Key Concepts in Chemistry & Biochemistry

Introduction

Chemistry and biochemistry are foundational to understanding anatomy and physiology. Life’s chemistry is intimately tied to water, and all living organisms require water for survival. Cells are composed of approximately 70% water, and water acts as a critical solvent in biochemical reactions, facilitating the movement and interaction of molecules.

Defining Matter

States and Properties of Matter

• Matter: Anything that occupies space and has mass.

• Mass: The amount of matter in an object.

• States of Matter relevant to physiology:

  • Solids: Defined shape and volume.

  • Liquids: Defined volume, undefined shape.

  • Gases: Undefined shape and volume.

• Chemistry: The study of matter and how its building blocks are put together.

Matter is Composed of Elements

Elements Essential for Human Life

Elements are pure substances that cannot be broken down by ordinary chemical means. About 24 elements are required to build a human body, and these are grouped based on their abundance and physiological importance.

• Major Elements (96.1% of body mass):

  • Oxygen (O)

  • Carbon (C)

  • Hydrogen (H)

  • Nitrogen (N)

• Minor Elements (3.9% of body mass):

  • Sodium (Na)

  • Chlorine (Cl)

  • Calcium (Ca)

  • Potassium (K)

  • Phosphorus, Sulfur, Magnesium, Iron, Iodine

• Trace Elements (<0.01% of body mass):

  • Copper, Zinc, Manganese, Cobalt, Chromium, Selenium, Molybdenum, Fluorine, Tin, Silicon, Vanadium

Application: Some trace elements are added to food and water to prevent disease (e.g., fluoride in water to reduce tooth decay, iodine in salt to prevent goiter).

Atoms and Subatomic Particles

Structure of the Atom

• Atom: The smallest unit of matter that retains the properties of an element.

• Subatomic particles:

  • Protons: Positively charged, located in the nucleus.

  • Neutrons: No charge, located in the nucleus.

  • Electrons: Negatively charged, orbit the nucleus.

• Mass number: Sum of protons and neutrons in the nucleus.

• Isotopes: Atoms of the same element with different numbers of neutrons.

Ions: Cations and Anions

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

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

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

Example: Sodium (Na+) is a cation; Chloride (Cl-) is an anion.

Chemical Bonds and Molecules

Types of Chemical Bonds

• Ionic Bonds: Complete transfer of electrons from one atom to another, resulting in oppositely charged ions that attract each other.

• Covalent Bonds: Atoms share electrons.

  • Non-polar covalent: Electrons shared equally.

  • Polar covalent: Electrons shared unequally, creating partial charges (polarity).

• Hydrogen Bonds: Weak attractions between a hydrogen atom in one molecule and an electronegative atom (like oxygen or nitrogen) in another.

Example: Water (H2O) molecules are held together by polar covalent bonds and form hydrogen bonds with each other.

Comparison of Bond Types

Chemical Reactions and Metabolism

Chemical Reactions

• Chemical reaction: Process that forms, breaks, or rearranges chemical bonds.

• Reactants: Starting substances.

• Products: Substances formed by the reaction.

• Metabolism: The sum of all chemical reactions in the body.

Anabolic vs. Catabolic Reactions

• Anabolic reactions: Build larger molecules from smaller ones; require energy.

• Catabolic reactions: Break down larger molecules into smaller ones; release energy.

Solutions and Concentration

Definitions

• Solution: A homogeneous mixture of two or more substances.

• Solvent: The substance present in the greatest amount (usually water in physiology).

• Solute: The substance dissolved in the solvent.

• Concentration: The amount of solute per volume of solution.

Properties of Water

Essential Properties for Life

• High heat capacity: Absorbs and releases heat slowly, helping maintain body temperature.

• High heat of vaporization: Evaporation of water removes heat from the body (sweating).

• Polar solvent properties: Dissolves ionic and polar substances, facilitating chemical reactions.

• Reactivity: Participates in many chemical reactions (e.g., hydrolysis, dehydration synthesis).

• Cushioning: Protects organs from physical trauma.

Acids, Bases, and pH

Definitions and pH Scale

• Acid: Substance that releases hydrogen ions (H+) in solution; increases [H+].

• Base: Substance that accepts hydrogen ions or releases hydroxide ions (OH-); decreases [H+].

• pH: A measure of hydrogen ion concentration; calculated as .

The pH scale ranges from 0 (most acidic) to 14 (most basic), with 7 being neutral (pure water).

Organic and Inorganic Molecules

Classification

• Organic molecules: Contain carbon, made by living things, usually large and complex (e.g., carbohydrates, lipids, proteins, nucleic acids).

• Inorganic molecules: Do not contain carbon (with some exceptions); include water, salts, acids, and bases.

Macromolecules: Structure and Function

Carbohydrates

• Composed of carbon, hydrogen, and oxygen (H:O ratio is 2:1).

• Polar and water-soluble.

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

• Disaccharides: Two monosaccharides joined by dehydration synthesis (e.g., sucrose, lactose, maltose).

• Polysaccharides: Long chains of monosaccharides (e.g., glycogen in animals for energy storage).

Lipids

• Composed mostly of carbon and hydrogen; non-polar and insoluble in water.

• Triglycerides: Glycerol + 3 fatty acids; energy storage, insulation, cushioning.

• Phospholipids: Glycerol + 2 fatty acids + phosphate group; form cell membranes (bilayers).

• Steroids: Four interlocking hydrocarbon rings; cholesterol is a key steroid, precursor for hormones and bile salts.

Proteins

• Composed of carbon, hydrogen, oxygen, nitrogen, and sulfur.

• Polymers of amino acids (20 types); joined by peptide bonds.

• Structure determines function; sequence of amino acids is critical.

• Functions: Enzymes, structural components, transport, signaling, immune response.

Nucleic Acids

• Polymers of nucleotides (monomers composed of a pentose sugar, phosphate group, and nitrogenous base).

• DNA (deoxyribonucleic acid): Double helix, stores genetic information, bases are adenine (A), guanine (G), cytosine (C), thymine (T).

• RNA (ribonucleic acid): Single strand, involved in protein synthesis, bases are adenine (A), guanine (G), cytosine (C), uracil (U).

Polymerization Reactions

Dehydration Synthesis and Hydrolysis

• Dehydration synthesis: Monomers are joined to form polymers by removing a water molecule.

• Hydrolysis: Polymers are broken down into monomers by adding a water molecule.

Summary Table: Macromolecules

Additional info:

• Electrolytes (ions like Na+, K+, Ca2+) are essential for nerve impulses, muscle contraction, and water balance.

• Mutations in protein amino acid sequence can alter structure and function, sometimes causing disease.