Chapter 2: The Chemical Level of Organization – Study Notes for Anatomy & Physiology I

Chemical Level of Organization

Introduction to Chemistry in Anatomy & Physiology

The study of living material in anatomy and physiology is fundamentally dependent on understanding chemistry, as all biological processes are governed by chemical interactions. The human body is composed of principal elements and compounds that interact at the molecular and atomic levels.

• Subatomic Particles: Protons (positive), Neutrons (neutral), Electrons (negative)

• Atoms: Smallest stable units of matter, made up of subatomic particles

• Molecules: Formed when atoms combine via chemical bonds

Atomic Structure and Isotopes

Atoms consist of a nucleus (protons and neutrons) and electron shells. The atomic number is the number of protons, while the mass number is the sum of protons and neutrons. Isotopes are variants of elements with the same number of protons but different numbers of neutrons.

• Atomic Weight: Expressed in Daltons

• Isotopes: Example: Hydrogen (0 neutrons), Deuterium (1 neutron), Tritium (2 neutrons)

Electron Shells and Stability

Electrons orbit the nucleus in shells, each with a specific capacity. Atoms are most stable when their outermost shell is full.

• 1st shell: max 2 electrons

• 2nd shell: max 8 electrons

• 3rd shell: max 8 electrons

• Atoms with full outer shells (e.g., Helium, Neon) are inert; those with incomplete shells are reactive.

Chemical Bonds

Types of Chemical Bonds

Chemical bonds are the forces that hold atoms together.

• Ionic Bonds: Formed by transfer of electrons (3-5 kcal/mol)

• Covalent Bonds: Formed by sharing electrons (50 kcal/mol)

• Hydrogen Bonds: Weak attractions between δ+ hydrogen and δ- atoms (3-5 kcal/mol)

Ionic Bonds

Ionic bonds occur when one atom donates an electron (becoming a cation) and another accepts it (becoming an anion). Example: Sodium chloride (NaCl).

• Cation: Positively charged ion

• Anion: Negatively charged ion

Covalent Bonds

Covalent bonds involve the sharing of electrons.

• Single Covalent Bond: Two atoms share one pair of electrons (e.g., H-H)

• Double Covalent Bond: Two atoms share two pairs of electrons (e.g., O=O)

Polar and Non-Polar Covalent Bonds

• Non-polar: Equal sharing of electrons

• Polar: Unequal sharing, resulting in partial charges (δ+ and δ-)

Hydrogen Bonds

Hydrogen bonds are weak attractions between the δ+ hydrogen of one molecule and the δ- atom of another. They are important for water properties and biological molecules.

• Reduce evaporation

• Create surface tension

Properties of Water

Water and Solutions

Water is a polar molecule, making it an excellent solvent. It dissolves ionic compounds (e.g., NaCl) and forms hydration spheres.

• Hydrophilic: Water-loving substances

• Hydrophobic: Water-repelling substances

pH and Acids, Bases, Salts

pH Scale

The pH scale measures hydrogen ion concentration, ranging from 0 (acidic) to 14 (basic).

• Neutral: pH = 7

• Acidic: pH < 7

• Basic: pH > 7

• Blood pH: 7.35–7.45

Organic Compounds

Carbohydrates

Carbohydrates are organic molecules containing carbon, hydrogen, and oxygen in a 1:2:1 ratio.

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

• Disaccharides: Two monosaccharides joined (e.g., sucrose)

• Polysaccharides: Many monosaccharides (e.g., starch, cellulose)

Lipids

Lipids are hydrophobic molecules with less oxygen than carbohydrates.

• Fatty Acids: Saturated (single bonds), Unsaturated (double bonds)

• Eicosanoids: Derived from arachidonic acid (prostaglandins, leukotrienes)

• Glycerides: Glycerol + fatty acids (mono-, di-, triglycerides)

• Steroids: Cholesterol, estrogen, testosterone

• Phospholipids & Glycolipids: Key components of cell membranes

Proteins

Proteins are the most abundant organic compounds, composed of amino acids.

• Functions: Support, movement, transport, buffering, metabolic regulation, coordination, defense

• Amino Acid Structure: Central carbon, amino group, carboxyl group, hydrogen, R group

• Peptide Bonds: Formed by dehydration synthesis

• Protein Structure: Primary, secondary, tertiary, quaternary

Nucleic Acids

Nucleic acids are large molecules made of nucleotides.

• DNA: Double-stranded, contains A, T, C, G

• RNA: Single-stranded, contains A, U, C, G

• Nucleotide Structure: 5-carbon sugar, phosphate group, base (purine or pyrimidine)

High Energy Compounds

Cells store energy in molecules like ATP, ADP, and AMP. Energy is released by breaking phosphate bonds.

• Phosphorylation: Addition of phosphate group

• ATP: Adenosine triphosphate, main energy carrier

Summary Table: Key Terms and Concepts

Term	Definition
Atom	Smallest unit of matter
Isotope	Element with same protons, different neutrons
Ionic Bond	Transfer of electrons
Covalent Bond	Sharing of electrons
Hydrogen Bond	Weak attraction between molecules
pH	Measure of hydrogen ion concentration
Carbohydrate	Organic molecule, energy source
Lipid	Hydrophobic molecule, energy storage
Protein	Organic molecule, structural and functional roles
Nucleic Acid	DNA/RNA, genetic information
ATP	Energy carrier molecule

Equations and Formulas

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

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

• Dehydration Synthesis: $\text{Monomer}_1 + \text{Monomer}_2 \rightarrow \text{Polymer} + \text{H}_2\text{O}$

• Hydrolysis: $\text{Polymer} + \text{H}_2\text{O} \rightarrow \text{Monomer}_1 + \text{Monomer}_2$

• ATP Hydrolysis: $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i + \text{Energy}$

Additional info:

• All content expanded and clarified for academic completeness.

• Images included only where directly relevant to the explanation.