Chem z Ch 22 Organic and Biological Chemistry - In-Depth Notes

Organic Chemistry and Biochemistry

• The focus is on molecules that bridge chemistry and biology.
• Common elements involved: C, H, O, N.
• Organic Chemistry: Study of carbon-containing compounds.
• Biochemistry: Study of chemistry in living systems.

General Characteristics of Organic Molecules (1 of 2)

• Carbon can make four bonds, allowing a diverse range of structures.
• Single bonds form a tetrahedral shape (109.5°) with sp³ hybridization.
• A single double bond gives a trigonal planar structure (120°) with sp² hybridization.
• A triple bond results in a linear structure (180°) with sp hybridization.
• Most common bond types involve C—H.
• Carbon forms strong, stable bonds with many elements including C, H, O, N, and halogens.
• Functional Groups: Groups of atoms that dictate the reactivity of organic molecules.

General Characteristics of Organic Molecules (2 of 2)

• Bond Angles:
  • Tetrahedral: 109.5°
  • Trigonal planar: 120°
  • Linear: 180°.

Solubility of Organic Molecules

• Predominantly nonpolar bonds (C—C, C—H) lead to low water solubility.
• Polar organic molecules (e.g., glucose) are soluble in polar solvents.
• Surfactants have long nonpolar and polar regions, allowing them to solubilize nonpolar substances in water (found in detergents and soaps).

Acid–Base Properties of Organic Molecules

• Many contain functional groups that can be acidic or basic.
• Carboxylic acids (—COOH) are common acids.
• Amines (R-NH₂) are prevalent bases.

Hydrocarbons (1 of 2)

• Composed solely of carbon and hydrogen.
• Classified by bond types between carbons:
  • Alkanes: Single bonds.
  • Alkenes: One double bond.
  • Alkynes: One triple bond.
  • Aromatic hydrocarbons: Contain resonance due to structure.

Hydrocarbons (2 of 2)

Properties Common to Hydrocarbons (1 of 2)

• Nonpolarity: Insoluble in water, soluble in nonpolar solvents.
• Melting and Boiling Points: Determined by dispersion forces; lower mass hydrocarbons are gases, mid-range are liquids, and high mass are solids.

Properties Common to Hydrocarbons (2 of 2)

Uses of Some Simple Alkanes

• Methane: Major component of natural gas; used for heating fuel.
• Propane: Commonly used as bottled gas for heating and cooking purposes.
• Butane: Found in disposable lighters and as fuel for camping.
• Alkanes with 5 to 12 Carbons: Main components of gasoline, including octane.

Methods for Writing Organic Formulas

• Structural formulas show bonding information explicitly.
• Condensed structural formulas give a simplified view that doesn’t explicitly show all C—H bonds but groups them (e.g., CH₃(CH₂)₄CH₃).

Structure of Alkanes

• Hybridization: Carbons in alkanes are sp³ hybridized with tetrahedral arrangement.
• Can be branched or straight chain.
• Structural isomers differ in the arrangement of atoms while possessing the same molecular formula.

Structural Isomers

• Molecules that share the same molecular formula but have different structural arrangements.

Systematic Nomenclature of Organic Compounds

• Base: Designates the greatest number of carbon atoms in the longest chain.
• Suffix: Indicates the type of compound/functional group.
• Prefix: Shows any substituents attached to the main chain.

Naming Organic Compounds (Steps)

1. Identify the longest continuous carbon chain.
2. Number the carbon atoms from the end closest to the first substituent.
3. Name the substituents, treating side chains from alkanes as alkyl groups.

Cycloalkanes

• Form rings with at least 3 carbon atoms.
• Stability decreases in smaller rings.
• Naming convention involves adding cyclo- to the alkane name.

Reactions of Alkanes

• Generally unreactive due to stability of C—C and C—H single bonds.
• Major reaction is combustion (reaction with oxygen).

Saturated vs. Unsaturated Hydrocarbons

• Saturated hydrocarbons: Only single bonds (alkanes).
• Unsaturated hydrocarbons: Have double or triple bonds (alkenes, alkynes) and are more reactive.

Alkenes

• Contain at least one C=C bond.
• Naming involves including the double bond in the longest chain, ending with -ene.

Geometric Isomers

• Present in alkenes due to hindered rotation around the double bond, leading to different spatial arrangements (cis and trans).

Alkynes

• Contain at least one C≡C bond.
• Naming follows a similar structure to alkenes, ending in -yne.

Addition Reactions of Alkenes and Alkynes

• Atoms can be added to the π bonds of double or triple bonds, saturating them.

Aromatic Hydrocarbons

• Characterized by delocalized electrons in a six-membered ring.
• More stable than alkenes and alkynes, and typically undergo substitution reactions.

Aromatic Nomenclature

• Many aromatic compounds have common names or are named as derivatives of benzene.

Functional Groups Overview

• The chemical behavior of organic molecules is influenced by functional groups.
• R represents the rest of the organic molecule, allowing various compounds to be identified (e.g., R-OH represents alcohols).

Common Functional Groups

• Alkene (-ene): C=C.
• Alkyne (-yne): C≡C.
• Alcohol (-ol): R-OH.
• Ether (-ether): R-O-R'.
• Aldehyde (-al): R-CHO.
• Ketone (-one): R-C(=O)-R'.
• Carboxylic acid (-oic acid): R-COOH.
• Ester (-oate): RCOOR'.
• Amine (-amine): R-NH₂.

Alcohols

• Contain hydroxyl groups (—OH) and are named based on the parent hydrocarbon, appending -ol.

Properties and Uses of Alcohols

• Polar molecules contributing to high water solubility.
• Examples include methanol (fuel), ethanol (alcoholic beverages), and glycerol (moisturizer).

Ethers

• Formed through dehydration between alcohols, typically unreactive aside from combustion, often used as solvents.

Nitrogen-Containing Organic Compounds

• Amines: Organic derivatives of NH₃ where one or more H atoms are replaced by R groups.
• An amide forms when a carbonyl group is bonded to an amine.

Biomolecules

• Major biopolymers include proteins, polysaccharides, and nucleic acids. Lipids are significant but not polymers.
• Proteins are made of amino acids, the building blocks.

Protein Structure

• Primary: Sequence of amino acids.
• Secondary: Formation of α-helices and β-sheets via hydrogen bonds.
• Tertiary: Folded 3D structure due to interactions between side chains.
• Quaternary: Combination of multiple polypeptide chains.

Carbohydrates

• Monosaccharides are the simplest sugars (e.g., glucose). Disaccharides form when two monosaccharides combine (e.g., sucrose). Polysaccharides (e.g., starch, cellulose) are long chains of monosaccharides.

Lipids

• Nonpolar molecules important for energy storage and structure in membranes.
• Fats (saturated) vs. Oils (unsaturated, healthier).

Phospholipids

• Similar to fats but with one phosphate group creating a polar head, essential for cell membrane structure.

Nucleic Acids

• Carries genetic information (DNA and RNA).
• Composed of nucleotides containing a sugar, phosphate, and nitrogenous base.

The Double Helix

• Structure of DNA with complementary base pairing (A-T, C-G) held together by hydrogen bonding and interactions.

Replication of DNA

• Essential process for cell division, where DNA unwinds and is replicated.