Chapter 5 Structure and Function of Large Biological Molecules

Four Major Classes: Carbohydrates, proteins, and nucleic acids are considered macromolecules and polymers. Lipids are large biological molecules but are not true polymers or macromolecules.
Polymer Chemistry:
* Monomer: A small molecule acting as a repeating unit.
* Polymer: A long molecule consisting of many similar building blocks (monomers).
* Dehydration Reaction: Synthesis of a polymer where two monomers bond through the loss of a water molecule ( $H_2O$ ).
* Hydrolysis: Disassembly of polymers into monomers by the addition of a water molecule.

Monosaccharides: Simple sugars (e.g., Glucose $C_6H_{12}O_6$ , Ribose $C_5H_{10}O_5$ ) serving as cell fuel and raw material. Formulas are typically multiples of $CH_2O$ .
Glycosidic Linkage: A covalent bond formed between two monosaccharides via dehydration to create disaccharides or polysaccharides.
Storage Polysaccharides:
* Starch: Glucose polymer in plants (e.g., Amylose, Amylopectin) linked by $\alpha$ glycosidic bonds.
* Glycogen: Extensively branched glucose storage polysaccharide in animals, found in liver and muscle cells.
Structural Polysaccharides:
* Cellulose: Unbranched glucose polymer with $\beta$ glycosidic bonds; provides rigidity to plant cell walls.
* Chitin: Found in arthropod exoskeletons and fungal cell walls.

General Traits: Hydrophobic, nonpolar molecules composed primarily of hydrocarbons.
Fats (Triacylglycerols): Formed from one glycerol (a 3-carbon alcohol) and three fatty acids joined by ester linkages.
* Saturated Fatty Acids: No double bonds; maximum hydrogen atoms; solid at room temperature (e.g., animal fats).
* Unsaturated Fatty Acids: One or more double bonds; liquid at room temperature (e.g., oils).
Phospholipids: Consist of two fatty acids (hydrophobic tails) and a phosphate group (hydrophilic head) attached to glycerol. They form the bilayer of cell membranes.
Steroids: Lipids characterized by a carbon skeleton consisting of four fused rings. Cholesterol is a crucial steroid for membrane fluidity and a precursor for other steroids.

Composition: Polymers of amino acids called polypeptides. There are $20$ standard amino acids differentiated by their R groups (side chains).
Amino Acid Anatomy: Contains an amino group ( $-NH_2$ ), a carboxyl group ( $-COOH$ ), and a central carbon.
Four Levels of Protein Structure:
* Primary: The unique linear sequence of amino acids.
* Secondary: Coils ( $\alpha$ -helix) and folds ( $\beta$ -pleated sheet) stabilized by hydrogen bonds between backbone atoms.
* Tertiary: The overall $3D$ shape resulting from R group interactions (hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges). * Quaternary: Results when two or more polypeptide chains form one functional macromolecule (e.g., Hemoglobin, Collagen).
Denaturation: Loss of a protein's native shape and function due to changes in pH, salt concentration, or temperature.
Functions: Include catalysis (enzymes like Alcohol dehydrogenase), defense (antibodies), transport (hemoglobin), movement (actin and myosin), and structural support (keratin).

Types: Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA).
Nucleotide Structure: Composed of a nitrogenous base, a pentose sugar (Deoxyribose in DNA; Ribose in RNA), and a phosphate group.
Nitrogenous Bases:
* Pyrimidines: Cytosine (C), Thymine (T, in DNA), and Uracil (U, in RNA).
* Purines: Adenine (A) and Guanine (G).
Polynucleotide Structure: Nucleotides are joined by phosphodiester linkages, creating a sugar-phosphate backbone with bases sticking out.
DNA Double Helix: Two antiparallel strands ( $5' \rightarrow 3'$ ) held by hydrogen bonds between complementary bases: $A-T$ and $G-C$ .

Definitions: Genomics is the study of whole sets of genes; Proteomics is the study of all proteins in an organism.
Bioinformatics: The use of computational tools to manage and analyze large biological datasets.
Applications: Sequencing helps trace evolutionary relationships and understand diseases like Alzheimer’s, Parkinson’s, and Sickle-Cell Disease (caused by a single amino acid substitution in hemoglobin).