BMB 507 Exam 1 | Questions and Answers

BMB 507 Exam 1 | Questions and Answers What does pH represent in relation to hydrogen ions? pH is the negative logarithm of the hydrogen ion concentration, expressed as pH = -log{H+}. What is the significance of pKa in relation to ionization? pKa is the pH at which a molecule is 50% ionized, indicating the strength of an acid. How does the dielectric constant affect pKa modulation? A lower dielectric constant increases electrostatic attraction, making it easier for charges to 'see each other' and thus increasing pKa. What role do hydrogen bonds play in pKa modulation? Hydrogen bonds can increase the pKa of acidic groups. How does temperature influence the pH of buffers? The pH of some buffers decreases as temperature increases. What is the effect of a hydrophobic environment on acidic side chains? In a hydrophobic environment, acidic side chains prefer to be uncharged, raising their pKa. What is the mechanism of aspartyl proteases? Aspartyl proteases use an acid-base mechanism involving two conserved aspartic acid residues in their active site to break peptide bonds. The pKa of the active site is 3.8, so most aspartyl proteases work best at low pHs hydrophobic amino acids alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, tryptophan, cysteine, glycine hydrophilic amino acids lysine, arginine, histidine, aspartate, glutamate, serine, threonine, asparginine, glutamine hydrophilic basic amino acids lysine, arginine, histidine hydrophilic acidic amino acids aspartate, glutamate hydrophilic amino acids with uncharged r groups serine, threonine, asparginine, glutamine amphipathic amino acids proline alanine ala, a hydrophobic Valine val, v hydrophobic isoleucine ile, i hydrophobic leucine leu, l hydrophobic methionine met, m hydrophobic phenylalanine Phe, F hydrophobic Tyrosine tyr, y hydrophobic tryptophan trp, w hydrophobic cysteine cys, c hydrophobic can form disulfide bonds between two cysteines to stabilize extracellular proteins glycine gly, g hydrophobic lysine lys, k basic hydrophilic Arginine arg, r basic hydrophilic aspartate asp, d acidic hydrophilic glutamate glu, e acidic hydrophilic serine ser, s hydrophilic polar with uncharged r groups threonine thr, t hydrophilic polar with uncharged R groups asparginine asn, n hydrophilic polar with uncharged R groups glutamine gln, q hydrophilic polar with uncharged R groups proline pro, p, hydrophobic and hydrophilic can also be found in cis confirmation due to steric hinderance of ring What are the characteristics of alpha helices in protein structure? Alpha helices are right-handed, counter clockwise and form a coiled structure. What distinguishes parallel from antiparallel beta strands? In parallel beta strands, all strands run in the same direction; in antiparallel strands, they run in opposite directions with hairpin turns. What is the Rossmann fold made of? The Rossmann fold consists of alternating beta strands and alpha helices, forming a concave active site that binds nucleotides.