Basic Biochemistry for Anatomy & Physiology

I. Chemistry – Science Dealing with the Properties and Transformation of Matter

A. Chemical Reactions and Elements

Chemistry studies the transformation and properties of matter, focusing on elements and their interactions.

• Chemical reactions: Processes in which different forms of matter combine or break apart, resulting in new substances.

• Element: A pure substance that cannot be broken down into simpler substances by chemical means.

• There are 92 naturally-occurring elements; about 25 are essential for life.

• Major elements in living organisms: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N).

• Other important elements: Calcium (Ca), Phosphorus (P), Potassium (K), Sulfur (S), Sodium (Na), Chlorine (Cl), Magnesium (Mg).

• Trace elements (needed in small amounts): Iron (Fe), Iodine (I), Zinc (Zn), Copper (Cu).

B. Atoms and Molecules

An atom is the smallest unit of an element that retains its properties. Molecules are assemblies of two or more atoms.

• Atom: Smallest unit of an element; properties are independent of the number of atoms present.

• Molecule: Assembly of two or more atoms (e.g., H2O, CO2).

• Compound: Substance formed from two or more different elements (e.g., H2O, CO2).

• Mixture: Assembly of two or more compounds; does not require a chemical reaction.

II. Properties of an Atom

A. Atomic Structure

Atoms consist of a mostly empty space with a central nucleus containing protons and neutrons, surrounded by electrons.

• Nucleus: Contains protons (positively charged, +1) and neutrons (neutral).

• Electrons: Negatively charged particles orbiting the nucleus.

B. Electron Shells and Energy Levels

Electrons occupy specific energy levels called shells, which determine the atom's chemical properties.

• Shells closest to the nucleus have the lowest energy; those farther have higher energy.

• Each shell contains a set number of electrons:

  • 1st shell: 2 electrons

  • 2nd shell: 8 electrons

  • 3rd shell: 18 electrons

• The outer shell (valence shell) is involved in chemical bonding.

III. Biomolecules

A. General Characteristics

Biomolecules are essential for life and are characterized by their carbon content and covalent bonds.

• Always contain carbon (C).

• Have covalent bonds.

• Large in size; associated with living organisms.

B. Classes of Biomolecules

• Carbohydrates

• Lipids

• Proteins

• Nucleic Acids

IV. Carbohydrates

A. Structure and Function

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen, typically in a 1:2:1 ratio. They serve as energy sources and structural components.

• General formula: $C_nH_{2n}O_n$

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

• Disaccharides: Two monosaccharides joined (e.g., sucrose, lactose, maltose).

• Polysaccharides: Three or more monosaccharides (e.g., starch, glycogen, cellulose).

• Covalent bond: Glycosidic bond.

• Functions: Energy storage and quick energy source.

V. Lipids

A. Structure and Classes

Lipids are hydrophobic molecules not soluble in water, important for energy storage, insulation, and cell membrane structure.

• 4 main classes:

  • Triglycerides (fats and oils)

  • Phospholipids

  • Steroids

  • Eicosanoids

• Triglycerides: 1 glycerol + 3 fatty acids; saturated (no double bonds) or unsaturated (one or more double bonds).

• Phospholipids: 2 fatty acids + 1 phosphate group; amphipathic (hydrophilic and hydrophobic ends); major component of cell membranes.

• Steroids: Found in cell membranes and hormones (e.g., cholesterol, estrogen, testosterone).

• Eicosanoids: Signaling molecules (e.g., prostaglandins).

VI. Proteins

A. Structure and Function

Proteins are the most abundant organic molecules, composed of chains of amino acids, and perform a wide variety of functions in the body.

• Composed of 20 different amino acids.

• Peptide bonds link amino acids; polypeptides are long chains.

• Structural levels:

  • Primary: Sequence of amino acids

  • Secondary: Alpha helix or beta pleated sheet

  • Tertiary: 3D folding

  • Quaternary: Multiple polypeptides

• Functions: Enzymes, transport, hormones, structure, defense, movement.

VII. Nucleic Acids

A. Structure and Function

Nucleic acids (DNA and RNA) store and transmit genetic information and are composed of nucleotides.

• Monomers: Nucleotides

• Each nucleotide: Sugar + phosphate + nitrogen base

• Sugar: Deoxyribose (DNA) or ribose (RNA)

• Bases:

  • Purines: Double ring (Adenine, Guanine)

  • Pyrimidines: Single ring (Thymine, Uracil, Cytosine)

• DNA: Genetic material in the nucleus

• RNA: Protein synthesis

VIII. Water

A. Properties and Importance

Water is vital for life, making up 70–90% of body weight, and acts as a universal solvent.

• Hydrophilic: "Water loving"

• Hydrophobic: "Water fearing"

• Solvent for ions and polar molecules; dissolves particles and solutes.

• Electrolyte: Any substance that dissociates in solution to form ions.

IX. Acids & Bases

A. Definitions and Properties

Acids and bases are important for maintaining pH balance in biological systems.

• Acids: Release H+ ions (e.g., HCl → H+ + Cl-); pH < 7; also called proton donors.

• Bases: Release OH- ions (e.g., NaOH → Na+ + OH-); pH > 7; also called proton acceptors.

• Neutrals: Equal H+ and OH- (e.g., H2O); pH = 7.

• Buffers: Stabilize pH by accepting or releasing H+ ions.

X. Chemical Bonds

A. Types of Chemical Bonds

Chemical bonds are forces that hold atoms together in molecules.

• Covalent bonds: Involve sharing of electrons between atoms.

  • Single covalent bond: Shares 1 pair of electrons (2 total)

  • Double covalent bond: Shares 2 pairs (4 total)

  • Triple covalent bond: Shares 3 pairs (6 total)

• Ionic bonds: Formed when one atom donates an electron to another, resulting in attraction between opposite charges.

  • Cation: Positively charged ion (e.g., Na+, K+)

  • Anion: Negatively charged ion (e.g., Cl-, OH-)

• Polar molecules: Molecules with uneven distribution of charges; dissolve well in water.

• Nonpolar molecules: Molecules with even charge distribution; do not mix with water and are hydrophobic.

B. Table: Comparison of Major Biomolecules

Biomolecule	Monomer	Main Elements	Function	Example
Carbohydrate	Monosaccharide	C, H, O	Energy storage, structure	Glucose, starch
Lipid	Fatty acid, glycerol	C, H, O (sometimes P)	Energy storage, insulation, membranes	Triglyceride, phospholipid
Protein	Amino acid	C, H, O, N, S	Enzymes, structure, transport	Hemoglobin, collagen
Nucleic Acid	Nucleotide	C, H, O, N, P	Genetic information, protein synthesis	DNA, RNA