Chapter 2: The Chemical Level of Organization – Study Notes

Chapter 2: The Chemical Level of Organization

Elements and Atoms: The Building Blocks of Matter

The study of the human body begins at the chemical level, focusing on the structure and properties of matter. Matter is anything that occupies space and has mass, and it exists in three primary states: solid, liquid, and gas.

• Solids: Maintain both shape and volume; particles are tightly packed (e.g., bone, brick).

• Liquids: Maintain volume but not shape; take the shape of their container (e.g., blood plasma, water).

• Gases: Have neither fixed shape nor volume; particles move freely (e.g., oxygen, carbon dioxide in air).

Matter is composed of elements, pure substances that cannot be broken down by ordinary chemical means. There are 92 naturally occurring elements, but only a few make up most of the human body:

• Major elements: Oxygen (65%), Carbon (18.6%), Hydrogen (9.7%), Nitrogen (3.2%)

• Other principal elements: Calcium, phosphorus, potassium, iron, sodium, chlorine

• Trace elements: Copper, zinc, manganese, fluorine (present in very small amounts)

Atoms are the smallest units of elements, consisting of subatomic particles:

• Protons (p+): Positive charge, high mass, found in the nucleus

• Neutrons (n0): No charge, high mass, found in the nucleus

• Electrons (e-): Negative charge, low mass, high energy, found in electron cloud

Atoms are structured with a central nucleus (protons and neutrons) and an electron cloud (electrons in energy levels or shells):

• K shell: Closest to nucleus, holds up to 2 electrons

• L shell: Holds up to 8 electrons (total 10 with K shell)

• M shell: Holds up to 8 electrons (total 18 with K-M shells)

• Valence shell: Outermost shell; determines chemical reactivity

Isotopes are atoms of the same element with different numbers of neutrons. The atomic number is the number of protons, and the mass number is the sum of protons and neutrons. The atomic weight is the average mass of all isotopes, measured in daltons (amu).

Ions are charged atoms:

• Cations: Positively charged (loss of electrons), e.g., Na+, Ca2+

• Anions: Negatively charged (gain of electrons), e.g., Cl-, SO42-

Chemical Bonds

Atoms combine to form molecules and compounds through chemical bonds, which stabilize their outer energy levels (valence shells).

• Ionic bonds: Formed by the transfer of electrons from one atom to another, creating oppositely charged ions that attract each other (e.g., NaCl).

• Covalent bonds: Formed by the sharing of electrons between atoms. Can be single, double, or triple bonds.

• Polar covalent bonds: Unequal sharing of electrons (e.g., H2O).

• Nonpolar covalent bonds: Equal sharing of electrons (e.g., O2, fats).

Molecules are substances of two or more atoms held by covalent bonds. Compounds are substances of two or more different elements, regardless of bond type.

Chemical Reactions

Chemical reactions involve the making or breaking of bonds, transforming reactants into products. All reactions in the body constitute metabolism.

• Work: Movement or change in matter's structure

• Energy: Capacity to do work; can be potential (stored) or kinetic (movement)

Chemical notation is used to represent reactions. Key rules include:

• Element symbol = one atom

• Number before symbol = multiple atoms

• Subscript = number of atoms in a molecule

• Arrow (→) = "yields"; separates reactants (left) from products (right)

• Superscript +/– = ion charge

• Balanced equations: same number of each atom on both sides

Types of Chemical Reactions

• Decomposition (Catabolism): Large molecules broken into smaller ones (e.g., hydrolysis)

  • Example: $ABC \rightarrow A + B + C$

• Synthesis (Anabolism): Small molecules joined to form larger ones (e.g., dehydration synthesis)

  • Example: $A + B + C \rightarrow ABC$

• Exchange: Parts of molecules are shuffled to produce new products

  • Example: $AB + CD \rightarrow AC + BD$

• Reversible: Reactions can proceed in both directions

  • Example: $A + B \rightleftharpoons AB$

Factors Affecting Chemical Reactions

• Properties of reactants

• Temperature

• Concentration and pressure

• Enzymes (biological catalysts) lower activation energy

• Exergonic reactions: Release more energy than they consume

• Endergonic reactions: Require more energy than they release

Metabolites are molecules synthesized or broken down in the body. Nutrients are essential metabolites from the diet, classified as:

• Organic: Contain carbon and hydrogen (e.g., sugars, fats, proteins)

• Inorganic: Do not contain both carbon and hydrogen (e.g., water, acids, bases)

Inorganic Compounds Essential to Human Functioning

Water

Water is the most abundant and vital inorganic compound in the body, with unique properties:

• States: Exists as solid, liquid, and gas at life-compatible temperatures

• Polarity: Held by polar covalent bonds; forms hydrogen bonds, leading to cohesion, adhesion, and surface tension

• Solubility: Universal solvent; dissolves many substances to form solutions

• Lubrication: Reduces friction (e.g., synovial fluid in joints)

• Reactivity: Participates in hydrolysis and dehydration synthesis

• High heat capacity: Absorbs and retains heat, contributing to thermal inertia

Water in Solutions

• Hydration spheres: Water molecules surround ions or polar molecules, aiding dissolution

• Hydrophilic: Molecules that dissolve in water (e.g., glucose)

• Hydrophobic: Molecules that do not dissolve in water (e.g., fats)

• Electrolytes: Soluble inorganic molecules whose ions conduct electricity (e.g., NaCl, K+, Ca2+)

• Colloid: Solution with large particles that remain suspended (e.g., Jell-O)

• Suspension: Large particles that settle out (e.g., blood cells in plasma)

pH and Homeostasis

• pH scale: Measures hydrogen ion (H+) concentration

• Acids: Release H+ in solution; pH < 7; proton donors (e.g., HCl)

• Bases: Release OH- in solution; pH > 7; proton acceptors (e.g., NaOH)

• Neutrals: Release equal H+ and OH-; pH = 7 (e.g., water)

• Salts: Electrolytes that release cations other than H+ and anions other than OH- (e.g., NaCl)

• Buffers: Substances that stabilize pH by absorbing or releasing H+

• Normal blood pH: 7.35–7.45; acidosis (<7.35) and alkalosis (>7.45) are harmful

Organic Compounds Essential to Human Functioning

Organic molecules contain carbon and are formed by covalent bonds. Four major classes are carbohydrates, lipids, proteins, and nucleic acids.

• Polymers: Large molecules made from monomers via dehydration synthesis; broken down by hydrolysis

Carbohydrates

• Composed of C, H, O in a 1:2:1 ratio

• Monosaccharides: Simple sugars (3–7 carbons); e.g., glucose, fructose, galactose

• Disaccharides: Two monosaccharides; e.g., lactose (glucose + galactose), sucrose (glucose + fructose), maltose (glucose + glucose)

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

Lipids

• Composed of C, H, O (not in 1:2:1 ratio); hydrophobic

• Fatty acids: Long hydrocarbon chains with carboxyl group; can be saturated (single bonds, solid) or unsaturated (double bonds, liquid)

• Glycerides: Fatty acids attached to glycerol (mono-, di-, triglycerides); energy storage, insulation

• Phospholipids & Glycolipids: Two fatty acids + phosphate (and sugar for glycolipids); main components of cell membranes

• Steroids: Four carbon rings; e.g., cholesterol, hormones, vitamin D

• Eicosanoids: Derived from arachidonic acid; include leukotrienes (immune response) and prostaglandins (local signaling)

Proteins

• Composed of C, H, O, N; most diverse biomolecules

• Functions: Enzymes, movement, transport, hormones, antibodies, structure

• Amino acids: Monomers with amine, carboxyl, and R group; 20 types

• Polypeptides: Chains of amino acids linked by peptide bonds

• Levels of structure:

  • Primary: Sequence of amino acids

  • Secondary: Helices or sheets (hydrogen bonding)

  • Tertiary: 3D folding (R group interactions)

  • Quaternary: Multiple polypeptides (e.g., hemoglobin, keratin)

• Denaturation: Loss of structure and function due to environmental changes

• Enzymes: Protein catalysts; lower activation energy, have active sites, form enzyme-substrate complexes

Nucleic Acids

• Composed of C, H, O, N, P; monomers are nucleotides

• Nucleotide structure: Five-carbon sugar (ribose or deoxyribose), phosphate group, nitrogenous base

• Nitrogenous bases: Purines (adenine, guanine), pyrimidines (cytosine, thymine [DNA], uracil [RNA])

• Base pairing: A–T (or A–U in RNA), C–G

• Major nucleic acids:

  • DNA: Double helix, stores genetic information

  • RNA: Single strand, involved in protein synthesis

  • ATP: Single nucleotide with three phosphates; energy currency of the cell

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Nitrogen Bases	A, C, G, T	A, C, G, U
Number of Nucleotides	>45 million	<50,000
Structure	Double-stranded helix (anti-parallel)	Single-stranded
Function	Stores genetic information	Protein synthesis

Example: ATP hydrolysis releases energy for cellular work: $\mathrm{ATP} + \mathrm{H}_2\mathrm{O} \rightarrow \mathrm{ADP} + \mathrm{P}_i + \text{energy}$

Additional info: Understanding the chemical level of organization is foundational for all subsequent study of anatomy and physiology, as all physiological processes are ultimately based on chemical interactions.