ACS BIOCHEMISTRY EXAM 2024, Exams of Biochemistry

Download ACS BIOCHEMISTRY EXAM 2024 and more Exams Biochemistry in PDF only on Docsity! ACS BIOCHEMISTRY EXAM 2024 1. Henderson-Hasselbach Equation: pH = pKa + log ([A-] / [HA]) 2. FMOC Chemical Synthesis: Used in synthesis of a growing amino acid chain to a polystyrene bead. FMOC is used as a protecting group on the N-terminus. 3. Salting Out (Purification): Changes soluble protein to solid precipitate. Protein precipitates when the charges on the protein match the charges in the solution. 4. Size-Exclusion Chromatography: Separates sample based on size with smaller molecules eluting later. 5. Ion-Exchange Chromatography: Separates sample based on charge. CM at- tracts +, DEAE attracts -. May have repulsion effect on like charges. Salt or acid used to remove stuck proteins. 6. Hydrophobic/Reverse Phase Chromatography: Beads are coated with a car- bon chain. Hydrophobic proteins stick better. Elute with non-H-bonding solvent (acetonitrile). 1 / 16 17. Ramachandran Plot: Shows favorable phi-psi angle combinatio "wells" for ±h-elices, ß-sheets, and left- handed ±h- elices. 18. Glycine Ramachandran Plot: Glycine can adopt more angles. (H's for R-group). 3 / 16 ns. 3 19. Proline Ramachandran Plot: Proline adopts fewer angles. Amino group is incorporated into a ring. 20. ±h-elices: Ala is common, Gly & Pro are not very common. Side- chain inter- actions every 3 or 4 residues. Turns once every 3.6 residues. Distance between backbones is 5.4Å. 21. Helix Dipole: Formed from added dipole moments of all hydrogen bonds in an ±h-elix. N-terminus is ´+and C-terminus is ´-. 22. ß-sheet: Either parallel or anti-parallel. Often twisted to increase strength. 23. Anti-parallel ß-sheet: Alternating sheet directions (C & N-termini don't line- up). Has straight H-bonds. 24. Parallel ß-sheet: Same sheet directions (C & N-termini line up). Has angled H-bonds. 25. ß-turns: Tight u-turns with specific phi-psi angles. Must have gly at position 3. Proline may also be at ß-turn because it can have a cis-omega angle. 26. Loops: Not highly structured. Not necessary highly flexible, but can occasionally move. Very variable in sequence. 27. Circular Dichroism: Uses UV light to measure 2° structure. Can measure destabilizatio n. be used to hat can be 41. ÀR-Àing Stacking: Weird interaction where aromatic rings stack on each other in positive interaction. 42. Ãh-ole: Methyl group has area of diminished electron density in center; attracts electronegative groups 43. Fe Binding of O2: Fe2+ binds to O2 reversible. Fe3+ has an additional + charge and binds to O2 irreversibly. Fe3+ rusts in O2 rich environments. 44. Ka for Binding: Ka = [PL] / [P][L] 45. ôv-alue in Binding: ô =b(ound / total)x100% ô =L[] / ([L] + 1/Ka) 46. Kd for binding: Kd = [L] when 50% bound to protein. Kd = 1/Ka 47. High-Spin Fe: Electrons are "spread out" and result in larger atom. 48. Low-Spin Fe: Electrons are less "spread out" and are compacted by electron rich porphyrin ring. 49. T-State: Heme is in high-spin state. H2O is bound to heme. 50. R-State: Heme is in low-spin state. O2 is bound to heme. 51. O2 Binding Event: O2 binds to T-state and changes the hat can be heme to R- state. Causes a 0.4Å movement of the iron. sites). Allows 52. Hemoglobin Binding Curve: 4 subunits present in hemoglobin t either T or R -state. Cooperative binding leads to a sigmoidal curve. 53. Binding Cooperativity: When one subunit of hemoglobin changes from T to R-state the other sites are more likely to change to R-state as well. Leads to sigmoidal graph. 54. Homotropic Regulation of Binding: Where a regulatory molecule is also the enzyme's substrate. 55. Heterotropic Regulation of Binding: Where an allosteric regulator is present that is not the enzyme's substrate. 56. Hill Plot: Turns sigmoid into straight lines. Slope = n (# of binding measurement of binding sites that are cooperative. 57. pH and Binding Affinity (Bohr Affect): As [H+] increases, Histidine group in hemoglobin becomes more protonated and protein shifts to T-state. O2 binding affinity decreases. 66. Chymotripsin: Cleaves proteins on C-terminal endof Phe, Trp, and Tyr 67. Competitive Inhibition Graph: Slope changes by factor of ±S. Km/Vmax. X-intercept becomes 1/±Km Y-intercept does not change. Vmax does not change. lope becomes 68. Uncompetitive Inhibition Graph: Does not change slope. Changes Km and Vmax. Results in vertical shift up and down. Y-intercept becomes ±V'/ max X-intercept becomes -±K'/ m 69. Mixed Inhibition Graph: Allosteric inhibitor that binds either E r o Pivot point is between X-intercept and Y-intercept. 70. Non-Competitive Inhibition Graph: Form of mixed inhibition where the pivot point is on the x-axis. Only happens when K1 is equal to K1'. 71. Ionophore: Hydrophobic molecule that binds to ions and carries them through cell membranes. Disrupts concentration gradients. 72. G” transport Equation: ”Gtransport = RTln([S]out / [S]in) + ZF”¨ 73. Pyranose vs. Furanose: Pyranose is a 6- membered ring. Furanose is a 5-membered ring. 74. Mutarotation: Conversion from ±to ß forms of the sugar at the anomeric carbon. 75. Anomeric Carbon: Carbon that is cyclized. Always the same as the aldo or keto carbon in the linear form. 76. ±vs. ß sugars: ±form has -OR/OH group opposite from the - CH2OH group. ß form has -OR/OH group on the same side as the -CH2OH group. 77. Starch: Found in plants. D-glucose polysaccharide. "Amylose chain". Un- branched. Has reducing and non-reducing end. 78. Amylose Chain: Has ±-1,4l-inkages that produce a coiled helix similar to an terminus inside and C-terminus outside 89. Type III Integral Membrane Protein: Membrane protein that contains connect- ed protein helices 90. Type IV Integral Membrane Protein: Membrane protein that contains uncon- nected protein helices 91. Bacteriorhodopsin: Type III integral membrane protein with 7 connected he- lices. 92. ß-Barrel Membrane Protein: Can act as a large door. Whole proteins can fit inside. 93. ±h-emolysin: Secreted as a monomer. Assembles to punch holes in membranes. 94. Cardiolipin: "Lipid staple" that ties two proteins (or complexes) together in a membrane. Formed from two phosphoglycerols. 95. Hydrolysis of Nucleotides: Base hydrolyzes RNA, but not DNA. DNA is stable in base because of 2' deoxy position. 96. Chargaff's Rule: Ratio of A:T and G:C are always equal or close to 1 97. DNA Double-Helix: Opposite strand direction. 3.4Å distance between comple- mentary bases. 36Å for one complete turn. 98. A-form DNA: Condensed form of DNA. Deeper major groove and shallower minor groove. 99. B-form DNA: Watson-Crick model DNA. Deep, wide major groove. 100. Z-form DNA: Left-handed helical form of DNA 110. Step 3 of Epinephrine Signal Transduction: Activated ±s-ubunit separates from ßc-complex and moves to adenylyl cyclase, activating it. 111. Step 4 of Epinephrine Signal Transduction: Adenylyl cyclase catalyzes the formation of cAMP from ATP 112. Step 5 of Epinephrine Signal Transduction: cAMP phosphorylates PKA, activating it 113. Step 6 of Epinephrine Signal Transduction: Phosphorylated PKA causes an enzyme cascade causing response to epinephrine 114. Step 7 of Epinephrine Signal Transduction: cAMP is degraded, reversing activation of PKA. ±s-ubunit hydrolyzes GTP to GDP and becomes inactivated. 115. cAMP: Secondary messenger in GPCR signalling. Formed from ATP by adeny- lyl cyclase. Activates PKA (protein kinase A). 116. AKAP: Anchoring protein that binds to PKA, GPCR, and adenylyl cyclase. 117. GAPs (GTPase activator proteins): Increase activity of GTPase activity in ±s-ubunit of GPCR. 118. ßARK and ßarr: Used in desensitization. ßARK phosphorylates receptors and ßarr draws receptor into the cell via endocytosis 119. RTKs (Receptor Tyrosine Kinases): Have tyrosine kinase activity that phos- phorylates a tyrosine residue in target proteins 120. INSR (Insulin Receptor Protein): Form of RTK. Catalytic domains undergo auto-phosphorylation. 121. INSR signalling cascade: INSR phosphorlates IRS-1 that causes a kinase cascade. 122. INSR cross-talk: INSR causes a kinase cascade that alters gene expression and phosphorlates ß-adrenergic receptor causing its endocytosis. 123. NADH: 124. FADH2: Single-electron transfer 125. NADPH: + glyceraldehyde 3- phosphate. Uses aldolase enzyme. 132. Step 5 of Glycolysis: Dihydroxyacetonephosphate <--> glyceraldehyde 3-phosphate Uses triose phosphate isomerase enzyme. 133. Step 6 of Glycolysis: Glyceraldehyde 3-Phosphate + Pi <-- > 1,3- biphospho- glycerate. Uses G3P dehydrogenase enzyme. NAD+ <--> NADH 134. First Energy Yielding Step of Glycolysis: Step 6 of Glycolysis. G3P + Pi <--> 1,3- bisphosphoglycerate 135. Step 7 of Glycolysis: 1,3-bisphosphoglycerate + ADP <--> 3- phosphoglycer- ate + ATP Uses phosphoglycerate kinase enzyme. 136. First ATP Yielding Step of Glycolysis: Step 7 of Glycolysis. 1,3-bisphosphoglycerate <--> 3- phosphoglycerate 137. Step 8 of Glycolysis: 3-phosphoglycerate <--> 2- phosphoglycerate Uses phosphoglycerate mutase enzyme. 138. Step 9 of Glycolysis: 2-phosphoglycerate <--> Phosphoenolpyruvate (PEP) Uses enolase enzyme. Dehydration reaction (loss of water). 152. Cost of Gluconeogenesis: 4 ATP, 2 GTP, and 2 NADH 153. Oxidative Pentose Phosphate Pathway: Uses glucose 6- phosphate to pro- duce 2 NADPH and ribose 5-phosphate used for biosynthesis 154. Non-Oxidative Pentose Phosphate Pathway: Regenerates glucose 6- phos- phate from ribose 5-phosphate. Uses transketolase and transaldolase enzymes. 155. Transketolase: Transfers a two-carbon keto group 156. Transaldolase: Transfers a three-carbon aldo group 157. Enzyme Km and Substrate Concentration: Most enzymes have a Km that is near the concentration of the substrate. 158. Fructose 2,6-bisphosphate: Not a glycolytic intermediate. Interconverts be- tween fructose 2,6-bisphosphate and fructose 6- phosphate using PFK-2 and FB- Pase-2 159. Regulation with fructose 2,6-bisphosphate: Activates PFK-1 encouraging glycolysis. Inhibits FBPase-1 discouraging gluconeogenesis 160. Regulation of Pyruvate Kinase: Inhibited by ATP, Acetyl- Coa, Alanine, long-chain FA's. 161. PDH (Pyruvate Dehydrogenase Complex): Large complex that converts pyruvate + Coa --> Acetyl-Coa + CO2 Uses pyruvate dehydrogenase, dihydolipoyl transacetylase, and dihydrolipoyl dehy- drogenase. 169. Step 4 of the Citric Acid Cycle: ±k-etoglutarate --> succinyl- CoA Uses ±k-etoglutarate dehydrogenase complex CoA + NAD+ --> NADH + CO2 170. Step 5 of the Citric Acid Cycle: Succinyl-CoA <--> Succinate Uses succinyl-CoA synthetase enzyme GDP + Pi <--> GTP + CoA 171. Step 6 of the Citric Acid Cycle: Succinate <--> Fumarate Uses succinate dehydrogenase FAD <--> FADH2 172. Step 7 of the Citric Acid Cycle: Fumarate <--> L- Malate Uses fumarase enzyme 1) OH- 2) H+ --> 173. Step 8 of the Citric Acid Cycle: L-Malate <--> Oxaloacetate Uses malate dehydrogenase enzyme NAD+ <--> NADH 174. Net Energy Gain of the Citric Acid Cycle: 3 NADH, FADH2, and GTP 175. NADH Producing Steps of the Citric Acid Cycle: Steps 3, 4, and 8. Isocitrate --> ±k-etoglutarate ±k-etoglutarate --> Succinyl- CoA L-Malate --> Oxaloacetate 176. FADH2 Producing Steps of the Citric Acid Cycle: Step 6 Succinate <--> Fumarate 188. Oxidation of Odd-numbered FA's: Results in propionyl-CoA formation. Pro- pionyl-CoA can be converted to succinyl-CoA and used in the CAC 189. Step 4 of ß-oxidation: ß-ketoacyl-CoA (+ CoA) --> Fatty acyl-Coa (shorter) Uses thiolase enzyme 190. ß-oxidation in plants: Electrons are passed directly to molecular oxygen releasing heat and H2O2 instead of the respiratory chain. 191. Éo-xidation: Similar to ß-oxidation but occurs simultaneously on both ends of the molecule. 192. ±o-xidation: Form of oxidation of branched FA's. Produced propionyl-CoA that must be converted to succinyl-CoA for use in the CAC 193. Ketone bodies: Consists of Acetoacetate, Acetone, and D-ß- hydroxybutryate. Formation begins from condensation of 2 acetyl-CoA --> Acetoacetyl-CoA (+ CoA) D-ß-hydroxybutryate can be broken into 2 acetyl-CoA and used as fuel. 194. Zymogen: An inactive precursor of an enzyme, activated by various methods (acid hydrolysis, cleavage by another enzyme, etc.) 195. PLP Structure: 196. Amidotransferase: Uses a PLP group to transfer amino group from an amino acid to ±k-etoglutarate to form L-glutamate and an ±k-etoglutarate. 202. Step 3 of the Urea Cycle: Arginosuccinate --> Argininine Uses arginosuccinase Produces fumarate byproduct 203. Step 4 of the Urea Cycle: Arginine --> Ornithine Uses arginase enzyme H2O --> Urea 204. N-acetylglutamate: Upregulates the production of carbamoyl phosphate and the urea cycle. Formed from acetyl-CoA and glutamate. 205. PCR (Protein Chain Reaction): Process by which DNA is replicated. Has melting step, annealing step, replication step. 206. pKa of Arginine R-group: 12.5 207. pKa of Aspartate R-group: 3.9 208. pKa of Cysteine R-group: 8 209. pKa of Glutamate R-group: 4 210. pKa of Histidine R-group: 6.1 211. pKa of Lysine R-group: 10.5 212. pKa of Tyrosne R-group: 10 213. FAD Structure: 214. Q (Ubiquinone/Coenzyme Q) Structure: 215. Q (Ubiquinone/Coenzyme Q) Function: Lipid soluble electron carrier. Carries 2 electrons with 2 H+. 216. ETC (Electron Transport Chain): Consists of 4 functional protein complexes. 217. Complex I in the ETC: Accepts two electrons from NADH via an FMN cofactor. Transfers 4H+ to Pside and 2H+ to Q 218. Complex II in the ETC: Succinate dehydrogenase. Accepts two electrons electrons from succinate via an FAD group. Q --> QH2 219. Complex III in the ETC: Transfers two electrons from QH2 to cytochrome c via the Q-cycle. Transfers 4H+ to Pside. 220. Complex IV in the ETC: Transfers electrons from cytochrome c to O2. Four electrons are used to reduce on O2 into two H2O molecules. Transfers 4H+ to Pside 221. Mitochondrial ATP Synthase: Consists of F1 and F0 domains 222. F1 Domain of Mitochondrial ATP Synthase: Hexamer of 3 ß± dimers. Catalyze ADP + Pi --> ATP via binding-change model 231. Stage 3 of the Calvin Cycle: Glyceraldehyde 3- phosphate --> Ribulose 1,5-bisphosphate Requires 3 ATP and uses transketolase (TPP). Only uses 8 of the 9 G3P's produced. One G3P is used to make starch/sucrose. 232. Energy Consumption of the Calvin Cycle: 9 ATP molecules and 6 NADPH molecules for every 3 CO2 molecules that are fixated. 233. Pi-Triose Phosphate Anti-porter: Maintains Pi balance in cytosol/chloroplast due to G3P export to the cytosol. Also exports ATP and NADH to the cytosol. 234. Oxygenase Activity in Rubisco: O2 competes with CO2 and reacts to form 2-phosphoglycerate 235. Glycolate Cycle: Process of converting 2- phosphoglycerate to 3- phospho- glycerate in chloroplast, peroxisome, and mitochondria. 236. C4 Plants: Fix CO2 into PEP to form oxaloacetate (via PEP carboxykinase) that is then converted to malate that carries CO2 to rubisco. Bypasses O2 binding. 237. CAM plants: Fix CO2 into PEP to form oxaloacetate (via PEP carboxykinase) that is converted to malate at night and stored until the day time. 238. Malonyl-CoA: Formed from Acetyl-CoA and HCO3 via the Acetyl-CoA car- boxylase (ACC). Serves as a regulator of FA catabolism and precursor in FA synthesis. 239. ACC (acetyl-CoA carboxylase) Regulation: Inhibited by PKA in glucagon chain and activated by pjhosphatase in INSR chain. 240. FAS (Fatty-acid Synthetase): Catalyzes condensation, reduction, dehydra- tion, and reduction of growing fatty acid chain. Requires activation by acetyl-CoA or malonyl-CoA 241. Additional Cost of FAS in Eukaryotes: Acetyl-CoA for lipid synthesis is made in mitochondria and must be transferred into the cytosol via citrate transporter. Costs 2 ATP. 242. Cost of FAS in Eukaryotes: 3 ATP's per 2 carbon unit added. 243. Phosphatidic Acid: Common precursor to TAGs and phospholipids. Consists of a glycerol 3-phosphate with two acyl groups that are attached via acyl transferas- es. 244. TAGs (Triacylglycerols): Made from phosphatidic acid by removing phos- phate with phosphatase and adding an acyl group with acyl transferase.