Chemistry Comes Alive: Biochemistry for Human Anatomy & Physiology

Part 2 – Biochemistry

Introduction to Biochemistry

Biochemistry is the study of the chemical composition and reactions of living matter. All chemicals in the body are classified as either organic or inorganic compounds. Both types are essential for life and play critical roles in physiological processes.

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

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

2.6 Inorganic Compounds

Water

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

• High heat capacity: Absorbs and releases heat with little temperature change, preventing sudden temperature shifts.

• High heat of vaporization: Requires significant energy to evaporate, providing an effective cooling mechanism.

• Polar solvent properties: Dissolves and dissociates ionic substances, forms hydration layers around large charged molecules (e.g., proteins), 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 called electrolytes because they conduct electrical currents in solution. Ionic balance is vital for homeostasis.

• Examples: NaCl, CaCO3, KCl, calcium phosphates.

• Specialized roles: Sodium, potassium, calcium, and iron ions are essential for nerve impulse transmission, muscle contraction, and other physiological functions.

Acids and Bases

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

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

• Bases: Proton acceptors; pick up H+ ions or 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– (e.g., 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.

• Buffers: Resist abrupt changes in pH by releasing or binding H+ ions. The carbonic acid–bicarbonate system is a key buffer in blood.

2.7 Organic Compounds: Synthesis and Hydrolysis

Polymers and Reactions

Many organic compounds are polymers—chains of similar units called monomers. They are synthesized by dehydration synthesis (removal of water) and broken down by hydrolysis (addition of water).

2.8 Carbohydrates

Overview

Carbohydrates include sugars and starches, containing carbon, hydrogen, and oxygen (H:O ratio is 2:1). They are classified as monosaccharides, disaccharides, or polysaccharides.

• Monosaccharides: Simple sugars (3–7 carbons), e.g., glucose, fructose, galactose, ribose, deoxyribose.

• Disaccharides: Double sugars, e.g., sucrose, maltose, lactose.

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

Monosaccharides

• General formula: (CH2O)n

• Pentoses: Ribose, deoxyribose

• Hexoses: Glucose (blood sugar)

Disaccharides

• Formed by dehydration synthesis of two monosaccharides.

• Examples: Sucrose (glucose + fructose), maltose (glucose + glucose), lactose (glucose + galactose).

Polysaccharides

• Polymers of monosaccharides, formed by dehydration synthesis.

• Examples: Starch (plants), glycogen (animals).

• Not very soluble in water.

2.9 Lipids

Overview

Lipids are hydrophobic molecules containing C, H, and O (less O than carbohydrates), and sometimes P. Main types include triglycerides, phospholipids, steroids, and eicosanoids.

Triglycerides

• Composed of three fatty acids bonded to a glycerol molecule by dehydration synthesis.

• Main functions: energy storage, insulation, protection.

Saturated and Unsaturated Fatty Acids

• Saturated fatty acids: Only single bonds between carbons; solid at room temperature (e.g., butter).

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

• Trans fats: Modified unsaturated fats, unhealthy.

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

Phospholipids

• Modified triglycerides with a glycerol, two fatty acids, and a phosphate group.

• Have polar (hydrophilic) heads and nonpolar (hydrophobic) tails.

• Major component of cell membranes.

Steroids

• Four interlocking hydrocarbon rings form the basic structure.

• Cholesterol is the most important steroid, serving as a precursor for vitamin D, steroid hormones, and bile salts.

Eicosanoids

• Derived from arachidonic acid (a fatty acid).

• Prostaglandins are the most important eicosanoids, involved in blood clotting, inflammation, and labor contractions.

• NSAIDs (e.g., aspirin) block prostaglandin synthesis.

2.10 Proteins

Overview

Proteins make up 20–30% of cell mass and have the most varied functions of any molecules, including structural, enzymatic, and contractile roles. They are polymers of amino acids joined by peptide bonds.

• Contain C, H, O, N, and sometimes S and P.

• Shape and function are determined by four structural levels.

Examples of Protein Functions

• Structural: Collagen provides tensile strength to connective tissues.

• Enzymatic: Enzymes catalyze biochemical reactions.

• Transport: Hemoglobin transports oxygen in blood.

• Contractile: Actin and myosin enable muscle contraction.

• Communication: Hormones and receptors transmit signals.

• Defensive: Antibodies protect against disease.

Amino Acids and Peptide Bonds

• 20 types of amino acids, each with an amine group, acid group, and unique "R group".

• Linked by peptide bonds via dehydration synthesis.

Structural Levels of Proteins

• Primary: Linear sequence of amino acids.

• Secondary: Alpha helices and beta sheets formed by hydrogen bonding.

• Tertiary: 3D folding due to interactions among R groups.

• Quaternary: Association of two or more polypeptide chains.

Fibrous and Globular Proteins

• Fibrous: Structural, water-insoluble, stable (e.g., collagen, elastin).

• Globular: Functional, water-soluble, sensitive to environmental changes (e.g., enzymes, antibodies).

Protein Denaturation

• Loss of 3D structure and function due to changes in pH or temperature.

• Usually reversible unless conditions are extreme.

Enzymes and Enzyme Activity

Enzymes are globular proteins that act as biological catalysts, increasing the speed of chemical reactions by lowering activation energy.

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

• Highly specific for their substrates.

• Names often end in –ase (e.g., hydrolase, oxidase).

Mechanism of Enzyme Action

1. Substrate binds to enzyme's active site, forming an enzyme-substrate complex.

2. Complex undergoes rearrangement, forming the product.

3. Product is released, and enzyme is free to catalyze another reaction.

2.11 Nucleic Acids

Overview

Nucleic acids (DNA and RNA) are the largest molecules in the body, composed of C, H, O, N, and P. They are polymers of nucleotides, each consisting of a nitrogen base, pentose sugar, and phosphate group.

• DNA: Double-stranded helix in the nucleus; stores genetic information for protein synthesis. Bases: adenine (A), guanine (G), cytosine (C), thymine (T).

• RNA: Single-stranded, active outside the nucleus; involved in protein synthesis. Bases: adenine (A), guanine (G), cytosine (C), uracil (U).

2.12 ATP (Adenosine Triphosphate)

Overview

ATP is the primary energy carrier in cells. It is an adenine-containing RNA nucleotide with two additional phosphate groups. Energy is released when phosphate bonds are hydrolyzed.

• ATP powers cellular work by transferring a phosphate group to other molecules (phosphorylation).

• ATP → ADP + Pi + energy

Examples of Cellular Work Driven by ATP

• Transport work: ATP phosphorylates transport proteins, enabling solute movement across membranes.

• Mechanical work: ATP phosphorylates contractile proteins in muscle cells.

• Chemical work: ATP drives endergonic chemical reactions.

Additional info: This summary covers the essential biochemical concepts foundational to human anatomy and physiology, including the structure and function of water, salts, acids, bases, carbohydrates, lipids, proteins, nucleic acids, and ATP. These topics are directly relevant to understanding cellular and systemic physiology.