Biochemistry and Classes of Compounds

Introduction to Biochemistry

Biochemistry is the study of the chemical composition and reactions of living matter. Understanding biochemistry is essential for grasping the molecular basis of physiological processes in the human body. All chemicals in the body are classified as either organic or inorganic compounds.

• 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.

Inorganic Compounds in the Body

Water

Water is the most abundant and important inorganic compound in living organisms, making up 60–80% of cell volume. Its unique properties are vital for life.

• High heat capacity: Absorbs and releases heat slowly, preventing sudden temperature changes.

• High heat of vaporization: Requires significant energy to evaporate, aiding in cooling mechanisms such as sweating.

• Polar solvent properties: Dissolves and dissociates ionic substances, forms hydration layers around large 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 around the brain).

Salts

Salts are ionic compounds that dissociate into ions (electrolytes) in water. These ions conduct electrical currents and are essential for various physiological functions.

• Common body salts: Sodium chloride (NaCl), calcium carbonate (CaCO3), potassium chloride (KCl), and calcium phosphates.

• Roles: Sodium and potassium are critical for nerve impulse transmission; calcium is vital for muscle contraction and blood clotting.

• Ionic balance: Essential for homeostasis.

Acids and Bases

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

• Acids: Proton donors; release H+ in solution (e.g., HCl → H+ + Cl–).

• Bases: Proton acceptors; take up H+ (e.g., NaOH → Na+ + OH–; OH– + H+ → H2O).

• Important acids: Hydrochloric acid (HCl), acetic acid (HC2H3O2), carbonic acid (H2CO3).

• Important bases: Bicarbonate ion (HCO3–), ammonia (NH3).

pH: Acid-Base Concentration

The pH scale measures the concentration of free hydrogen ions [H+] in a solution, ranging from 0 (most acidic) to 14 (most basic). The scale is logarithmic; each unit change represents a tenfold difference in [H+].

• Acidic solutions: pH 0–6.99; higher [H+].

• Neutral solutions: pH 7; equal [H+] and [OH–].

• Alkaline (basic) solutions: pH 7.01–14; lower [H+], higher [OH–].

The equation for pH is:

Buffers and Acid-Base Homeostasis

Buffers are systems that resist abrupt changes in pH by releasing or binding hydrogen ions. The carbonic acid-bicarbonate buffer system is especially important in blood.

• Buffers: Convert strong acids/bases into weak ones, minimizing pH changes.

• Homeostasis: pH is regulated by the kidneys, lungs, and chemical buffers; even slight deviations can be fatal.

Organic Compounds in the Body

General Properties

Organic compounds always contain carbon (except CO2 and CO) and are unique to living systems. Many are polymers, built from repeating monomer units. They are synthesized by dehydration synthesis and broken down by hydrolysis.

• Dehydration synthesis: Removal of water to join monomers.

• Hydrolysis: Addition of water to break bonds between monomers.

Carbohydrates

Structure and Classification

Carbohydrates are sugars and starches composed of carbon, hydrogen, and oxygen (CH2O)n. They are classified by size and complexity:

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

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

• Polysaccharides: Long chains of monosaccharides; e.g., starch, glycogen.

Functions include serving as a major energy source (especially glucose) and as structural molecules (e.g., ribose in RNA).

Monosaccharides

• Pentoses: Ribose, deoxyribose (important in nucleic acids).

• Hexoses: Glucose (blood sugar), fructose, galactose.

Disaccharides

• Formed by joining two monosaccharides via dehydration synthesis.

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

• Too large to pass through cell membranes; must be digested to monosaccharides.

Polysaccharides

• Polymers of monosaccharides; large and insoluble.

• Examples: Starch (plant storage), glycogen (animal storage in liver and muscle).

Lipids

Structure and Types

Lipids are hydrophobic molecules containing carbon, hydrogen, and oxygen (less oxygen than carbohydrates), and sometimes phosphorus. Main types include triglycerides, phospholipids, steroids, and eicosanoids.

Triglycerides (Neutral Fats)

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

• Main functions: energy storage, insulation, protection.

Phospholipids

• Modified triglycerides: glycerol + two fatty acids + phosphate group.

• Have polar (hydrophilic) "head" and nonpolar (hydrophobic) "tail" regions.

• Major component of cell membranes.

Steroids

• Four interlocking hydrocarbon rings.

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

Eicosanoids

• Derived from arachidonic acid (a fatty acid).

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

Proteins

Structure and Function

Proteins are polymers of amino acids (20 types), containing carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur and phosphorus. Amino acids are joined by peptide bonds. Proteins serve as structural materials, enzymes, hormones, and more.

• General structure: Amine group, acid group, and variable R group.

Levels of Protein Structure

• Primary: Sequence of amino acids.

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

• Tertiary: Folding of secondary structures into a 3D shape.

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

Fibrous vs. Globular Proteins

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

• Globular proteins: Functional, compact, 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.

Molecular Chaperones

• Assist in proper folding of proteins, prevent incorrect folding, and help repair damaged proteins.

• Produced in response to stress (stress proteins).

Enzymes

Structure and Function

Enzymes are globular proteins that act as biological catalysts, increasing the speed of chemical reactions by lowering activation energy. They are highly specific for their substrates and reactions.

• Holoenzyme: Consists of an apoenzyme (protein) and a cofactor (metal ion or coenzyme).

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

Mechanism of Enzyme Action

1. Substrates bind to the enzyme's active site, forming an enzyme-substrate complex.

2. The complex undergoes internal rearrangements to form the product.

3. The enzyme releases the product and is free to catalyze another reaction.

Nucleic Acids

DNA and RNA

Nucleic acids store and transmit genetic information. They are polymers of nucleotides, each consisting of a nitrogenous base, a pentose sugar, and a phosphate group.

• DNA (Deoxyribonucleic acid): Double-stranded helix; bases are adenine (A), guanine (G), cytosine (C), and thymine (T). A pairs with T, G pairs with C. Stores genetic instructions for protein synthesis.

• RNA (Ribonucleic acid): Single-stranded; bases are adenine (A), guanine (G), cytosine (C), and uracil (U). Three types: mRNA, tRNA, rRNA. Carries out DNA instructions for protein synthesis.

Adenosine Triphosphate (ATP)

Structure and Function

ATP is the primary energy carrier in cells. It is an adenine-containing RNA nucleotide with three phosphate groups. Energy is released when the terminal phosphate bond is hydrolyzed.

• Phosphorylation: Transfer of a phosphate group to other molecules, energizing them to perform cellular work.

• ATP functions: Powers transport work (e.g., ion pumps), mechanical work (e.g., muscle contraction), and chemical work (e.g., synthesis of macromolecules).

Summary Table: Major Classes of Organic Compounds