The Chemistry of Living Things: Foundations for Anatomy & Physiology

Matter and Elements

Introduction to Chemistry in Biology

Chemistry is fundamental to understanding biological processes, as living organisms are composed of matter and governed by chemical principles. Matter consists of elements, which are the simplest forms of substances and cannot be broken down further by ordinary chemical means.

• Chemistry: The study of matter and energy.

• Matter: Anything that has mass and occupies space; composed of elements.

• Energy: The capacity to do work.

• Elements: Pure substances that cannot be broken down into simpler substances; listed in the periodic table.

The Periodic Table of Elements

The periodic table organizes all known elements by increasing atomic number, providing essential information for understanding their properties and roles in biological systems.

• Atomic number: Number of protons in the nucleus.

• Element symbol: One or two-letter abbreviation (e.g., Na for sodium).

• Atomic mass: Approximately the sum of protons and neutrons.

Atoms: Structure and Function

Atomic Structure

Atoms are the smallest functional units of elements, consisting of a central nucleus and surrounding shells.

• Nucleus: Contains protons (positive charge, have mass) and neutrons (no charge, have mass).

• Shells: Surround the nucleus and contain electrons (negative charge, very small mass).

• Electrons and Energy: Electrons in outer shells have more potential energy; moving shells requires absorbing/releasing energy.

Atomic Models

Atoms are depicted with a nucleus at the center and electrons in shells around it. The arrangement of electrons determines chemical behavior.

• Hydrogen: 1 proton, 1 electron.

• Oxygen: 8 protons, 8 neutrons, 8 electrons in 2 shells.

• Sodium: 11 protons, 12 neutrons, 11 electrons in 3 shells.

Key Atomic Properties

• Atomic number: Defines element.

• Atomic mass: Protons + neutrons.

• Neutral atom: Protons = electrons.Electrically neutral atom: Number of protons equals number of electrons.

Isotopes

• Same element, different neutron numbers.

• Stable isotopes: Do not change over time.

• Radioisotopes: Unstable isotopes that emit radiation; used in medical imaging, cancer treatment, and dating biological materials.

Free Radicals:

• Atoms/molecules with unpaired electrons.

• Highly reactive → damage proteins, DNA, membranes.

• Linked to aging, cancer, degenerative diseases.

Atoms, Molecules, and Chemical Bonds

Atoms Combine to Form Molecules

Molecules: Stable associations of 2+ atoms

• Examples: Oxygen molecule (O2), Water (H2O), Table salt (NaCl).

Chemical Bonds

Chemical bonds are attractive forces that hold atoms together in molecules. There are three main types:

Bond Type	Description	Examples
Covalent	Atoms share electrons; very strong bonds	Water (H2O), Oxygen (O2)
Ionic	Attraction between oppositely charged ions	Table salt (NaCl)
Hydrogen	Weak attraction between polar molecules	Between water molecules

• Covalent: Atoms share electrons.

  • Nonpolar: Equal sharing (O2, H2).

  • Polar: Unequal sharing (H2O).

• Ionic: Attraction between oppositely charged ions (Na+ Cl–).

• Hydrogen: Weak attractions between polar molecules (important in water, DNA, proteins).

Covalent Bonds

• Nonpolar covalent bonds: Electrons shared equally (e.g., O2, H2).

• Polar covalent bonds: Electrons shared unequally, creating partial charges (e.g., H2O).

Ionic Bonds

• Ions: Electrically charged atoms or molecules.

• Cation: Positively charged ion (loses electrons).

• Anion: Negatively charged ion (gains electrons).

• Ionic bond: Attraction between cations and anions (e.g., Na+ and Cl-).

Hydrogen Bonds

• Polar molecules: Have regions of partial positive and negative charge.

• Hydrogen bond: Weak attraction between oppositely charged regions of polar molecules (important in water and biological macromolecules).

Elements Essential for Life

Major Elements in Living Organisms

Although nearly 100 elements exist, only a few are essential for life. About 99% of body weight consists of six elements:

• Oxygen (O)

• Carbon (C)

• Hydrogen (H)

• Nitrogen (N)

• Calcium (Ca)

• Phosphorus (P)

Why Life is Carbon-Based:

• Carbon forms 4 covalent bonds → linear, branched, rings.

• Can form double/triple bonds (unlike silicon).

• Basis for complex molecules.

Water: The Biological Solvent

Properties of Water

Water is vital for life due to its unique chemical and physical properties.

• Excellent solvent: Dissolves many substances.

• Liquid at body temperature: Facilitates transport and chemical reactions.

• High heat capacity: Absorbs and holds heat, helping regulate body temperature.

• Participates in chemical reactions: Involved in synthesis and breakdown of biological molecules.

Hydrophilic and Hydrophobic Substances

• Hydrophilic: Polar molecules that interact easily with water.

• Hydrophobic: Nonpolar molecules that do not dissolve in water.

Water in the Body

• About 60% of body weight is water.

• Main constituent of intracellular and extracellular spaces.

• Body distribution: 90% of blood is water; major part of intra- and extracellular fluids.

Acids, Bases, and pH

Hydrogen Ions and pH

Hydrogen ions (H+) play a critical role in biological systems. The concentration of H+ in solution is measured by pH.

• Acid: Donates H+ ions; increases H+ concentration.

• Base: Accepts H+ ions; decreases H+ concentration.

• pH scale: Ranges from 0 (acidic) to 14 (basic); pH 7 is neutral.

• Buffers: Stabilize pH. Example: carbonic acid–bicarbonate buffer in blood.

$\text{pH} = -\log_{10}[\text{H}^+]$

Buffers

Buffers help maintain stable pH in body fluids by minimizing changes in H+ concentration.

• Example: Carbonic acid-bicarbonate buffer system in blood.

• $\text{HCO}_3^- + \text{H}^+ \rightleftharpoons \text{H}_2\text{CO}_3$

Organic Molecules in Living Organisms

Introduction to Organic Molecules

• Organic molecules are carbon-based compounds essential for life. They include carbohydrates, lipids, proteins, and nucleic acids.

• Carbon: Forms four covalent bonds; can create linear, branched, or ring structures.

• Macromolecules: Large molecules built from smaller subunits (monomers).

Synthesis and Breakdown of Macromolecules

• Dehydration synthesis: Links monomers by removing water; requires energy.

• Hydrolysis: Breaks polymers by adding water; releases energy.

Carbohydrates

Structure and Function

Carbohydrates are energy sources and provide structural support. General formula: Cn(H2O)n.

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

• Disaccharides: Two monosaccharides linked (e.g., sucrose, maltose, lactose).

• Polysaccharides: Long chains for energy storage (starch, glycogen) or structural support (cellulose).

Lipids

Structure and Function

Lipids are hydrophobic molecules important for energy storage, cell membranes, and signaling.

• Triglycerides: Glycerol + 3 fatty acids; stored in adipose tissue.

• Phospholipids: Glycerol + 2 fatty acids + phosphate; main component of cell membranes.

• Steroids: Four carbon rings; includes cholesterol and hormones (estrogen, testosterone).

Proteins

Structure and Function

Proteins are polymers of amino acids, essential for structure, function, and regulation of tissues and organs.

• Amino acids: 20 types; joined by peptide bonds.

• Polypeptide: Chain of 3-100 amino acids.

• Protein: Polypeptide longer than 100 amino acids with complex structure.

Levels of Protein Structure

• Primary: Amino acid sequence.

• Secondary: Alpha helix, beta sheets (hydrogen bonds).

• Tertiary: 3D shape (covalent, ionic, hydrophobic, hydrogen bonds).

• Quaternary: Multiple polypeptide chains joined.

Denaturation

• Permanent disruption of protein structure (by heat or pH change) leads to loss of function.

Enzymes

Role in Biochemical Reactions

Enzymes are proteins that act as biological catalysts, speeding up chemical reactions without being consumed.

• Enzyme activity: Depends on shape, temperature, pH, ion concentration, and inhibitors.

• Homeostasis: Critical for maintaining enzyme function.

Nucleic Acids

Structure and Function

Nucleic acids store and transmit genetic information. They are polymers of nucleotides.

• DNA (deoxyribonucleic acid): Double-stranded; contains deoxyribose, bases (adenine, guanine, cytosine, thymine).

• RNA (ribonucleic acid): Single-stranded; contains ribose, bases (adenine, guanine, cytosine, uracil).

• Information flow: DNA → RNA → Protein

ATP: The Energy Carrier

Adenosine triphosphate (ATP) is the universal energy currency of the cell.

• Structure: Nucleotide with three phosphate groups.

• Function: Stores and releases energy for cellular processes.

• $\text{ATP} \rightarrow \text{ADP} + P_i + \text{energy}$

• $\text{ADP} + P_i + \text{energy} \rightarrow \text{ATP}$

Summary Table: Major Biological Molecules

Type	Subunits	Main Functions
Carbohydrates	Monosaccharides	Energy, structural support
Lipids	Fatty acids, glycerol	Energy storage, membranes, hormones
Proteins	Amino acids	Structure, enzymes, transport
Nucleic acids	Nucleotides	Genetic information, energy (ATP)