Cheat Sheet Test 1 - Intermolecular interactions Covalent bonds and ionic bonds hold molecules together Other bonds determine the associations between

Intermolecular interactions: Covalent bonds and ionic bonds hold molecules together. Other bonds determine the associations between different molecules Electrostatic interactions: Strong bonds, but easily separated in water. Acidic (-) and basic (+) functional groups can form “salt bridges” Hydrogen bonds - Weak, straight-line interactions. “Hydrogen sandwich” Weakened* by competition with water van der Waals attractions - Weak interactions between nonpolar atoms. Transient fluctuations in electron cloud. Not affected by presence of water Hydrophobic forces - “Anti-hydrogen bonding” Not really a force, but a phenomenon occurring due to lowest energy conformations. Breaking a hydrogen bond requires energy. Clustering limits disruptions to water hydrogen bonding Each amino acid has its own chemical behavior based on its side chain: Basic, Acidic, Uncharged polar, Nonpolar. Peptide bonds and ends have their own properties and interactions as well Subunit advantage: Small amount of DNA can produce large structures. Assembly and disassembly are controllable. Growth and shrinkage of cytoskeletal fibers. Error correction. Badly made subunits simply won’t be used Control of enzymatic activity: Change the shape! Multiple binding sites: Favorable linkage, Negative linkage. Phosphorylation: Addition of a charged functional group. Change shape. Provide new recognition/bonding opportunities Hsp 70: Works with Hsp 40 early in protein folding Hsp 60: Provides a special space for folding, Prevents aggregation, Favorable environment Ubiquitylation: Three proteins required for tagging: E1 = ubiquitin-activating enzyme, E2 + E3 = ubiquitin ligase, Various combinations of E2 and E3 allow for multiple pathways to feed into proteosome. Both enthalpy (H) and entropy (S) values of free energy (G) favor clustering of hydrophobic molecules Lipid tails: Straight-tailed phospholipids can pack closer together (less lateral fluidity). Long tails have more van der Waal opportunities. Tail length and saturation can alter membrane thickness Cholesterol: Decreases permeability to small water-soluble molecules. Prevents crystallization / gelling by acting as a spacer Helix vs. barrel: α helix proteins are suitable for transmitting signals from one side of a membrane to the other. Possible even with oliogmerized single-pass proteins. β barrel protein structure tends to be too rigid. Mobility is variable: Different proteins will exhibit different diffusion coefficients, Interactions with other proteins, Areas of mobility are not unlimited, Bacteriorhodopsin forms clusters, Tight junctions, Molecular fences. Both concentration gradient and electrical gradients impact diffusion of charged molecules: Electro chemical gradient Coupled transporters utilize the potential energy of one gradient to move other molecules Na+-driven Cl--HCO3- exchanger: In: Na+ and HCO3- (NaHCO3), HCO3- + H+ ◊ H2O + CO2. Out: Cl- and H+ (HCl) Na+-independent Cl--HCO3- exchanger: Lowers pH by moving HCO3- out of the cell. Band 3 of RBCs P-type Na + -K + pump: K + is high inside, Na + outside, Electrogenic 1.