Chapter 2: The Chemistry of Life

Introduction to Chemistry in Anatomy & Physiology

The chemical level of organization is the most fundamental structural level in the human body. Understanding chemistry is essential for comprehending the structure and function of biological molecules and physiological processes.

• Key Point: All anatomical structures and physiological functions are based on chemical interactions.

• Example: Bones are strong due to minerals and collagen, both of which are chemical substances.

Atoms and Elements

Atoms are the smallest units of matter, and elements are substances composed of identical atoms. The human body is primarily composed of a few key elements.

• Atom: Smallest unit of matter retaining its properties.

• Element: Substance made of atoms with the same number of protons; cannot be broken down by chemical means.

Atomic Structure

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

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

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

• Electron Shells: 1st shell holds 2 electrons, 2nd holds 8, 3rd holds 18 (satisfied with 8).

Elements in the Human Body

• Major Elements (96%): Oxygen (O), Carbon (C), Hydrogen (H), Nitrogen (N).

• Mineral Elements (<4%): Sodium (Na), Potassium (K), Calcium (Ca), Chlorine (Cl), Magnesium (Mg), Phosphorus (P), Sulfur (S).

• Trace Elements: Iron (Fe), Copper (Cu), Iodine (I), Zinc (Zn), and others.

Isotopes and Radioactivity

Isotopes are atoms of the same element with different numbers of neutrons. Some isotopes are unstable and emit radiation, which is used in medical applications.

• Mass Number: Sum of protons and neutrons.

• Isotope: Same atomic number, different mass number.

• Radioisotopes: Unstable, release energy as radiation.

• Applications: Cancer radiation therapy, radiotracers, treatment of thyroid disorders.

Mixtures and Chemical Bonds

Matter can be combined physically (mixtures) or chemically (molecules and compounds). Mixtures retain the properties of their components, while chemical bonds create new substances.

• Mixture: Physical combination; components can be separated.

• Molecule: Chemical combination; new properties, separation requires chemical means.

Types of Mixtures

• Suspensions: Liquid with visible solid particles that settle out.

• Colloids: Liquid with small, invisible solid particles; remains dispersed.

• Solutions: Liquid (usually water) with dissolved solute; appears translucent.

Chemical Bonds

Chemical bonds are attractive forces between atoms, forming molecules and compounds. The stability of atoms is governed by the octet rule (8 electrons in the valence shell).

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

• Octet Rule: Atoms are most stable with 8 electrons in the valence shell.

• Duet Rule: Atoms with 5 or fewer electrons are stable with 2 electrons in the first shell.

Ionic Bonds

Ionic bonds form when electrons are transferred between a metal and a nonmetal, resulting in charged ions (cations and anions) that attract each other.

• Cation: Positively charged ion.

• Anion: Negatively charged ion.

• Example: Sodium chloride (NaCl) is formed by ionic bonding.

Covalent Bonds

Covalent bonds involve the sharing of electrons between nonmetal atoms. They are the strongest type of chemical bond and can be single, double, or triple bonds.

• Single Bond: One pair of electrons shared (e.g., H2).

• Double Bond: Two pairs shared (e.g., O2).

• Triple Bond: Three pairs shared (e.g., N2).

Nonpolar and Polar Covalent Bonds

• Nonpolar Covalent Bond: Electrons shared equally (e.g., H2, C-H bonds).

• Polar Covalent Bond: Electrons shared unequally; one atom attracts electrons more strongly (e.g., H2O).

• Dipole: Molecule with partially positive and negative ends.

Hydrogen Bonds

Hydrogen bonds are weak attractions between partially positive and negative atoms in polar covalent molecules, such as water. They are crucial for surface tension and many biological processes.

• Example: Hydrogen bonding between water molecules creates surface tension.

Determining Bond Types

• Ionic: Metal + nonmetal.

• Nonpolar: Two identical nonmetals, or mostly C and H.

• Polar: Two nonmetals with different electronegativities.

Chemical Notation and Reactions

Chemical reactions involve the formation, breaking, or rearrangement of chemical bonds. Chemical equations represent these reactions, showing reactants and products.

• Reversible Reactions: Proceed in either direction (⇌).

• Irreversible Reactions: Proceed left to right (→).

Energy and Chemical Reactions

Energy is required for chemical reactions. It exists as potential (stored) or kinetic (in motion) energy. Chemical, electrical, and mechanical energy are important in physiology.

• Endergonic Reactions: Require energy input; products have more energy.

• Exergonic Reactions: Release energy; products have less energy.

Types of Chemical Reactions in the Body

• Catabolic Reactions: Break down larger substances; generally exergonic.

• Exchange Reactions: Atoms or electrons are transferred; includes redox reactions.

• Anabolic Reactions: Build new chemical bonds; generally endergonic.

Reaction Rates and Enzymes

Enzymes are biological catalysts that increase reaction rates by lowering activation energy. They are highly specific, not altered by the reaction, and speed up reactions dramatically.

• Activation Energy (Ea): Energy required for reactants to collide and react.

• Enzyme Properties: Specificity, not altered, speeds up reactions.

• Induced Fit Mechanism: Enzyme changes shape to fit substrate.

Enzyme Deficiencies

• Tay-Sachs Disease: Deficiency of hexosaminidase; fatal by age 3.

• SCIDS: Deficiency of adenosine deaminase; severe immune deficiency.

• Phenylketonuria: Deficiency of phenylalanine hydroxylase; can be managed by diet.

Inorganic Compounds: Water, Acids, Bases, and Salts

Inorganic compounds do not contain carbon bonded to hydrogen. Water, acids, bases, and salts are essential for physiological functions.

Water

• Properties: Absorbs heat, carries heat, cushions, lubricates, primary solvent.

• Hydrophilic: Dissolves in water (polar/charged).

• Hydrophobic: Does not dissolve (nonpolar).

Acids and Bases

• Acids: Proton donors; increase H+ in water.

• Bases: Proton acceptors; decrease H+ in water.

• pH: Negative logarithm of H+ concentration; scale from 0 (acidic) to 14 (basic).

• Buffers: Resist changes in pH; important for blood pH homeostasis.

Salts and Electrolytes

• Salt: Metal cation and nonmetal anion held by ionic bonds.

• Electrolytes: Conduct electric current in water; essential for organ function.

Organic Compounds: Hydrocarbons, Carbohydrates, Lipids, Proteins, Nucleic Acids

Organic compounds contain carbon bonded to hydrogen. The four main types are carbohydrates, lipids, proteins, and nucleic acids.

Monomers and Polymers

• Monomer: Single subunit.

• Polymer: Many monomers linked together.

• Dehydration Synthesis: Links monomers, releases water.

• Hydrolysis: Breaks polymers, adds water.

Carbohydrates

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

• Disaccharides: Two monosaccharides (sucrose, lactose).

• Polysaccharides: Long chains (starch, glycogen).

• Function: Fuel, structural roles, cell recognition.

Lipids

• Fatty Acids: Hydrocarbon chains; saturated (no double bonds), monounsaturated (one double bond), polyunsaturated (multiple double bonds).

• Triglycerides: Three fatty acids + glycerol; energy storage.

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

• Steroids: Four-ring structure; cholesterol, hormones.

Proteins

• Amino Acids: Monomers; 21 types.

• Peptide Bonds: Link amino acids.

• Protein Structure: Primary (sequence), secondary (folding), tertiary (3D shape), quaternary (multiple chains).

• Denaturation: Loss of shape/function due to heat, pH, chemicals.

Nucleotides and Nucleic Acids

• Nucleic Acids: DNA and RNA; store and execute genetic code.

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

• ATP: Main source of chemical energy; synthesized from ADP and phosphate.

• DNA: Double helix; complementary base pairing (A-T, G-C).

• RNA: Single strand; uracil replaces thymine; carries genetic instructions.

Summary Table: Organic Compounds