Chemistry Comes Alive: Biochemistry and Molecular Foundations for Human Anatomy & Physiology

Biochemistry: The Chemical Basis of Life

Overview of Biochemistry

Biochemistry is the study of the chemical composition and reactions of living matter, forming the foundation for understanding physiological processes in the human body. All chemicals in living organisms are classified as either organic or inorganic compounds.

• Inorganic compounds: Include water, salts, acids, and bases; do not contain carbon.

• Organic compounds: Include carbohydrates, lipids, proteins, and nucleic acids; contain carbon and are usually large, covalently bonded molecules.

• Both types are essential for life and homeostasis.

Inorganic Compounds

Water: Properties and Functions

Water is the most abundant inorganic compound in living cells, accounting for 60–80% of cell volume. Its unique properties make it vital for life.

• High heat capacity: Absorbs and releases heat with minimal temperature change, stabilizing body temperature.

• High heat of vaporization: Requires significant energy to evaporate, enabling cooling mechanisms like sweating.

• Polar solvent properties: Dissolves and dissociates ionic substances, forms hydration layers around charged molecules, and serves as the body's major transport medium.

• Reactivity: Participates in hydrolysis and dehydration synthesis reactions.

• Cushioning: Protects organs from physical trauma (e.g., cerebrospinal fluid cushions the nervous system).

Salts

Salts are ionic compounds that dissociate into cations and anions in water, excluding H+ and OH–.

• All ions are electrolytes and conduct electrical currents in solution.

• Ions such as sodium, potassium, calcium, and iron play specialized roles in body functions.

• Ionic balance is vital for homeostasis.

• Common salts: NaCl, CaCO3, KCl, calcium phosphates.

Acids and Bases

Acids and bases are electrolytes that ionize and dissociate in water.

• Acids: Proton donors; release H+ ions. Examples: HCl, acetic acid (HAc), carbonic acid (H2CO3).

• Bases: Proton acceptors; release OH– ions. Examples: bicarbonate (HCO3–), ammonia (NH3).

pH: Acid-Base Concentration

The pH scale measures the concentration of hydrogen ions ([H+]) in a solution, ranging from 0 (most acidic) to 14 (most basic).

• Each pH unit represents a tenfold difference in [H+].

• Acidic solutions: pH 0–6.99; high [H+], low pH.

• Neutral solutions: pH 7; equal H+ and OH– ions (pure water).

• Alkaline (basic) solutions: pH 7.01–14; low [H+], high pH.

Neutralization and Buffers

• Neutralization: Mixing acids and bases forms water and a salt via displacement reactions.

• Buffers: Resist abrupt changes in pH by releasing or binding H+ ions; convert strong acids/bases into weak ones. The carbonic acid–bicarbonate system is a key buffer in blood.

Organic Compounds: Synthesis and Hydrolysis

Polymer Formation and Breakdown

Many organic compounds are polymers, chains of similar units called monomers.

• Dehydration synthesis: Monomers are joined by removal of water (H2O).

• Hydrolysis: Polymers are broken down by addition of water.

Carbohydrates

Structure and Classification

Carbohydrates are sugars and starches containing C, H, and O, with hydrogen and oxygen in a 2:1 ratio.

• Monosaccharides: Simple sugars (3–7 carbon atoms); monomers of carbohydrates. Examples: glucose, fructose, galactose, ribose, deoxyribose.

• Disaccharides: Double sugars; formed by dehydration synthesis of two monosaccharides. Examples: sucrose, maltose, lactose.

• Polysaccharides: Polymers of monosaccharides; formed by dehydration synthesis. Examples: starch (plants), glycogen (animals).

Lipids

Types and Functions

Lipids contain C, H, O (less O than carbohydrates), and sometimes P. They are insoluble in water and serve as energy storage, insulation, and protection.

• Triglycerides: Composed of three fatty acids bonded to a glycerol molecule. Fats (solid) and oils (liquid).

• Phospholipids: Modified triglycerides with a phosphorus-containing group; essential for cell membrane structure.

• Steroids: Four interlocking ring structures; cholesterol is the most important steroid, precursor for vitamin D, steroid hormones, and bile salts.

• Eicosanoids: Derived from arachidonic acid; prostaglandins play roles in blood clotting, inflammation, and labor contractions.

Saturated vs. Unsaturated Fatty Acids

• Saturated fatty acids: All carbons linked by single bonds; linear molecules; solid at room temperature (e.g., butter).

• Unsaturated fatty acids: One or more double bonds; kinked molecules; liquid at room temperature (e.g., olive oil).

• Trans fats: Modified unsaturated fats; unhealthy.

• Omega-3 fatty acids: Heart-healthy unsaturated fats.

Phospholipids and Steroids

• Phospholipids: Glycerol, two fatty acids, and a phosphorus group; head is hydrophilic, tails are hydrophobic; form cell membranes.

• Steroids: Four-ring structure; cholesterol is the basis for all steroids formed in the body.

Proteins

Structure and Functions

Proteins comprise 20–30% of cell mass and have diverse functions: structural, enzymatic, contractile, transport, communication, and defense.

• Polymers of amino acids held together by peptide bonds.

• Shape and function determined by four structural levels: primary, secondary, tertiary, quaternary.

Amino Acids and Peptide Bonds

• All proteins are made from 20 amino acids, each with an amine group, acid group, and unique R group.

• Peptide bonds form via dehydration synthesis; hydrolysis breaks them.

Levels of Protein Structure

• Primary: Linear sequence of amino acids.

• Secondary: Alpha helix (spring) or beta sheet (accordion); stabilized by hydrogen bonds.

• Tertiary: Folding of secondary structures into a compact shape.

• Quaternary: Two or more polypeptides combine to form a functional protein.

Fibrous vs. Globular Proteins

• Fibrous proteins: Strandlike, water-insoluble, stable; provide mechanical support (e.g., collagen).

• Globular proteins: Compact, spherical, water-soluble; functional regions (active sites); sensitive to environmental changes (e.g., enzymes, antibodies).

Protein Denaturation

• Globular proteins unfold and lose their functional shape due to changes in pH or temperature.

• Usually reversible unless changes are extreme.

Enzymes and Enzyme Activity

Enzymes are globular proteins acting as biological catalysts, lowering activation energy and increasing reaction speed.

• Most enzymes are holoenzymes (protein + cofactor/coenzyme).

• Highly specific for substrates; names often end in -ase.

• Three steps: substrate binds to active site, rearrangement occurs, product is released.

Nucleic Acids

Structure and Function

Nucleic acids (DNA and RNA) are polymers of nucleotides, each composed of a nitrogen base, pentose sugar, and phosphate group.

• DNA: Double-stranded helix; genetic blueprint for protein synthesis; located in nucleus; bases: adenine (A), guanine (G), cytosine (C), thymine (T).

• RNA: Single-stranded; links DNA to protein synthesis; bases: adenine (A), guanine (G), cytosine (C), uracil (U); types: mRNA, tRNA, rRNA.

ATP: The Energy Currency of Cells

Structure and Function

ATP (adenosine triphosphate) stores and releases energy for cellular work.

• Composed of adenine, ribose, and three phosphate groups.

• Energy is released when phosphate bonds are hydrolyzed.

• ATP can be converted to ADP and AMP by loss of phosphate groups.

Cellular Work Driven by ATP

ATP powers transport, mechanical, and chemical work in cells.

• Transport work: Phosphorylates membrane proteins to move substances.

• Mechanical work: Phosphorylates contractile proteins for muscle contraction.

• Chemical work: Phosphorylates reactants to drive endergonic reactions.

Summary Table: Major Classes of Biomolecules

Class	Monomer	Polymer	Main Functions
Carbohydrates	Monosaccharide	Polysaccharide	Energy, structure
Lipids	Fatty acid, glycerol	Triglyceride, phospholipid	Energy storage, membranes, signaling
Proteins	Amino acid	Polypeptide	Structure, enzymes, transport, defense
Nucleic Acids	Nucleotide	DNA, RNA	Genetic information, protein synthesis

Key Equations

• pH calculation: $pH = -\log_{10}[H^+]$

• ATP hydrolysis: $ATP + H_2O \rightarrow ADP + P_i + \text{energy}$

• General formula for monosaccharides: $(CH_2O)_n$

Clinical Relevance

• Enzymes function within a narrow pH range; extreme deviations can be life-threatening.

• Arterial pH below 6.85 is rarely compatible with survival.

Conclusion

Understanding the molecular foundations of biochemistry is essential for grasping the physiological processes that sustain life. Mastery of these concepts is critical for further study in human anatomy and physiology.