-G); stores genetic code.

• RNA: Single strand; types include mRNA, tRNA, rRNA; involved in protein synthesis.

Characteristic	RNA	DNA
Sugar	Ribose	Deoxyribose
Nitrogenous Bases	A, G, C, U	A, G, C, T
Number of Nucleotides	<100 to ~50,000	>45 million
Shape	Single strand, variable	Double helix
Function	Protein synthesis	Genetic information storage

High-Energy Compounds

ATP and Energy Transfer

• High-energy compounds (e.g., ATP) are derived from nucleotides and store energy in covalent bonds.

• Phosphorylation: Addition of a phosphate group to a molecule.

• ATP (adenosine triphosphate): Main energy currency; formed from ADP and phosphate; broken down by ATPase to release energy.

Class	Building Blocks	Sources	Functions
Water	H, O	Diet, metabolism	Solvent, transport, chemical reactions
Acids, Bases, Salts	H+, OH-, ions	Diet, metabolism	Buffers, structural, ion sources
Carbohydrates	C, H, O (1:2:1)	Diet, body synthesis	Energy, structure, storage
Lipids	C, H, O (not 1:2:1)	Diet, body synthesis	Energy, structure, messengers
Proteins	Amino acids	Diet, body synthesis	Enzymes, structure, movement
Nucleic acids	Nucleotides	Diet, body synthesis	Genetic information
High-energy compounds	Nucleotides + phosphates	Cell synthesis	Energy storage/transfer