Basic Chemistry for Anatomy & Physiology: Foundations for Understanding Biological Processes

Basic Chemistry Part I

Overview

Chemistry forms the foundation for understanding the structure and function of the human body. The study of Anatomy & Physiology begins at the simplest level of organization: atoms and molecules. The types of atoms and the ways they combine to form molecules determine the characteristics of all substances in the body.

• Levels of Organization: The human body is organized hierarchically from chemicals (atoms and molecules) to cells, tissues, organs, organ systems, and the complete organism.

• Importance: Understanding basic chemistry is essential for grasping how biological molecules interact and function in living systems.

Matter

Definition and Properties

Matter is anything that has mass and takes up space. All living and non-living things are composed of matter, which exists in three states: solid, liquid, and gas.

• Mass: The amount of matter in an object; remains constant regardless of location.

• Weight: The measurement of the pull of gravity on an object; can change with location (e.g., weightless in space, but mass remains the same).

• States of Matter:

  • Solid: Definite shape and volume (e.g., bones).

  • Liquid: Definite volume, no definite shape (e.g., blood).

  • Gas: No definite shape or volume (e.g., oxygen in lungs).

Elements

Definition and Biological Relevance

Elements are pure substances that cannot be broken down into simpler substances by ordinary chemical reactions. All matter is composed of elements.

• Element: A substance made of only one type of atom (e.g., carbon, oxygen).

• Periodic Table: Organizes all known elements by their properties and atomic structure.

• Biological Elements: About 25 elements are essential for life. Four elements—carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)—make up about 96% of the human body.

• Element Symbols: Each element is represented by a one- or two-letter symbol (e.g., H for hydrogen, Na for sodium).

Periodic Table of Elements

The periodic table provides information about each element, including its atomic number, symbol, and atomic weight.

• Atomic Number: Number of protons in the nucleus of an atom; determines the element's identity.

• Atomic Weight (Mass): Average mass of the element's atoms, accounting for isotopes.

Atoms

Structure and Subatomic Particles

An atom is the smallest unit of an element that retains the properties of that element. Atoms are composed of three major subatomic particles:

• Protons (p): Positively charged particles located in the nucleus.

• Neutrons (n): Neutral particles (no charge) also located in the nucleus.

• Electrons (e): Negatively charged particles that orbit the nucleus in electron shells.

Atoms are electrically neutral when they have equal numbers of protons and electrons.

Atomic Number and Mass Number

• Atomic Number (Z): Number of protons in the nucleus; unique to each element.

• Mass Number (A): Total number of protons and neutrons in the nucleus.

• Atomic Mass: Average of the mass numbers of all isotopes of an element.

Formula:

• Mass Number: $A = Z + N$ where $A$ = mass number, $Z$ = number of protons, $N$ = number of neutrons

Isotopes and Radioactivity

• Isotopes: Atoms of the same element with different numbers of neutrons (and thus different mass numbers).

• Radioactive Isotopes: Unstable isotopes that emit radiation as their nuclei break down; used in medical imaging and cancer treatment (e.g., Technetium-99, Iodine-131).

Electron Shells and Valence Electrons

Electron Arrangement

Electrons orbit the nucleus in specific energy levels called electron shells. The arrangement of electrons determines how atoms interact with each other.

• First shell: Holds up to 2 electrons.

• Second shell: Holds up to 8 electrons.

• Third shell: Holds up to 18 electrons.

• Valence Shell: The outermost electron shell; electrons here are called valence electrons and determine chemical reactivity.

Atoms are most stable when their valence shell is full. Atoms with incomplete valence shells tend to interact with other atoms to achieve stability.

Molecules and Compounds

Definitions and Examples

• Molecule: Two or more atoms joined by chemical bonds (e.g., O2, H2).

• Compound: A molecule that contains atoms of more than one element (e.g., H2O, CO2).

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

Chemical Bonds

Types of Chemical Bonds

Chemical bonds are forces that hold atoms together in molecules and compounds. The main types are:

• Ionic Bonds: Formed when one atom donates an electron to another, creating oppositely charged ions (cations and anions) that attract each other.

• Covalent Bonds: Formed when two atoms share one or more pairs of electrons. Can be single, double, or triple bonds depending on the number of shared electron pairs.

• Polar Covalent Bonds: Electrons are shared unequally, resulting in partial charges (e.g., water molecule).

• Hydrogen Bonds: Weak attractions between a slightly positive hydrogen atom in one molecule and a slightly negative atom (usually oxygen or nitrogen) in another molecule. Important in stabilizing the structure of proteins and DNA.

Ions, Cations, and Anions

• Ion: An atom or molecule with a net electric charge due to the loss or gain of electrons.

• Cation: Positively charged ion (loss of electrons).

• Anion: Negatively charged ion (gain of electrons).

Chemical Reactions

Types and Mechanisms

Chemical reactions involve the making or breaking of chemical bonds, resulting in new substances.

• Reactants: Starting substances in a chemical reaction.

• Products: Substances formed as a result of the reaction.

General Reaction Formula:

• $\text{A} + \text{B} \rightarrow \text{AB}$

Types of Reactions

• Decomposition (Catabolic) Reactions: Break down larger molecules into smaller parts. Often involve hydrolysis (addition of water to break bonds). Example: Digestion of food.

• Synthesis (Anabolic) Reactions: Combine smaller molecules to form larger, more complex molecules. Often involve dehydration synthesis (removal of water to form bonds).

• Reversible Reactions: Can proceed in both directions, forming and breaking down products as needed. Example: $\text{A} + \text{B} \rightleftharpoons \text{AB}$

Enzymes and Activation Energy

• Enzymes: Biological catalysts that speed up chemical reactions by lowering the activation energy required for the reaction to occur.

• Activation Energy: The minimum amount of energy needed to start a chemical reaction.

• Enzymes are not consumed or permanently changed during the reaction.

Effect of Enzymes on Activation Energy:

• With enzyme: Lower activation energy, faster reaction.

• Without enzyme: Higher activation energy, slower reaction.

Summary Table: Types of Chemical Bonds

Bond Type	How Formed	Example	Strength
Ionic	Transfer of electrons between atoms	NaCl (table salt)	Strong (in solid state)
Covalent	Sharing of electron pairs between atoms	H2O (water), O2	Very strong
Hydrogen	Attraction between polar molecules (H and O/N/F)	Between water molecules	Weak (individually), strong in large numbers