Cellular Metabolism Exam 1 Gift

Cellular Metabolism Exam 1: The Gift N.B.: Due to randomization, questions may not appear in the exact order shown. The notation “[REDACTED” indicates one or more words are not shown in that position. Any questions that involve figures will not have the figures shown. Please color code your answers: ( green=99% certain, orange=50-75% certainty, red=uncertain ) TEAMwork is Dreamwork! Let’s get some :) Please include alternative questions/answers and not just the answer to old test questions! Cursor parking lot: ` S Parking R Parking Gold Zone Note: This was copy/pasted from when I took Biochemistry from a previous semester with Dr. Daniel lol ~What does this mean? 1. From the biomolecules listed, identify those that can [REDACTED]: (Select all that apply) be used for energy ~assuming from challenges overview questions ● Proteins - structure/catalysis ● Nucleic acids - information storage/ coenzyme ● Lipids - cell signaling/ membranes ● Carbohydrates - storage/ source of electrons 2. Match the eukaryotic subcellular structure with its function. **This was a question on the overview quiz** Nucleus: Genetic Expression Lysosome: Cellular Digestion Mitochondria: ATP Production Rough ER: Secreted Protein Production Cytoplasm: Cellular Protein Synthesis

3. How was metabolism to be determined to be [REDACTED] a highly conserved system across species? ** This was a quiz question on the overview quiz** Glycolysis was found in yeast and animals 4. Which of the lysosomal-based diseases manifests due to [REDACTED] dramatically reduced but still present activity of a particular enzyme? **This was a quiz question on the overview quiz** Cholesterol Ester Storage Disease 5. What is the best way to distinguish between Wolman's Disease and Cholesterol Ester Storage Disease? Wolman’s Cholesterol Ester Both - Premature Stop Codon - Lethal by Age 1 - Point Mutation instead of a stop codon - Can be managed with dietary managing and pharmacologics - Exon Splice Error - Involve enzyme failure in the lysosome 6. From the elements presented below, identify those elements that are needed in trace amounts [REDACTED]: ** This was a quiz question on the overview quiz** - Oxygen - Phosphorous - Cobalt - Selenium - Carbon - Zinc Potentially Other: Needed in trace amounts by humans: · Mg, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Se, Mo, I Primary elements of life: · H, C, N, O, Na, K, Ca, P, S, Cl (mainly H, C, N, O)

13. If there was an increase in substrate C, which enzyme is likely to [REDACTED] likely to decrease activity in the forward direction? ** Question in Ebb and Flow Quiz** Enzyme 2 14. A technician, [REDACTED], performs an experiment on this pathway and notes enzyme 8 is inhibited and accumulation of C occurs with acceleration of enzyme 4 in the forward direction. [REDACTED] states that this is due to reverse flow of enzyme 6 and substrate F being converted to substrate C via enzyme 6. What error if any has [REDACTED] made? 15. If concentration of C decreases, which pathway [REDACTED] first? 16. Which of the following could result in a Km [REDACTED] of enzyme [REDACTED]? (End of Ebb and Flow Question set) ---------- 17. From the list below, select the reasons that [REDACTED] do not apply to cellular systems. (Select all that apply) The Le Chatelier principle doesn't apply to cellular systems because cells are not at equilibrium and do not try to reach equilibrium; they try to achieve a steady state. OR - Cellular systems are open systems with large interconnected pathways - ‘Irreversible’ reactions NOT found in beaker - No equilibrium in cell 18. In a cellular system, the concentration of a metabolite is noted to be 50mM. Over time this metabolite drops to 25mM. What is the expected response of the system? Km represents the concentration so if it lowering then the active site and the ES complex are strong (stronger binding affinity) The System is expected to take the product and flow back to the metabolite to try and achieve its steady state again or pull metabolite from upstream reactions to achieve its steady state. 19. Evaluate the provided statement. Determine if the statement is correct or incorrect. If the statement is incorrect determine if the error is in clause (A) or clause (B). (A) Km is a value that [REDACTED] 1/2 of Vmax; (B) if Vmax is 200 units per second then [REDACTED]. A) is; B) is 100 units per second **Question from Enzyme 1 quiz** Both (A) and (B) are incorrect 20. [REDACTED] is an electron carrier with a similar purpose to NAD. However, what distinguishes [REDACTED] from NAD? - FAD, contains higher oxidative activity than NAD

- FAD is tightly or covalently bound to the enzyme and does not get released. NAD is not tightly or covalently bound and can be released into a pool of coEnzymes. - FAD accommodates 2 Hydrogens; NAD accepts 1 Hydrogen - OR if it refers to NADP v NAD: NADP is anabolic and NAD is catabolic 21. Match the free energy term with the free energy value: ΔG>0 - reaction is non spontaneous or unfavorable ΔG<0 - reaction is spontaneous or favorable ΔG=0 - reaction at equilibrium 22. Evaluate the provided statement. Determine if the statement is correct or incorrect. If the statement is incorrect determine if the error is in clause (A) or clause (B). (A) An isozyme is a [REDACTED] enzyme found in [REDACTED] cellular location; (B) therefore, isozymes [REDACTED] gene. A) variant, different; B) come from the same gene ~question from enzyme 1 quiz B) is incorrect 23. Given the following determine if the overall reaction (A --> D) is favorable, unfavorable, or at equilibrium. A --> B --> C --> D • A --> B [REDACTED] • B --> C [REDACTED] • C --> D [REDACTED] If you add all the steps (A—>B,B→C,C→D) and the number is positive it is un favorable If you add all the steps (A—>B,B→C,C→D) and the number is negative it is favorable If you add all the steps (A—>B,B→C,C→D) and the number is zero it is at equilibrium 24. At which point is an enzyme is most likely in [REDACTED] conformation? ~from enzymes 1 quiz If REDACTED refers to “Lowest energy” the answer would be transition state 25. Given the following determine the [REDACTED]. Provide only a numerical answer. Km = [REDACTED] M Vmax = [REDACTED] units/second S = [REDACTED] M What is [REDACTED] → Potentially asking for the velocity

If two compounds from two substrates, its Transferases - Example (hexokinase, aminotransferases) If one compound from two substrates, its Ligases - Example (synthetases) 28. Which of the following inhibitors are likely to [REDACTED]? Bind covalently to the enzyme? - Suicide inhibitors Bind to the active site? - Competitive inhibitors Bind to a site other than the active site? - Allosteric Inhibitors Aid in substrate binding but hinder catalysis? - Uncompetitive Inhibitors Put the enzyme in its relaxed state so it becomes inactive? - Transition State Inhibitors 29. In ethanol sensitivity, there are two enzymes that clear the dangerous material. Why doesn't the [REDACTED] isozyme clear the material even though [REDACTED]? - Cytoplasmic aldehyde dehydrogenase and mitochondrial aldehyde dehydrogenase clear it, but cytoplasmic has a high Km meaning it has a low affinity. The mitochondrial fails due to having a single A.A. mutation even though it has a high affinity and low Km causing only the cytoplasmic to be working 30. A technician is examining the amino acid sequence of a mutated enzyme cannot be inactivated by protein kinase A. The technician reports that an amino acid [REDACTED] has been mutated to [REDACTED] and this [REDACTED]. Is this statement reasonable or has an error been made? The mutated enzyme might be referring to glycogen synthase, as it is typically inactivated by protein kinase A. 31. Which type of inhibitor would provide the best starting point for developing a therapy [REDACTED]? For Ethanol Sensitivity ~from enzymes 2-3 quiz Uncompetitive inhibition 32. Examination a Lineweaver Burk plot for an enzyme system after an inhibitor is added reveals a sudden [REDACTED]. Which of the following statements best describes what is happening at the enzyme level? Increase in the Y-intercept. ~from enzymes 2-3 quiz The inhibitor is binding at a site that is not the active site and disrupting catalysis An Increase in the y intercept, indicates a decrease in Vmax, if this is observed it is likely that a non competitive (allosteric) inhibition is occurring, wherein a molecule is binding a distal non active site which prevents catalysis from occurring, but the substrate is still able to bind to the active site 33. Which enzyme class uses [REDACTED]? Class 1: Oxidoreductases ● Catalyze (break down) Oxidation-Reduction rxns

○ Oxidation = electron loss ■ dehydrogenases ○ Reduction = electron gain ● Example: Cytochrome P450 ○ Metabolizes everything; xenobiotics → saturated compound converted to an alcohol Class 2: Transferases ● Transfers chemical group from one molecule to another ○ Two substrates & products ■ Hexokinase (transfer phosphate from ATP to glucose) ○ Aminotransferases ■ Move amino groups (i.e. keto acid to amino acid) ■ Needs pyridoxal phosphate (B6) as coenzyme Class 3: Hydrolases ● Catalyze addition of -OH from water to substrate ( Note: NOT a transferases ) ● IRREVERSIBLE ● RNases and DNases hydrolyze phospho-ester bond Class 4: Lyases ● Catalyze carbon-carbon bond cleavage ○ C-N bond cleavage ○ Release CO2 from beta-keto acid ○ Some reversible ● Synthase → ATP is NOT INVOLVED in new bond formation ● Synthetase → ATP IS INVOLVED in new bond formation Class 5: Isomerase ● Moving of groups or double bonds within a molecule ○ Example: Glucose-6-phosphate → Fructose-6-phosphate ● Mutases → moves phosphate group from one C to another in SAME MOLECULE ● Racemerases & Epimerase : changes stereochemistry ● Other examples of isomerases: ○ Phosphoglyceromutase ○ Epimerase ○ Racemase Class 6: Ligases ● Join C atoms together ○ Needs energy (usually ATP ) ○ Synthetases ● Examples: ○ Adding CO2 to pyruvate requires coenzyme biotin & ATP

● Km decreases ● Vmax decreases (remember: it’s in the reciprocal!) ● Mode of inhibition = uncompetitive ● Vmax decrease ● Km stays the same ● Mode of inhibition = allosteric / non-competitive Notes: remember that both transition state inhibitors and suicide inhibitors focus on its POTENCY, therefore a graph is not usually used 37. Considering a muscle cell [REDACTED] ATP. What is the likely form and state of phosphorylase? Stimulated by epinephrine but is overloaded by **Enzymes 2-3 Quiz** A form to R state 38. Determine if the provided statement is correct or incorrect. If the statement is incorrect, determine if clause (A) or (B) or both possesses an error.

(A) Glucose is removed from glycogen by the enzyme phosphorylase [REDACTED], (B) this is how we know phosphorylase uses [REDACTED]. To make this sentence fully correct, both [REDACTED] must be glycogen! - I don’t agree with this answer, in the enzymes 2-3 quiz its redacted parts say A) creating glucose-6-phosphate; B) ATP for the cutting - Therefore the statement is completely false 39. If protein kinase A is active what is the likely state, form, and activity of [REDACTED]? (Select state, form, activity) If redacted is phosphorylase; then phosphorylase A form (active) in R state If redacted is glycogen synthase, glycogen synthase is in b form (inactive and phosphorylated) and in T state 40. Why can liver cells generate glucose, but muscle cells cannot? Muscle cells lack Glucose-6-phosphatase. Liver cells contain Glucose-6-phosphatase. 41. Considering a muscle [REDACTED]. What is the likely form and state of phosphorylase? (Choose form and state) Muscle phosphorylase enzymes generally are in “B” form and “T” state Liver phosphorylase enzymes generally are in “A” form and “R” state during fasting This question could be asking if hormones or cofactors are acting on the muscle cells which could change the form and state of the enzyme phosphorylase in the muscle cell. If asking about energy levels… High AMP levels: favor R state High ATP levels: favor T state If asking about levels of G-6-Phosphate… Abundance: favor T state Scarce: favor R state 42. In [REDACTED] disease, what is the enzymatic failure? If this is the quiz question the enzymatic failure for “HERS DISEASE” is absence or deficiency of Liver enzyme phosphorylase 43. Both Hers disease and Type 1 Von Gierke disease possess the symptom of hypoglycemia. Why does [REDACTED]? Von Gierke also have the threat of lactic acidosis ~enzyme 2-3 question Von Gierke clears glucose-6-phosphate by glycolysis rather than export 44. Which of the following diseases tends to resolve positively over time? Hers Disease

Glucose-6-Phosphate→Glucose-6-Phosphatase→Glucose Hexokinase (ATP)→ Glucose-6-Phosphate