Chapter 2: Chemistry Comes Alive – Study Notes for Anatomy & Physiology

Atoms and Elements

Overview of Elements

All matter is composed of elements, which are substances that cannot be broken down into simpler substances by ordinary chemical means. In the human body, four elements—carbon, oxygen, hydrogen, and nitrogen—make up about 96% of body mass, with approximately 20 other elements present in smaller amounts.

• Periodic Table: Lists all known elements (118 recognized, 92 naturally occurring).

• Atomic Symbol: One- or two-letter shorthand for each element (e.g., O for oxygen, C for carbon; some from Latin names, e.g., Na for sodium).

Common Elements in the Human Body

Elements are classified by their abundance and function in the body.

Element	Atomic Symbol	Approx. % Body Mass	Functions
Oxygen	O	65.0	Component of organic/inorganic molecules; needed for cellular energy (ATP) production.
Carbon	C	18.5	Component of all organic molecules (carbohydrates, lipids, proteins, nucleic acids).
Hydrogen	H	9.5	Component of all organic molecules; influences pH of body fluids.
Nitrogen	N	3.3	Component of proteins and nucleic acids (genetic material).

Additional info: Lesser elements (e.g., calcium, phosphorus, potassium, sulfur, sodium, chlorine, magnesium) and trace elements (e.g., iron, iodine, zinc) are essential for specific physiological functions such as nerve conduction, blood clotting, and hormone production.

Structure of Atoms

Subatomic Particles

Atoms are composed of three subatomic particles:

Particle	Charge	Mass (amu)	Located in Nucleus?
Proton (p+)	+1	1	Yes
Neutron (n0)	0	1	Yes
Electron (e-)	-1	~0 (0.0005)	No

• Atoms are electrically neutral: number of protons equals number of electrons.

• Protons and neutrons are located in the nucleus; electrons orbit the nucleus (orbital model).

Combining Matter: Molecules and Compounds

Definitions

• Molecule: Two or more atoms bonded together.

• Compound: A molecule containing two or more different kinds of atoms.

Chemical Bonds

Electron Shells and Bonding

Chemical bonds are energy relationships between electrons of reacting atoms. Electrons occupy electron shells around the nucleus, with each shell holding a specific number of electrons:

• Shell 1: max 2 electrons

• Shell 2: max 8 electrons

• Shell 3: max 18 electrons

Octet Rule

Atoms tend to gain, lose, or share electrons to achieve stability with 8 electrons in their valence shell.

Types of Chemical Bonds

Ionic Bonds

• Ions: Atoms that have gained or lost electrons and become charged.

• Anion: Negative charge (gained electrons).

• Cation: Positive charge (lost electrons).

• Attraction of opposite charges forms an ionic bond.

• Most ionic compounds are salts (e.g., NaCl).

Covalent Bonds

• Formed by sharing of two or more valence shell electrons between atoms.

• Stronger when more pairs of electrons are shared.

• Types: Polar covalent bonds (unequal sharing) and Nonpolar covalent bonds (equal sharing).

Hydrogen Bonds

• Attractive force between electropositive hydrogen of one molecule and an electronegative atom of another.

• Important for water's liquid state and for stabilizing large molecules (e.g., proteins, DNA).

Summary Table: Major Chemical Bond Types

Type	Description	Strength
Covalent bonds	Sharing of pairs of electrons (polar or nonpolar)	Strongest
Ionic bonds	Attraction between two oppositely charged ions	Intermediate
Hydrogen bonds	Attraction between a hydrogen atom and an electronegative atom	Weakest

Chemical Reactions

Chemical Equations

• Chemical reactions occur when chemical bonds are formed, rearranged, or broken.

• Written as chemical equations: Reactants (starting substances) and Products (resulting substances).

Types of Chemical Reactions

1. Synthesis (Combination) Reactions: Atoms/molecules combine to form larger molecules. Used in anabolic (building) processes. $A + B ightarrow AB$

2. Decomposition Reactions: Breakdown of molecules into smaller molecules or atoms. Used in catabolic (bond-breaking) processes. $AB ightarrow A + B$

3. Exchange (Displacement) Reactions: Involve both synthesis and decomposition; bonds are made and broken. $AB + C ightarrow AC + B$ $AB + CD ightarrow AD + CB$

Redox Reactions

• Reduction-oxidation reactions: Atoms are reduced when they gain electrons and oxidized when they lose electrons.

• Example: $C_6H_{12}O_6 + 6O_2 ightarrow 6CO_2 + 6H_2O + ATP$ (Glucose is oxidized, oxygen is reduced)

Energy Flow in Chemical Reactions

• Exergonic reactions: Net release of energy; products have less potential energy than reactants (catabolic, oxidative).

• Endergonic reactions: Net absorption of energy; products have more potential energy than reactants (anabolic).

Reversibility and Rate of Chemical Reactions

• All chemical reactions are theoretically reversible: $A + B ightleftharpoons AB$

• Chemical equilibrium: Forward and reverse reactions are balanced.

• Rate affected by temperature, concentration, particle size, and catalysts (enzymes).

Biochemistry: Organic and Inorganic Compounds

Inorganic Compounds

• Water: Most abundant inorganic compound (60–80% of cell volume). Key properties: high heat capacity, high heat of vaporization, polar solvent, reactivity, cushioning.

• Salts: Ionic compounds that dissociate into ions (electrolytes) in water; essential for nerve conduction, muscle contraction, and fluid balance.

• Acids and Bases: Both are electrolytes; acids are proton donors (release $H^+$), bases are proton acceptors (release $OH^-$). pH scale: Measures $[H^+]$ concentration, ranges from 0–14. Acidic: pH 0–6.99; Neutral: pH 7; Alkaline: pH 7.01–14.

• Buffers: Resist changes in pH by releasing or binding $H^+$ ions.

Organic Compounds

• Contain carbon; include carbohydrates, lipids, proteins, and nucleic acids.

• Usually large and covalently bonded; essential for life.

Summary

• Understanding atomic structure and chemical bonding is foundational for studying physiology and the molecular basis of life.

• Biochemical reactions underpin all cellular processes, including metabolism, energy production, and homeostasis.

Additional info: These notes provide a comprehensive overview of the chemical principles relevant to human anatomy and physiology, focusing on the elements, atomic structure, chemical bonds, reactions, and the distinction between organic and inorganic compounds.