Module 2 Biochemistry - Notes PDF

MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec I. Introduction other (like dissolves...

MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec I. Introduction other (like dissolves like); Pharmaceutical Biochemistry hydrophobic interaction – involves physical Science concerned with the chemical reaction only, no basis of life, as applied to pharmacy and chemical bond pharmaceutical biological sciences. building block: fatty acids and fatty alcohols Science concerned with the chemical connecting constituents of living cells and the bond/covalent bo0nd: reactions they undergo. none The application of chemistry to the study lipids are esters (usually of biological processes at the cellular triester) and molecular level. Central Dogma of Molecular Biology – central Biomolecules - chemical constituents of the principle of life; how cell is made. living cells; biopolymer o Starts with the DNA (book of life) o Polymer – made from repeating o Then, the DNA will undergo replication monomeric units (building blocks) (one copy will be transcribed as protein, connected to one another by covalent the other will be stored at the daughter bond. cell) o Biopolymer - polymers made of o DNA will become mRNA via biomolecules that are bonded covalently transcription (other names: RNA and obtained from natural sources such synthesis, RNA Assembly) as carbohydrates, proteins, and fats. o mRNA will become protein via Carbohydrates (CHO’S) translation (other names: Protein o building block: monosaccharides Synthesis / Amino Acid Assembly) o connecting bond/covalent bond: o When RNA is made, it goes through the glycosidic bonds ribosomes to become protein (this is Proteins (CHONS) where translation occurs) o building block: amino acids ▪ Site of protein synthesis: o connecting bond/covalent bond: peptide Ribosomes bonds o Protein – the most biologically active Nucleic Acids (DNA and RNA) biomolecule, indicates that a cell is alive o building block: nucleotides o Replication / DNA Assembly / DNA o connecting bond/covalent bond: Synthesis – synthesis from DNA from phosphodiester bonds DNA Enzymes o Majority of enzymes are proteins Cells Vitamins o Essential – molecules needed by the Basic units of life body but cannot be produced by the 2 major classifications of cells: PROKARYOTIC body, which is why it is obtained from AND EUKARYOTIC food. Prokaryotes include bacteria; lack o B Vitamins (water-soluble) becomes co- nucleus and organelles enzyme ▪ Co-enzyme – helps enzymes Lipids o NOT TRUE BIOPOLYMER ▪ because they are not chemically related but physically related ▪ they don’t have a covalent bond water molecules tend to make lipids aggregate physically with each MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec Cosmid – hybrid plasmid that serves as a cloning vector for recombinant DNA technology o plasmid + cos gene Eukaryotic Cell Eukaryotes have a nucleus and organelles (plants, fungi, animals, protozoans, helminths) NOTE: Acellular entities – VIRUSES (they are not eukaryotic nor prokaryotic) Cell wall of bacteria component: Peptidoglycan Plant cell wall component: Cellulose Fungal cell wall component: Chitin These components are all CARBOHYDRATES Explanation sa pic: Outer cellular envelope 1. Glycocalyx / Glycocalices i. Capsule – offers resistance to phagocytosis ii. Slime layer - Capsule and slime layer can both maintain water inside the bacterial cell and serve for attachment - Capsule is firmly attached (rigid) while the slime layer is water-washable (not rigid). 2. Cell wall – offers rigidity to the cell; made from peptidoglycan 3. Cell membrane – allows the entry of selected substances; keeps out toxic substances both in Explanation sa pic: and out of the cells 4. Ribosomes – not true organelles - DNA is located at the nucleus i. used to make proteins (for human and o Site of DNA synthesis: nucleus bacteria) o Site of RNA synthesis: nucleolus ii. site of protein synthesis - Protein folding / Protein maturation / Protein 5. Pili – used for attachment processing / Post-translational modification 6. Flagella – motility o This happens in the Golgi apparatus 7. Cytoplasm – semi-solid matrix o Protein that is linear is inactive, it has to 8. Cytosol – liquid part of the cytoplasm undergo folding 9. Nucleoid – region where genetic material is ▪ Needs ATP’s to undergo folding concentrated 10. Plasmid – small, circular, extrachromosomal 5 Pathways that are ATP-producing (nasa labas ng chromosome) DNA molecules - Mnemonics: miTOKondRiA that can be transcribed independent of the major o T – ricarboxylic Acid / Citric Acid / Krebs’ chromosome. Cycle i. Used as cloning vector o O – xidation of fatty acids / Beta oxidation Recombinant DNA Technology / Cloning / Genetic of fatty acids Engineering o K – etogenesis o R – espiratory chain / Electron Transport - Drug first produced by genetic engineering: Chain Insulin (protein hormone) o A – TP synthase MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec Stages of Protein Synthesis This is where replication o Initiation happens o Elongation o Termination Nucleolus – where transcription - All of these stages happen in the ribosome happens / RNA synthesis Mitochondrion Human Eukaryotic Cell Has series of folds called Plasma Membrane cristae; for ATP production Provides a barrier; contains transport and Rough Endoplasmic signaling systems. Reticulum (RER) TRANSPORT MECHANISMS Covered with ribosomes (Movement of Solute) Ribosomes 1.) Passive diffusion – movement of solute from high to low concentration Protein and RNA complex (thermodynamically downhill) responsible for protein - doesn’t require ATP, carriers, synthesis. (No nor active transporters membranes) 2.) Active transport 3 RNA’s read by ribosome to - movement of solute from low assemble amino acids to high concentration gradient together: (thermodynamically uphill) - mRNA (messenger) - requires ATP and active - rRNA (ribosomal, most transporters (protein) abundant) - proteins are limited in supply - tRNA (transfers amino acids inside the 3.) Facilitation diffusion ribosome) - similar to passive diffusion but requires carriers Prokaryotic Eukaryotic ribosomes Ribosomes Carrier-mediated transport -Has 30s -Has 40s and mechanisms obey Zero Order and 50s 60s Kinetics (low concentration, concentration independent) s means - Zero Order Kinetics also Svedberg obey Michelis-Menten unit – unit of Kinetics / Capacity- time limited kinetics / (sedimentati Saturation Kinetics on rate - Phenytoin – obeys zero 1x10^-13 order kinetics secs) Sedimentati Sedimentatio First Order Kinetics – on rate of n rate of concentration dependent Prokaryotic Eukaryotic ribosomes: ribosomes: Nucleus 70s 80s BACTERIAL PROTEIN SYNTHESIS INHIBITORS Contains chromosomes and the nucleolus which 1.Kumakabit sa 30s (30s is the site for RNA inhibitors) synthesis. - Tetracyclines (ex. Doxycyline which is MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec used to treat - Dominant organ for leptospirosis, cholera, drug metabolism: liver and 30 day therapy for Golgi Apparatus pimples if paired with Clindamycin roll-on) - Aminoglycosides (ex. Processes/modify Streptomycin) proteins to mature forms. 2.Kumakabit sa 50s (50s For protein maturation and inhibitors) post-translational modification - Lincomycin / Lysosomes Lincosamides (ex. Clindamycin) - Chloramphenicol Degrades proteins, - Macrolides (first nucleic acids and discovered macrolide: membranes in the cell, erythromycin) and helps degrade - Pleuromutilines (for materials ingested by the infectious disease in pets) cell. - Streptogramins (ex. - Suicide bag (kills cells Dalfopristin and that are old or Quinopristin) malfunctioning) - Important in apoptosis 3.Kumakabit sa 23s (23s (cell death) inhibitors) Peroxisomes or - Linezolid (drug Microbodies Smooth Endoplasmic Reticulum (SER) Degrade hydrogen peroxide Site for lipid metabolism; contains enzymes for GSH (Glutathione) – used to detoxify reactive oxygen detoxifying xenobiotics species - Lipid metabolism (both synthesis and H-O-O-H – thiol breakdown) Cytoplasm - Used to detox xenobiotics (anything foreign) Houses organelles; liquid - Fatty acid elongation portion called cytosol - MICROSOMES – smaller aggregates of Smooth Endoplasmic Cytoskeleton Reticulum with aqueous cores Protein filaments that - Cytochrome P450 – provide rigidity and mixed function oxidase; shape, a basis for a dominant enzyme movement and facilitates used to oxidize drugs for drugs to be water- mitosis. E.g. microtubules soluble. (DRUG - Microtubule - gives the METABOLISM) cell shape, rigidity, and - The aim of drug form. metabolism is to make - 3 uses of microtubule the drug HIPE (3 M’s) (hydrophilic, ionized, -Morphology polar, excretable) -Mitosis -Movement MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec - Tubulin – used to make microtubule (structural protein) - If a drug is attached to tubulin, it prevents the assembly of microtubules. SAMPLE DRUGS THAT BIND TUBULIN (Microtubule Synthesis Inhbitor) - Colchicine = former - Lipids are not joined by covalent bonds, only DOC for acute gout physical interaction (NSAID’s except - Membrane is made from phospholipid bilayer salicylates are the new DOC for acute gout) Membrane Proteins - Purines (Adenine, Guanine) Pumps/Active Transporters o AKA “ATPase Pumps” - Griseofulvin = ringworms (fungi); o For active transport needs high fat diet to Carriers absorb o For facilitated diffusion Ion Channels - Vinca Alkaloids = vincristine and Membrane fluidity is controlled by fatty vinblastine; attaches to acid composition and cholesterol the microtubules of content. cancer cells (source of o Fatty acids may be: Vinca alkaloids: ▪ Saturated (membranes that are Catharanthus roseus) highly saturated becomes rigid) - Benzoimidazole / ▪ Unsaturated (membranes that Benzimidazole = are highly unsaturated becomes antihelmintics (ex. fluid) Mebendazole) ▪ High cholesterol = rigid ▪ Low cholesterol = fluid Centriole – holds the spindle fiber during mitosis ▪ Conversion of a rigid membrane to a fluid membrane can occur Membranes spontaneously = FALSE, it is not a spontaneous process. Spontaneously formed due to ▪ 2 phases of the membrane are hydrophobicity always the same = FALSE Existing potentials facilitate transport Test Manship guessing and excitability technique: pag may ALWAYS sa question, Membrane lipids are amphipathic due to mas madalas na sagot phospholipids. ay FALSE. Others: glycolipids and cholesterol II. Carbohydrates General Functions Energy stores o Glycogen - storage carbohydrates for human and animals ▪ Found in liver and muscles o Starch - storage carbohydrates for plants Fuels MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec o Glucose is the most readily available fuel for cells - Pag aldehyde nasa dulo yung Metabolic intermediates - D and L = describes the OH or the alcoholic Intermediates – means it is a part of the functional group located at the highest numbered biochemical pathway but not yet a final product chiral carbon (from book) Ex. GLYCOLYSIS = Glucose → Glyceraldehyde - It describes the penultimate OH (from sir nix) → Dihydroxyacetone → Pyruvate (final product) o “D” (dextro) – the penultimate OH is - Glycerol – most common fat alcohol pointing to the right Structural elements o “L” (levo) – the penultimate OH is o Most common structural element: Protein pointing to the left o Penultimate – second to the last carbon Receptors Blood typing o Antigen (foreign substances) Carbohydrates Polyhydroxy aldehydes and ketones o o Should have a chiral carbon o Dihydroxyacetone is ACHIRAL, which is why it doesn’t have D or L. Polyhydroxy groups account for sweet taste. o - Pag ketone nasa gitna yung C=O (automatically Make up most of the organic matter on position 2) the earth Cellulose - most abundant carbohydrate - found in plant cell wall and purest source is cotton - - Glyceraldehyde is called aldotriose and Carbohydrates are hydrated carbon (CH2O) dihydroxyacetone is called ketotriose because Monosaccharides they each have 3 carbons. - D-glyceraldehyde is more common in humans than L-glyceraldehyde Smallest monosaccharide found in humans – glyceraldehyde (synonym: glycerose) and dihydroxyacetone Smallest monosaccharide but NOT found in humans - hydroxyacetaldehyde Explanation sa pic: MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec - - Pag aldose, palaging constant: o yung carbon 1 (carbonyl group) o “D” (nakaturo sa kanan yung OH = dextro) second to the last carbon / penultimate carbon o Terminal carbon (CH2OH) - Aldotetroses (4 carbons) o D-Erythrose (OH is both at the right side) ▪ Erytho SAME SIDES o D-Threose (OH of carbon 2 is at the left, OH of the second to the last carbon is at the right) ▪ Threo OPPOSITE SIDES - - Pag ketose, palaging constant: - Aldopentoses (5 carbons) o Carbon 1 (CH2OH) o D-Ribose (lahat RIGHT SIDE) o Carbon 2 (Carbonyl) o D-Arabinose (Carbon 2 nasa left) o 2nd to the last (penultimate carbon) is o D-Xylose (Carbon 3 nasa left) always “D” (dextro) o D-Lyxose (lahat LEFT SIDE) o Terminal carbon (CH2OH) o Mnemonics: ▪ R,2,3,BOTH - Ketopentoses (5 carbons) ▪ RAXL o D-Ribulose (Carbon 3 RIGHT SIDE) o D-Xylulose (Carbon 3 LEFT SIDE) - Aldohexoses (6 carbons) o D-Allose (sana all RIGHT SIDE) - Ketohexoses (6 carbons) o D-Altrose (Carbon 2 nasa left) o D-Psicose (lahat RIGHT SIDE) o D-Glucose (Carbon 3 nasa left) o D-Fructose (Carbon 3 nasa LEFT SIDE) o D-Mannose (lahat nasa LEFT SIDE) ▪ Sweetest monosaccharide o Mnemonics: o D-Tagatose (lahat nasa LEFT SIDE) ▪ R,2,3,BOTH o D-Sorbose (Carbon 4 nasa LEFT SIDE) o D-Gulose (nangGULO nang pattern) o Mnemonics: o D-Idose (Gulose na pinihit yung Carbon ▪ R,3,4,BOTH 2) o D-Galactose (Gulose na pihitin yung - Ketoheptoses (7 carbons) Carbon 3) o Sedoheptulose o D-Talose (lahat nasa LEFT SIDE) o Mannoheptulose NOTE: D-Glucose and D-Mannose are EPIMERS - Ketononose o Derivative – Sialic Acid o They differ in the 2nd carbon only o Mnemonics: SIAm carbons o Epimers – carbohydrates that differ in the configuration of a single carbon atom Cyclization of Glucose other than the terminal and penultimate - Full name of Glucose is β-D-Glucopyranose carbon NOTE: D-Glucose and D-Galactose are EPIMERS o They differ in the 4th carbon only MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec o α- anomer α- anomer Haworth projection - a method used to show the 3D stereochemistry of cyclic sugars / closed-chain (from google) Fischer projection – a way of depicting compounds in organic chemistry with stereocenter or chiral centers, without explicitly drawing out wedges or dashes / open- chain (from google) - The penultimate carbon reacts with the carbonyl carbon - If the OH is pointing to the right, pag hiniga downwards. - If the OH is pointing to the left, pag hiniga, upwards. - Anomeric carbon – an achiral carbonyl that has - Ribose → RNA (Carbon 2 has oxygen) become chiral after cyclization - Deoxyribose → DNA (Carbon 2 of has no o The only carbon that has 2 oxygen after oxygen) cyclization - Glucose = 3rd carbon OH left side o Reducing agent - Mannose = 2nd carbon OH left side ▪ Ex. Benedict’s and Fehling’s - Galactose = 4th carbon OH left side reagent both have CuSO4 2+ → Cu2O (brick red precipitate) ISOMERS OF SUGAR - D and L - Epimers – wala sa terminal and penultimate yung difference - Anomers – anomeric carbon yung difference - Anomeric carbon is carbon 1 o If the OH is pointing upward, it is called β-anomer (beta anomer) Cyclization of Fructose o If the OH is pointing downward, it is - Full name of Fructose is β-D-Fructofuranose called α- anomer (alpha anomer) MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec - Fructose is a ketose - Anomeric carbon is Carbon 2 - o Product of complete starch digestion = β-D-glucopyranose GLUCOSE o Product of partial starch digestion = MALTOSE (dominant) Fructose (a.k.a. Levulose, Fruit Sugar) - Levulose, because it is strongly levorotatory. - Constituent of table sugar and inulin ▪ Inulin – a polyfructan, used for the evaluation of glomerular filtration rate (GFR). It is called Inulin Filtration Test. Important Points on Monosaccharides ▪ Inulin Filtration Test – most accurate test for kidney function. Glucose (a.k.a. Blood Sugar, Physiological ▪ Creatinine – common marker to Sugar, Dextrose) diagnose kidney problem - Sweetest monosaccharide - Most abundant and important - Can be converted to glucose in the monosaccharide; occurs in the form of liver. β-D-glucose (Mnemonics: aβunDant) - Fructose intolerance leads to - Optical activity is dextrorotatory (+) hypoglycemia - Stored as starch by plants or used to - Glucose intolerance leads to hyperglycemia synthesize cellulose (diabetes mellitus) - Stored as glycogen in the liver and Common types of DN muscles of animals - Precursor for all other carbohydrates o Type 1 DM (Insulin-dependent DM) in the body ▪ Etiology: auto-immune destruction of β-cells of pancreas - Produced from complete hydrolysis of o Type 2 DM (Non-insulin dependent DM) starch and in the hydrolysis of maltose, sucrose and lactose Glyceraldehyde/Glycerose and Dihydroxyacetone - Aldo-keto Isomers - Important intermediates of glycolysis - Precursors for glycerol Ribose - Components of nucleic acids Galactose MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec - Produced from hydrolysis of lactose ▪ Ex. Glucuronic acid - Can also be converted to glucose in - -aric acid - oxidation at carbon 1 and 6 ▪ Ex. Glucaric acid, Galactaric acid the liver and metabolized - Biosynthesized in the mammary Disaccharides glands - Sugars which yield two same or - Failure to metabolize causes different monosaccharide galactosemia and further, cataracts. - Galactose intolerance leads to cataracts. units/residues on hydrolysis. ▪ Too much galactosemia becomes o Homodisaccharide - same monosaccharide galactaric acid, which causes ▪ Ex. Maltose (glucose + glucose) cataracts. o Heterodisaccharide – different monosaccharide Xylose ▪ Ex. Sucrose (glucose + fructose) - Found in wood gums - AKA Wood Sugar - Obtained by boiling corn cobs - Diagnostic aid for malabsorption studies - Treatment of cystitis o Cystitis – inflamed urinary bladder Important Sugar Modifications: - Maltose (a.k.a. Malt Sugar, Beer Sugar) Product of partial starch hydrolysis by amylase - Glycosidic bond of maltose: α-1→ 4 - Cellobiose Product of partial cellulose hydrolysis - Deoxyribose – deoxy sugar - Glycosidic bond of cellobiose: β-1→ 4 - Glycerol – sugar alcohol; produced by - We cannot digest cellulose because we do not addition of hydrogen (reduction) have cellulase in our body - Glucuronate – sugar acids; produced by oxidation NOTE: Maltose and cellobiose has a free anomeric carbon, which makes them reducing sugars. SUGAR ACID SUBTYPES - -onic acid - oxidation at carbon 1 ▪ Ex. Gluconic acid - -uronic acid - oxidation at carbon 6 MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec - Lactase and Sucrase Deficiency both leads to diarrhea and flatulence. Polysaccharides Function: Storage and Structural Types of Units: Homopolysaccharide / Homoglycan (1 unit, ex. Glycogen, Inulin) and Heteropolysaccharide (2 or more units) STRUCTURAL POLYSACCHARIDES Inulin Polyfructan and used in the evaluation of - Sucrose (a.k.a. Table sugar, Beet glomerular filtration Sugar, Saccharum) rate - Most common disaccharide - Also called invert sugar since on Inulin is homoglycan (made from one kind of sugar) hydrolysis, optical activity is inverted. - Glycosidic bond of sucrose: α-1→ 2 Most accurate method for - Sucrose has NO free anomeric carbon, which monitoring kidney function: is why it is NOT a reducing sugar. Inulin filtration ▪ If you don’t see a brick red - Not commonly precipitate in Benedict’s or Fehling’s used because reagent, the correct answer is the process is sucrose because it is not a reducing tedious and sugar and it is not capable of costly. reducing metals. - Commonly used - Trehalose – has NO free anomeric carbon, is creatinine which is why it is NOT a reducing sugar. measurement. Dextrin Polyglucan intermediary products of starch hydrolysis Limiting dextrins: matagal ma-digest ng bituka Homoglycan Dextran Polyglucan synthesized from the - action of - Lactose (a.k.a. Milk Sugar) Alkali nonpathogenic gram- rearrangement produces lactulose positive cocci on (galactose + fructose = lactulose) sucrose ▪ Lactulose – indigestible colloid; bulk-forming laxative A homoglycan, microbial gum, produced from the ▪ Patients with severe liver action of Leuconostoc disease: cannot convert NH3 → mesentoroides. (microbes) urea ▪ Accumulation of NH3 causes IV colloid = plasma hepatic encephalopathy. expander (increases blood DOC: Lactulose volume) - Lactose has a free anomeric carbon, which makes it a reducing sugar. MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec Xanthan – Xanthomonas administration campestris site Agar Sulfated galactose units; from seaweeds An enzyme that breaks hyaluronic acid. Synonym: Japanese Heparin & Heparan N-acetylglucosamine + Isinglass (Japanese ice in glucuronate + glass) iduronate Chitin Principal component of the exoskeleton of Heparin and heparan has 2 arthropods, sugar acids: glucoronate and iduronate crustaceans and some mushrooms Heparin: Made from glucosamine anticoagulant mucopolysaccharide Homoglycan Used as an emergency management for stroke and Peptidoglycan/Murein N-acetylglucosamine + heart attack N-acetylmuramic acid Peptidoglycan is made Heparan: ubiquitous, from NAG-NAMA (N- recruits leucocytes acetylglucosamine+1- Part of the immune acetylmuramic acid) response (WBC) GLYCOSAMINOGLYCANS Heteropolysaccharide 1. Warfarin – PO Hyaluronic Acid N-acetylglucosamine + (dose: mg) glucuronate (prevention or units/glucuronic acid; prophylaxis: tissue barrier outpatient) contributor, joint 2. Heparin – IV (dose: lubricant and shock units) absorbent (administered pag nastroke na) Hyaluronic acid has 1 Chondroitin N-acetylgalactosamine sugar acid: glucuronate + glucuronate units Used for osteoarthritis (inflammation of joints; old For osteoarthritis age related). HYALURONIC ACID AND Heteropolysaccharide CHONDROITIN DIFFERENCE Heteropolysaccharides that - Hyaluronic acid are found inside the human is glucosamine + body are called glucuronic acid glycosaminoglycans - Chondroitin is (GAG’s) galactosamine + glucuronic acid Hyaluronidase / Clinically used to Spreading Factor increase absorption of solutions administered Keratan N-acetylglucosamine + by clysis (IM and ID) galactose - IM = slow release from the Has no sugar acid MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec Corneal development Starch Components: Amylose vs. Dermatan N-acetylgalactosamine Amylopectin + iduronate Amylose Amylopectin Wound repair, 15-20% of the starch 80-85% of starch coagulation regulation molecule LMW, insoluble in HMW, soluble in water, swells up water Starch vs. Glycogen Linear/Non- Branching branching Deep blue with Blue violet with Iodine Iodine Iodine is non-polar Linked by α-1,4 Linked by α-1,4 in the glycosidic bonds main stem and α-1,6 at the branch points Like maltose Digestion of Carbohydrates STORAGE POLYSACCHARIDES Polysaccharides & disaccharides need Starch Glycogen to be hydrolyzed before absorption can Storage form of CHO Storage form of CHO occur. in plants in animals o Should be converted to monosaccharide Glycogen is stored in the liver and muscles Composed of 2 Resembles polymeric glucose amylopectin units (amylose and amylopectin) Amylopectin Branching frequency branching frequency = 8-12/10 -15 = 25 – 30 glucose glucose units units Glycogen has more Explanation sa pic: branch points than - Starch is digested by amylase amylopectin ▪ Digestion of carbohydrates begin Forms deep blue Forms a deep red with the mouth complex of Starch-I2 color with I2 solution ▪ Salivary amylase: Ptyalin with I2 solutions due ▪ Pancreatic amylase: Amylopsin to amylose - Electrolyte needed for carbohydrate Confirmatory / Qualitative / Identification test for absorption: Sodium STARCH and GLYCOGEN - Most rapidly absorbed carbohydrate/monosaccharide: Galactose - Lugol’s (Iodine) test - α-glucosidase inhibitor: inhibits glucose; ▪ Starch forms a complex with iodine used for post-prandial hyperglycemia / to produce a deep blue color, ketoacidosis specifically, amylose reacts with o Members of α-glucosidase inhibitor: iodine to form a deep blue color. Acarbose ▪ Glycogen forms a complex with Glucobay iodine to produce a deep red color. Voglibose MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec Miglotol Contains bismuth ▪ This should be taken at the first bite Positive result: Black of your meal Bi 3+ → Bi ▪ ADR: Diarrhea (due to normal flora) 5. Barfoed’s Test Test for reducing monosaccharides (+) Chemical Tests for Carbohydrates brick red ppt 1. Molisch Test/α- General test for naphthol reaction CHO’s involving the Acidified CuSO4 formation of furfurals or hydroxyfurfurals Test used to differentiate Lactose (+) purple ring at the and Galactose: junction of two liquids Barfoed’s test All carbohydrates will Positive result: Brick red produce a positive result ppt Reagent used: α-naphthol 6. Mucic Acid Test Specific test for galactose (+) sandy Will involve dehydration crystals reaction; Sulfuric acid (H2SO4) is the Mnemonic: Galak na dehydrating acid. galak sa music 2. Anthrone Test Also a general test for carbohydrates (+) Mucic acid is a crytallized form of galactose’s sugar green or blue green acid when oxidized. colored solution (Galactaric acid) without a precipitate 3. Benedict’s Test Test for reducing Acid used: HNO3 sugars (+) brick red (Oxidizing agent) ppt. 7. Fehling’s Test Test for reducing sugars (+) brick red Balikan nalang yung ppt. tinype ko kanina CuSO4 CuSO4 2+ → Cu 1+ Sequestering agent of Positive result: Brick red Fehling’s: Potassium precipitate Sodium Tartrate (Rochelle’s Salt) Sucrose and trehalose doesn’t produce a 8. Seliwanoff’s Specific test for positive result Test/Resorcinol Test ketoses (+) red color Preservative of Fehling’s Mnemonics: Off kay and Benedict’s reagent: aldose, gusto niya ketose Sequestering agent (organic substances that Test used to differentiate temporarily inhibit glucose and fructose: reactivity of metals) Seliwanoff’s test - Sequestering 9. Bial’s Test Specific test for agent of pentoses (+) green Benedict’s: color w/ ppt. Citrate (C6H5O7 +3) Pentoses: 4. Nylander’s Test Test for reducing - Ribose sugars (+) black ppt. - Arabinose  MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec - Xylose 1. Storage fuels (stored in unlimited amounts) - Lyxose 2. Paddings & insulators for internal organs 10. Osazone Means of producing 3. Building materials for active materials Formation/Kowarsky precipitated sugar a. Eicosanoids (from Arachidonic acid → fatty Reaction derivatives esp. acid) mannose i. Prostaglandins – pain and inflammation ii. Leukotrienes - bronchoconstriction iii. Thromboxane – blood clotting 4. Nervous system components 5. Utilization of fat-soluble vitamins a. Vitamins ADEK 6. Membranes and organelles Used for monosaccharides and Lipids disaccharides Biopolymers related by their physical Reagent used: rather than chemical properties Phenylhydrazine HCl Esters of long chain fatty acids and fatty Mannose produces alcohols osazone rapidly Principal stored forms of energy 11. Tauber’s Test/ Also a test for o Triacylglycerol / Triglyceride (most Aminoguanidine ketoses (+) bright common lipid molecule in the human Reaction reddish purple color body) Fats Test for ketose and Esters of saturated fatty acids with fatty pentose alcohols o Solid at room temp except for cod liver Positive result: Bright reddish purple Fixed Oils Esters of unsaturated fatty acids with Ketoses: fatty alcohols - Ribulose o Liquid at room temp except for - Xylulose Theobroma oil 12. Tollen’s Test / Test for aldoses (+) ▪ Theobroma oil / Food for the Gods – used as suppository Silver mirror test silver mirror base Reagent used: Tollen’s Waxes reagent / Howe’s solution Esters of fatty acids with high molecular / Ammoniacal AgNO3 weight monohydric alcohols 13. Maillard’s Reaction of reducing o Has 1 OH (Ex. Cholesterol) Reaction sugars with amino acids (+) brown color Fatty Alcohols 14. Phloroglucinol Also a test for Test pentoses (+) brown ppt. III. Lipids General Functions MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec Phospholipids Basic unit / Building block: Phosphatidic acid Lecithin Most abundant phospholipid of the cell membrane Source of choline, may be converted to acetylcholine. Chemical name: Phosphatidylcholine Cephalin Essential for blood clotting. 1st pic: Glycerin / Glycerol Chemical name: P. ethanolamine 2nd pic: Sphingol 3rd pic: Cholesterol Complex Lipids / Compound Lipid Contain other groups in addition to the alcohol and the fatty acid. Phospholipids Contain fatty acids, glycerol or sphingol/sphingosine, PO4 3- , and nitrogenous compounds, or alcoholic compounds Basic unit: Phosphatidic Acid Major component of cell membranes - Serine is converted to ethanolamine by e.g. glycerophospholipids, sphingolipids removal of carbon dioxide (CO2) / Glycolipids/Glycosphingolipids decarboxylation via the enzyme, Serine Contain fatty acids, sphingol and decarboxylase. carbohydrates - Ethanolamine is converted to choline by N- methylation, via the enzyme, N- Phosphatidic Acid methyltransferase. Glycolipids/Glycosphingolipids Basic unit / Building block: Ceramide (fatty acid + sphingol) 1. Cerebrosides Lipids w/ gluc/galac or both + ceramide Simplest 2. Gangliosides Lipids w/ gluc/galac + ceramide + one or more molecules of neuraminic acid (Sialic acid = 9 carbon) 3. Cytolipins Gluc + galac + ceramide Mnemonic: cy2 (kasi dalawang sugar) 4. Globosides MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec Contain N-acetylglucosamine or Oleic Acid Δ9 18:1 – most abundant Nacetylgalactosamine + ceramide o Found in plants o Omega = 7 Fatty Acids Linoleic Acid Δ9,12 18:2 - dietary precursor for arachidonic acid Building blocks for lipids o Dietary precursor for eicosanoids: Obtained from hydrolysis of fats linoleic acid Biosynthesized from acetyl CoA o Omega = 6 (last location of double bond Saturated fatty acids: – total number of carbon) (18-12 = 6) Regular carboxylic acids Linolenic Acid Δ9,12,15 18:3 o Omega = 3 Even number of C atoms o First member of the omega-3 fatty acids Impart high melting points o Vitamin F o Solid o Omega 3 = Good for the heart Unsaturated fatty acids: Arachidonic Acid Δ5,8,11,14 20:4 - Can be monounsaturated and precursor for eicosanoids polyunsaturated o Omega = 6 Impart low melting points o Also known as: Eicosatetraenoic Acid o Liquid o o COX inhibitors: NSAID’s o NSAID that can lower thromboxane: Aspirin (lowers platelet aggregation) o Blocker of leukotriene: Montelukast and Zafirlukast (leukotriene receptor blockers) Timnodonic Acid Δ5,8,11,14,17 20:5 - Pic: Lauric acid important component of fish oils Omega = end carbon o Omega = 3 o Chemical name: Eicosapentaenoic Acid (EPA) Cervonic Acid Δ4,7,10,13,16,19 22:6 - important component of fish oils Pic: Palmitoleic Acid o Omega = 3 o Chemical name: Docosahexanoic acid Unsaturated Fatty Acids (DHA) Palmitoleic Acid Δ9 16:1 or 16:1;9 or Omega 3 fatty acids have fibrinolytic effect ω7, C16:1 or n-7, 16:1 (blood thinner) o Δ9 = location of double bond o 16 = total number of carbons Fat Alcohols o 1 = number of double bonds o ω = omega 1. Glycerol/Glycerin ▪ To get the omega designation: Simplest trihydric alcohol ID Test: total number of carbons – Acrolein Test (heating with location of double bond (ex. 16- 9 = 7) KHSO4 ) (+) pungent odor 2. Sterols – ALL have a CPPP ring MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec Occurs as unsaponifiable matter Cholelithiasis in lipid samples Synthesized from Acetyl-CoA Other Sterols 1. 7-dehydrocholesterol Present in skin; precursor for vitamin D3 2. Ergosterol Present in fungi; precursor for vitamin D2 3. Stigmasterol/Phytosterol/Sitosterol Present in plants; no nutritional value but appears to decrease blood cholesterol Chemical Tests for Sterols 1. Liebermann- (+) red → blue → Burchard Test (Acetic bluish green colored Acid-Sulfuric Acid solution IV. Amino Acids and Proteins Test) Proteins: Foundations of the Working Cell 2. Salkowski Test (+) bluish red → (Sulfuric Acid Test) cherry red and purple Catalysis (enzymes) color of CHCl3 layer, Chemical storage and transport (plasma green fluorescence in albumin, ion channel pumps) Structure the acid layer (structural proteins) Mechanical work (contractile proteins) Digestion and Absorption of Dietary Lipids Information storage and retrieval (histones) Cholesterol Intercellular communication (hormones Triacylglycerol → Monoacylglycerol + 2 and neurotransmitters) F.A.’s Defense (fibrinogen) Phospholipid → Lysophospholipid + F.A. Particles emulsified by bile acids and Basic Composition of Amino Acids transported into the intestinal cell ▪ Chylomicrons – Dietary TAGs to peripheral tissues ▪ VLDL – TAGs to peripheral tissues ▪ LDL – Cholesterol to peripheral tissues ▪ HDL – Cholesterol from tissues to the liver  MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec The Twenty-Two Major Amino Acids (A) Ala alanine (C) Cys cysteine (D) Asp aspartate Non-polar Amino Acids: Branched Chain (E) Glu glutamate Aliphatic Amino Acids (F) Phe phenylalanine Accumulation leads to Maple Syrup Urine (G) Gly glycine Disease (MSUD), a genetic deficiency of Branched Chain Keto-acid Dehydrogenase (H) His histidine (BCKDH) (I) Ile isoleucine (K) Lys lysine (L) Leu leucine (M) Met methionine (N) Asn asparagine (O) Pyl pyrrolysine Non-polar Amino Acids: Imino Acid (P) Pro proline α-helix breakers Puts kinks in polypeptides (Q) Gln glutamine (R) Arg arginine (S) Ser serine (T) Thr threonine (U) Sec selenocysteine (V) Val valine Aromatic Amino Acids (W) Trp tryptophan All absorb UV light esp. Trp (Y) Tyr tyrosine Phe Hydroxylase deficiency leads to Non-polar Amino Acids: Small Aliphatic Amino phenylketonuria. Acids Tyr is polar & is the precursor for Catecholamines, Thyroid Hormones, Gly is an inhibitory neurotransmitter & is the Melanin & Homogentisate precursor for heme Trp is the precursor for 5-HT, B3 , Found in sharp protein folds Melatonin  MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec Polar Amino Acids: Basic Amino Acids Sulfur-Containing Amino Acids Positively charged at neutral pH Methionine - Non-polar Initiator amino acid Cysteine - Polar Polar Amino Acids: Amide-containing Amino Acids Isosteres of Asp and Glu Amide group can’t ionize New Amino Acids Polar Amino Acids: Alcoholic Amino Acids Polar Amino Acids: Acidic Amino Acids Negatively charged at neutral pH Found in mammalian glutathione Glu is a stimulatory NT peroxidase MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec 4. Millon-Nasse Test Test for phenolic amino acid (+) flesh ppt turning red 5. Hopkins- Test for indole Cole/Glyoxylic Acid containing amino Rxn acid (+) violet ring at the junction of two liquids 6. Sakaguchi Test Test for guanidium containing amino acid (+) red color 7. Sodium Test for amino acid Nitroprusside Test with sulfhydryl group Found in Methanosarcina barkeri’s (+) red to purple color enzyme monomethylamine 8. Basic Lead Test for sulfur methyltransferase AcetateTest containing amino Peptide Bond Formation acids (+) black ppt 9. Pauly Diazo Test Test for His & Tyr (+) blue to red color 10. Schiff’s Test Test for Lys (+) pink violet color Purification of Proteins: Column Chromatography Primary Structure of Proteins Describes the linear sequence of amino acids in a polypeptide chain. Peptide bonds do not dissociate Has double bond characteristics (planar), resonance stabilized and polar Assumes trans configuration (more stable) Chemical Tests for Peptides & Amino Acids 1. Biuret Test Test for peptide bonds (+) violet 2. Ninhydrin/ Test for α-amino Triketohydrindene acids (+) blue/violet Purification of Proteins: Size Exclusion Test except Pro Chromatography 3. Xanthoproteic Test Test for amino acids with benzene ring (+) Separation depends on Stokes radius: yellow to orange due the diameter of the sphere of space they to nitration occupy when in solution or when they tumble. MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec Purification of Proteins: HPLC Other Methods of Protein Purification 1. Partition Chromatography 2. Ion-exchange Chromatography 3. Adsorption Chromatography Purification of Proteins: Sodium Dodecyl 4. Hydrophobic Interaction Chromatography Sulfate-Polyacrylamide Gel Electrophoresis 5. Affinity Chromatography (SDS-PAGE) Protein Structures Determination 1. X-ray crystallography - Most common; proteins can form highly defined crystals when highly purified then precipitated - Advantage: Large proteins can be analyzed - Disadvantage: Difficulty of crystallization 2. NMR - Examines structure of proteins in solution - Advantage: Structures are determined in solution. Separation is based on differences in - Disadvantage: Size of proteins that molecular mass. can be analyzed are limited to smaller SDS-PAGE is the most widely employed proteins. method for determining protein purity Ways of Representing Protein Structures Purification of Proteins: Two Dimensional Electrophoresis MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec Prion: abnormal form of Prion-related Protein (PrP) produced by mutations in genes that code for PrP. Convert normal PrPs to prions Creutzfeldt-Jakob Disease and Bovine Spongiform Encephalopathy Alzheimer’s Disease Secondary Structure of Proteins Refers to the spatial arrangements of amino acid residues located near each other in the linear sequence of the polypeptide chain. Stabilized by extensive H-bonding α-helix, β-sheet, and β-bends Tertiary Structure Overall arrangement & inter relationship of various regions or domains & individual amino acid residues Stabilized by hydrophobic interactions and disulfide bonds Quaternary Structure Arrangement of polypeptide chains in relation to one another in a multi- chained protein Stabilized by H-bonds, hydrophobic interactions, ionic bonds and disulfide Fibrous Proteins bonds. Simpler than globular proteins but water Protein Denaturation insoluble. Structural proteins Unfolding & disorganization of protein Collagen structure without hydrolysis of peptide bonds Most abundant protein in vertebrates Present in skin, cartilage and tendons Alterations of Protein Conformation Basic Unit: Tropocollagen Prion Diseases Vitamin C is for Pro hydroxylation, key step in tropocollagen formation MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec Elastin Responsible for A, B, AB & O blood groups Found in lungs, blood vessel walls & largest Ig ligaments Capable of opsonization Keratin 3. IgA Found in exocrine gland secretions (saliva, tears, sweat) Found in hair, nails and horny tissues 4. IgD Least common of the skin 5. IgE Participates in reactions that distorts mast cells & basophils Globular Proteins More complex in structure but water ABO Blood Groups soluble. Heme proteins Fibrous and Globular proteins are described by tertiary structures Myoglobin Stores oxygen in muscle. (monomeric) Hemoglobin Transports oxygen to tissues and returns CO2 to the lungs.(tetrameric) Biomedical Implications of Hemoglobin and Myoglobin Methemoglobinemia Sickle-cell anemia: caused by mutations that exchange Val for Glu. Not Leu Important Pharmaceutical Points on Thalassemias: absence of one or more Proteins peptide chains in Hgb. Myoglobinuria is indicative of muscle Classification According to Solubility injury, colors the urine dark brown. 1. Albumins Iron deficiency or impaired synthesis of - Soluble in water and salt solutions RBC (due to B9 and B12 Deficiency) 2. Globulins causes anemia. - Sparingly soluble in water but soluble HbA1C indicates the mean blood in salt solutions glucose concentration during the past 3. Histones 6-8 weeks. - Soluble in salt solutions Antibodies 4. Prolamines 1. IgG Major form - Soluble in 70-80% ethanol; insoluble Only Ig that crosses in water and absolute alcohol placenta 2. IgM 1st Ig formed during immunization but later gives way to IgG MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec General Classes of Proteins Nitrogen from the alpha amino group becomes ammonia 1. Simple Proteins - Yields amino acids or their derivatives on hydrolysis 2. Conjugated Proteins - Contain non-protein groups or prosthetic groups 3. Derived Proteins - Formed by action of heat, alkali, Nitrogen Balance: Intake - Output of acids, water, enzymes or mechanical nitrogenous compounds shock on proteins Positive Nitrogen Balance: Intake > Output Hormonal Control of Protein Digestion Marasmus vs. Kwashiorkor 1. Gastrin - Secreted by pancreas on entry of Marasmus: chronic deficiency of dietary proteins calories despite adequate intake of Stimulates: proteins. - Parietal cells → HCl Kwashiorkor: sufficient calorie intake in - Chief cells → Pepsinogen the presence of a negative protein 2. Secretin consumption - Secreted by duodenum V. Nucleic Acids - Stimulates pancreas to secrete H2O & HCO3 – Nucleic Acids 3. Cholecystokinin - Secreted by duodenum Nitrogenous Base: most fundamental - Releases trypsinogen, component chymotrypsinogen, pro-elastase and Nucleoside: base attached to pentose pro-carboxypeptidases from pancreas sugar. Protein Digestion Nucleotide: nucleoside with one or more Endopeptidases phosphates First enzymes to act Nitrogenous Base→Pentose Sugar β-N- a. Pepsin in the gastric juice glycosidic bond b. Trypsin, Chymotrypsin, and Elastase Pentose Sugar →Phosphate secreted into the small intestine by the Phosphoester Bond pancreas Pentose Sugar→Pentose Sugar (in polynucleotides) 3’→5’ Phosphodiester Exopeptidases bonds a. Carboxypeptidases secreted into the Additional phosphates are linked by small intestine by the pancreas phosphoric anhydride bonds. (in b. Aminopeptidases secreted by intestinal mononucleotides) mucosal cells MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec Nitrogenous Bases The information inherited by the daughter cell or offspring. (replicated) Replication occurs in a semi- conservative manner. DNA Gene: DNA segment that contains the info required for biosynthesis of a specific RNA and a specific protein. DNA DNA is usually double stranded May be linear or circular Formed by nucleotides joined together by 3’-5’ phosphodiester linkages forming Nucleic Acids the “backbone”. Polymers of nucleotides Molecular repositories for genetic information. Protein structure and cell constituents are products of info programmed into the nucleotide sequence of a cell’s nucleic acid. Nucleic acids are either: DNA (made up of deoxyribonucleotides) RNA (made up of ribonucleotides) DNA The genetic info stored in the DNA’s Strands are anti-parallel. nucleotide sequence serves as Chargaff’s rule A - T G - C templates for: No. of Purines = No. of Pyrimidines The information for the synthesis of all Template/Anti-sense/Non-coding Strand: proteins in cells and the entire organism. transcribed (transcribed) Coding Strand: opposing complementary strand MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec More G-C interactions: minor groove DNA occur in 6 forms but the DNA within our cells is normally in B configuration B-DNA is the most stable form RNA Second major form of nucleic acid Products of transcription and are single stranded, but can fold back to itself forming a hair-pin like structure having double strand characteristics Its purine content need not necessarily equal its pyrimidine content. G pairs with C; A pairs w/ U. Types: 1. Ribosomal RNA (rRNA)- Most abundant Serve as adaptor molecules for mRNA Other Types of RNA 2. Transfer RNA (tRNA) Carries specific sequences of amino acids to ribosomes 3. Messenger RNA (mRNA) Templates for protein synthesis mRNA Processing Heteregeneous nuclear RNA (hnRNA) comes first before mRNA. 5’ terminal is “capped” by 7- methylguanosine triphosphate. 3’ end is usually attached with “poly A tail” Breakdown of Dietary Nucleic Acids Double helix structure was first proposed by James Watson & Francis Crick Grooves serve as attachment for regulatory proteins. More A-T interactions: major groove  MODULE 2 | BIOCHEMISTRY RWB & RDC ☺ notes in red are from the recorded lec Co-enzymes Provide reactive groups not found in amino acid side chains present in the enzyme. Classes: 1. Co-substrates Freely dissociate from apoenzymes and regenerated by another enzyme. (eg. NAD) 2. Prosthetic Groups Remain bound to its apoenzyme and regenerated during each full catalytic event. (eg. FAD) Pyrimidine bases are catabolized to Thiamine Pyrophosphate form intermediates of central Vitamin Precursor: Thiamine (B1 ) metabolism, purines don’t. Vitamin Deficiency: Beriberi, Wernicke- Degradation of Purines Korsakoff Syndrome Sources include rice polishings and wheat Flavin Adenine Dinucleotide and Flavin Mononucleotide Vitamin Precursor: Riboflavin (B2 ) Vitamin Deficiency: Growth Retardation, Cheilosis, Glossitis, Seborrheic Dermatitis, Photophobia Rich source is yeast, milk and dairy products. Colored intensely yellow. Nicotinamide Adenine Dinucleotide VI. Vitamins, Co-enzymes and Enzymes Vitamin Precursor: Nicotinic Acid/Niacin Vitamins (B3 ) Vitamin Deficiency: Pellagra (3 D’s) Cannot be synthesized by the body Co-substrate for dehydrogenases (except vitamin D3 and B3 )