Carbon and the Molecular Diversity of Life & The Structure and Function of Large Biological Molecules

Chapter 4: Carbon and the Molecular Diversity of Life

Introduction to Organic Chemistry

Organic chemistry is the study of carbon-based compounds, which are fundamental to all living organisms. Carbon's unique bonding properties allow for the formation of a wide variety of molecular structures essential for life.

• Cells are composed of approximately 70% water, but the majority of the remaining mass consists of carbon compounds.

• Organic chemistry: The study of compounds containing carbon.

• Carbon can form four covalent bonds, allowing for diverse molecular shapes such as straight chains, branched chains, and rings.

• Oxygen forms two covalent bonds; Nitrogen forms three covalent bonds.

Hydrocarbons and Isomers

• Hydrocarbon: A compound made only of hydrogen and carbon. These are nonpolar and hydrophobic.

• Isomers: Compounds with the same molecular formula but different structures.

  • Structural isomers: Differ in the covalent arrangements of their atoms.

  • Geometric (cis-trans) isomers: Same covalent partnerships but differ in spatial arrangements around a double bond.

  • Enantiomers: Mirror images of each other; often have different effects in biological systems.

• Example: L-dopa and D-dopa are enantiomers; only L-dopa is biologically active in treating Parkinson's disease.

Functional Groups

Functional groups are specific groups of atoms within molecules that determine the chemical properties and reactions of those molecules.

• Hydroxyl (–OH): Hydrogen and oxygen

• Carbonyl (C=O): Carbon and oxygen

• Carboxyl (–COOH): Carbon, two oxygens, and hydrogen

• Amino (–NH2): Nitrogen and two hydrogens

• Sulfhydryl (–SH): Sulfur and hydrogen

• Phosphate (–PO4): Phosphorus and oxygen

• Methyl (–CH3): Carbon and three hydrogens

ATP: The Energy Currency of the Cell

• ATP stands for Adenosine Triphosphate.

• Function: Main energy source for cellular processes.

• Energy extraction: Energy is released when a phosphate group is removed, converting ATP to ADP (Adenosine Diphosphate).

Chapter 5: The Structure and Function of Large Biological Molecules

Introduction to Macromolecules

All living things are composed of four major classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids. These macromolecules are essential for structure, function, and regulation of the body's cells, tissues, and organs.

• Macromolecule: A large molecule made of many smaller subunits.

• Polymer: A long molecule consisting of many similar or identical building blocks (monomers) linked by covalent bonds.

• Classes of polymers: Carbohydrates, proteins, nucleic acids.

Polymerization and Depolymerization

• Condensation (Dehydration) Reaction: Joins monomers by removing a water molecule.

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

• Enzymes: Proteins that act as catalysts to speed up chemical reactions without being consumed.

Carbohydrates

Carbohydrates serve as fuel and building material. They include sugars and their polymers.

• Monosaccharides: Single sugars (e.g., glucose, fructose, galactose).

• Disaccharides: Two monosaccharides joined together (e.g., sucrose, lactose, maltose).

• Polysaccharides: Many monosaccharides linked together.

  • Starch: Plant energy storage.

  • Glycogen: Animal energy storage.

  • Cellulose: Structural component of plant cell walls. Some bacteria and protists in termite guts can digest cellulose.

  • Chitin: Structural component in fungal cell walls and arthropod exoskeletons.

Cis-Trans Isomerism in Functional Groups

• Cis: Hydrogens on the same side of a double bond.

• Trans: Hydrogens on opposite sides of a double bond.

Lipids

Lipids are hydrophobic molecules important for energy storage, membrane structure, and signaling.

• Fats: Composed of glycerol and fatty acids.

  • Triacylglycerol: Glycerol + 3 fatty acids.

  • Saturated fatty acids: No double bonds; solid at room temperature (e.g., butter, animal fat).

  • Unsaturated fatty acids: One or more double bonds; liquid at room temperature (e.g., olive oil, vegetable oil).

  • Hydrogenation: Converts unsaturated fats to saturated fats; can produce trans fats.

• Phospholipids: Major component of cell membranes; have hydrophilic heads and hydrophobic tails, forming a bilayer.

• Steroids: Lipids with a carbon skeleton of four fused rings (e.g., cholesterol, steroid hormones).

Proteins

Proteins are polymers of amino acids and perform a vast array of functions within organisms, including catalysis, structure, transport, and regulation.

• Enzymes: Proteins that speed up reactions by lowering activation energy.

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

• Amino acids: Can be nonpolar, polar, or electrically charged.

• Protein structure:

  • Primary: Sequence of amino acids.

  • Secondary: Alpha helix and beta pleated sheet (hydrogen bonding).

  • Tertiary: 3D folding due to side chain interactions (e.g., disulfide bridges).

  • Quaternary: Multiple polypeptide chains assembled together.

• Example: A single amino acid substitution in hemoglobin can cause sickle-cell disease.

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

• Chaperonins: Proteins that assist in the proper folding of other proteins.

Nucleic Acids

Nucleic acids store and transmit hereditary information. The two types are DNA and RNA.

• Gene: Segment of DNA that codes for a protein or trait.

• DNA (Deoxyribonucleic acid): Stores genetic information.

• RNA (Ribonucleic acid): Controls protein synthesis.

• Central Dogma: DNA → mRNA (in nucleus) → amino acids (in ribosomes).

• Polynucleotides: Long chains of nucleotides.

• Nucleotide: Consists of a phosphate group, sugar, and nitrogenous base.

• Nitrogenous bases:

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

  • Purines: Adenine (A), Guanine (G)

• Sugar: Deoxyribose in DNA, ribose in RNA.

• Double helix: DNA's twisted ladder shape; strands run antiparallel (5' to 3' and 3' to 5').

• Base pairing: A pairs with T (DNA) or U (RNA); C pairs with G.

• Thymine: Only in DNA; Uracil: Only in RNA.

Summary Table: Major Classes of Biological Molecules

Class	Monomer	Polymer	Function	Example
Carbohydrates	Monosaccharide	Polysaccharide	Energy, structure	Starch, cellulose
Lipids	Fatty acid, glycerol	Triacylglycerol, phospholipid	Energy storage, membranes	Fats, oils, cholesterol
Proteins	Amino acid	Polypeptide	Catalysis, structure, transport	Enzymes, hemoglobin
Nucleic Acids	Nucleotide	Polynucleotide	Genetic information	DNA, RNA

Key Equations and Concepts

• Dehydration Synthesis:

  • $\text{Monomer}_1 + \text{Monomer}_2 \rightarrow \text{Polymer} + H_2O$

• Hydrolysis:

  • $\text{Polymer} + H_2O \rightarrow \text{Monomer}_1 + \text{Monomer}_2$

• Base Pairing in DNA:

  • $A = T$

  • $C = G$

Additional info: Some explanations and examples have been expanded for clarity and completeness, such as the central dogma, the role of chaperonins, and the significance of isomers in biology.