Organic Molecules and Macromolecules: Properties, Structure, and Function

Properties of Molecules

Carbon and Organic Molecules

Organic molecules are primarily composed of carbon atoms, which have unique properties that allow them to form a wide variety of stable and complex structures essential for life.

• Carbon: Carbon atoms can form four covalent bonds, allowing for diverse molecular shapes and the formation of large, complex molecules.

• Organic molecules: Compounds containing carbon, typically bonded to hydrogen, oxygen, nitrogen, and other elements.

• Molecular shape: The three-dimensional arrangement of atoms in a molecule, determined by the bonding and hybridization of carbon atoms.

Functional Groups

Functional groups are specific groups of atoms within molecules that have characteristic properties and chemical reactivity. They are key to the function and classification of organic molecules.

Functional Group	Formula	Examples of Where Found
Amino	R–NH2	Amino acids (proteins)
Carbonyl (Ketone)	R–CO–R'	Steroids, waxes, proteins
Carbonyl (Aldehyde)	R–CHO	Sugars, some proteins
Carboxyl	R–COOH	Amino acids, fatty acids
Hydroxyl	R–OH	Alcohols, carbohydrates
Methyl	R–CH3	DNA, proteins, carbohydrates
Phosphate	R–O–PO32−	Nucleic acids, ATP
Sulfate	R–SO4−	Carbohydrates, proteins, lipids
Sulfhydryl	R–SH	Proteins (cysteine)

Isomers

Isomers are molecules with the same molecular formula but different structures or spatial arrangements, resulting in different properties.

• Structural isomers: Differ in the covalent arrangement of atoms. Example: n-propyl alcohol and isopropyl alcohol.

• Stereoisomers: Same covalent arrangement but differ in spatial orientation.

  • Geometric isomers: Differ in arrangement around a double bond (cis/trans isomers).

  • Enantiomers: Mirror-image isomers, important in biological systems due to their different interactions with enzymes and receptors.

Atomic Structure and Bonding

Electron Orbitals and Energy Shells

Atoms consist of a nucleus surrounded by electrons in specific energy levels or shells. The arrangement of electrons determines the chemical properties of an atom.

• The first shell holds up to 2 electrons (lowest energy).

• The second shell can hold up to 8 electrons, with orbitals filled in order of increasing energy.

• Electron configuration influences bonding and molecular shape.

Bond Polarity

The type of bond formed between atoms depends on their electronegativity.

• Nonpolar covalent bonds: Electrons are shared equally (e.g., C–C, C–H bonds).

• Polar covalent bonds: Electrons are shared unequally due to differences in electronegativity (e.g., O–H bond in carboxyl group).

Macromolecules

Overview of Macromolecules

Macromolecules are large, complex molecules essential for life. They are typically polymers, made by joining smaller units called monomers.

• Four major types: Proteins, carbohydrates, lipids, nucleic acids

• Roles: Energy storage, structural support, catalysis (enzymes), transport, protection, regulation, movement, heredity

Polymerization and Depolymerization

• Condensation (dehydration) reaction: Joins monomers by removing water.

• Hydrolysis reaction: Breaks polymers into monomers by adding water.

• Enzymes: Biological catalysts that facilitate these reactions.

Proteins

Structure and Function

Proteins are polymers of amino acids with diverse structures and functions, including catalysis, transport, and structural support.

• Amino acids: Building blocks of proteins, each with a central carbon, amino group, carboxyl group, hydrogen, and variable R group (side chain).

• Polypeptide: Linear chain of amino acids linked by peptide bonds.

• Folding: The three-dimensional shape is crucial for protein function.

Levels of Protein Structure

• Primary structure: Sequence of amino acids.

• Secondary structure: Localized patterns (α-helix, β-pleated sheet) stabilized by hydrogen bonds.

• Tertiary structure: Overall 3D shape formed by interactions among R groups.

• Quaternary structure: Association of multiple polypeptide subunits (e.g., hemoglobin).

Protein Denaturation and Chaperones

• Denaturation: Loss of structure and function due to heat, pH, or chemicals.

• Chaperonins/Heat shock proteins: Assist in proper protein folding.

Carbohydrates

Structure and Types

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen, often with the general formula (CH2O)n.

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

• Disaccharides: Two monosaccharides joined by glycosidic linkage (e.g., sucrose, lactose).

• Oligosaccharides: Short chains of monosaccharides, often attached to proteins/lipids.

• Polysaccharides: Long chains (e.g., starch, glycogen, cellulose).

Isomerism in Carbohydrates

• Structural isomers: Different arrangement of atoms.

• Stereoisomers: Same formula, different spatial arrangement (e.g., α- and β-glucose).

Glycosidic Linkages

• Formed by condensation reactions between monosaccharides.

• α-1,4 and β-1,4 linkages determine structure and function (e.g., starch vs. cellulose).

Lipids

Structure and Types

Lipids are hydrophobic molecules with diverse structures, not true polymers. They play roles in energy storage, membrane structure, and signaling.

• Fats and oils (triglycerides): Glycerol + 3 fatty acids.

• Saturated fatty acids: No double bonds, straight chains, solid at room temperature.

• Unsaturated fatty acids: One or more double bonds, kinks, liquid at room temperature.

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

• Steroids: Four fused rings (e.g., cholesterol, hormones).

• Carotenoids: Pigments in plants, precursors to vitamin A.

Phospholipid Bilayer

• Phospholipids arrange in bilayers with hydrophilic heads outward and hydrophobic tails inward, forming the basis of biological membranes.

Nucleic Acids

Structure and Function

Nucleic acids store and transmit genetic information. They are polymers of nucleotides.

• DNA (deoxyribonucleic acid): Double-stranded, stores genetic information.

• RNA (ribonucleic acid): Single-stranded, involved in protein synthesis.

• Nucleotide: Monomer with a nitrogenous base, pentose sugar, and phosphate group.

Nitrogenous Bases

• Pyrimidines: Cytosine (C), Thymine (T), Uracil (U)

• Purines: Adenine (A), Guanine (G)

DNA Structure

• Double helix with antiparallel strands (5' to 3' and 3' to 5').

• Complementary base pairing: A–T (2 H-bonds), G–C (3 H-bonds).

• Phosphodiester linkages form the sugar-phosphate backbone.

RNA Structure

• Single-stranded.

• Ribose sugar instead of deoxyribose.

• Uracil replaces thymine.

Other Roles of Nucleotides

• ATP (adenosine triphosphate): Cellular energy currency.

• GTP (guanosine triphosphate): Energy transfer and signaling.

• cAMP (cyclic adenosine monophosphate): Second messenger in signaling pathways.