The Structure and Function of Large Biological Molecules: Carbon, Water, and Macromolecules

Section I: Carbon

Overview: Carbon—The Backbone of Life

Carbon is fundamental to life, forming the backbone of biological molecules. Although cells are mostly water, the remaining mass is primarily carbon-based compounds. Carbon enters the biosphere through photosynthesis, enabling the diversity of organic molecules essential for life.

• Carbon-based compounds include proteins, DNA, carbohydrates, and other molecules distinguishing living matter from inorganic material.

• Common elements bonded to carbon: hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), phosphorus (P).

Concept 4.1: Organic Chemistry—The Study of Carbon Compounds

Organic chemistry focuses on compounds containing carbon, ranging from simple molecules (e.g., CH4) to complex macromolecules (e.g., proteins).

• Major elements of life (C, H, O, N, S, P) are uniform across organisms.

• Carbon's versatility allows for an immense variety of organic molecules.

• Early chemists distinguished between organic (living origin) and inorganic (nonliving origin) compounds.

• Vitalism (belief in a life force) was replaced by mechanism (physical and chemical laws govern all phenomena).

• Key experiments: Wöhler synthesized urea; Kolbe synthesized acetic acid; Stanley Miller simulated early Earth conditions, demonstrating abiotic synthesis of organic compounds.

Additional info: Mechanism is now the accepted view; organic chemistry studies carbon compounds regardless of origin.

Concept 4.2: Carbon's Bonding Versatility

Carbon atoms can form diverse molecules by bonding to four other atoms, enabling complex molecular architectures.

• Carbon has 6 electrons: 2 in the first shell, 4 in the second shell.

• Forms four covalent bonds (single or double), rarely forms ionic bonds.

• Bond angles in tetrahedral geometry: $109.5^\circ$.

• Carbon skeletons vary in length, branching, and ring formation.

• Hydrocarbons: molecules of only carbon and hydrogen; hydrophobic, major component of petroleum and fats.

• Hydrocarbons release energy upon reaction.

Isomers

• Structural isomers: same formula, different covalent arrangement.

• Cis-trans isomers: differ in spatial arrangement around double bonds.

• Enantiomers: mirror images, possible with asymmetric carbon; often only one is biologically active.

Example: Methamphetamine enantiomers have vastly different biological effects.

Concept 4.3: Functional Groups and Molecular Function

The properties of organic molecules depend on their carbon skeleton and attached chemical groups. Functional groups are key to molecular function.

• Seven important chemical groups: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl.

• Functional groups (first six) are hydrophilic, increase solubility.

• Methyl groups are nonreactive, serve as markers.

Functional Group	Structure	Properties	Example
Hydroxyl	—OH	Polar, forms alcohols, increases solubility	Ethanol
Carbonyl	>CO	Polar, forms aldehydes (end) or ketones (within)	Acetone (ketone), Propanal (aldehyde)
Carboxyl	—COOH	Acidic, forms carboxylic acids	Acetic acid
Amino	—NH2	Basic, forms amines	Glycine
Sulfhydryl	—SH	Forms thiols, stabilizes proteins	Cysteine
Phosphate	—OPO32−	Transfers energy, forms anions	ATP
Methyl	—CH3	Nonreactive, marker	5-methyl cytosine

ATP (Adenosine Triphosphate) is a key energy transfer molecule. Hydrolysis of ATP releases energy:

$\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i + \text{energy}$

Section II: Water and Macromolecules

Overview: The Molecules of Life

Cells assemble small organic molecules into large macromolecules: carbohydrates, lipids, proteins, nucleic acids. These macromolecules exhibit unique properties due to their atomic arrangement.

Concept 5.1: Macromolecules—Polymers Built from Monomers

Three classes of macromolecules (carbohydrates, proteins, nucleic acids) are polymers made from monomers.

• Polymer: long molecule of repeating monomers.

• Monomer: small molecule serving as a building block.

• Enzymes facilitate polymerization and depolymerization.

• Dehydration reaction: joins monomers by removing water.

• Hydrolysis: breaks polymers by adding water.

Example: Digestion involves hydrolysis of polymers into monomers for absorption.

Concept 5.2: Carbohydrates—Fuel and Building Material

Carbohydrates include sugars and their polymers, serving as energy sources and structural materials.

• Monosaccharides: simple sugars (e.g., glucose, C6H12O6).

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

• Polysaccharides: polymers of many monosaccharides (e.g., starch, glycogen, cellulose).

Type	Structure	Function	Example
Monosaccharide	Single sugar unit	Energy source	Glucose
Disaccharide	Two sugars	Transport/storage	Sucrose, Lactose
Polysaccharide	Many sugars	Storage/structure	Starch, Cellulose, Glycogen

• Starch: storage polysaccharide in plants; composed of α-glucose monomers.

• Glycogen: storage polysaccharide in animals; highly branched.

• Cellulose: structural polysaccharide in plant cell walls; composed of β-glucose monomers.

• Chitin: structural polysaccharide in arthropod exoskeletons and fungal cell walls; contains nitrogen appendage.

Example: Cellulose is indigestible by humans but digestible by some microbes and fungi.

Concept 5.3: Lipids—Hydrophobic Molecules

Lipids are diverse, hydrophobic molecules that do not form polymers. They include fats, phospholipids, and steroids.

• Fats: constructed from glycerol and fatty acids; energy storage, insulation, cushioning.

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

• Unsaturated fatty acids: one or more double bonds, kinked chains, liquid at room temperature (oils).

• Trans fats: unsaturated fats with trans double bonds, associated with health risks.

• Phospholipids: two fatty acids, glycerol, phosphate group; major component of cell membranes.

• Steroids: four fused carbon rings; includes cholesterol and hormones.

Lipid Type	Structure	Function	Example
Fat (Triglyceride)	Glycerol + 3 fatty acids	Energy storage	Animal fat, plant oil
Phospholipid	Glycerol + 2 fatty acids + phosphate	Membrane structure	Cell membrane
Steroid	Four fused rings	Hormones, membrane component	Cholesterol, testosterone

Example: Phospholipid bilayer forms the basis of cell membranes.

Concept 5.4: Proteins—Diversity of Structure and Function

Proteins are polymers of amino acids, accounting for more than half the dry mass of cells. They perform structural, catalytic, transport, and regulatory functions.

• Amino acids: monomers with amino, carboxyl, and variable R group.

• Polypeptides: chains of amino acids linked by peptide bonds.

• Protein structure:

  • Primary: sequence of amino acids.

  • Secondary: α-helix and β-pleated sheet, stabilized by hydrogen bonds.

  • Tertiary: 3D folding due to R group interactions (hydrogen bonds, ionic bonds, hydrophobic interactions, disulfide bridges).

  • Quaternary: aggregation of multiple polypeptides.

• Denaturation: loss of structure due to environmental changes (pH, temperature, solvents).

• Chaperonins: proteins assisting in proper folding.

Structure Level	Description	Example
Primary	Linear sequence of amino acids	Insulin sequence
Secondary	α-helix, β-sheet	Keratin, silk
Tertiary	3D folding	Antibody, enzyme
Quaternary	Multiple polypeptides	Hemoglobin, collagen

Example: Sickle-cell disease results from a single amino acid substitution in hemoglobin.

Additional info: Protein structure is determined by primary sequence and assisted by chaperonins; misfolded proteins are linked to diseases like Alzheimer's.

Concept 5.5: Nucleic Acids—Hereditary Information

Nucleic acids (DNA and RNA) store, transmit, and express genetic information. They are polymers of nucleotides.

• Nucleotide: nitrogenous base (purine or pyrimidine), pentose sugar (ribose or deoxyribose), phosphate group.

• DNA: double helix, antiparallel strands, base pairing (A-T, G-C).

• RNA: single strand, base pairing (A-U, G-C).

• Gene expression: DNA → RNA → protein.

• Phosphodiester linkage: joins nucleotides (3' OH to 5' phosphate).

Type	Sugar	Bases	Structure
DNA	Deoxyribose	A, T, G, C	Double helix
RNA	Ribose	A, U, G, C	Single strand

Example: mRNA carries genetic instructions from DNA to ribosomes for protein synthesis.

$\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$

Concept 5.6: Genomics and Proteomics

Advances in sequencing have enabled the study of entire genomes (genomics) and protein sets (proteomics). These fields use computational tools to analyze large datasets.

• Genomics: analysis of large sets of genes or whole genomes.

• Proteomics: analysis of large sets of protein sequences.

• Bioinformatics: computational analysis of biological data.

• DNA and protein sequences are used to trace evolutionary relationships.

Species	Hemoglobin Amino Acid Differences (vs. Human)
Gorilla	1
Mouse	25
Chicken	45
Frog	67

Example: Molecular genealogy uses DNA/protein sequence similarity to infer evolutionary relationships.