The Chemistry of Life

Introduction

Chemistry is fundamental to understanding human anatomy and physiology because all biological structures and functions are based on chemical principles. The chemical level of organization is the most basic structural level in the human body, forming the foundation for all higher levels of organization.

Atoms and Elements

Definitions and Importance

• Matter: Anything that has mass and occupies space.

• Chemistry: The study of matter and its interactions.

• Atom: The smallest unit of matter that retains its original properties.

• Element: A substance composed of one or more identical atoms; cannot be broken down into simpler substances by chemical means.

Elements are defined by the number of protons in their atomic nucleus, known as the atomic number. The periodic table organizes elements by increasing atomic number and recurring chemical properties.

Atomic Structure

• Atoms are composed of three types of subatomic particles:

  • Protons (p+): Positively charged, located in the atomic nucleus.

  • Neutrons (n0): Uncharged, slightly larger than protons, also in the nucleus.

  • Electrons (e-): Negatively charged, tiny, orbit the nucleus in electron shells.

• Atoms are electrically neutral when the number of protons equals the number of electrons.

• Most atomic mass comes from protons and neutrons.

• Electrons occupy electron shells:

  • 1st shell: up to 2 electrons

  • 2nd shell: up to 8 electrons

  • 3rd shell: up to 18 electrons (but is stable with 8)

Example: A carbon atom has 6 protons, 6 neutrons, and 6 electrons.

Elements in the Human Body

• Four major elements make up 96% of body mass:

  • Oxygen (O): 65%

  • Carbon (C): 18%

  • Hydrogen (H): 10%

  • Nitrogen (N): 3%

• Seven mineral elements (less than 4%): Sodium (Na), Potassium (K), Calcium (Ca), Chloride (Cl), Magnesium (Mg), Phosphorus (P), Sulfur (S)

• Thirteen trace elements (less than 1%): Iron (Fe), Copper (Cu), Iodine (I), Zinc (Zn), etc.

Isotopes and Radioactivity

Definitions

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

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

• Radioisotopes: Unstable isotopes that emit radiation; used in nuclear medicine.

Example: Hydrogen has three isotopes: Protium (no neutrons), Deuterium (1 neutron), Tritium (2 neutrons).

Applications in Medicine

• Radiotracers: Used in imaging to detect organ function and structure.

• Radiation Therapy: Used to treat cancer by damaging cancerous cells.

Matter Combined: Mixtures and Chemical Bonds

Mixtures

• Mixture: Physical combination of two or more substances; can be separated physically.

• Molecule: Chemical combination of two or more atoms; can only be separated by chemical means.

Types of Mixtures

• Suspensions: Liquid mixed with large solid particles that settle out (e.g., blood cells in plasma).

• Colloids: Liquid mixed with small solid particles that do not settle (e.g., milk).

• Solutions: One substance dissolves in another (e.g., salt water).

Chemical Bonds

• Chemical Bond: Energy relationship between atoms.

• Molecule: Two or more atoms of the same element bonded.

• Compound: Two or more atoms of different elements bonded.

• Macromolecule: Very large compound made of many atoms.

Valence Electrons and the Octet Rule

• Valence Electrons: Electrons in the outermost shell; involved in bonding.

• Octet Rule: Atoms are most stable with 8 electrons in their valence shell (2 for very small atoms).

Ions and Ionic Bonds

• Ionic Bond: Electrons are transferred from a metal to a nonmetal.

• Ion: Atom that has gained or lost electrons and is charged.

• Cation: Positively charged ion (lost electrons).

• Anion: Negatively charged ion (gained electrons).

• Oppositely charged ions attract to form salts.

Covalent Bonds

• Covalent Bond: Electrons are shared between two nonmetals; strongest type of bond.

• Can be single, double, or triple bonds (sharing 1, 2, or 3 pairs of electrons).

• Nonpolar Covalent Bond: Electrons shared equally (e.g., O2, H2).

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

• Electronegativity: The ability of an atom to attract electrons; higher in elements like oxygen.

Hydrogen Bonds

• Weak attractions between partially positive hydrogen atoms and partially negative atoms in polar molecules.

• Responsible for properties like water's surface tension.

Summary Table: Types of Chemical Bonds

Chemical Reactions and Energy

Chemical Notation

• Chemical Reaction: Occurs when chemical bonds are formed, broken, or rearranged.

• Chemical Equation: Shows reactants (left) and products (right).

• Reversible Reaction:

• Irreversible Reaction:

Energy in Chemical Reactions

• Energy: The capacity to do work.

• Potential Energy: Stored energy.

• Kinetic Energy: Energy of motion.

• Chemical Energy: Energy stored in chemical bonds.

• Electrical Energy: Movement of charged particles.

• Mechanical Energy: Direct transfer between objects.

Types of Chemical Reactions

• Catabolic (Decomposition) Reactions: Break down larger substances into smaller ones; generally exergonic (release energy).

• Exchange Reactions: Atoms or electrons are exchanged between reactants.

• Anabolic (Synthesis) Reactions: Build new chemical bonds; generally endergonic (require energy).

• Redox (Oxidation-Reduction) Reactions: Involve electron transfer; one reactant is oxidized (loses electrons), the other is reduced (gains electrons).

Reaction Rates and Enzymes

• Activation Energy (): Minimum energy required for a reaction to occur.

• Factors Affecting Rate: Concentration, temperature, properties of reactants, presence of catalysts.

• Enzymes: Biological catalysts (usually proteins) that lower activation energy and speed up reactions without being consumed.

• Enzymes are highly specific, not permanently altered, and can increase reaction rates by millions of times.

• Induced Fit Model: Enzyme changes shape to fit the substrate during the reaction.

Enzyme Deficiencies

• Tay-Sachs Disease: Deficiency of hexosaminidase; leads to brain cell damage.

• SCID: Deficiency of adenosine deaminase; severely impairs immune function.

• Phenylketonuria: Deficiency of phenylalanine hydroxylase; can cause mental retardation if untreated.

Inorganic Compounds: Water, Acids, Bases, and Salts

Water

• Makes up 50-65% of body mass.

• Absorbs heat, carries heat, cushions, protects, and lubricates body structures.

• Solvent: Dissolves hydrophilic (polar) solutes; does not dissolve hydrophobic (nonpolar) solutes.

Acids and Bases

• Acid: Proton (H+) donor; increases H+ in solution.

• Base: Proton acceptor; decreases H+ in solution.

• pH Scale: Measures hydrogen ion concentration;

• pH 7 is neutral; below 7 is acidic; above 7 is basic.

• Buffers: Resist changes in pH; important for maintaining blood pH (7.35-7.45).

Salts and Electrolytes

• Salt: Compound formed from a metal cation and nonmetal anion (ionic bond).

• Electrolytes: Ions in solution that conduct electricity; essential for nerve and muscle function.

Organic Compounds

Hydrocarbons

• Organic compounds containing only carbon and hydrogen; form chains and rings; backbone of organic molecules.

Monomers and Polymers

• Monomer: Single subunit; can be combined to form polymers.

• Polymer: Large molecule made of many monomers.

• Dehydration Synthesis: Links monomers by removing water.

• Hydrolysis: Breaks polymers by adding water.

Carbohydrates

• Composed of carbon, hydrogen, and oxygen (1:2:1 ratio); polar and hydrophilic.

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

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

• Polysaccharides: Long chains (e.g., starch in plants, glycogen in animals).

• Glycoproteins and glycolipids are carbohydrates covalently bonded to proteins and lipids, important for cell recognition.

Lipids

• Composed of carbon, hydrogen, and some oxygen; nonpolar and hydrophobic.

• Fatty Acids: Hydrocarbon chains with a carboxylic acid group.

• Saturated: No double bonds; solid at room temperature.

• Monounsaturated: One double bond; liquid at room temperature.

• Polyunsaturated: Two or more double bonds; liquid at room temperature.

• Triglycerides: Three fatty acids linked to glycerol; energy storage.

• Phospholipids: Glycerol backbone, two fatty acids, phosphate group; amphiphilic; main component of cell membranes.

• Steroids: Four-ring structure; includes cholesterol, bile acids, and hormones.

Proteins

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

• Amino Acids: 21 types; central carbon, amino group, carboxyl group, R group.

• Peptide Bonds: Link amino acids via dehydration synthesis.

• Protein Structure:

  • Primary: Amino acid sequence

  • Secondary: Alpha helix or beta sheet (hydrogen bonds)

  • Tertiary: 3D folding (R group interactions)

  • Quaternary: Multiple polypeptide chains

• Denaturation: Loss of structure due to heat, pH, or chemicals; results in loss of function.

Nucleotides and Nucleic Acids

• Composed of carbon, hydrogen, oxygen, nitrogen, phosphorus.

• Nucleotide: Nitrogenous base, five-carbon sugar, phosphate group.

• Pyrimidines: Cytosine, Thymine, Uracil

• Purines: Adenine, Guanine

• ATP (Adenosine Triphosphate): Main energy currency of the cell.

• DNA: Double helix, deoxyribose sugar, bases A, T, C, G; stores genetic information.

• RNA: Single strand, ribose sugar, bases A, U, C, G; involved in protein synthesis.

Summary Table: Major Organic Compounds