BMS 531 Medical Biochemistry Review Spring 2025 (PDF)

Block 1 Review BMS 531 Medical Biochemistry Spring 2025 BMS 531.01 Objectives The overall goal of this packet is to introduce you to graduate level medical biochemistry. This packet will establish a few baseline expectations and overall course goals. Upon completion of this lectur...

Block 1 Review BMS 531 Medical Biochemistry Spring 2025 BMS 531.01 Objectives The overall goal of this packet is to introduce you to graduate level medical biochemistry. This packet will establish a few baseline expectations and overall course goals. Upon completion of this lecture students will be able to: Understand course expectations and goals Summarize the foundation of knowledge to build from for success in the course 1. Define and explain terms associated with biochemistry and chemical compounds and explain the connection between biochemistry and the requirements of living systems i.e. Define stereochemistry and explain its importance in biochemical reactions 2. Summarize the naming of carbons in carbon chains 3. Summarize the basic functional groups important in biochemistry and explain their reactivity in key processes 4. Demonstrate the transfer of electrons in oxidation-reduction reactions and determine which molecule/compound was oxidized and which was reduced LO1, LO2 Some Organic Chemistry Reminders: Helpful Terminology Alpha carbon (α-carbon): carbon bonded to functional group Naming continues down the carbon chain (α, β, γ, etc...) More than one alpha carbon can be present in a carbon chain The label applies to any carbon bonded to a functional group Numbering of carbons begins so that the lowest number is assigned to the carbon at the functional group/reaction end or branch point  Structure and Function Relationship Stereochemistry = structural configuration at the alpha-carbon Key Functional Groups in Biology/Biochemistry: Hydroxyl – DNA and RNA synthesis, dehydration synthesis Amino – protein synthesis/peptide bond, considered basic because it can accept H+ to generate NH3+ Carboxyl – Acidic, protein synthesis/peptide bond Phosphate – regulation, energy (i.e. ATP) LO1, LO4 Oxidation-Reduction Reactions Transfer of electrons is of significant consideration in Biochemistry Loses Electrons Oxidized and Gains Electrons Reduced Represents a form of energy transfer (along with phosphorylation) Transfer of a hydrogen can also be considered electron transfer (H = H+ + e-) The reactions are coupled so as each oxidation is accompanied by a reduction (a) Structural isomers Pentane 2-methyl butane (b) Cis-trans isomers cis isomer: The two Xs trans isomer: The two Xs are on the same side. are on opposite sides. (c) Enantiomers CO2H CO2H C C H NH2 NH2 H CH3 CH3 L isomer isomer D Inc. © 2016 Pearson Education, BMS 531.02 Objectives 1. Compare and contrast the chemical and structural features of amino acids and describe how these features contribute to behavior with particular emphasis on functional groups 2. Explain the role of side chains in amino acids and how they contribute to the chemical and functional behavior of amino acids 3. Summarize the generation of peptide bonds and explain the process from the perspective of the functional groups involved 4. Evaluate protein structure by doing the following: List and describe the levels of protein structure and the importance of amino acid structure to protein structure Explain how each level of structure is defined and influenced by the lower level structures Compare and contrast denaturation and renaturation/folding Describe examples where altered folding affects protein function with an impact on human health 5. Explain how proteins are classified and list the types/categories of proteins based on the classification system 6. Determine and describe the changes in behavior of amino acids as changes in environmental conditions (i.e. pH) occur (Henderson-Hasselbalch) Calculate pH, pKa, and pI values Calculate changes in pH and pKa BMS531.03 Objectives Overall Goal: Evaluate the structure and function of carbon-based molecules and identify the features that enable unique chemical behaviors Carbohydrates 1. Summarize the common carbohydrates in the body and diet 2. Explain carbohydrate structure by the following: Compare and contrast linear and cyclic forms Identify the anomeric carbon Differentiate between aldehydes and ketones Describe the type of bond formed between monosaccharides Explain the difference between alpha and beta conformations in monosaccharides and alpha and beta linkages in polysaccharides Lipids 3. Compare and contrast types of lipids and their uses in biological systems 4. Compare and contrast saturated and unsaturated forms of lipids 5. Compare and contrast types of adipose tissue and explain the role of adipose in energy storage 6. Explain how lipid structure contributes to lipid behavior and location/localization, storage, and usage in biological systems  BMS 531.04 and 531.05 Concepts Includes Learning Activity 1 These are the objectives utilized from all 3 topics: (numbers do NOT match original numbers) 1. Describe the relationship between pH and hydrogen ion concentration and Relate pKa to the ratio of associated and dissociated compounds. 2. If given the pKa and pH, be able to estimate the percentage of a compound that will be dissociated and/or associated. 3. Describe the function of a buffer in a biological system. Explain how the bicarbonate system is an effective physiological bu ffer. 4. Describe why a buffer is more effective near its pKa(s). 5. Define osmotic pressure, osmosis, isotonic, hypertonic, hypotonic, molarity, molality, osmolarity and osmolality. 6. Show the direction of water flow in a solute gradient and explain the effect on the cell. Describe the effect of antidiuretic hormone (ADH)/arginine vasopressin (AVP) on cell volume. 7. Explain the role of water, salt and aquaporin in diabetes insipidus. 8. Define and contrast hypertonic, hypotonic, and isotonic 9. Explain the role of water, salt, and aquaporins in diabetes insipidus and Recall the underlying cause(s) of central and nephrogenic diabetes insipidus Additional objectives (Calculations): 1. Describe the concept of chemical equilibrium and Define the equation for chemical equilibrium 2. Describe a general acid/base reaction 3. Identify the components of a weak acid/base conjugate pair 4. Evaluate pH and changes in pH and the role of biological buffers in pH regulation Calculate pH and pKa of weak acid/base pairs Calculate and estimate relative concentrations of a conjugate acid/base pair Understand the Henderson-Hasselbalch equation Calculate pH change of a buffer solution when exposed to strong acid or strong base 5. Compare and contrast acidosis and alkalosis types, causes, consequences, and compensatory changes Overview Properties of water Cohesion, surface tension, high specific heat, high heat of vaporization, crystalizes and expands when freezes, and polar solvent Movement of water across semi-permeable membrane pH, equilibrium, and Henderson-Hasselbalch LO7 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 Acid-Base Example Alkalosis = decrease of hydrogenResulting Cause ion Change Compensation Disorder Metabolic Inability to remove acid from plasma Decreased plasma Decreased pCO2 (hyperventilation/increased Acidosis (kidney dysfunction) bicarbonate breathing rate) Metabolic Dietary intake of too much bicarbonate Increased plasma Increased pCO2 (hypoventilation/decreased Alkalosis (antacids)/too much acid from plasma bicarbonate breathing rate) Respiratory Hypoventilation Increased pCO2 Increased renal bicarbonate generation to Acidosis increase plasma bicarbonate Respiratory Hyperventilation Decreased pCO2 Decreased renal bicarbonate generation to Alkalosis decrease plasma bicarbonate  Acid Dissociation Constant (Ka) Describes the affinity of an acid for the dissociable H+ ions The equilibrium constant for the reaction is called the acid dissociation constant Weak acids have a low Ka due to a corresponding high concentration of HA Strong acids have a high Ka due to a corresponding high concentration of A- Due to the small size of Ka, it is typically presented as pKa Weak acids have a high pKa Strong acids have a low pKa  BMS 531.06 Objectives 1. Define and apply the following terms: ribozyme, enzyme-substrate complex, activation energy, active site, apoenzyme, cofactor, coenzyme, and holoenzyme 2. List the 6 categories of enzymes, connect each category with the type of reaction catalyzed, compare/contrast the categories, and determine the most likely category for a hypothetical enzyme based on activity described 3. Assess the impact of environmental conditions on enzyme activity (i.e. what impact will a change in pH have on the activity of an enzyme and how will that change in enzyme activity impact the corresponding system?) 4. Compare and contrast covalent and noncovalent mechanisms of enzyme activity and explain the role of functional groups within an enzyme’s active site 5. Explain the concept of enzyme specificity and describe the factors that generate or influence it 6. Compare and contrast protein-derived enzymes with ribozymes and explain the unique features of ribozymes 7. Discuss the use of enzymes clinically in disease diagnostics and therapeutics and determine whether a test would be direct or indirect assessment of function/activity 8. Explain the relationship between enzyme kinetics, affinity for substrate, and the enzyme’s Km value AND identify whether an enzyme will have a high or low affinity for substrate based on the provided relative Km value 9. Evaluate enzyme kinetics by: Explain the influence of substrate concentration on reaction rates Apply the Michaelis-Menten equation to given scenarios Calculate Vmax, Km, or [S] from provided information LO2 Enzyme Basics Terminology **Enzymatic activity is Coenzyme conferred by functional groups Enzyme partner with enzymatic of the amino acids along with activity or critical to enzymatic partner molecules such as activity Holoenzyme coenzymes Complex of enzyme + all coenzymes; represents the active form Apoenzyme Holoenzyme without coenzyme; represents an inactive form Cofactor OR Prosthetic Group Cofactors OR Coenzyme Inorganic ions needed for enzyme Apoenzyme Holoenzyme function *Catalytically Inactive *Catalytically Active LO3 Enzyme Classification CLASSIFICATION 4 Digit Number CLASS General Reaction Example Human Membership in 1 of 6 classes Genes Substrate sub-class Substrate sub-sub-class (est.) Specific Enzyme Serial 1. Oxidoreductases Dehydrogenases 656 Number The numbers are 2. Transferases Transaminases 610 underrepresented in terms of number of human genes 3. Hydrolases Trypsin 1227 Represent rough estimates that do not account for 4. Lyases Fumarase 117 genes identified after (Synthases) classification was updated Lets highlight the first 3… 5. Isomerases Phosphoglucomutase 163 6. Ligases DNA Ligases 56 (synthetases) LO9 Double Reciprocal Plot (inverse of reaction This linear version of analysis rate plotted against inverse of substrate does not compress data at high concentration) [S] but does not treat all aspects y=mx + b as independent variables y=1/v, x=1/[S] y-intercept = Vmax Slope = Km/Vmax Linear regression for goodness of **Small experimental error expected at fit (R) is not applicable low [S] can result in large error in Vmax ALSO compresses data for high [S]  Past Objective Relevant to the Section: ◦ List the 6 categories of enzymes, connect each category with the type of reaction catalyzed, compare/contrast the BMS 531.07 categories, and determine the most likely category for a hypothetical enzyme based on activity described ◦ Evaluate enzyme kinetics by: ◦ Explain the influence of substrate concentration on reaction rates Objectives ◦ ◦ Apply the Michaelis-Menten equation to given scenarios Calculate Vmax, Km, or [S] from provided information 1. Summarize the laws of thermodynamics and apply them to biological processes including considerations for potential and kinetic energy in biological systems 2. Determine when potential energy is maximum vs kinetic energy given biological examples 3. Using delta G, evaluate the change in free energy of a reaction and determine whether a reaction will occur spontaneously 4. Explain how energy is conserved and unfavorable reactions are enabled through coupling reactions to ATP hydrolysis 5. Compare and Contrast Basal Metabolic Rate (BMR) and Resting Metabolic rate as well as direct and indirect methods of measuring BMR 6. Summarize and explain mechanisms of regulation for enzymes by: List and explain the strategies for biological catalysis Predict the impact for a biochemical pathway or activity under conditions of enzymatic regulation or loss of regulation of a given enzyme* Evaluate conditions that affect enzymatic reactions and determine the most likely outcome following changes in conditions in terms of the corresponding process overall or the enzyme specifically 7. Explain how enzyme structure contributes to function and summarize the common functional groups in catalysis and the role of cofactors in enzyme activity 8. Apply enzymatic regulation to real world situations and use specific examples to summarize the role of enzyme-substrate complexes in enzymatic reactions 9. Compare and contrast competitive, noncompetitive inhibition, and allosteric regulation and determine the outcomes on reaction rates for each type of regulation LO1, LO2 ENERGY Potential Kinetic Chemical Mechanical Stored in bonds of atoms and molecules Electrical Nuclear Thermal Stored in nuclei of atoms Radiant/Light Energy Gravitational Stored in object’s interaction with other Sound objects (i.e. height from gravitational forces of Earth) Elastic Energy stored in elasticity of objects What is a slight misunderstanding regarding the laws of thermodynamics and human health? LO3 Free Energy ΔG = change in free energy represents the driving force toward equilibrium starting at ANY concentration of reactants and products ΔG0’ = Amount of energy that is available for useful work Change in Gibbs free energy at pH 7 and standard conditions (25°C) Equal to chemical bond energy of products minus the reactants (corrected for energy lost to entropy) Exergonic vs. endergonic ΔG0’ in a series = ADDITIVE Pearson 2016 LO6, LO7 Introducing Metabolism: Strategies for Catalysis Acid-Base Catalysis Donate or accept a proton Covalent Catalysis Covalent linkage through amino acid side chain Metal-Ion Catalysis Uses metal ion By Approximation Orient substrates via hydrogen bonds and ionic interactions Cofactor Catalysis Requires cofactor to orient substrate LO6, LO9