Topnotch Medical Board Prep Biochemistry Main Handout (Part 1) PDF

TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries, visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next bat...

TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries, visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. IMPORTANT LEGAL INFORMATION The handouts, videos and other review materials, provided by Topnotch Medical Board Preparation Incorporated are duly protected by RA 8293 otherwise known as the Intellectual Property Code of the Philippines, and shall only be for the sole use of the person: a) whose name appear on the handout or review material, b) person subscribed to Topnotch Medical Board Preparation Incorporated Program or c) is the recipient of this electronic communication. No part of the handout, video or other review material may be reproduced, shared, sold and distributed through any printed form, audio or video recording, electronic medium or machine-readable form, in whole or in part without the written consent of Topnotch Medical Board Preparation Incorporated. Any violation and or infringement, whether intended or otherwise shall be subject to legal action and prosecution to the full extent guaranteed by law. DISCLOSURE The handouts/review materials must be treated with utmost confidentiality. It shall be the responsibility of the person, whose name appears therein, that the handouts/review materials are not photocopied or in any way reproduced, shared or lent to any person or disposed in any manner. Any handout/review material found in the possession of another person whose name does not appear therein shall be prima facie evidence of violation of RA 8293. Topnotch review materials are updated every six (6) months based on the current trends and feedback. Please buy all recommended review books and other materials listed below. THIS HANDOUT IS NOT FOR SALE! INSTRUCTIONS To scan QR codes on iPhone and iPad 1. Launch the Camera app on your IOS device 2. Point it at the QR code you want to scan 3. Look for the notification banner at the top of the screen and tap To scan QR codes on Android 1. Install QR code reader from Play Store 2. Launch QR code app on your device 3. Point it at the QR code you want to scan 4. Tap browse website Approach to Topnotch Biochemistry by Dr. Banzuela • Please have the following Topnotch materials at hand o Topnotch main handout will serve as your main reference material o Topnotch supplement handout will serve as a quick refresher prior (few weeks) before the board. • Please buy the following: o Michael W. King, Integrative Medical Biochemistry Examination & Board Review o Lieberman & Ricer, Biochemistry, Molecular Biology & Genetics Board Review Series 7th edition o USMLE first aid • Study smart! o Memorization is not enough; you must listen & understand the concepts well. o Comprehend the applications of biochemistry in certain disease conditions. BIOCHEMISTRY PART 1 – STRUCTURAL BIOCHEMISTRY & NUTRITION By Frinz Moey C. Rubio, MD Contributors: Ronnie E. Baticulon, MD; James Daniel E. Omalin, MD, Madelaine Johanna Abraham, MD Champion, 27th Dr. Adrian C. Peña PCP Medical Quiz Contest (National Internal Medicine Quiz Contest by the Philippine College of Physicians) Internal Medicine Resident, St. Luke’s Medical Center – Quezon City (2022 – present) Junior Faculty, San Beda College of Medicine (2020 – 2021) University of the Philippines College of Medicine Class 2020, Cum Laude (5th Rank) UP Manila Gawad Chancellor Most Outstanding Student AY 2019-2020 Awardee Ten Outstanding Medical Students, APMC-SN NCR-SL AY 2019-2020 Awardee Champion, National Medical Quiz Bee, APMC-SN, (2018, 2019) IMPORTANT: READ THIS FIRST! This handout is designed to discuss the basic concepts of chemistry, the structures and properties of biomolecules, and important topics of nutrition in the clinical and public health settings. Moreover, this handout also caters to students who cannot or do not want to watch my lecture videos (since we all have unique learning styles). This handout will be sufficient to cover the basic concepts of biochemistry. Please note that the lecture videos only cover high-yield and confusing topics. Therefore, it is important to read this handout before watching my lecture video. This handout is also important for re-establishing the fundamentals of biochemistry before discussing Metabolism and Genetics with Dr. Baticulon. Additionally, make sure not to miss Dr. Baticulon's handout, as the bulk of Metabolism and Genetics will not be discussed in my handout or lecture. After reading the handout, please take the time to review the appendix, which provides a summary of important board correlates. I hope that this handout will be very useful for your Biochemistry Exam. MODULE 1. Review of Chemistry Concepts 2. Structure of Amino Acids & Proteins 3. Structure of Carbohydrates 4. Structure of Lipids 5. Structure of Nucleotides 6. Nutrition 7. Vitamins & Minerals 8. Complex Molecules 9. General Enzymology 10. Digestion & Absorption of Macronutrients 11. Expanded National Nutritional Survey (ENNS) 12. Immunology Appendix: Board Correlates & Quick Review PAGE 1 4 12 15 17 20 29 31 34 37 38 40 Appendix This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. 1. REVIEW OF CHEMISTRY CONCEPTS 1. 2. Chemical Reactions Thermodynamics and Thermoregulation 3. Water 4. Acids and Bases 5. Functional Groups FUNDAMENTAL LAWS Law of Conservation of Mass Law of Definite Composition Law of Multiple Proportion GENERAL CHEMISTRY https://qrs.ly/czez8yj DEFINITION Mass of material before reaction = after reaction Mass is neither created nor destroyed Chemical compound, regardless of source or method of preparation, have the same composition (proportion by mass) If two elements form more than one compound, masses of one element combined with fixed mass of another are in ratio of small whole numbers 1.1 CHEMICAL REACTIONS CHEMICAL REACTION • Refers to a process in which a substance (or substances) is changed into one or more new substances • Example: burning love letters from your ex Tip: On the other hand, physical change occurs when you simply cut the love letters of your ex (lalo na if umaasa ka na magkakabalikan pa kayo! 🤡) I know this is a very basic concept, but this is very important to strengthen your basic chemistry concepts! Moreover, not all medical students have a BS degree in Science. Chill lang tayo! 😎 Dr. Rubio CHEMICAL EQUATION • A standard method for communicating with one another about chemical reactions • Uses chemical symbols to show what happens during a chemical reaction From Chang General Chemistry: The Essential Concepts, 6th edition “plus” sign • Means “reacts with” “arrow” sign • Means “to yield” • The symbolic expression, chemical equation, can be read as: Molecular hydrogen reacts with molecular oxygen to yield water • In the equation above, we refer to H2 and O2 as reactants, while H2O as products: From Chang General Chemistry: The Essential Concepts, 6th edition • Starting materials in a chemical reaction • Substance formed as a result of a Products chemical reaction REVERSIBLE VS IRREVERSIBLE REACTIONS • Irreversible reactions are usually represented by a single arrow (→) wherein the tail-side represents the side of the reactants, while the arrowhead-side represents the side of the products • Reversible reactions are usually represented by a bidirectional arrow (⇌) Reactants REACTANTS PRODUCTS Arrow pointing to the • Represents FORWARD REACTION RIGHT • Reactants → Products Arrow pointing to the • Represents REVERSE REACTION See you around... virtually! 😉 Dr. Rubio LEFT • Products → Reactants TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD Page 1 of 43 For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries, visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. Remember: When the rates of the FORWARD and REVERSE reactions are EQUAL, and the concentrations of the reactants & products no longer change with time, CHEMICAL EQUILIBRIUM IS ACHIEVED. Steady-state process Dr. Rubio ENERGY CHANGES IN CHEMICAL REACTIONS • Heat refers to the transfer of thermal energy between bodies that are at different temperatures Exothermic process Endothermic process Heat generated by the combustion process is transferred from the SYSTEM OF CHEMICAL REACTION → SURROUNDINGS Heat is supplied by the SURROUNDINGS → SYSTEM OF CHEMICAL REACTION Occurs without a change in the internal energy All parameters are held constant (heat, enthalpy, pressure, volume, etc.) SIGN CONVENTIONS FOR HEAT • Endothermic process Enthalpy (H) (+) • Heat is absorbed by the SYSTEM OF Entropy (S) (-) CHEMICAL REACTION Enthalpy (H) (-) • Exothermic process Entropy (S) (+) • Heat is released to the SURROUNDINGS Remember: If the FORWARD REACTION is an exothermic process; the REVERSE REACTION is an endothermic process; vice versa 1.2 THERMODYNAMICS AND THERMOREGULATION Dr. Rubio DEFINITION OF TERMS TERM DEFINITION Energy transfer between two bodies at Heat (q) different temperatures Energy transfer between a system and its Work (w) surroundings in the form of compression or expansion of gas Total energy attributed to particles of Internal matter & their interactions within a system, Energy (U) composed of thermal energy & chemical energy Enthalpy(H) Energy of a reaction Entropy (S) Degree of disorderliness Heat Amount of heat required to raise temperature Capacity (c) of an object/substance by 1 degree Specific Amount of heat required to raise temperature Heat of an object per gram ENTROPY AND THE LAWS OF THERMODYNAMICS • Thermodynamics: study of the interconversion of heat and other kinds of energy o The laws of thermodynamics provide useful guidelines for understanding the energetics and direction of processes THERMOCHEMISTRY https://qrs.ly/ztez8zo METHODS OF HEAT TRANSFER • There are three basic methods involved in the transfer of heat from the heat source to another object CONDUCTION Heat transfer between objects via direct contact Touching heated pan ZEROTH LAW OF THERMODYNAMICS • States that if two bodies are each in thermal equilibrium with a third body, they are also in equilibrium with each other Tip: To simplify this, remember your transitive property in Math (ugh) – If A = C, and B = C, then A = C Dr. Rubio 1ST LAW OF THERMODYNAMICS • Energy can be converted from one form to another, but cannot be created nor destroyed ENTROPY • Measure of the change in randomness or disorder of the reactants and products • The greater the randomness or disorder, the greater the entropy 2ND LAW OF THERMODYNAMICS • The entropy of the universe increases in a spontaneous process, and remains unchanged in an equilibrium process • In simpler terms: Entropy of the universe = Entropy of the reaction + Entropy of the surroundings 3RD LAW OF THERMODYNAMICS • The entropy of a system approaches a constant value when absolute temperature reaches absolute zero Tip: And this actually makes sense, because in absolute zero temperature, the molecules are not moving, hence entropy is zero (there is no chaos). Pero walang masama mag-move… on 😜 Dr. Rubio THERMODYNAMIC PROCESS • Defined as the energetic evolution of a thermodynamic system proceeding from an initial state to a final state • Commonly studied thermodynamic processes: Occurs without loss or gain of Adiabatic process energy by heat Isenthalpic process Occurs at constant enthalpy Isentropic process Occurs at constant entropy Isobaric process Occurs at constant pressure Isochoric (isometric, Occurs at constant volume isovolumetric) process Isothermal process Occurs at constant temperature CONVECTION Heat transfer by movement of fluid – air or water – when the heated fluid is caused to move away from the heat source Evaporation of air from hot water surface, and precipitating as rain when air is cooled Evaporative cooling from perspiration RADIATION Heat transfer by which heat is transmitted without any medium Heat from the sun or lightbulb via electromagnetic waves Clinical Correlates: Ultraviolet A – accelerates Aging Ultraviolet B – associated with skin malignancies Ultraviolet C – screened by ozone layer Dr. Rubio THERMOREGULATION IN HUMANS • Hypothalamus is the major organ responsible for controlling body temperature HEAT LOSS IN HUMANS • Convection Avenues for heat loss in • Conduction humans • Radiation • Evaporation Mode of heat loss in humans if skin • Radiation (major) temperature > • Conduction environment temperature Mode of heat loss in humans if environment • Evaporation (major) temperature > skin • Convection temperature • May affect thermoregulation Humidity by limiting sweat evaporation and thus heat loss HEAT GAIN IN HUMANS • Shivering thermogenesis is the major mechanism of the hypothalamus in generating heat for the body • There are 2 types of shivering: • Primarily uses fats • For long-term use • Primarily uses glucose High-intensity shivering • For short-term use • Non-shivering thermogenesis is a minor mechanism of heat generation mostly seen in babies of lower mammals o Produced by brown adipocytes Low-intensity shivering TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. Page 2 of 43 TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries, visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. FACTORS AFFECTING THE CHEMICAL EQUILIBRIUM • Chemical equilibrium represents a balance between forward and reverse reactions: Shift to the • Net reaction favored is from LEFT → RIGHT RIGHT • Formation of PRODUCTS is favored Shift to the • Net reaction favored is from RIGHT → LEFT LEFT • Formation of REACTANTS is favored LE CHATELIER’S PRINCIPLE • General rule that helps us to predict the direction in which an equilibrium will move when there is a change in: o Concentration o Pressure o Volume o Temperature • States that if an external stress is applied to a system at equilibrium, the system adjusts in such a way that the stress is partially offset as it tries to reestablish equilibrium (stress: change in concentration, pressure, volume, or temperature that removes a system from the equilibrium state RESPONSE OF A CHEMICAL EQUILIBRIUM TO STRESSORS Increase in concentration of a Shifts AWAY from the substance substance Decrease in concentration of a Shifts TOWARDS the substance substance Increase in pressure Shifts TOWARDS fewer moles of gas of the system Decrease in pressure Shifts TOWARDS more moles of gas of the system Increase temperature Favors ENDOTHERMIC REACTION of the system Decreases temperature Favors EXOTHERMIC REACTION of the system NO SHIFT A catalyst increases the rates of both Catalyst forward and reverse reactions by the same amount LE CHATELIER’S PRINCIPLE https://qrs.ly/meezhh0 Tip: To have a visual understanding of Le Chatelier’s Principle. Please watch the attached QR code! Dr. Rubio OXIDATION & REDUCTION OXIDATION • Losing electrons • Losing hydrogen • Gaining oxygen Increase in oxidation number (e.g., Fe2+ → Fe3+) Reaction RELEASES ENERGY Oxidized agent = Reducing agent REDUCTION • Gaining electrons • Gaining hydrogen • Losing oxygen Decrease in oxidation number (e.g., Fe3+ → Fe2+) Reaction STORES ENERGY Reduced agent = Oxidizing agent MNEMONIC REDOX REACTIONS LEORA: Loses Electrons, Oxidized = serves as Reducing Agent GEROA: Gains Electrons, Reduced = serves as Oxidizing Agent • Hydrogen atoms: Partially positive • Unpaired electrons of oxygen: Partially negative • Here you can see two molecules of water joined by a hydrogen bond (dotted line), because the partially positive end attracts the partially negative end Remember: The oxygen found at the center attracts more electron (negatively charged particle) towards it; this makes the oxygen side a (-) pole; and hydrogen side a (+) pole → making water a POLAR substance. The concept of polarity is very important when we talk about solubility: “LIKE DISSOLVES LIKE!” Substances w/ similar characteristics will dissolve in each other: polar substances dissolve with polar substances; non-polar substances dissolve with non-polar substances. Remember: opposites attract! The partially positive end of one water molecule attracts the partially negative end of another water molecule → forming a hydrogen bond Dr. Rubio ✔ KEY CONCEPTS • Hydro-PHILIC (water-loving): compounds that dissolve easily in water; generally charged or polar • Hydro-PHOBIC (water-fearing): nonpolar molecules such as lipids and waxes, which dissolve in chloroform and benzene 1.4 ACIDS AND BASES pH pH = – log [H+] • Defined as the negative log of the hydrogen ion concentration • Measure of acidity or alkalinity • Physiologic pH: 7.35 to 7.45 ✔ KEY CONCEPTS • Acids: low pH, high H+ concentration [H+] • Bases: high pH, low H+ concentration [H+] • ACIDS are proton donors • BASES are proton acceptors • pKa values express the strengths of acids Smaller pKa value The STRONGER the acidity of a substance Larger pKa value The WEAKER the acidity of a substance HENDERSON-HASSELBALCH EQUATION • Used to calculate the concentration of a weak acid [HA] and its conjugate base [A-] in an aqueous solution o An increase in [HA] lowers pH, while an increase in [A-] elevates pH • Useful for: o Titration of amino acids o Predicting shifts in the bicarbonate buffer system CO2 + H2O ↔ H2CO3 ↔ H+ + HCO3o Predicting distribution of drugs OXIDATION AND REDUCTION https://qrs.ly/j3ezhh7 1.3 WATER WATER • Predominant chemical component of living organisms • A molecule with electrical charge distributed asymmetrically about its structure pKA Table From https://www.masterorganicchemistry.com/2010/09/29/how-to-use-a-pka-table/ TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. Page 3 of 43 TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries, visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. ✔ KEY CONCEPTS • The STRONGER THE ACID, the WEAKER ITS CONJUGATE BASE • The WEAKER THE ACID, the STRONGER ITS CONJUGATE BASE BUFFERS From Klein Organic Chemistry, 3rd Edition From Harper’s Illustrated Biochemistry. 30th ed. 2015 • Resist a change in pH when protons are produced or consumed • Maximum buffering occurs ± 1 pH unit on either side of pKa • Physiologic buffers include bicarbonate, orthophosphate, and proteins 1.5 FUNCTIONAL GROUPS • A functional group is a characteristic group of atoms or bonds that possess a predictable chemical behavior • “R-“: refers to the remainder of the compound, usually a hydrocarbon (made up of hydrogen and carbon) Tip: Above are the common functional groups encountered in biochemistry. Familiarize yourselves on their structures so that you will have an idea on how they look like as you read the rest of this handout. Enjoy! 😎 Dr. Rubio • Other terminologies important in understanding the structure of biomolecules: • An organic chemical compound Hydrocarbon exclusively of hydrogen and carbon chains atoms • Composed of straight-chained, Aliphatic branched, or cyclic compounds compounds • Can be saturated (alkanes) or unsaturated (alkenes, alkynes) Aromatic • Contains benzene rings compounds Monomer • Basic unit of a polymer • Represents 2 monomers attached to Dimer each other • Represents more than 2 monomers Polymer attached to each other • Polymer made up of identical Homopolymer monomers • Polymer made up of 2 or more Heteropolymer different monomers • Also known as an asymmetric carbon • Refers to a carbon which has 4 different atoms or groups of atoms attached to it Chiral carbon Structure of 2-butanol. (Center of the structure represents a chiral carbon with 4 different atoms/groups of atoms attached to it) From Klein Organic Chemistry, 3rd Edition α-carbon • It refers to the 1st carbon atom that attaches to a functional group in an organic compound • The 2nd carbon atom is termed as βcarbon… and so on! 2. STRUCTURE OF AMINO ACIDS & PROTEINS 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. General Structure of Amino Acids Classification of Amino Acids Essential and Non-Essential Amino Acids Properties of Amino Acids Abbreviations of Amino Acids Overview of Proteins Structural Organization of Proteins Globular Proteins Fibrous Proteins Structure of Immunoglobulins 2.1 GENERAL STRUCTURE OF AMINO ACIDS • More than 300 amino acids have been described • Only 20 are commonly found in mammalian proteins • Except for proline, each amino acid has: o A carboxyl group (COOH): an acid (can donate a proton) o An amino group (NH2): a base (can accept a proton) o A distinctive side chain (R-group): structure of R-group dictates the function of the amino acid in the protein TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. Page 4 of 43 TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries, visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. • Most of the amino acids are α-amino acids o It means both amino and carboxyl groups are attached to the α-carbon atom • In non-α-amino acids, neither carboxyl group nor amino group is attached to the α-carbon atom Remember: Non-α-amino acids present in tissues in free form are: βalanine, β-aminoisobutyrate, and γ-aminobutyrate. Dr. Rubio • At physiologic pH (7.4): o Carboxyl group is dissociated or deprotonated → COOo Amino group is protonated → NH3+ General Structure of α-Amino Acids From Self-Assessment and Review of Biochemistry, 2nd Edition 2.2 CLASSIFICATION OF AMINO ACIDS NON-POLAR AMINO ACIDS POLAR UNCHARGED AMINO ACIDS Zero net charge Zero net charge Forms hydrophobic interactions Found in the interior of the protein Glycine Phenylalanine Alanine Tryptophan Valine Methionine Isoleucine Proline Leucine Forms hydrogen bonds Found on the surface of a protein -OH -SH AMIDE Serine Cysteine Asparagine Threonine Glutamine Tyrosine NONPOLAR AMINO ACIDS GLYCINE ALANINE LEUCINE VALINE ISOLEUCINE GLYCINE • Has the smallest side chain; only achiral amino acid among the 20 AAs • Used in the first step of heme synthesis Glycine + Succinyl CoA à δ-ALA • Used in synthesis of purines and creatine • Conjugated to bile acids, drugs, and other metabolites • Major inhibitory neurotransmitter in the spinal cord Remember: Tetanospasmin (product of C. tetani) prevents the release of glycine from Renshaw cells. Thus, muscle will continuously contract leading to spastic paralysis. Dr. Rubio ALANINE • Carrier of ammonia and of the carbons of pyruvate from skeletal muscle to liver • Together with glycine, constitutes a major fraction of free amino acids in the blood Remember: Alanine, Glutamine, Glutamate are important in ammonia disposal in the body. This will be further discussed by Dr. Baticulon. CHARGED AMINO ACIDS Positive or negative net charge (acidic or basic) Forms ionic interactions Found on the surface of a protein ACIDIC BASIC Aspartate Arginine Glutamate Lysine Histidine METHIONINE • Source of methyl groups in metabolism: o Involved in transfer of methyl groups as S-adenosylmethionine (SAM) • Precursor of homocysteine and cysteine PROLINE • Not an amino, but an imino acid • Contributes to the fibrous structure of collagen and interrupts αhelices in globular proteins UNCHARGED POLAR AMINO ACIDS SERINE THREONINE SERINE, THREONINE, TYROSINE • Contain a polar hydroxyl group • Site for O-linked glycosylation and phosphorylation of proteins • Tyrosine is the precursor of several compounds: o Phenylalanine → Tyrosine → L-dopa → Dopamine → Norepinephrine → Epinephrine o Also a precursor for thyroxine and melanin PHENYLALANINE / TYROSINE DERIVATIVES Pare, True Love Does Not Exist Phenylalanine →Tyrosine → L-dopa → Dopamine → Norepinephrine → Epinephrine MNEMONIC Dr. Rubio VALINE, LEUCINE, ISOLEUCINE • Branched-chain amino acids whose metabolites accumulate in maple syrup urine disease PHENYLALANINE TRYPTOPHAN METHIONINE PROLINE PHENYLALANINE • Accumulates in phenylketonuria • Precursor of tyrosine TRYPTOPHAN • Has the largest side chain • Precursor for niacin, serotonin, and melatonin TRYPTOPHAN DERIVATIVES TRYp Mo Siya, ‘No? TRYptophan Melatonin Serotonin Niacin MNEMONIC TYROSINE CYSTEINE ASPARAGINE GLUTAMINE ASPARAGINE, GLUTAMINE • Have a carbonyl group and an amide group that can also form hydrogen bonds • Asparagine is the site for N-linked glycosylation of proteins • Glutamine is deaminated by glutaminase resulting in the formation of ammonia, and is a major carrier of nitrogen to the liver from peripheral tissues CYSTEINE • Contains a sulfhydryl group that is an active part of many enzymes • Participates in the biosynthesis of coenzyme A • Two cysteines can be connected by a covalent disulfide bond to form cystine Remember: Disulfide bonds formed by cystine residues causes kinking of hair. Disruption of these bonds (using heat) may straighten hair temporarily. Dr. Rubio TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. Page 5 of 43 TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries, visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. Semi-essential amino acid Non-essential amino acids ACIDIC AMINO ACIDS ASPARTATE Warning: Please take note that in some Biochemistry textbooks, they include arginine as an essential amino acid. Hence, this can be a cause of confusion. GLUTAMATE ASPARTATE, GLUTAMATE • Negatively charged at neutral pH because of the carboxylate group • Participate in ionic interactions • Serve as proton donors • Glutamate is the precursor for GABA and glutathione Remember: Glutamate is the major excitatory neurotransmitter of the CNS. GABA is the major inhibitory neurotransmitter of the BRAIN. Glycine is the major inhibitory neurotransmitter of the SPINE. Dr. Rubio BASIC AMINO ACIDS HISTIDINE • Arginine • All other amino acids ARGININE LYSINE Dr. Rubio ESSENTIAL & SEMI-ESSENTIAL AMINO ACIDS PVT TIM HALL, always ARGues, never TYRes (A is always ARGinine, T is never TYRosine) MNEMONIC Phenylalanine Valine Threonine Tryptophan Isoleucine Methionine Histidine Arginine (semi-essential) Leucine Lysine 2.4 PROPERTIES OF AMINO ACIDS • Except for glycine, all amino acids are chiral o L-configuration: all amino acids in human proteins o D-configuration: bacterial cell walls, antibiotics Remember: Chiral carbon has 4 different atoms or group of atoms around it. Glycine’s alpha carbon is not chiral (achiral) since two H’s (which are similar) are attached around that carbon hence Glycine has no chiral center. All the rest are chiral, and if chiral it will have a nonsuperimposable mirror image (enantiomer). Dr. Rubio HISTIDINE, ARGININE, LYSINE • Proton acceptors • At neutral pH: o Arginine and lysine are positively charged o Histidine, being a weak base, has no charge HISTIDINE • Precursor of histamine • Also used in the diagnosis of folic acid deficiency (FIGLU excretion test) • Concentration in the brain hypothalamus varies in accordance with the circadian rhythm ARGININE • Precursor of creatinine, urea, citrulline, and nitric oxide LYSINE • Precursor of carnitine Adapted from Lippincott Illustrated Reviews Biochemistry, 7th Edition • Amino acids can have negative, zero, or positive charge depending on pH of the aqueous environment • An amino acid bears no net charge (zwitterion) at its isoelectric pH (pI) • Because they can accept or donate protons, amino acids can serve as buffers in aqueous solutions Remember: Acids: donates protons (H+) Bases: accepts protons (H+) Remember: Form II is the zwitterion for alanine (neutral charge overall). Acidic amino acids have a pI <7. Basic amino acids have pI> 7. Dr. Rubio 2.5 ABBREVIATIONS OF AMINO ACIDS AMINO ACIDS WITH UNIQUE FIRST LETTER 21ST AMINO ACID SELENOCYSTEINE • Found in a handful of proteins, including certain peroxidases and reductases, where it participates in the catalysis of electron transfer reactions • A selenium atom replaces the sulfur of its structural analog, cysteine • Inserted into polypeptides during translation but is not specified by a simple three-letter codon CLASSIFICATION OF AMINO ACIDS https://qrs.ly/s6ezhit 2.3 ESSENTIAL AND NON-ESSENTIAL AMINO ACIDS • Essential: refers to amino acids which cannot be synthesized in the body; hence they are ESSENTIAL IN DIET • Non-essential: refers to amino acids which can be synthesized in the body; hence they are NON-ESSENTIAL IN DIET • Semi-essential: refers to amino acids which are required in growing children, but not essential in adults • Phenylalanine • Valine • Threonine • Tryptophan Essential amino acids • Isoleucine • Methionine • Histidine • Leucine • Lysine 3-LETTER ABBREVIATION 1-LETTER ABBREVIATION Cysteine Cys C Histidine His H Isoleucine Ile I Methionine Met M Serine Ser S Valine Val V AMINO ACIDS ABBREVIATED BASED ON THE COMMONLY OCCURRING AMINO ACIDS 3-LETTER ABBREVIATION 1-LETTER ABBREVIATION Glycine Gly G Alanine Ala A Leucine Leu L Proline Pro P Threonine Thr T AMINO ACIDS ABBREVIATED BASED ON PHONETICALLY SOUNDING LETTERS Arginine Asparagine Aspartic acid Glutamic acid Glutamine Phenylalanine Tyrosine Tryptophan Lysine 3-LETTER ABBREVIATION 1-LETTER ABBREVIATION Arg Asn Asp Glu Gln Phe Tyr Trp Lys R (aRginine) N (asparagiNe) D (asparDic acid) E (glutEmic acid) Q (Qtamine) F (Fenylalanine) Y (tYrosine) W (tWiptophan) K (letter close to L) Tip: Read the phonetic mnemonic aloud while studying this portion of the handout! It helps! TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. Dr. Rubio Page 6 of 43 TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries, visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. 2.6 OVERVIEW OF PROTEINS • Most abundant and functionally diverse molecules in living systems • Proteins are linear polymers of amino acids o Monomers: amino acids o Polymers: proteins • Perform diverse functions: o Regulate metabolism o Facilitate muscle contraction o Provide structural framework o Shuttle molecules in the bloodstream (especially hydrophobic molecules) o Serve as component of the immune system Proteome Proteomics • Refers to the set of all the proteins expressed by an individual cell at a particular time • Aims to identify the entire complement of proteins elaborated by a cell under diverse conditions • A major goal is the identification of proteins and of their posttranslational modifications whose appearance or disappearance correlates with physiologic phenomena, aging, or specific diseases SECONDARY STRUCTURE The folding of short (3–30 residue) contiguous segments of polypeptide into geometrically ordered units • Stabilized by hydrogen bonding ALPHA HELIX • Most common secondary structure • Spiral structure with polypeptide backbone core, with side chains extending outward • 3.6 AA per turn • Examples: o Keratin (100% α-helix) o Hemoglobin (80% α-helix) Remember: The amino acids that can disrupt the α-helix structure are proline and glycine Dr. Rubio BETA SHEET • Amino acid residues form a zigzag or pleated pattern • R groups of adjacent residues project in opposite directions • Sheets can be parallel or antiparallel • Examples: o Amyloid o Immunoglobulin Remember: Genome contains the manuscript of life. It remains the same throughout. Proteome refers to the variety of proteins formed from the genome. Dr. Rubio 2.7 STRUCTURAL ORGANIZATION OF PROTEINS PRIMARY STRUCTURE • Determined by the amino acid sequence of a protein • Peptide bonds attach the α-amino group of one amino to the αcarbonyl group of another PEPTIDE BONDS • Partial double-bond character (represents 1.5 bonds) • Rigid and planar • Generally, in the trans-configuration • Disrupted by hydrolysis through prolonged exposure to a strong acid or base at elevated temperatures Remember: Peptide bond formation is a dehydration chemical reaction. Hence, addition of water can cause lysis or destruction of this bond (hydrolysis) (when exposed to strong chemicals at elevated temperatures or catalyzed by enzymes) Dr. Rubio N-TERMINUS AND C-TERMINUS • Proteins are naturally synthesized from the N-terminus (NH3 end) to the C-terminus (COOH end) • Read the amino acid sequence of a primary structure from the Nterminus to C-terminus NON-REPETITIVE SECONDARY STRUCTURES • Less regular structures forming loops and bends MOTIFS • Supersecondary structures produced by packing side chains from adjacent secondary structural elements close to each other • Examples are β-α-β unit, Greek key, β-meander, β-barrel TERTIARY STRUCTURE • Overall 3-dimensional shape of the protein o Globular proteins vs Fibrous proteins • The assembly of secondary structural units into larger functional units such as the mature polypeptide and its component domains • Stabilized by disulfide bonds, hydrophobic interactions, hydrogen bonds, and ionic interactions Remember: Recall that amino acids that can disrupt the α-helix structure are proline and glycine. Dr. Rubio • Salient functions of N- and C-terminus of AA sequences: • Contains targeting signals (targets protein N-terminus to a specific organelle) • Contains retention signals for protein sorting (keeps the protein in the endoplasmic reticulum) C-terminus • Can be modified post-translationally to allow the protein to be inserted into a membrane without having a transmembrane domain N-TERMINUS VS. C-TERMINUS N-TERMINUS – allows N-try of protein into an organelle MNEMONIC C-TERMINUS – C-ontains protein inside the organelle Mnemonic: N-terminus – allows N-try of protein into an organelle via targeting signals; C-terminus Contains protein inside the organelle via retention signals Dr. Rubio DOMAINS • Fundamental functional and three-dimensional structural units of polypeptide Tip: Motifs refer to structural modifications Domains may vary and have specific functional effect Dr. Rubio QUATERNARY STRUCTURE • Number and types of polypeptide units of oligomeric proteins and their spatial arrangement o Monomeric vs Dimeric proteins o Homodimers vs Heterodimers Tip: A protein can form quaternary structure if there are 2 or more chains. Hemoglobin A1 has 2 alpha & 2 beta chains; thus, it can form quaternary structure. Monomeric means having only 1 polypeptide chain/subunit; so it cannot form quaternary structure (ex. Myoglobin). TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. Dr. Rubio Page 7 of 43 TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries, visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. CHAPERONES • Specialized group of proteins required for the proper folding of many species of proteins • Prevent aggregation, thus providing an opportunity for the formation of appropriate secondary structural elements and their subsequent coalescence into a molten globule • Can also “rescue” proteins that have become thermodynamically trapped in a misfolded dead end by unfolding hydrophobic regions ALZHEIMER DISEASE • Most common and most important degenerative disease of the brain, presenting with diffuse cerebral atrophy with dementia • The characteristic senile plaques and neurofibrillary bundles contain aggregates of the protein β-amyloid • Apolipoprotein E has been implicated as a potential mediator of this conformational transformation Remember: Amyloid plaques & neurofibrillary tangles in Alzheimer disease are aggregates of protein B-amyloid Dr. Rubio Tip: In short, chaperones help fold proteins to their final configuration. Dr. Rubio DENATURATION • Results in the unfolding and disorganization of the protein’s secondary and tertiary structures • Not accompanied by hydrolysis of peptide bonds • Results from denaturing agents: o Heat, organic solvents, mechanical mixing, strong acids or bases, detergents, ions of heavy metals (e.g., lead, mercury) • May be reversible, but most proteins remain permanently disordered STRUCTURAL ORGANIZATION OF PROTEINS https://qrs.ly/ktezhla 2.8 GLOBULAR PROTEINS GLOBULAR VS FIBROUS PROTEINS GLOBULAR PROTEIN Shape Spherical Solubility General Function MORE SOLUBLE Has dynamic functions Hemoglobin Myoglobin Albumin Globulin Most enzymes Examples • • • • • FIBROUS PROTEIN Elongated or needleshaped MINIMALLY SOLUBLE Structural proteins • Collagen fibers • Elastin fibers • Keratin Remember: Note that denaturation does not affect a protein’s primary structure. Dr. Rubio PROTEIN-FOLDING DISORDERS PRION DISEASES Remember: Majority of oxygen is transported in the blood through hemoglobin. In contrast, majority of carbon dioxide is transported as dissolved bicarbonate anion. Note that carboxyhemoglobin refers to carbon monoxide bound to hemoglobin, while carbaminohemoglobin refers to carbon dioxide bound to hemoglobin. Dr. Rubio • Fatal neurodenegerative diseases characterized by spongiform changes, astrocytic gliomas, and neuronal loss resulting from the deposition of insoluble protein aggregates in neural cells • Examples: o Creutzfeldt-Jakob disease (humans) o Kuru (cannibalistic tribes of Papua New Guinea) o Scrapie (sheep) o Bovine spongiform encephalopathy (cattle) Remember: This will be discussed more extensively in Microbiology. But what I want you to remember here are the forms of normal and abnormal prion protein. PrPc represents the normal protein which has an α-helix structure; on the other hand, PrPsc represents the abnormal protein which has a β-sheet structure. The shift from α-helix → β-sheet makes PrPsc resistant from proteases and other chemicals. Accumulation of PrPsc would lead to spongiform neurodegeneration of the brain → CNS dysfunction → coma → death. HEMOGLOBIN • Heme protein found exclusively in red blood cells (RBCs) • Functions: o Transport of O2 from the lungs to capillaries o Transport of CO2 from tissues to the lungs • Exists in 2 configurations o T (taut) form: low oxygen affinity o R (relaxed) form: high oxygen affinity (300x) • Hemoglobin binds up to 4 molecules of O2 with increasing affinity (positive cooperativity) Remember: Heme has iron and histidine. Hemoglobin has 4 polypeptides hence can form quaternary structure. Oxygen binds to Hb if Hb is in the R state, & its iron is in the Fe2+ or ferrous state! Positive cooperativity: 1st to commit is the hardest to let go (it is the rationale for the sigmoidal configuration of the O2 dissociation curve) Dr. Rubio OVERVIEW OF HEMOGLOBIN FORMATION • Basic steps in the formation of hemoglobin A (1) 2 succinyl coenzyme A + 2 glycine → 1 pyrrole (2) 4 pyrroles → protoporphyrin IX (3) Protoporphyrin IX + Fe2+ → Heme (4) Heme + Polypeptide → Hemoglobin chain (α or β) (5) 2 α chains + 2 β chains → Hemoglobin A Dr. Rubio TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. Page 8 of 43 TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries, visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. STRUCTURE OF PORPHYRINS (PROTOPORPHYRIN IX) Structure of Porphyrin From Self-Assessment and Review of Biochemistry, 2nd Edition • Porphyrin are cyclic compounds formed by the linkage of 4 aromatic pyrrole rings by methenyl (methyne) bridges • Porphyrins are colored compounds that emit a strong red fluorescence when illuminated by UV light after being dissolved in strong acids or inorganic solvents • Porphyrins have a maximum characteristic electronic absorption spectrum of around 400 nm known as the Soret peak • Porphyrins causes photosensitivity STRUCTURE OF HEME • Heme is a metalloporphyrin containing iron Structure of Heme From Self-Assessment and Review of Biochemistry, 2nd Edition MYOGLOBIN • Heme protein present in heart and skeletal muscle • Functions: o Reservoir of oxygen o Oxygen carrier that increases the rate of transport of O2 within the muscle cell • Consists of a single polypeptide chain (monomeric) • Following massive crush injury, myoglobin released from damaged muscle fibers colors the urine dark red (myoglobinuria) • Myoglobin can be detected in plasma following a myocardial infarction CHARACTERISTICS MYOGLOBIN HEMOGLOBIN Structure 1 polypeptide only 4 polypeptides O2 Bound 1 O2 only 4 O2 Sigmoidal O2 Dissociation Hyperbolic Shows Curve Shows saturation cooperativity Main Purpose For O2 storage For O2 transport Heart and skeletal Where Found Red blood cells muscle Allosteric Effects Absent Present • Factors that cause a shift to the RIGHT: o ↑ CO2 o ↑ 2,3 BPG o ↑ Acidity (↓pH) o ↑ Exercise o ↑ Temperature A: Shift to the right (P50 is increased) B: Shift to the left (P50 is decreased) O2-HgB DISSOCIATION CURVE “CABET, do the RIGHT thing, LET GO” CO2, Acidosis, BPG (2,3 BPG), Exercise, Temperature MNEMONICS 2,3-BISPHOSPHOGLYCERATE • Stabilizes the T structure of hemoglobin by forming additional salt bridges that must be broken prior to conversion to the R state • A low pO2 in peripheral tissues promotes the synthesis in erythrocytes of 2,3-bisphosphoglycerate from the glycolytic intermediate 1,3-bisphosphoglycerate • Effects: o In infants, 2,3-BPG binds weaker to HbF than to HbA. Hence, HbF has a higher affinity for O2 than HbA. o Prolonged exposure to high altitude increases the number of erythrocytes. ↑hemoglobin and ↑ BPG lowers the affinity of HbA for O2 TYPES OF HEMOGLOBIN HEMOGLOBIN IN THE EMBRYO Gower I hemoglobin Gower II hemoglobin Hemoglobin Portland I Hemoglobin Portland II IN THE FETUS Hemoglobin F (HbF) COMPONENTS • ζ2 - ε2 • α2 - ε2 • ζ2 - γ2 • ζ2 - β2 • α2 - γ 2 • binds less with 2,3-BPG AFTER BIRTH Hemoglobin A (HbA) Hemoglobin A2 (HbA2) Hemoglobin F (HbF) • α2 - β 2 • binds more with 2,3-BPG • 95% of hemoglobin after birth • α2 -δ2 • 1.5-3.5% of hemoglobin after birth • α2 - γ 2 • can be elevated in persons with sickle cell disease & beta-thalassemia MNEMONICS BLOOD CELL FORMATION YOUNG LIVER SYNTHESIZES BLOOD. Yolk Sac à Liver, Spleen à Bone Marrow GLYCATED HEMOGLOBIN (HbA1C) • When blood glucose enters the erythrocytes, it glycates the ε-amino group of lysine residues and the amino terminals of hemoglobin • ↑ glycation of hemoglobin noted in patients with diabetes mellitus due to ↑ glucose in blood Clinical Correlate: HbA1c allows us to determine the glycemic control of DM patients over the past 3 months Dr. Rubio CLINICAL CORRELATES Comparison of Myoglobin and Hemoglobin O2 Dissociation Curve ALLOSTERIC FACTORS • Factors whose interaction with one site of hemoglobin affects the binding of O2 to heme groups at other locations • Effect may be positive or negative CARBOXYHEMOGLOBIN • Form of hemoglobin bound to carbon monoxide in place of O2 • Hb becomes “cherry pink” in color • CO has 200x greater affinity for Hgb than O2 • Treatment: 100% O2 therapy Remember: carbon monoxide also inhibits complex IV of the electron transport chain. TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. Dr. Rubio Page 9 of 43 TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries, visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. METHEMOGLOBIN • Oxidized form of hemoglobin (Fe3+) that does not bind O2 as readily, but has ↑ affinity for cyanide • Methemoglobinemia o Symptoms: anxiety, headache, and dyspnea, o Signs: chocolate cyanosis, O2 saturation is at 85% o Treatment: § Mild: oral methylene blue or ascorbic acid, both reducing agents § Acute massive, due to ingestion of chemicals: IV methylene blue Remember: In methemoglobin, ferrous (Fe2+) becomes ferric (Fe3+) Dr. Rubio HEREDITARY SPHEROCYTOSIS • Disorder characterized by an inherited (intrinsic) defect in the RBC membrane that renders the erythrocytes spheroidal, less deformable, and vulnerable to splenic sequestration and destruction • Multiple mutations have been described: ankyrin (most common), spectrin, band 4.1 and band 3 • Clinical manifestations: o Anemia, splenomegaly, jaundice • Diagnosed: Osmotic fragility test • Treatment: No cure o Splenectomy for symptomatic patients Remember: Splenectomy only provides symptomatic relief, since splenic infarcts may cause pain. Spherocytes also hemolyze earlier in the circulation due to the absence of biconcavity which allows RBCs to squeeze through small vessels Dr. Rubio SICKLE CELL DISEASE • Results from a point mutation (missense) in both genes coding for the β-chain that results in a change from glutamate → valine (at the 6th position) • Homozygous recessive disorder 1 missing allele 2 missing alleles Silent carrier α-Thalassemia trait (mild anemia) Hemoglobin H disease (moderate to severe 3 missing alleles anemia) Contains Hb H (β4), Hydrops fetalis (lethal in utero without 3 missing alleles transfusions) (not in photo above) Contains Hb Bart (γ4) Remember: Hb Bart, which is made up of 4 gamma-globin chains, becomes prominent when alpha- and beta-globin chains become deficient Dr. Rubio BETA THALASSEMIA • Inadequate synthesis of β-chains • Leads to anemia, accumulation of Hb Barts and α-chain precipitation • Physical manifestations appear only after birth Remember: Symptoms only manifest at around 6 months of age because before then, you rely on fetal hemoglobin that doesn’t contain beta chains. Dr. Rubio • Two alleles are responsible for the production of β-globin o Both alleles are found in chromosome 11 o The number of missing alleles contributes to the overall presentation of β-thalassemia Adapted from Ferrier DR. Lippincott Illustrated Reviews: Biochemistry. 7th ed. 2017. Remember: The change from glutamate → valine is significant because there is a change from a charged amino acid → nonpolar amino acid Dr. Rubio • Effect on RBC: o Polymerization & decreased solubility of the deoxy form of Hb in times of low oxygen tension → distortion of the RBC membrane → sickling of the RBCs → occlusion of capillaries • Clinical Manifestations: o Anemia, tissue anoxia, painful crises o Protective against malaria • Treatment: hydration, analgesics, antibiotics if with infection, transfusions, hydroxyurea Remember: Hydroxyurea causes increased production of hemoglobin F, which has increased affinity to oxygen (which is what we want to prevent sickling) Dr. Rubio HEMOGLOBIN C DISEASE • Hemoglobin variant that has a single amino acid substitution in the 6th position of the β-globin chain, in which glutamate → lysine • Patients homozygous for hemoglobin C present with mild hemolytic anemia 1 missing allele 2 missing alleles β-Thalassemia minor / trait (mild anemia) β-Thalassemia major (moderate or severe anemia) 2.9 FIBROUS PROTEINS COLLAGEN • Most abundant protein in the body • A long stiff extracellular structure in which 3 polypeptides (αchains) each 1000 AA in length are wound around one another in a triple helix • At least 28 distinct types made up of over 30 distinct polypeptide chains have been identified in human tissues • Most common form is type I collagen Remember: Hemoglobin C disease is benign compared to sickle cell disease because the replacement of glutamate, lysine (lyCine), is also a charged amino acid. In simpler terms, it is not so different from the original amino acid (glutamate) at the 6th position, hence the presentation is mild. Dr. Rubio ALPHA THALASSEMIA • Inadequate synthesis of α-chains • Leads to anemia, accumulation of Hb Bart (γ4) and Hb H (β4), and β-chain precipitation • Symptoms appear at birth because α-chains are needed for HbF and HbA Remember: The name of the thalassemia tells you what is deficient. In alpha thalassemia, you don’t have alpha chains. In beta thalassemia, beta chains. Dr. Rubio • Four alleles are responsible for the production of α-globin o All four alleles are found in chromosome 16 o The number of missing alleles contributes to the overall presentation of α-thalassemia Structure of Collagen Remember: Hydrogen bonding stabilizes the 3-part structure of the collagen. Dr. Rubio • Rich in glycine and proline o Gly: glycine o X: proline (facilitates kinking) o Y: hydroxyproline or hydroxylysine • Formed in fibroblasts (or in the osteoblasts of bone and chondroblasts of cartilage) TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. Page 10 of 43 TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries, visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. SYNTHESIS OF COLLAGEN 1. 2. 3. 4. 5. 6. Synthesis of pre-procollagen in the rough endoplasmic reticulum, and cleavage of the signal (pre) sequence Hydroxylation of proline and lysine residues, which requires vitamin C Glycosylation (addition of galactose and glucose) to hydroxylysine residues → Formation of triple helix Exocytosis of procollagen from the cell into the extracellular matrix Proteolytic processing (cleavage of disulfide-rich terminal regions of procollagen) → insoluble tropocollagen Cross-linking of tropocollagen fibers via copper-containing lysyl oxidase → collagen fibrils Synthesis of Collagen From First Aid for the USMLE 2020, 30th Edition DISEASES ASSOCIATED WITH COLLAGEN SYNTHESIS • Problem in hydroxylation step Scurvy • Due to vitamin C deficiency Discussed further in Vitamins & Minerals module Osteogenesis imperfecta Menkes disease • Problem in formation of triple helix step Discussed further in Clinical Correlates part of this module • Problem in cross-linking step • Due to deficiency in copper → dysfunction of lysyl oxidase Discussed further in Clinical Correlates part of this module SYNTHESIS OF COLLAGEN https://qrs.ly/lxezhmn TYPES OF COLLAGEN I Bone, skin, tendon, dentin, fascia, cornea, late wound repair II Cartilage (including hyaline), vitreous body, nucleus pulposus (Reticulin) Skin, blood vessels, uterus, fetal tissue, III granulation tissue (early wound repair) IV Basement membrane or basal lamina Anchoring fibrils – found beneath the stratified VII squamous epithelium TYPES OF COLLAGEN Type One is in b-ONE and tend-ONE. Type Two is in Car TWO-lage. Type Three has THREE-ticulin. Type Four is under the FLOOR (FOUR), which is your basement MNEMONIC EHLERS-DANLOS SYNDROME • Group of inherited disorders characterized by: o Hyperextensibility of the skin o Abnormal tissue fragility o Increased joint mobility CLASSICAL Defect in types I and V collagen • Similar to hypermobility subtype but more severe skin abnormalities and less severe joint changes HYPERMOBILITY Defect in type III collagen • Joint hypermobility • skin abnormalities • osteoarthritis • severe pain Most common VASCULAR Defect in type III collagen • Fragile blood vessels and organs • small stature • thin and translucent skin, easy bruising • Increased risk of intracranial aneurysms Most serious • Manifestations: o Multiple fractures (need to rule out child abuse) o Blue sclerae o Hearing loss o Dental imperfections ALPORT SYNDROME • Genetic disorders affecting the structure of type IV collagen fibers, the major collagen found in the basement membranes of the renal glomeruli • Manifestations: o Hematuria (main presenting sign) o Ocular lesions o Hearing loss o Patients may eventually develop end-stage renal disease Remember: Al-FOUR-th syndrome involves Type 4 collagen. The glomerular and cochlear basement membranes are also affected. Dr. Rubio GOODPASTURE SYNDROME • A form of pulmonary-renal syndrome due to autoantibodies to the glomerular basement membrane (anti-GBM autoantibodies) • Manifestations: o Hemoptysis o Gross hematuria Clinical Correlate: In a patient with gross hematuria and hemopytis, always think of a pulmonary-renal syndrome that could cause this presentation Dr. Rubio DYSTROPHIC EPIDERMOLYSIS BULLOSA (DEB) • The skin breaks and blisters as a result of minor trauma • Dystrophic form is due to mutations affecting the structure of type VII collagen, which anchors the basal lamina to collagen fibrils in the dermis SCURVY • Hydroxylation of collagen is a post-translational modification requiring ascorbic acid • Vitamin C deficiency causes ↓ cross-linking of collagen fibers • Manifestations: o Sore spongy gums, Loose teeth o Poor wound healing o Petechiae on skin and mucous membranes MENKES DISEASE • Characterized by kinky hair and growth retardation • Reflects a dietary deficiency of the copper required by lysyl oxidase o Catalyzes a key step in formation of the covalent cross-links that strengthen collagen fibers OSTEOGENESIS IMPERFECTA • Brittle bone disease • Mutation in collagen genes → problem in triple helix formation → result to bones that easily bend and fracture • Most common form is autosomal dominant with abnormal collagen type I TYPES OF COLLAGEN https://qrs.ly/v8ezhmv TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. Page 11 of 43 TOPNOTCH MEDICAL BOARD PREP BIOCHEMISTRY MAIN HANDOUT (PART 1) BY FRINZ MOEY C. RUBIO, MD For inquiries, visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for the October 2023 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. Fab & Fc REGIONS ELASTIN • Connective tissue protein with rubber-like properties, responsible for extensibility and elastic recoil in tissues • Found in tissues where elastic recoil is needed o Lungs, large arteries, elastic ligaments, vocal cords, ligamentum flavum • Rich in proline and lysine, but contains little hydroxyproline and no hydroxylysine • Precursor tropoelastin is deposited into an irregular fibrillin scaffold cross-linked by desmosine Structure Function Fab Contains both light and heavy chains Contains variable and constant regions Contains antigenbinding site Fc Contains heavy chains only Contains constant region only Site of complement & macrophage binding Determines the isotype (class) Remember: Fab = contains antigen-binding site Fc = contains complement-binding site Dr. Rubio HINGE REGION • Region found between CH1 and CH2 domains • Confers flexibility and allows both Fab arms