BMS 531 Block 1 Live Review PDF

The Review: An In-Person Exploration of Introductory Medical Biochemistry B LO C K 1 B M S 5 3 1 M E D I C A L B I O C H E M I S T RY SPRING 2025 Exam Breakdown 54 Total Questions BMS 531.01 Introduction: 4 BMS 531.02 Amino Acids and Proteins: 9 BMS 531.03 Carbohydrates and Lipids:...

The Review: An In-Person Exploration of Introductory Medical Biochemistry B LO C K 1 B M S 5 3 1 M E D I C A L B I O C H E M I S T RY SPRING 2025 Exam Breakdown 54 Total Questions BMS 531.01 Introduction: 4 BMS 531.02 Amino Acids and Proteins: 9 BMS 531.03 Carbohydrates and Lipids: 10 BMS 531.04 Acids and Bases: 10 BMS 531.05 Properties of Water: 6 Calculations/Learning Activity: 6 BMS 531.06 Enzymes: 9 BMS 531.07 Bioenergetics: 8  Importance of Acid-Base Balance Changes in pH are monitored and play a role in biological processes including the regulation of breathing Acidosis vs Alkalosis ◦ Acidosis = accumulation of hydrogen ion ◦ Alkalosis = decrease of hydrogen ion Acid- Example Cause Resulting Compensation Base Change Disorder Metabolic Inability to remove acid from Decreased Decreased pCO2 Acidosis plasma (kidney dysfunction) plasma (hyperventilation/increased breathing bicarbonate rate) Metabolic Dietary intake of too much Increased Increased pCO2 Alkalosis bicarbonate (antacids)/too much plasma (hypoventilation/decreased breathing acid from plasma bicarbonate rate) Respirato Hypoventilation Increased pCO2 Increased renal bicarbonate ry generation to increase plasma Functional Groups (so many objectives!) Tell me everything you can think of for each of the following: Amino Carboxyl Hydroxyl Phosphate LO2 Enzyme Classification CLASSIFICATION ◦ 4 Digit Number CLASS General Reaction Example Huma ◦ Membership in 1 of 6 classes n ◦ Substrate sub-class Genes ◦ Substrate sub-sub-class (est.) ◦ Specific Enzyme Serial Number 1. Dehydrogenases 656 The numbers are Oxidoreductase underrepresented in terms of s number of human genes 2. Transferases Transaminases 610 ◦ Represent rough estimates that do not account for 3. Hydrolases Trypsin 1227 genes identified after 4. Lyases Fumarase 117 classification was updated (Synthases) Lets highlight the first 3… 5. Isomerases Phosphoglucomu 163 tase 6. Ligases DNA Ligases 56 (synthetases) Explain how energy is conserved and unfavorable reactions are enabled through coupling reactions to ATP hydrolysis Under which of the following scenarios would a reaction be coupled to ATP hydrolysis? A. Low pH B. High pH C. Endergonic reaction D. Exergonic reaction E. Low temperatures F. High temperatures G. 3 of these are correct Lipids joining the game… Which of the following would decrease membrane fluidity? ◦ Unsaturated hydrocarbons in the phospholipid head ◦ Unsaturated hydrocarbons in the phospholipid tails ◦ Saturated hydrocarbons in the phospholipid head ◦ Saturated hydrocarbons in the phospholipid tails A triglyceride is composed of? ◦ 3 fatty acids bound to a glycerol Esterification of fatty acids to glycerol produces which of the following: ◦ Water ◦ Oxygen ◦ Carbon Dioxide ◦ Glyceraldehyde Km and Substrate Affinity What will happen to an enzyme with a low Km if… ◦ Substrate concentrations increase ◦ Increase in reaction rate ◦ Substrate concentrations decrease to low levels ◦ Low Km = high affinity; reaction can still progress An enzyme has the ability to bind 2 different substrates. The enzyme has a low Km in regards to substrate 1 and a high Km in regards to substrate 2. ◦ At low concentrations of both substrates, which substrate is most likely to bind? ◦ Substrate 1 ◦ Under what conditions might the other substrate have favorable binding? ◦ Low or no substrate 1 and high substrate 2 (competitive) Evaluate Enzyme Kinetics: Apply the Michaelis-Menten equation to given scenarios The Michaelis constant for a given enzyme tells you: ◦ A. the corresponding concentration of the substrate. ◦ B. the estimated affinity for a corresponding substrate. ◦ C. the rate of the reaction based on the substrate. ◦ D. the rate limiting step of a reaction in a pathway. ◦ E. the likelihood that an enzymatic reaction will occur. A reaction is capable of proceeding efficiently only when there are large concentrations of substrate when: ◦ A. the corresponding enzyme has a high Km. ◦ B. the corresponding enzyme has a low Km. ◦ C. the reaction is coupled to ATP hydrolysis. Don’t forget that Km is when ◦ D. the change in free energy is negative. Vmax is at 50% or ½ Vmax! ◦ E. the change in free energy is positive. There are lots of ways to say this in a question to raise the difficulty! structural features of amino acids and describe how these features contribute to behavior with particular emphasis on functional groups Which of the following amino acids would be of interest to pI considerations if present in the center of a short polypeptide? Alanine Arginine Asparagine Aspartic acid Glutamine Glutamic acid Glycine Explain carbohydrate structure α-glycosidic bond Hemiacetal carbon has different stereochemistry as second sugar (different sides; different β-glycosidic bond stereochemistry, etc…) Hemiacetal carbon with same stereochemistry as second sugar N-linked (same side; matching stereochemistry, etc…) Attachment of a monosaccharide at a O-linked residue of another molecule involving nitrogen Attachment of a monosaccharide at a residue of another molecule involving oxygen Assess the impact of environmental conditions on enzyme activity A human is experiencing a high fever. 1) What is the anticipated impact of this fever if the body returns to normal temperatures within a short period of time? 2) What is the anticipated impact if the fever is prolonged or excessively high? ◦ A. carbohydrates structure and therefore function will be adversely affected ◦ B. enzyme activity will increase increasing metabolism ◦ C. enzyme function may be adversely altered or suppressed ◦ D. Protein folding and therefore function will be adversely affected ◦ E. there are no adverse consequences as fever help combat infection Summarize and explain mechanisms of regulation for enzymes by: List and explain the strategies for biological catalysis Acid-Base Catalysis Uses partner to orient substrate Covalent Catalysis Involves partners like Fe, Cu, Zn, Mg, etc… Metal-Ion Catalysis Hydrogen bonds and ionic interactions help orient substrates By approximation Donate or accept protons Cofactor Catalysis Generate strong bonds through amino acid side chains Compare and contrast competitive, noncompetitive inhibition, and allosteric regulation and determine the outcomes on reaction rates for each type of regulation Allosteric regulation: Suppression of enzyme activity via ◦ Heterotropic adversarial binding within the active ◦ Homotropic site Enzyme activity modulated (either increased or decreased) by binding of Competitive Inhibition an effector that is NOT the substrate Enzyme activity modulated (either increased or decreased) by binding of Noncompetitive Inhibition an effector that IS the substrate Suppression of enzyme activity via binding external to active site A bit more… Multiple choice without the choices Which of the following sugars is most likely to be incorporated into a structure within a human? ◦ D form/D conformation is most likely Which of the following amino acids would be most likely to be found attached to a human tRNA molecule? ◦ L form due to the chirality of human enzymes Which of the following functional groups are involved in the generation of water during peptide synthesis? ◦ Amino and carboxyl; amino group supplies the hydrogen while carboxyl supplies the oxygen Which of the following functional groups are involved in the bipyramidal intermediate of the ribozyme catalyzed reaction? ◦ Phosphate and hydroxyl Buffering and Acid-Base HA A- Ways to talk about this… Protonated vs deprotonated Acid vs conjugate base Associated vs disassociated proton Where will the water go… Cell in a hypertonic solution ◦ Solution has increased osmolarity ◦ Water will flow out of cell and into solution Cell in an isotonic solution ◦ Solution and cell have same osmolarity and no expected change in solutes ◦ Net water movement is equal (no change in cell volume) Cell in a hypotonic solution ◦ Solution has decreased osmolarity ◦ Water will flow into the cell from the solution Natural examples: ◦ Change in ECF ◦ RBC in pure water ◦ Other examples? Additional thoughts… Only a glycine is small enough to fit into an active site. What is the consequence for loss of the glycine? ◦ If the glycine is on the substrate, the substrate will not associate with the enzyme ◦ If the glycine is part of the necessary structure for folding or generating the functional enzyme, then inappropriate or absent folding could be expected ◦ Both would potentially reduce enzyme activity When is the buffering potential on an amino acid the least? ◦ At the pI Diseases discussed and features especially Diabetes Insipitus! ◦ Central vs Nephrogenic ◦ Lack of ADH release vs resistance to ADH