Biomolecules and Hydrocarbons: Core Concepts

Macromolecules: proteins, nucleic acids (RNA and DNA), carbohydrates, lipids.
Organic molecules important for life; carbon is the fundamental backbone.
Carbon’s tetravalence allows up to four covalent bonds; enables diverse macromolecule structures.
Carbon atomic basics: atomic number 6; inner shell filled, four in the second shell; octet rule satisfied by forming up to four covalent bonds.
Methane example: $ext{CH}_4$ ; each H forms a single covalent bond with C, sharing a pair of electrons.
Overall concept: three-dimensional shape and bonding patterns determine macromolecule function.

Hydrocarbons = organic molecules composed of carbon and hydrogen; store a lot of chemical energy in C–C and C–H bonds.
Methane geometry: tetrahedral around carbon; bond angles $109.5^ ext{°}$ .
Hydrocarbon backbones can be linear chains, rings, or combinations.
Bond types: single (C–C), double (C=C), triple (C≡C) affect geometry.
Prefixes/suffixes: two-carbon hydrocarbons start with $ext{eth-}$ ; suffixes $- ext{ane}, - ext{ene}, - ext{yne}$ denote single, double, and triple bonds, respectively (e.g., $ext{ethane} o ext{C}2 ext{H}6, ext{ ethene } o ext{C}2 ext{H}4, ext{ ethyne } o ext{C}2 ext{H}2$ ).
Geometry by bond type: single bonds allow rotation; double bonds are planar; triple bonds are linear.
Aliphatic vs aromatic hydrocarbons: aliphatic = chains, rings with single bonds (e.g., cyclopentane, cyclohexane); aromatic = rings with alternating single/double bonds (e.g., benzene).
Benzene-containing molecules appear in biology (some amino acids, cholesterol, hormones like estrogen and testosterone) and in some herbicides (e.g., 2,4-D); benzene is a natural crude oil component and a carcinogen.
Isomerism in hydrocarbons: same formula, different structure leads to different properties (e.g., butane vs isobutane).

Isomers: molecules with same formula but different arrangement of atoms/bonds.
Structural isomers: different covalent connectivity (e.g., butane vs isobutane).
Geometric (cis/trans) isomers: different arrangement around a double bond (e.g., butene, C$4$H$8$; cis vs trans).
Enantiomers: non-superimposable mirror images; true for many chiral molecules.
Cis/trans and geometric considerations affect molecular shape and biological interactions.

Enantiomers are mirror images; often have different biological effects.
Thalidomide example: the drug exists as R- and S- forms; interconversion can occur; different enantiomers can have very different effects.
In biology, usually only one enantiomer is utilized (e.g., only L-forms of amino acids in proteins; some D-forms appear in bacteria).
In fats, cis/trans configurations in fatty acids influence properties:
- Unsaturated fats have double bonds; cis double bonds cause bends, keeping fats liquid at room temperature.
- Trans fats have more linear chains; pack tightly and are solid at room temperature; linked to cardiovascular risk.
- Saturated fats have no double bonds; typically solid at room temperature and of animal origin.
Common examples: cis-oleic acid vs trans-elaidic acid; trans fats are nutritionally undesirable.

Functional groups confer specific chemical properties and reactivity to carbon backbones.
Key functional groups include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, sulfhydryl.
They are responsible for the characteristic chemistry of each macromolecule class (proteins, lipids, carbohydrates, nucleic acids).
Hydrophobic vs hydrophilic classification:
- Hydrophobic example: nonpolar methyl group.
- Hydrophilic examples: carboxyl group (COOH) which ionizes to COO$^-$, and carbonyl group which can form hydrogen bonds with water.
Hydrogen bonds between functional groups help folding, structure, and recognition (e.g., DNA base pairing; enzyme–substrate interactions).

Hydrogen bonds connect DNA strands, enabling the double-helix structure.
Complementary base pairing relies on hydrogen bonding between bases.
Hydrogen bonds also stabilize protein folding and specific interactions in biomolecules.

Thalidomide enantiomers demonstrate differential biological activity and safety.
Carboxyl and other groups drive solubility and reactivity in biomolecules.
Ring structures (benzene) contribute to properties of fatty acids, amino acids, cholesterol, and drugs.
Isomerism (structural, geometric, enantiomeric) is central to understanding reactivity and pharmacology.