Biochemistry and Classes of Compounds

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 distinct 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.

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 maintaining 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 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 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: NaCl, CaCO3, KCl, calcium phosphates.

• Roles: Sodium, potassium, calcium, and iron ions are critical for nerve impulse transmission, muscle contraction, and other processes.

• Ionic balance: Vital for homeostasis.

Acids and Bases

Acids and bases are electrolytes that ionize and dissociate in water. They are crucial for maintaining the body's pH balance.

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

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

pH: Acid-Base Concentration

The pH scale measures the relative concentration of free hydrogen ions [H+] in a solution. It ranges from 0 (most acidic) to 14 (most basic), with 7 being neutral.

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

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

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

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

• The pH scale is logarithmic: a change of 1 pH unit equals a tenfold change in [H+].

Neutralization and Acid-Base Homeostasis

Mixing acids and bases results in neutralization, forming water and a salt. The body's pH is tightly regulated by the kidneys, lungs, and chemical buffers, as even slight deviations can be harmful or fatal.

Buffers

Buffers are systems that resist abrupt changes in pH by releasing or binding hydrogen ions. They convert strong acids or bases into weak ones, maintaining acid-base balance.

• Example: The carbonic acid-bicarbonate buffer system is crucial in blood:

$H_2CO_3 \rightleftharpoons HCO_3^- + H^+$

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.

Carbohydrates

Carbohydrates are sugars and starches that serve as major sources of cellular fuel and structural molecules. They contain carbon, hydrogen, and oxygen in a 1:2:1 ratio (CH2O)n.

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

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

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

Lipids

Lipids are hydrophobic molecules that include fats, oils, phospholipids, steroids, and eicosanoids. They contain carbon, hydrogen, and oxygen (less than carbohydrates), and sometimes phosphorus.

• Triglycerides (neutral fats): Composed of three fatty acids bonded to glycerol; function in energy storage, insulation, and protection.

• Phospholipids: Modified triglycerides with two fatty acids and a phosphate group; major components of cell membranes.

• Steroids: Four interlocking hydrocarbon rings; cholesterol is the most important steroid, serving as a precursor for vitamin D, steroid hormones, and bile salts.

• Eicosanoids: Derived from arachidonic acid; include prostaglandins, which regulate blood clotting, inflammation, and other processes.

• Other lipids: Fat-soluble vitamins (A, D, E, K) and lipoproteins (fat transporters in blood).

Proteins

Proteins are polymers of amino acids (20 types), containing carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur and phosphorus. They are essential for structure, function, and regulation of the body's tissues and organs.

• Amino acids: Contain an amine group, acid group, and unique R group; linked by peptide bonds.

• Structural levels:

  • Primary: Sequence of amino acids.

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

  • Tertiary: 3D folding of the polypeptide.

  • Quaternary: Combination of two or more polypeptide chains.

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

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

• Denaturation: Loss of protein structure and function due to pH or temperature changes; may be reversible or irreversible.

• Molecular chaperones: Assist in protein folding, repair, and immune response.

Enzymes

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 may require cofactors or coenzymes.

• Mechanism of action: Substrates bind to the enzyme's active site, forming an enzyme-substrate complex, which undergoes rearrangement to form products.

Nucleic Acids

DNA and RNA

Nucleic acids are polymers of nucleotides, containing carbon, hydrogen, oxygen, nitrogen, and phosphorus. They store and transmit genetic information.

• DNA (Deoxyribonucleic acid): Double-stranded helix; bases are adenine (A), guanine (G), cytosine (C), and thymine (T); stores genetic instructions.

• RNA (Ribonucleic acid): Single-stranded; bases are adenine (A), guanine (G), cytosine (C), and uracil (U); involved in protein synthesis (mRNA, tRNA, rRNA).

Adenosine Triphosphate (ATP)

ATP is the primary energy carrier in cells, composed of an adenine-containing RNA nucleotide with two additional phosphate groups. It powers cellular work by transferring phosphate groups to other molecules (phosphorylation).

• Functions of ATP:

  • Transport work: Phosphorylates transport proteins to move solutes across membranes.

  • Mechanical work: Phosphorylates contractile proteins in muscle cells.

  • Chemical work: Phosphorylates reactants to drive energy-absorbing reactions.