MCB 2000 Exam 1

MCB 2000 Exam 1 Alanine (ala) nonpolar aliphatic Glycine (gly) nonpolar aliphatic Valine (val) nonpolar aliphatic branched chain Leucine (leu) nonpolar aliphatic branched chain Isoleucine (ile) nonpolar aliphatic branched chain Proline (pro) nonpolar aliphatic ring structure that is not aromatic Phenylalanine (phe) nonpolar aromatic permits absorption of UV light at 280 nm Tyrosine (tyr) polar and nonpolar properties -amphipathic uncharged aromatic OH group Tryptophan (trp) nonpolar aromatic permits absorption of UV light at 280 nm Serine (ser) polar uncharged OH group Threonine (thr) polar uncharge OH group Cysteine (cys) polar uncharged SH group -groups can become oxidized and form disulfide bonds to each other (S-S) Asparagine (asn) polar uncharged carboxamide group Methionine (met) nonpolar aliphatic thioether Glutamine (gln) polar uncharged carboxamide group Lysine (lys) polar charged positive Arginine (arg) polar charged positive Histidine (his) polar charged positive pKa 6, close to physiological can act as acid or base Aspartic acid (asp) polar charged negative Glutamic acid (glu) polar charged negative What makes water essential for life? -solvent -organizing principle -can be reactant or product in reaciton Common electronegative atoms in biological systems OxygenNitrogenSulfur Types of Noncovalent Interactions Hydrogen Bonding Electrostatic, Ionic interactions Van der Waals force Hyrdrophobic interactions Hydrogen bonds btwn electronegative atom (acceptor) and an H atom that is covalently bonded to another atom (donor) -dont last very long -weak association -bond is strongest at 180 degrees Importance of Hydrogen bonds -solvent properties of water -structure of proteins and nucleic acids Electrostatic, Ionic interactions Occur btwn atoms with a complete - charge and complete + charge -strength of interaction determine by distance and solvent Importance of electrostatic interactions protein-protein interactions DNA protein interactions Catalytic mechanisms Van der Waals forces charge fluctuations transiently produces + or - poles even in nonpolar molecules -weakest -present with snug fit btwn atoms -interactions in membranes - contributes to how permeable it is Hydrophobic interactions Nonpolar molecules that can not form H bonds -form spontaneously Hydrophobic interactions importance allow for an increase in entropy in water The hydrophobic effect Entropy driven association -structure function of proteins - hydrophobic amino acids on inside Importance of noncovalent interactions flexibility stability to large molecules essential to specificity 4 properties of all living organisms Chemical and energy transformation adaptation replication organization and complexity What determines polarity electronegative atoms -electrons not being shared equally Properties of polar molecules partial charges noncovalent interactions hydrophilic reactivity amphipathic both polar and nonpolar molecule Myoglobin stores O2 and releases it under extreme excursion globular protein that is hydrophobic on inside has 8 alpha helixes has high affinity to O2 bc it is tertiary and cant do coopertivity Reversible ionization unique property of water H2O - H+ + OH- Molarity of water 55.5 M Keq of water 1.8 x 10^-16 -indicates that number of dissociate molecules are very small -always products over reactants Kw 1 x 10^-14 will always be the concentration of H+ times concentration of OH- -central role of water as biological solvent pH -log[H+] range 0-14 How does Metabolism change pH? Metabolism produces changes in [H+] which would make the body very acidic without buffers Changes of pH (by .2 -.3) in body Is a signaling mechanism Promotes cell proliferation, migration, assembly of actin Regulates specific proteins binding affinity, activity, recruitment High pH can cause what disease? Cancer Low pH can cause what disease? Neurodegenerative diseases Metabolic acidosis acid-base pathological disorder where there is an increase in the production of acid or a loss of bicarbonate -may cause lactic acidosis, ketoacidosis, complication with drugs, diarrhea, and altered kidney function Acid substance that can release H ion Base substance that can accept H ions Ka expression of the extent of ionization dissociates on top, acid on bottom -used to compare strengths of acids Henderson-Hasselbalch equation pH = pKa + log [A-]/[HA] Applies to weak acids and bases Indicates relationship btwn Ka and pH When pH = pKa the acid is 50% dissociated will be the point of inflection on a concentration curve How is knowledge of pKa important in aspirin? It's a weak acid with pKa 3.5 and has hydrophobic character. Absorbed through cell lining the stomach and small intestine Absorption requires passage through plasma membrane which rate is determined by polarity and charge of molecule. When aspirin is protonated it can pass through membrane since it has no charge. It will be absorbed better through stomach since it has a low pH. Selective avantage for cancer cells proliferation avoiding apoptosis migration and invasion avoiding immune detection Intra and extracellular pH of normal cells IC pH ~ 7.2 EC pH ~ 7.4 Intra and extracellular pH of cancer cells IC pH 7.4 EC pH ~ 6.7-7.1 Will have a reverse pH gradient that benefits the cells Equilibrium no net change in concentration Buffer that your body uses Bicarbonate Amino group weak organic base Carboxylic group weak organic acid Which carboxylic acid will lose a proton first in glutamic acid?