Spring 2004 BCHS 3304 Final Exam Review Student Copy-1). The TR transition of hemoglobin upon binding of oxygen to the heme has been thoroughly investigated. On a thermodynamic level, this TR transition can be described as (primarily) an enthalpically driven process. Which of the following phenomena in the TR transition of hemoglobin is the likely enthalpic driving force?a). Movement of the heme iron into the plane of the heme upon oxygen binding.b). The binding of oxygen by the distal histidine (E7).c). The exclusion of water from the oxygen-binding pocket.d). The breaking of pre-existing and making of new C-terminal salt bridges at the / interfaces.e). The occlusion of the heme pocket by valine (E11).2). At a pH more acidic than its isoelectric point, a protein will carry:a). no ionic charge b). a net positive chargec). a net negative charge d). a positive charge equal to the negative chargee). I have no clue, where am I, who are all of these people3). Match the following protein with its appropriate characteristic.a). Collagen I). 2 right-handed -helices forming a left-handedb). Chymotrypsin coiled structure c). -Keratin II). Left-handed proline helices d). RNase A III). oxonium intermediate e). Silk Fibroin IV). catalyzes 2 ADP  AMP + ATP f). Creatine Kinase V).stabilizes collagen structure using ascorbic g). Lysozyme acid h). Prolyl Hydroxylase VI). catalytic triad i) Carbonic Anhydrase VII). pair of catalytic histidine residues j). Adenylate Kinase VIII). solubilizes CO2 as bicarbonate anion k). IgG Antibody IX). antiparallel -sheet structure comprised of primarily small, aliphatic residues X). maintains the muscle “energy reserve” XI). Sandwiched -sheet structure with high-affinity ligand binding loops. 4). Which of the following statements accurately describes the nature of a biologically active protein?a). A biologically active protein is composed of a branching sequence of amphoteric, L-amino acids joined together by resonant amide bonds between neighboring residues, each exhibiting free rotation.b). A biologically active protein is composed of a non-branching sequence of amphipathic, D-amino acids joined together by resonant amide bonds between neighboring residues, with each exhibiting no free rotation.c). A biologically active protein is composed of a non-branching sequence of amphoteric, L-aminoacids joined together by resonant amide bonds between neighboring residues, with each exhibiting no free rotation.d). A biologically active protein is composed of a branching sequence of amphipathic, D-amino acids joined together by non-resonant amide bonds between neighboring residues, each exhibiting free rotation.e). A biologically active proteins is composed of a non-branching sequence of amphoteric, L-amino acids joined together by non-resonant amide bonds between neighboring residues, with each exhibiting no free rotation.5). Consider the following proteins of the TCA cycle:Protein- Mass (kDa)- pI- Solubility Limit (% Salt)-Pyruvate Dehydrogenase 1,100 8.3 25Aconitase 15 5.0 35-ketoglutarate Dehydrogenase 1,080 6.0 27Succinyl-CoA Thiokinase 357 7.5 20Fumarase 353 7.3 40Malate Dehydrogenase 14 7.7 15Outline a procedure to separate all of the enzymes of the TCA cycle from a crude mitochondrial homogenate, paying specific attention to separating Pyruvate Dehydrogenase from -ketoglutarate Dehydrogenase, Aconitase from Malate Dehydrogenase, and Succinyl-CoA Thiokinase from Fumarase in their native states, using affinity chromatography only as a last resort.6). Consider the following Lineweaver-Burk Plot:1/[S] (uM)-1-0.15 -0.12 -0.09 -0.06 -0.03 0.00 0.03 0.06 0.09 0.121/Vo ([nmole/min./mg.]-1)1.990e-43.990e-45.990e-47.990e-49.990e-41.199e-3●= no inhibitor. ▼= 300 nM inhibitor. ■ = 650 nM inhibitor. ◆= 900 nM inhibitor.a). What type of inhibition is seen at low inhibitor concentrations?b). What type of inhibition is seen at higher inhibitor concentrations?c). Going from the absence of inhibitor to 300 nM inhibitor, is the apparent Km increasing or decreasing? Is the presence of the inhibitor making the substrate bind tighter or looser?d). Going from 300 nM inhibitor to 650 nM and 900 nM inhibitor, is the apparent Km increasing or decreasing? Is the presence of the inhibitor making the substrate bind tighter or looser?e). Going from the absence of inhibitor to the presence of inhibitor (300-900 nM inhibitor), is the apparent Vmax of the reaction increasing or decreasing?7). Match the following reagent with its utility in protein primary structure determination.a). Dansyl Chloride I). cuts on the C-terminal side of R or K residues if b). Carboxypeptidase A they are not on the N-terminal side of P c). Chymotrypsin II). labels the N-terminal residue d). -mercaptoethanol III). cuts on the C-terminal side of M residues e). Trypsin IV). cuts off all C-terminal residues except R, K, P, f). Phenyl Isothiocyanate or residues on the C-terminal side of P g). Cyanogen Bromide V). cleaves oxidized disulfide bonds VI). cuts on the C-terminal side of W, Y, or F residues if they are not on the N-terminal side of P 8). 2-phosphoglycate inhibits TIM. In an anaerobic system that is metabolizing glucose as a substrate, which of the following compounds would you expect to increase in concentration rapidly following the addition of 2-phosphoglycate?a). dihydroxyacetone phosphate d). glyceraldehyde-3-phosphateb). 1, 3-bisphosphoglycerate e). 2-phosphoglyceratec). phosphoenolpyruvate9). When the pH is 2 units below the pKa of a specific group, the ratio of protonated to deprotonated species in solution is:a). 10:1 in favor of the protonated form b). 100:1 in favor of the deprotonated formc). 1000:1 in favor of the protonated form d). 100:1 in favor of the protonated forme). 10:1 in favor of the deprotonated form10). Name the following amino acid and denote its’ absolute configuration:COO---- H C NH3+---CH311). Consider the following hemoglobin fractional saturation profile:pO2 (torr)0 20 40 60 80YO2020406080100Curve ACurve BCurve CCurve Da). Which curve represents a person at rest near sea level? b). Which curve represents a person running a marathon at high altitude? c). Which curve represents a person resting at high altitude? d). Which curve represents a person running a marathon near sea level? e). As the graph shifts to the right, is the p50 value increasing or decreasing? Is the affinity of hemoglobin for