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Biochemistry Topics & Concepts Covered

TOPICS	CONCEPTS
Biomolecules	Proteins, Nucleic Acids, Lipids, Carbohydrates
Enzymes	Enzyme Kinetics, Inhibition, Catalysis
Metabolism	Glycolysis, TCA Cycle, Oxidative Phosphorylation
Molecular Genetics	DNA Replication, Transcription, Translation
Cell Signaling	Signal Transduction Pathways, Cellular Communication
Biochemical Pathways	Biosynthesis of Macromolecules, Metabolic Pathways
Protein Structure & Function	Primary, Secondary, Tertiary, Quaternary Structure
Enzyme Mechanisms	Active Sites, Substrate Binding, Catalytic Reactions
Bioenergetics	ATP, Thermodynamics, Energy Conversion
Carbohydrate Metabolism	Glycogenesis, Glycogenolysis, Gluconeogenesis
Lipid Metabolism	Fatty Acid Synthesis, β-Oxidation, Lipid Signaling
Amino Acid Metabolism	Amino Acid Catabolism, Biosynthesis, Urea Cycle
DNA Replication & Repair	DNA Polymerases, Proofreading, Mismatch Repair
RNA Transcription & Processing	Promoters, RNA Splicing, Ribosome Biogenesis
Protein Synthesis	Translation Initiation, Elongation, Termination
Cell Cycle & Division	Cell Cycle Phases, Cell Cycle Regulation
Hormones & Signaling Peptides	Endocrine Signaling, Hormone Classes, Signal Cascade
Membrane Structure & Function	Fluid Mosaic Model, Transport Mechanisms
Enzyme Regulation	Allosteric Regulation, Covalent Modification
Biochemical Techniques	Spectroscopy, Chromatography, Electrophoresis

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Recently Asked Biochemistry Questions

Expert help when you need it

Q1: Explain the role of eicosanoids formed as a result of metabolism of n-3and n-6 fatty acids in human physiological processes. In your answer consider data from relevant observational (epidemiological) studies alongside explanation of mechanism of action of these eicosanoids.2.See Answer
Q2:Calculate the plasma osmolality and comment on its significance. See Answer
Q3:Explain the pathophysiology of the different types of Diabetes Mellitus. See Answer
Q4:Consider the enzyme-catalyzed reaction AB. You determine experimentally that the maximal initial velocity. Vmax for the amount of enzyme you have added is 50 mM of B appearing per minute. You also determine that the Michaelis constant, K. for this enzyme is 20 mM of A. What concentration of A will give an initial velocity of 25 mM of B appearing per minute?See Answer
Q5: Short Answer 1. A study on rat metabolism is being conducted. There are 3 different groups of rats involved. Group 1 Diet rich in fat but normal in carbohydrates and protein Group 2 Diet rich in protein but normal in carbohydrates and fat Group 3 Diet rich in carbohydrates and normal protein and fat a. The three groups are kept in identical environments with opportunities for physical activity. Write a hypothesis, predicting the expected energy levels for each group for the first 4 days of the experiment. Please explain your predictions. (A-4, 2-C) 3 Scanned with CamScanner b. You run the experiment for 20 days and then analyze the results. How do you expect the three groups to compare in terms of body size/mass and general health? (A-4, 2-C) de toutes 2. Track athletes often say that the 400m sprint is much more exhausting and harder on the legs than the 100m sprint. What type of respiration would a 400m sprinter rely mostly on as they reach the end of the race? Explain. (A-4, 2-C) 3. Several anti-nuclear war protesters claim that inhabitants of the earth did not perish from nuclear bombs or the radiation afterwards, that the people would slowly succumb to changes brought on during the "nuclear winter". During a "nuclear winter", a lot of dust would be drifting in the atmosphere causing the blockages of the sun's electromagnetic spectrum. Based on your knowledge of photosynthesis, what impact would this have on humans that are still alive and why? (A-4, 2-C) Scanned with CamScannerSee Answer
Q6:a) Briefly describe the overall tertiary structure of MHETase. (Approach this as in Problem 1.) How many and what kind of domains does the polypeptide have (e.g., what class)? Even if you think that there is a single domain, would there be a way to divide it into 2 sub-domains? Specify which parts of the polypeptide below to each domain or sub- domain (unless you think that there is only 1 domain and no sub-domains).See Answer
Q7:b) MHETase is believed to use a catalytic triad to hydrolyze the ester linkage in MHET, just like the catalytic triad in the serine proteases. Examine the structure of MHETase complexed with the analog and identify the 3 residues in the catalytic triad. For each one, find the most important distance between that residue and its partner in the mechanism and fill out the chart, identifying the 2 atoms used and the distance between them. Also identify the secondary structure in which it is found (e.g., a-helix, ß-strand, tight turn, or loop). Residue (name & #) Ser His Asp Identify the most relevant inter-atomic distance and identify the atom name (click on it in PyMOL) (e.g., "CB" or "C4" or "OG") Atom in Ser: Atom in substrate analog: Atom in His: Atom in Ser: Atom in Asp: Atom in His: distance between atoms (Å) 2° structural context/nWhat other residues in the enzyme are important for binding MHET? Identify at least 4 that seem to play an important role. Residue (chain, name & #) Atom of the residue and the substrate analog? distance Type(s) of interaction (e.g., H-bond, between charge-charge, coordination bond, van der Waals) atoms (Å) 2⁰ structural context Which, if any, of these residues might explain why MHET is a good substrate, but BHET is not? And how would it explain the substrate specificity?See Answer
Q8:c) The enzyme contains 5 disulfide bonds. Given that this is a secreted enzyme, is this expected or surprising? List the 5 disulfide bonds below (e.g., "Cys41 - Cys142") and circle the one that you would expect to be most important for enzyme activity.See Answer
Q9:d) Going back to the first question, briefly discuss the roles of the 2 (sub)domains in the mechanism of MHET hydrolysis. Broadly speaking, what role does each one play?See Answer
Q10:Assigned topic- Alcoholic Liver Disease Assigned Section- Treatments and Conclusion |See Answer
Q11:Consider the reaction mechanism shown below for this question: CH₂ CH₂ NH₂ CH₂ CH₂ Lyase O Ligase 6 Oxidoreductase Transferase O Hydrolase CH₂₂ CH₂ 0,PO 5 CH CH₂ What class of enzyme does this belong to? O Translocase CH₂ 20,P H₂C CH₂ CH₂ 2 CH₂ 20,PO CH₂ 20,PO Net₂See Answer
Q12:Bonus: Determine the primary sequence of the following peptide. (10 Pts) A. Trypsin treatment generated the following fragments: (LFVCYMGFR) (HDITNAATYR) (AEK) (CPS) (K) (QIVAAR) (LWVANK) B. Chymotrypsin treatment generated the following fragments: (AEKL) (F) (VCY) (MGF) (RHDITNAATY) (RL) (W) (VANKKQIVAARCPS) C. Thermolysin treatment generated the following fragments: (LF) (VCY) (MGFRHD) (ITNAATYR) (AEK) (LW) (VANKKQ) (1) (V) (AARCPS) Legend: Trypsin = Lys & Arginine (R.) Chymotrypsin = Tyr, Trp, Phe, Leu (R.) Thermolysin = Leu, Val, lle, Met (R₂)See Answer
Q13:1. Why does EDTA (structure shown below) quench DNA polymerization reactions at physiological pH? Show the mechanism involving the atoms in EDTA that may be responsible (3 points) میری HO HO OH OHSee Answer
Q14:2. A DNA polymerase is isolated and found to have an error rate of 1 in 106. (6 points, 3 each) A. Suppose that the error rate is determined solely by the relative stabilities of incorrect and correct base pairs. What would the difference in free energy between correct and incorrect nucleotides incorporated by the polymerase have to be in order to explain the error rate? B. Solution studies of isolated oligonucleotides indicate that the energetic difference is actually -1.2 kJ.mol-1. What is the equilibrium constant of correct-incorrect base pair discrimination based on these solution studies?See Answer
Q15:3. The direction of RNA synthesis was determined by growing bacteria for a short period of time with trinucleotides labeled with tritium (³H) on their bases. The structure of RNA looks like : 5' pppNpNpNpNp...N-OH 3' (N = nucleosides; p = phosphates). Cleavage of RNA by a base occurs after the 3' phosphate. (8 points, 2 each) A. What products are produced if RNA is digested with a base? B. The products obtained in Part A can be distinguished by thin layer chromatography. Which of the products would you expect to be differentially labeled if new nucleotides are added at the 5' end (i.e., synthesis is in the 3' to 5' direction)?/nC. Which products would be differentially labeled if RNA is synthesized from the 5' to 3' direction? D. When the experiment was done the tritium label was found in the spot containing N-OH? In which direction is RNA synthesized.See Answer
Q16:4. Reto is an aspiring medicinal chemist whose project involves screening a library of compounds to find molecules that bind with high affinity to the opioid receptor (a membrane protein). Based on our discussion of the thermodynamics of binding, answer the following questions (10 points) A. Reto titrated a candidate compound C (fluorescently tagged) against the purified receptor and obtained the isotherm below. Reto concluded that he found a high affinity specific binder. Is Reto's conclusion correct? Why or Why not? What is missing from the experiment? (2) 1/Fluorescence polarization 450 400 350 300 250 200 150 100 50 0 0 10 20 30 40 [Ligand] (n) 50 60 70/nB. After performing the required controls, Reto obtained the following binding isotherm (left) and the associated Scratchard plot (right). What is the value of K, for the interaction between C and the receptor? What is the total protein concentration used in this experiment? (2) Binding isotherm Scratchard plot 1/Fluorescence anisotropy 300 250 200 150 100 50 0 0 10 20 30 40 [Ligand] (nM) 50 60 [bound ligand]/[free ligand] 0.6 0.5 0.4 0.3 0.2 0.1 0 1 2 3 4 bound ligand [L]bound (nM) in 6/nC. Next, Reto performed the affinity measurements on mammalian cells that express the opioid receptor. He is surprised to find that the K, from these measurements is over 10-fold higher than what he measured with the purified protein. Can you speculate a possible reason that could explain this observation? D. Given the poor affinity of the compound C, Reto modified the library, rescreened and found a candidate molecule R that binds the opioid receptor with a K, of 2nM. A high throughput measurement of binding isotherms of R and other receptors revealed that R also binds to the glucagon receptor with a K₁ of 5 μM. Based on this data, what should be the concentration of R that Reto should recommend for further testing of the compound R in vivo (i.e. in a living human body)? (2)/nE. In an in vitro experiment with R and the opioid receptor, what is the fractional saturation of the receptor, when the concentration of R is 200 nM? (2)See Answer
Q17:5. p53 is activated under cellular stress, and turns on genes involved in stress response. In the absence of stress its levels are kept low by proteasomal degradation through interactions with MDM2 ubiquitin ligase that marks it for degradation. (17 pts) A. Identify at least three hydrogen bonding interactions that stabilize the p53-MDM2 complex? (3 pts)/nB. Use the secondary structure prediction web server Proteus (http://www.proteus2.ca/proteus2/) and underline the residues that will participate in helix formation (2 pts): SQETFSDLWKLLPEN SQETFSDLWKLLAEN C. Based on Borcherds et al, which residue in the peptide can be mutated to increase the helical structure of the peptide? Is this in line with the prediction from (2) above (2 pts)? D. How does the Kd between p53 and MDM2 change upon mutating Pro27 to Ala (3 pts)?/nE. What assay was used by Boercherd's et al to determine the effect of Pro27Ala mutation on DNA replication post DNA damage (3 pts)? F. What is the effect of Pro27Ala mutant on cell cycle progression post DNA damage? Based on this result what is the mechanism by which p53 regulates cell fate after DNA damage? (4 pts)See Answer
Q18:Q6. The World Health Organization (WHO) has conducted worldwide clinical trial for the usage of potential SARS-CoV-2 main protease inhibitors as COVID therapeutics. (14 pts) A. Briefly explain (in 1-2 sentences) why viral proteases are important in the replication cycles of viruses like HIV and SARS-CoV-2. (3 pts)/nB. IC50 values were measured for new compounds designed as inhibitors for SARS-CoV-2 main protease, as shown below: P3 P3 cythe highe 14b 11r P2 13b P1 H₂N Compound 11r 13b 14b IC50 (μM) 0.18 0.67 >50 Based on this data, what type(s) of modifications are NOT tolerated by the main protease at the "P3" functional group of the inhibitor? Provide a brief hypothesis for how the P3 site interacts with the protease. (5 pts) (from Zhang et al., Science 2020, 368, 409.)/nC. You synthesize an analog of one of the compounds from part B called 15L and discover that it binds SARS-CoV-2 main protease with a KD of 250 nM. What concentration of 15L would result in ~50% saturation of the main protease? Briefly explain your answer. (4 pts) D. What enzyme that violates the central dogma can be used in an assay to measure SARS-COV2 RNA levels? (2 pts)See Answer
Q19:Q7. The notion of treating sickle cell disease (SCD) by stabilizing the R (oxy) conformation was introduced by Beutler. He proposed that converting a fraction of sickle hemoglobin (HbS) to the oxidized form or to the carbon monoxide complex of HbS would reduce sickling by maintaining a fraction of HbS molecules in the nonpolymerizing R conformation of oxyhemoglobin, while understanding that such a treatment would compromise oxygen delivery to the tissues. Solution 000 ↑↓ от R Polymer/nA. How will you measure the kinetics of this reaction? Below are only one of the two options available to you (3+3 = 6 points total). i. Oxygen tank and the dark (non fluorescent) dye shown below ii. Ultracentrifuge and uv-vis absorbance Juge R Fluorescent Dark/nCompound 9; compound 23; Len 2 Val 73 Ser 131 Ser 131 Arg 141 The 134 Au 78 Ser 131 al Asp 75 Val 1 al Met 76 Val 73 B. Based on the PDB structures, which compound will have higher affinity for Hb? Explain your answer based on molecular interactions between the compound and the structure of Hb (you may need to look at the relevant paper from hints)See Answer
Q20:Q8. 5E83 - (10 points total; 2 points each) A. Based on this PDB, does the compound GBT440 stabilize the S or the R state?/nB. Draw an arrow pushing mechanism for the reaction between GBT440 and the alpha subunit residue amine group. % O₂ Saturation 100 80 60 40 20 0 p50 (mmHg) -30 μmol/l -10 μmol/l -6 μmol/l -0 μmol/l 20 40 15 10 -6 -5 GBT440 Log [M] 60 pO₂ (mmHg) 80 100 120/nC. Based on this experiment, what state does GBT440 stabilize? D. Why is more GBT440 needed in the blood compared to purified protein? 100 80 60 %0₂ Saturation 20 0 0 20 (6Hww) od -1000 μmol/l - 600 μmol/l - 300 μmol/l - 0 μmol/l 40 60 20 10 45-40 -35 -30 -25 GBT440 [Log M 80 pO₂ (mm Hg) 100 120/nE. What could be a side effect of GBT440? Will you want this person to do much exercise when taking this drug? Why?See Answer

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