Biochemistry: Chemical Composition and Reactions of Living Matter

Biochemistry and Classes of Compounds

Introduction to Biochemistry

Biochemistry is the study of the chemical composition and reactions that occur in living matter. All chemicals in the body are classified as either organic or inorganic compounds, both of which are essential for life.

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

• Organic compounds: Include carbohydrates, fats, proteins, and nucleic acids. They contain carbon, are usually large, and are covalently bonded.

Inorganic Compounds

Water in Living Organisms

Water is the most abundant inorganic compound in living cells, making up 60%–80% of cell volume. Its unique properties make it the most important inorganic compound in biological systems.

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

• High heat of vaporization: Evaporation requires large amounts of heat, providing a useful cooling mechanism.

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

• Reactivity: Involved in hydrolysis and dehydration synthesis reactions.

• Cushioning: Protects organs from physical trauma, such as cerebrospinal fluid cushioning the brain.

Salts

Salts are ionic compounds that dissociate into ions in water. These ions, known as electrolytes, conduct electrical currents in solution and play specialized roles in body functions (e.g., sodium, potassium, calcium, and iron). Ionic balance is vital for homeostasis.

• Common salts in the body include NaCl, CaCO3, KCl, and calcium phosphates.

Acids and Bases

Both acids and bases are electrolytes that ionize and dissociate in water.

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

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

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

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

pH: Acid-Base Concentration

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

• As [H+] increases, acidity increases and pH decreases.

• As [H+] decreases, alkalinity increases and pH increases.

• The pH is calculated as the negative logarithm of [H+] in moles per liter: $pH = -\log_{10}[H^+]$

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

Neutralization and Acid-Base Homeostasis

Neutralization occurs when acids and bases mix, forming water and a salt. Maintaining acid-base homeostasis is critical, as even slight changes in pH can be fatal. The kidneys, lungs, and chemical buffers regulate pH in the body.

Buffers

Buffers resist abrupt and large swings in pH by releasing or binding hydrogen ions. They convert strong acids or bases into weak ones. The carbonic acid-bicarbonate system is an important buffer in blood:

$\mathrm{H_2CO_3 \rightleftharpoons HCO_3^- + H^+}$

Organic Compounds

General Properties

Organic compounds contain carbon (except CO2 and CO, which are inorganic). Carbon forms four covalent bonds, allowing for a diversity of stable compounds. Many organic compounds are polymers, synthesized by dehydration synthesis and broken down by hydrolysis reactions.

Carbohydrates

Carbohydrates are sugars and starches composed of carbon, hydrogen, and oxygen (CH2O)n. They are classified as monosaccharides, disaccharides, or polysaccharides.

• Monosaccharides: Simple sugars with three to seven carbon atoms (e.g., glucose, fructose, ribose, deoxyribose).

• Disaccharides: Double sugars formed by joining two monosaccharides (e.g., sucrose, maltose, lactose).

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

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

Lipids

Lipids are insoluble in water and contain carbon, hydrogen, and oxygen (less than carbohydrates), and sometimes phosphorus. Main types include triglycerides, phospholipids, steroids, and eicosanoids.

• Triglycerides: Composed of three fatty acids bonded to a glycerol molecule. Function in energy storage, insulation, and protection.

• Phospholipids: Modified triglycerides with two fatty acids and a phosphorus-containing group. Essential for cell membrane structure.

• 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 play roles in blood clotting, inflammation, and other processes.

Proteins

Structure and Function

Proteins are polymers of amino acids, containing carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur and phosphorus. Amino acids are joined by peptide bonds. The structure of a protein determines its function and can be described at four levels:

• Primary structure: Sequence of amino acids in a polypeptide chain.

• Secondary structure: Formation of alpha-helices and beta-sheets stabilized by hydrogen bonds.

• Tertiary structure: Folding of the polypeptide into a three-dimensional shape.

• Quaternary structure: Association of two or more polypeptide chains.

Types of Proteins

• Fibrous (structural) proteins: Strandlike, water-insoluble, and stable. Provide mechanical support and tensile strength (e.g., collagen, keratin).

• Globular (functional) proteins: Compact, spherical, water-soluble, and sensitive to environmental changes. Include enzymes, antibodies, and hormones.

Protein Denaturation

Denaturation is the unfolding and loss of functional shape of globular proteins, often caused by changes in pH or temperature. It is usually reversible unless the changes are extreme.

Enzymes

Enzymes are globular proteins that act as biological catalysts, increasing the speed of chemical reactions by lowering activation energy. They are specific to their substrates and often require cofactors or coenzymes to function.

Nucleic Acids

DNA and RNA

Nucleic acids include deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), which are the largest molecules in the body. They are polymers of nucleotides, each composed of a nitrogen base, a pentose sugar, and a phosphate group.

• DNA: Double-stranded helix found in the nucleus. Bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T). Stores genetic information and directs protein synthesis.

• RNA: Single-stranded, mostly active outside the nucleus. Bases: Adenine (A), Guanine (G), Cytosine (C), Uracil (U). Types include mRNA, tRNA, and rRNA.

Adenosine Triphosphate (ATP)

ATP is the primary energy carrier in cells, capturing chemical energy from glucose and making it available for cellular work. It consists of an adenine-containing RNA nucleotide with two additional phosphate groups.

Function of ATP

ATP powers cellular work by transferring a phosphate group to other molecules (phosphorylation), energizing them to perform transport, mechanical, and chemical work.

Additional info: This guide covers the essential biochemistry concepts relevant to ANP college courses, including the chemical basis of life, the structure and function of major biomolecules, and the importance of water, acids, bases, and buffers in maintaining homeostasis.