Chemical Level of Organization: Atoms, Molecules, and Biochemistry in Anatomy & Physiology

Chapter 2: Chemical Level of Organization

Atoms: The Smallest Stable Units of Matter

Atoms are the fundamental building blocks of all matter, including the human body. Understanding their structure is essential for grasping the chemical basis of physiology.

• Subatomic Particles:

  • Protons: Positively charged particles

  • Neutrons: Neutral particles (no charge)

  • Electrons: Negatively charged particles

• Atomic Structure: Atoms normally contain equal numbers of protons and electrons, making them electrically neutral.

• Atomic Number: The number of protons in an atom; determines the element.

• Mass Number: The sum of protons and neutrons in the nucleus.

Example: Hydrogen (H) has 1 proton and 1 electron. Its atomic number is 1.

Elements and Isotopes

An element is a pure substance consisting of only one kind of atom, defined by its atomic number. Elements cannot be broken down by ordinary chemical processes.

• 13 elements are most abundant in the human body.

• Isotopes: Atoms of the same element with different numbers of neutrons. The main difference is mass.

• Some isotopes are radioactive (unstable), releasing energy as they decay. These are called radioisotopes.

Example: Hydrogen has three isotopes: 1H (protium): 1 proton, 0 neutrons; 2H (deuterium): 1 proton, 1 neutron; 3H (tritium): 1 proton, 2 neutrons (radioactive).

Atomic Mass and the Mole

Atomic mass unit (amu): 1 amu is approximately the mass of one proton or neutron. For example, oxygen has 8 protons and 8 neutrons, so its atomic mass is about 16 amu.

• Mole: A unit of measurement for amount of substance. 1 mole = $6.023 \times 10^{23}$ particles (Avogadro's number).

• Mass in grams of 1 mole of an element equals its atomic mass.

Example: 1 mol O = 16g; 1 mol H = 1g.

Electron Shells and Valence

Electrons occupy energy levels (shells) around the nucleus. The arrangement of electrons determines chemical reactivity.

• 1st shell: up to 2 electrons

• 2nd and 3rd shells: up to 8 electrons each

• Valence shell: Outermost shell; unfilled shells are unstable and more likely to react.

Molecules, Compounds, and Chemical Bonds

Molecules and Compounds

• Molecule: Two or more atoms held together by shared electrons (e.g., O2).

• Compound: Atoms of at least two different elements bonded together (e.g., NaCl).

• All compounds are molecules, but not all molecules are compounds.

Molecular Weight

The sum of the atomic weights of all atoms in a molecule, measured in amu.

• Example: H2O: 2(1) + 16 = 18 amu

Chemical Bonds

Atoms bond to achieve stable electron configurations. The main types of bonds are:

1. Ionic Bonds: Formed by the transfer of electrons from one atom to another, creating ions.

   • Cation: Positively charged ion (e.g., Na+)

   • Anion: Negatively charged ion (e.g., Cl-)

   • Example: Na+ + Cl- → NaCl (table salt)

2. Covalent Bonds: Atoms share electrons to fill their valence shells.

   • Single, double, or triple bonds possible (e.g., H2, O2).

   • Nonpolar covalent: Equal sharing of electrons (e.g., H2).

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

3. Hydrogen Bonds: Weak attractions between a slightly positive hydrogen and a slightly negative atom (e.g., O, N, F). Important in water and biological molecules.

Water and Its Properties

Water is the most abundant compound in the body and is essential for life.

• High heat capacity and reactivity

• Excellent solvent: dissolves more substances than any other liquid

• Lubricant: reduces friction between body surfaces

• Participates in hydrolysis and dehydration synthesis reactions

Water as a Solvent

• Hydrophilic compounds: Polar molecules that dissolve in water (e.g., glucose)

• Hydrophobic compounds: Nonpolar molecules that do not dissolve in water (e.g., fats, oils)

Electrolytes

• Ions that conduct electrical currents in solution

• Essential for muscle contraction and nerve function

• Examples: sodium, potassium, magnesium, chloride, calcium

Types of Mixtures

Type	Description	Example
Solution	Solute dissolves in solvent; does not settle	Saltwater, Kool-Aid
Colloid	Large molecules; does not settle	Jello, plasma proteins
Suspension	Large particles; will settle	Blood cells in plasma

pH and Buffers

• pH: Measure of hydrogen ion concentration; pure water is neutral (pH 7)

• Acid: pH < 7; Base: pH > 7

• Normal blood pH: 7.35–7.45

• Buffer: Stabilizes pH by adding or removing H+ ions

Carbonic Acid–Bicarbonate Buffer System:

$\mathrm{CO_2 + H_2O \leftrightarrow H_2CO_3 \leftrightarrow H^+ + HCO_3^-}$

Energy and Chemical Reactions

Energy in Biological Systems

• Energy: The ability to do work

• Kinetic energy: Energy of motion

• Potential energy: Stored energy

• Law of Conservation of Energy: Energy cannot be created or destroyed, only converted from one form to another

Chemical Reactions

Chemical reactions involve the making and breaking of bonds, transforming reactants into products.

• Decomposition (Catabolic) Reactions: Break molecules into smaller components; release energy (exergonic)

  • Example: $2H_2O_2 \rightarrow 2H_2O + O_2$

• Synthesis (Anabolic) Reactions: Join smaller molecules to build larger ones; require energy (endergonic)

  • Example: $2Na + Cl_2 \rightarrow 2NaCl$

• Exchange Reactions: Atoms are rearranged to produce new molecules

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

• Reversible Reactions: Can proceed in both directions until equilibrium is reached

  • Example: $2Na + 2H_2O \rightleftharpoons 2NaOH + H_2$

Enzymes and Metabolism

• Enzymes: Biological catalysts that speed up chemical reactions without being consumed

• Enzymes are usually proteins

• Enzymatic reactions are often reversible

• Metabolism: All chemical reactions within the cells and tissues of the body

• Metabolites: Substances involved in or produced by metabolism

• Nutrients: Substances from food required for normal body function

Organic and Inorganic Compounds

Inorganic Compounds

• Do not contain both carbon and hydrogen as primary structural components

• Examples: water, salts, acids, bases

Organic Compounds

• Contain carbon and hydrogen as primary structural components

• Examples: carbohydrates, lipids, proteins, nucleic acids

Macromolecules

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

Monomer: A single subunit of a macromolecule Polymer: Many monomers joined together

Summary Table: Key Chemical Concepts

Term	Definition	Example
Atom	Smallest unit of matter	Oxygen atom
Element	Pure substance of one kind of atom	Hydrogen (H)
Compound	Atoms of different elements bonded	NaCl
Molecule	Two or more atoms bonded	O2
Ion	Atom with a charge	Na+
Isotope	Atoms with same protons, different neutrons	Carbon-12, Carbon-14

Additional info: Some explanations and examples have been expanded for clarity and completeness, including the summary tables and the Law of Conservation of Energy.