Unit 2- Basic Chemistry for Anatomy & Physiology: Structure, Bonds, and Biological Molecules

A) Structure of an Atom

Atomic Structure and Subatomic Particles

All matter, including the human body, is composed of atoms. Understanding atomic structure is foundational for grasping chemical processes in anatomy and physiology.

• Atoms are made of three types of subatomic particles:

  • Protons: Positively charged particles located in the nucleus.

  • Neutrons: Neutral particles also found in the nucleus.

  • Electrons: Negatively charged particles orbiting the nucleus.

• Atoms are electrically neutral when the number of protons equals the number of electrons.

• Isotopes: Atoms of the same element with different numbers of neutrons.

Example: Carbon-12 and Carbon-14 are isotopes of carbon.

B) Ions

Formation and Importance of Ions

Ions are atoms or molecules that have gained or lost electrons, resulting in a net electrical charge. They play crucial roles in physiological processes.

• If an atom loses or gains electrons, it becomes an ion:

  • Anion: Atom gains electrons (negative charge).

  • Cation: Atom loses electrons (positive charge).

• Important ions (electrolytes) in the body:

  • Calcium: Ca2+

  • Sodium: Na+

  • Potassium: K+

  • Hydrogen: H+

  • Chloride: Cl-

Example: Sodium ions (Na+) are essential for nerve impulse transmission.

C) Chemical Bonds

Types and Functions of Chemical Bonds

Chemical bonds hold atoms together to form molecules, which are the basis of biological compounds.

• Ionic Bonds: Formed by the transfer of electrons from one atom to another, resulting in oppositely charged ions that attract each other.

• Covalent Bonds: Formed by the sharing of electrons between atoms.

• Examples:

  • NaCl (table salt): Ionic bond between Na+ and Cl-.

  • H2O (water): Covalent bonds between hydrogen and oxygen.

Additional info: Chemical bonds allow the formation of organic and inorganic compounds essential for life.

D) Water (Inorganic)

Properties and Biological Importance of Water

Water is the most abundant substance in cells and is vital for many physiological processes.

• Composed of hydrogen and oxygen (H2O).

• Universal solvent: Dissolves many substances due to its polarity.

• Participates in chemical reactions and helps transport nutrients and wastes.

• Maintains body temperature due to high heat capacity.

Example: Water dissolves electrolytes like Na+ and Cl- for nerve function.

E) Acids and Bases

Definitions, Properties, and Biological Roles

Acids and bases are important for maintaining pH balance in the body, which is critical for cellular function.

• Acids: Substances that release H+ ions in solution.

• Bases: Substances that accept H+ ions or release OH- ions.

• pH Scale: Measures acidity or alkalinity.

$\text{pH} = -\log_{10}[\text{H}^+]$

• pH < 7: Acidic

• pH = 7: Neutral

• pH > 7: Basic/Alkaline

• Normal blood pH: 7.35 – 7.45

• Buffers: Substances that help maintain stable pH by neutralizing acids or bases.

Example: Bicarbonate buffer system in blood: $\text{HCO}_3^- + \text{H}^+ \rightarrow \text{H}_2\text{CO}_3$

F) Important Organic Substances

Major Classes of Biological Molecules

Organic molecules are essential for structure and function in living organisms. The main classes include carbohydrates, lipids, proteins, and nucleic acids.

1) Carbohydrates

• Consist of carbon, hydrogen, and oxygen (C, H, O).

• General formula: $\text{C}_n(\text{H}_2\text{O})_n$

• Functions:

  • Source of energy (e.g., glucose)

  • Cellular structures (e.g., DNA, RNA)

• Types:

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

  • Disaccharides: Two monosaccharides covalently bonded (e.g., sucrose, lactose)

  • Polysaccharides: Many monosaccharides bonded together (e.g., glycogen, starch)

2) Lipids

• Consist mainly of C, H, O (ratio differs from carbohydrates).

• Functions:

  • Energy storage

  • Insulation and protection (padding)

  • Cell membrane structure

• Types:

  • Glycerides: Most common lipid, composed of glycerol and fatty acids.

  • Phospholipids: Major component of cell membranes; have hydrophilic (water-soluble) head and hydrophobic (water-insoluble) tails.

  • Cholesterol: Found in membranes, precursor for steroid hormones.

  • Steroids: Derived from cholesterol (e.g., bile salts, vitamin D, testosterone, estrogen).

3) Proteins

• Consist of C, H, O, N (sometimes S).

• Functions:

  • Structural materials (e.g., collagen)

  • Enzymes, hormones, transporters

  • Source of energy (especially when carbs & lipids are low)

• Structure:

  • Amino acids: Building blocks of proteins; 20 different types.

  • Peptides: Chains of amino acids.

  • Polypeptides: Many amino acids joined together; fold into specific shapes for function.

4) Nucleic Acids

• Consist of C, H, O, N, P.

• Types:

  • DNA (deoxyribonucleic acid): Stores genetic information.

  • RNA (ribonucleic acid): Involved in protein synthesis.

• Building blocks: Nucleotides (composed of a sugar, phosphate group, and nitrogenous base).

• Nitrogenous bases:

  • Adenine (A)

  • Thymine (T) – DNA only

  • Uracil (U) – RNA only

  • Cytosine (C)

  • Guanine (G)

• Structure:

  • DNA: Double-stranded helix; base pairs A-T, G-C.

  • RNA: Single-stranded; base pairs A-U, G-C.

• Functions:

  • DNA: Cellular reproduction, template for RNA synthesis.

  • RNA: Protein synthesis.

5) Adenosine Triphosphate (ATP)

• Modified RNA nucleotide; primary energy carrier in cells.

• Structure: Adenosine (adenine + ribose) + 3 phosphate groups.

• Energy is released when ATP is broken down:

$\text{ATP} \rightarrow \text{ADP} + \text{P}_i$

• ATP hydrolysis provides energy for cellular activities.

Summary Table: Major Biological Molecules

Class	Elements	Building Blocks	Main Functions	Examples
Carbohydrates	C, H, O	Monosaccharides	Energy, structure	Glucose, starch, glycogen
Lipids	C, H, O	Fatty acids, glycerol	Energy storage, membranes	Triglycerides, phospholipids, cholesterol
Proteins	C, H, O, N, (S)	Amino acids	Structure, enzymes, transport	Collagen, hemoglobin, enzymes
Nucleic Acids	C, H, O, N, P	Nucleotides	Genetic information, protein synthesis	DNA, RNA, ATP