Atomic Structure and Subatomic Particles

Overview of Atomic Structure

Atoms are the fundamental units of matter, composed of subatomic particles that determine their chemical properties and behavior. Understanding atomic structure is essential for grasping the principles of organic chemistry.

• Protons: Positively charged particles located in the nucleus; the number of protons defines the atomic number and thus the element.

• Neutrons: Uncharged particles in the nucleus; varying the number of neutrons creates isotopes of an element.

• Electrons: Negatively charged particles found in orbitals around the nucleus; their arrangement in shells determines chemical reactivity.

• Atomic Mass: The sum of protons and neutrons, measured in daltons (Da).

• Isotopes: Atoms of the same element with different numbers of neutrons. Some isotopes are radioactive (radioisotopes).

Example: Carbon has three naturally occurring isotopes: , , and .

Key Equations

• Atomic Number ():

• Mass Number ():

Chemical Bonding and Molecular Structure

Types of Chemical Bonds

Chemical bonds are forces that hold atoms together in molecules and compounds. The type of bond influences molecular properties and reactivity.

• Ionic Bonds: Formed by the transfer of electrons from one atom to another, resulting in oppositely charged ions (cation and anion).

• Covalent Bonds: Formed when atoms share electrons. Can be polar (unequal sharing) or nonpolar (equal sharing).

• Hydrogen Bonds: Weak attractions between a partially positive hydrogen atom and an electronegative atom (e.g., O or N) in another molecule.

• Van der Waals Forces: Weak, transient attractions due to temporary shifts in electron density.

Example: Table salt () is held together by ionic bonds, while water () molecules are held together by polar covalent bonds and interact via hydrogen bonds.

Bonding Capacity and the Octet Rule

• Atoms tend to form bonds to fill their outermost electron shell (the octet rule).

• Carbon: Has 4 valence electrons and forms up to 4 covalent bonds (e.g., methane, ).

Properties of Water and Solutions

Water as a Solvent

Water is the universal solvent in biological systems due to its polarity and ability to form hydrogen bonds.

• Hydrophilic: Molecules with ionic or polar covalent bonds dissolve in water.

• Hydrophobic: Nonpolar molecules (mainly hydrocarbons) do not dissolve in water.

• Amphipathic: Molecules with both hydrophilic and hydrophobic regions (e.g., phospholipids).

Concentration and Molarity

• Molarity (M):

Example: Dissolving 45 g of glucose (molecular mass = 180 g/mol) in 0.5 L of water yields a 0.5 M solution.

pH, Acids, Bases, and Buffers

pH Scale and Calculations

The pH scale measures the concentration of hydrogen ions () in a solution.

• pH Equation:

• Acidic: pH < 7

• Neutral: pH = 7

• Basic (Alkaline): pH > 7

Example: If , then and pH = 5.

Buffers

• Buffers: Pairs of substances (weak acid and its conjugate base) that minimize pH changes in biological fluids.

• Function: Absorb excess when acidic, release $\text{H}^+$ when basic.

Organic Molecules: Structure and Function

Carbon: The Basis of Organic Chemistry

Organic chemistry centers on carbon-containing molecules, which form the backbone of all biological macromolecules.

• Tetravalency: Carbon forms four covalent bonds, allowing for diverse molecular structures (chains, rings, branches).

• Bond Types: Carbon can form single, double, or triple bonds with other atoms.

• Isomers: Molecules with the same chemical formula but different structures (e.g., enantiomers are non-superimposable mirror images).

Functional Groups

Functional groups are specific groups of atoms within molecules that confer characteristic chemical properties and reactivity.

Major Classes of Organic Molecules

• Carbohydrates: Sugars and polymers of sugars; energy storage and structural roles.

• Lipids: Nonpolar molecules (fats, phospholipids, steroids, waxes); energy storage, membrane structure, signaling.

• Proteins: Polymers of amino acids; catalysis, structure, transport, signaling.

• Nucleic Acids: DNA and RNA; storage and transmission of genetic information.

Synthesis and Breakdown of Macromolecules

Polymerization and Hydrolysis

• Dehydration (Condensation) Reactions: Join monomers to form polymers by removing water.

• Hydrolysis Reactions: Break polymers into monomers by adding water.

Example: Breaking a polysaccharide of 74 glucose units into monomers requires 73 hydrolysis reactions.

Carbohydrates

Structure and Function

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

• Disaccharides: Two monosaccharides joined by a glycosidic bond (e.g., sucrose).

• Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen for energy storage; cellulose for structure).

Lipids

Classes and Properties

• Fats (Triglycerides): Glycerol + 3 fatty acids; energy storage.

• Saturated Fatty Acids: Only single C–C bonds; straight chains; solid at room temperature.

• Unsaturated Fatty Acids: One or more C=C double bonds; kinks in chains; liquid at room temperature.

• Phospholipids: Glycerol + 2 fatty acids + phosphate group; amphipathic; form cell membranes.

• Steroids: Four fused carbon rings; hormones (e.g., estrogen, testosterone).

• Waxes: Long-chain lipids; waterproof coatings.

Proteins

Structure and Function

• Amino Acids: Monomers of proteins; 20 types with different side chains (R groups).

• Peptide Bonds: Link amino acids via condensation reactions.

• Levels of Structure:

  • Primary: Amino acid sequence

  • Secondary: α-helix and β-pleated sheet (hydrogen bonding)

  • Tertiary: 3D folding of a single polypeptide

  • Quaternary: Association of multiple polypeptides

• Domains: Regions of a protein with specific structure and function.

Example: A change in the primary structure (amino acid sequence) can alter secondary, tertiary, and quaternary structures, affecting protein function.

Nucleic Acids

DNA and RNA

• Nucleotides: Monomers composed of a phosphate group, a five-carbon sugar (deoxyribose or ribose), and a nitrogenous base.

• DNA: Double helix; bases A, T, G, C; stores genetic information.

• RNA: Single strand; bases A, U, G, C; involved in protein synthesis.

• Base Pairing (Chargaff’s Rules): %A = %T, %G = %C in DNA.

Example: If 30% of DNA bases are guanine (G), then 30% are cytosine (C), and 20% each are adenine (A) and thymine (T).

Isomerism in Organic Molecules

Types of Isomers

• Structural Isomers: Same molecular formula, different connectivity.

• Stereoisomers: Same connectivity, different spatial arrangement.

• Enantiomers: Non-superimposable mirror images (important in biological activity).

Summary Table: Key Functional Groups in Organic Chemistry

Additional Info

• Organic chemistry is foundational for understanding the structure and function of biological macromolecules.

• Knowledge of atomic structure, bonding, and functional groups is essential for predicting molecular behavior and reactivity in biological systems.