Plant Biochemistry Lecture 1: General Introduction
ant BiochemistryLecture 1: General IntroductionCatalaseThe conversion of substratesto products throughbiochemical reactions whichcatalyzed by enzymesScience without religion is lame,religion without science is blind.--Albert EinsteinBalasubramanian & Ponnuraj, 2010These are my rules Come on time ( 10’)with a proper dress Get into the lectureroom, don’t hangaround Use English in mylecture and exam (7599%) These are myphilosophiesTurn your enemies tobe your friendsTurn your useless timeto be useful timeMake big problems tobe small problemsSimplify the systems orproblems1
2/12/2016STRUCTURED TASK1. English Presentation Every student hasPresentationto make English2. Dictionary Take your English dictionary every time I give mylecture3. My Dictionary Buy a writing book (100-pages) and name it MYDICTIONARYWrite down all English words with Indonesianmeanings that you do not know yet4. Literature Study Every student has to undertake literaturestudy to obtain more and detail informationas to the lecture materials5. Study GroupsOrganize your study group, 5 member eachto discuss the lecture materials6. Paper (NO COVER) Write a paper about Plant Biochemistry or a summaryof a published papers in international Journal(internet) One (1) page only, (single space) arranged in severalparagraphs (4-5 sentences/ paragraph), font (TimesNew Roman 12)2
2/12/2016EXAMPLEUreaseSitiParagraf 1. Uraikan informasi umum mengenai Urease(kapan ditemukan & siapa penemunya, dimana terdapatumumnya, dll)Paragraf 2-3. Uraikan fungsi catalase khususnya padatanaman termasuk reaksi yang dikatalisis dan pengaruh faktorlingkungan (mis. pH, temperatur, dll.)Paragraf 4-5. Uraikan perkembangan hasil penelitiantentang urease paling terakhir termasuk gambar kristalmya)Paragraf 5. KesimpulanReferences (3 at least for paper, and 1 for a f/program/papers.htmPAPER TOPICSENZYMES1. Catalase2. Amylase3. Urease4. Sucrase5. Cellulase6. Lipase7. Lactase8. Pectinase9. Phytase10. Pectinase11. 4.25.26.27.Nitrate ninedeiminseFicin3
39.40.COMPOUNDSChemical Structure, Functionand Synthesis31. Cathecin32. Theaflavins33. Capsaicinoids34. Berberine35. Capsidiol36. tinJasmonic acidAnthraquinonesDiosgeninRosmarinic leinSalidrosideShikoninLEARNING OUTCOMESStudents, after mastering materials of the presentlecture, should be able1. to explain plant biochemistry in general2. to identify the basic molecules which make upplant3. to describe the way in which chemicalcomponents are synthesized and utilized byplants in the life process4. to describe the process of pant life on a chemicallevel5. to initiate ways from the standpoint ofbiochemistry to improve the growth of plants or tosolve problems in plant growth4
2/12/2016LECTURE OUTLINESUMMARYLEARNING OUTCOMESSTRUCTURED TASKCOURSE PLANREFERENCESI. INRODUCTION1. Definition2. Basic PrincipleII. BIOMOLECULES1. Carbohydrates2. Lipids3. Proteins4. Nucleic acidsIII. BICHEMISTRYIMPORTANCE1. Biochemistry Use2. The Core of PlantBiochemistryIV. BREAKTHROUGHS INBIOCHEMISTRY1. Enzyme and DNA2. Genetic EngineeringExamples of BiochemistryCOURSE CSINTRODUCTIONENZYME IENZYME IIENZYME IICARBOHYDRATE ICARBOHYDRATE IIMETABOLIC ENERGYMID SMESTER EXAMLIPIDAMINO ACIDSBIOLOGICAL N FIXATIONNUCLEIC ACIDPROTEIN SYNTHESIS IPROTEIN SYNTHESIS IISECONDARY METABOLITESEND SMESTER EXAMSubjectIntroductionKineticsMechanism & InhibitorIntroductionClassificationRNA and DNAGenome and genTranscription and Translation5
2/12/2016REFERENCESBerg, J.M., Tymoczko, J.L. and Stryer, L., 2002. Biochemistry.5th edition: W.H. Freeman and Co,. New YorkBuchanan, B.B., Gruissem, W. and Jones, R.L., 2000.Biochemistry and Molecular Biology of Plants. AmericanSociety of Plant BiologistsConn, E.E. & Stumpf, P.K., 1976. Outlines of Biochemistry.John Wiley & Sons, New York.Goodwin, T.W. & Mercer, E.I., 1990. Introduction to PlantBiochemistry. Pergamon Press, Oxford.Stryer, L., 1975. Biochemistry. W.H. Freeman and Company,San FranciscoWood, W.B., Wilson, J.H., Benbow, R.M., & Hood, L. E., 1981.Biochemistry A Problems Approach.1.2.3.4.5.6.I. INTRODUCTION1. DefinitionWhat is Plant Biochemistry ?1.2.Biochemistry is the study of molecular basis oflife (Stryer, 1975)Biochemistry is the study of the way in whichchemical components are synthesized andutilized by the organism in the life process(Goodwin & Mercer, 1990).Plant Biochemistry is the study of molecular basis ofplant life that includes the synthesis and utilizationof compounds in the life process of plants (growth &development).6
2/12/20162. Basic Principle Living organisms, whether they are plants, animalsor microbes, are made up basically of the samechemical components The formation of compounds (biomolecules)required in the living process of plants, from thechemical components, occurs through biochemicalreactions catalyzed in most cases by enzymesunder genetic control and environmental influence. Enzymes, therefore, are crucial in the biochemical processof plant life. For example, the break down of urea to beammonium occurs through a hydrolysis reaction catalyzedby enzyme urease.H2NUreaseC O 3 H2O Urease 2NH4 OH- HCO3H2N Urease from jack beans (Canavaliaensiformis) was the first enzyme everpurified and crystallised, anachievement of James B. Sumner in1926 who earned a Nobel Prize inChemistry in 1946Balasubramanian & Ponnuraj, 20107
2/12/2016II. BIOMOLECULESWhat are Types of Molecules studied in Biochemistry? The principal types of biological molecules, orbiomolecules are: carbohydrateslipidsproteinsnucleic acidsMany of these molecules are complex moleculescalled polymers which are made up of monomersubunitsBiochemical molecules are principally based oncarbon.carbolipidsproteinsnucleic acidsmonomerglucosefatty acidamino acidnucleotidepolymercellulosephospholipidprotein subunitDNAsupramolecularstructurecell wallmembraneprotein complexchromosome8
2/12/2016monomer glucosepolymer cellulosesupramolecularstructure cell wall Cellulose is the majorstructural material of plants.Wood is largely cellulose,and cotton is almost purecellulose.One Fatty Acid The “head” of the molecule is a carboxyl groupwhich is hydrophilic.The “tail” of a fatty acid is a long hydrocarbonchain, making it hydrophobic. Fatty acids are the main component of soap, wheretheir tails are soluble in oily dirt and their heads aresoluble in water to emulsify and wash away the oilydirt. However, when the head end is attached toglycerol to form a fat, that whole molecule ishydrophobic.9
2/12/2016fatty acidmonomerpolymer tionDefinition:Health:Cholesterol:Form:Derived from:Saturated FatsUnsaturated FatsSaturated fats are fats with asingle bond between thecarbon atoms of the fatty acidsExcessive consumption is notgood because of theirassociation withatherosclerosis and heartdiseases.Saturated fats increase LDL(bad cholesterol) and decreasethe HDLSolid at room temperatureUnsaturated fats are fats withone or more double bondsbetween the fatty acidsMostly from animal productsPlantscontains one or more doublebonds between carbon atoms-monounsaturated polyunsaturatedUnsaturated fats areconsidered good to eat if youare watching your cholesterolUnsaturated fats increase HDL(good cholesterol) anddecrease LDLLiquid at room temperatureHydrocarbonchain:contains only single bondsbetween carbon atoms, nodouble bonds (ex: stearic acis)Commonlyfound in:Butter, coconut oil, breast milk, Avocado, soybean oil, canolameatoil, olive oilLife:Recommendedconsumption:These are long lasting and donot get spoiled quicklyThese get spoiled quicklyNot more than 10% of totalcalories per day.Not more than 30% of totalcalories per day10
2/12/2016lipidsSaturatedFormulaCommon NameMelting PointCH3(CH2)10CO2Hlauric acid45 ºCCH3(CH2)12CO2Hmyristic acid55 ºCCH3(CH2)14CO2Hpalmitic acid63 ºCCH3(CH2)16CO2Hstearic acid69 ºCCH3(CH2)18CO2Harachidic acid76 ºCMelting PointUnsaturatedFormulaCommon NameCH3(CH2)5CH CH(CH2)7CO2Hpalmitoleic acid0 ºCCH3(CH2)7CH CH(CH2)7CO2Holeic acid13 ºCCH3(CH2)4CH CHCH2CH CH(CH2)7CO2Hlinoleic acid-5 ºCCH3CH2CH CHCH2CH CHCH2CH CH(CH2)7CO2Hlinolenic acid-11 ºCCH3(CH2)4(CH CHCH2)4(CH2)2CO2Harachidonic acid-49 ºCOmega-3 and Omega-6 Fatty Acids11
2/12/2016Cis and Trans Bondsmonomeramino acidpolymer protein subunitsupramolecularstructure Enzyme complex12
eotideDNAchromatinIII. THE IMPORTANCE OFBIOCHEMISTRY1. Biochemistry UseWhat Is Biochemistry Used For?1. Biochemistry is used to learn about the biologicalprocesses which take place in cells and organisms.2. Biochemistry may be used to study the propertiesof biological molecules, for a variety of purposes.-3.For example, a biochemist may study the characteristicsof the keratin in hair so that a shampoo may be developedthat enhances curliness or softness.Biochemists find uses for biomolecules.-For example, a biochemist may use a certain lipid as afood additive.13
2/12/20164.Alternatively, a biochemist might find a substitutefor a usual biomolecule. For example, biochemistshelp to develop artificial sweeteners.5.Biochemists can help cells to produce newproducts. Gene therapy is within the realm ofbiochemistry. The development of biologicalmachinery falls within the realm of biochemistry.2. Molecular CharacterizationThe core of biochemistry is the characterization oforganismal life at molecular level including theconversion mechanism of substrates to productsthrough biochemical reactions catalyzed byenzymes under genetic control and environmentalinfluence.1. Isolation and Identification Biochemistry is firstly concerned with the isolationand identification of all different substances whichmake up plant and animal organisms- A living organism is composed of more than justfasts, carbohydrates and protein. Hundreds ofother substances are necessary to the properfunctioning of the organisms2. Chemical Changes Secondly, biochemistry is concerned with all chemicalchanges which take place in the cells to provide forenergy, growth, reproduction, and aging.- Protoplasm is an aqueous solution of certainsubstances with other colloidally dispersedsubstances14
2/12/2016Chemical Changes:Metabolism(146 pathways)117481. Carbohydrate Metabolism (17)2. Energy Metabolism (8)3. Lipid Metabolism (14)4. Nucleotide Metabolism (2)5. Amino Acid Metabolism (16)6. Metabolism of Other AminoAcids (9)7. Glycan Biosynthesis and Metabolism(18)8. Biosynthesis of Polyketides andNonribosomal Peptides (9)9. Metabolism of Cofactors and Vitamins(11)10. Biosynthesis of SecondaryMetabolites (21)1635911. Biodegradation of Xenobiotics (21)210http://manet.illinois.edu/pathways.phpPLANT BIOCHEMISTRYAssume 10 reactions/pathway (glycolysis has 11reactions), then 146 x 10 1460 reactions/cell15
2/12/2016IV. BREAKTHROUGHS INBIOCHEMISTRY1. Enzyme and DNA Two notable breakthroughs in the history ofbiochemistry1.2. Discovery of the role of enzymes as catalystsIdentification of nucleic acids as informationmoleculesFlow of information: from nucleic acids toproteinsAt lunch Francis [Crick] winged into the Eagle to tell everyone withinhearing distance that we had found the secret of life. — James Watson Two polynucleotidesassociate to form adouble helix Genetic information iscarried by the sequenceof base pairs16
2/12/20162. Genetic Engineering and Cloning Advances in the study of genetics (DNA) have led tothe development of genetic engineering and cloning Genetic engineering is the manipulation of genes tocreate purposefully versions of organisms Cloning is to make a genetically identical organismthrough non-sexual means. Cloning of African violets:1. Take a leaf from a plant2. Immerse the stalk inwater- Roots start to formafter a week3. Pot the plant- A new plant isproducedThe new plant isgenetically identicalto the parental plantThe color of theflowers are thesame17
2/12/2016How Dolly was cloned?Egg cellParent cellSel telur dengan inti dari induk yang berkembangmenjadi anak domba yang sama dengan induknyaHow Dolly was cloned?18
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2/12/2016EXAMPLES OF PLANTBIOCHEMISTRY1. Gugur Daun Perusakan dinding selpada lapisan absisioleh aktivitas enzimCellulase danPolygalacturonaseSintesis kedua enzimtersebut terhambatjika kadar hormontumbuh auxin cukuptinggiAuxinEthyleneLapisan absisiCellulase/Polygalacturonase Transpor auxin dari tempat ujung daun (tempatsintesis) ke lapisan absisi dihambat ethylene20
2/12/20162. The Narcotic Analgesics Narcotics block the transmission of thenerve signal across nerve gaps, [the minoranalgesics blocked prostaglandinsynthesis]The more important ones: Morphine, codeine, oxycodone (PERCODAN), hydromorphone (DILAUDID),methadone, heroin [ not legal] meperidine (DEMEROL), pentazocine (TALWIN), fentanyl (SUBLIMAZE), buprenorphine (BUPRENEX) Morphine: Opium [est. 10,000 tons] extracted from thepoppy Papaver somniferum, Afghanistan spring 066100 tons alone.21
2/12/2016Morphine goes to receptors (opiate receptors) whichcontrol passage of Ca2 and K through channels, which inturn control acetylcholine (nerve transmitter) flow acrosssynapses.DEPRESSES RESPIRATORY SYSTEM - usual overdoseeffect; some euphoria - plus is addictiveKomunikasi saraf (neuron & nerve cells) antara satu dengan yanglain, atau dengan yang lain (kelenjar, otot & organ tubuh lain) terjadimelalui pelepasan zat, “neurotransmitters”, pada reseptor dari neuronatau organ bersangkutan. Suatu zat yang secara mengyakinkanberfungsi sebagai neurotransmitter adalah Acetylcholine.c. Cyanide Poisoning Disrupts metabolism by inhibiting metalcontaining enzymes, most notably,cytochrome oxidase.A3 catalyzes O2 H2Oability of mitochondria to use O2 O2 saturation may be normal Cytochrome Blocks Poisoning can occur throughpercutaneous absorption and inhalation.Degree of symptoms depends onseverity of exposure.22
2/12/2016AntidoteSpecific antidotes available1. Sodium nitrite reacts with hemoglobin to formmethemoglobin that removes cyanide ions from varioustissues to form cyanmethemoglobin (relatively low toxicity).2. The function of Sodium thiosulfate is to convert cyanide tothiocyanate, by an hepatic enzyme known as rhodanesed. Methanol Poisoning Methanol itself has a relatively low degree of toxicity,but it is metabolized to formic acid which is responsiblefor the acidosis and blindness that characterizesmethanol poisoning.The initial step in the metabolism of methanol occurs bythe action of alcohol dehydrogenase (ADH).23
2/12/2016e. What is Biodiesel? Alternative fuel for diesel engines Made from vegetable oil or animal fat Meets health effect testing (CAA) Lower emissions, High flash point ( 300F), Safer Biodegradable, Essentially non-toxic. Chemically, biodiesel molecules are mono-alkyl estersproduced usually from triglyceride estersBiodiesel Samples24
2/12/2016Chemistry of Triglycerides Biodiesel is made from the combination of a triglyceridewith a monohydroxy alcohol (i.e. methanol, ethanol ).What is a triglyceride? Made from a combination ofglycerol and three fatty acids:TransesterificationWhile actually a multi-step process, the overallreaction looks like this:CH2OOR1CHOOR2 3CH3OHCH2OH3CH3OORx CHOHCH2OOR3Triglyceride MethanolCH2OHBiodieselGlycerinR1, R2, and R3 are fatty acid alkyl groups (could bedifferent, or the same), and depend on the type of oil.The fatty acids involved determine the final properties ofthe biodiesel (cetane number, cold flow properties, etc.)25
2/12/2016Individual step of TransesterificationFirst step, triglyceride turned into diglyceride, methoxide (minus Na) joinsfreed FA to make biodiesel, Na joins OH from water (from methoxideformation) to make NaOH. Other H joins the diglyceride.H OHCOR1HHHCOOR2 HCONa H2OHCOR3HH OTriglyceride MethoxideHCOH OCHOOR2 HCOR1 NaOHHCOR3H ODiglycerideHBiodieself. Penyakit encok (gout) yang mengakibatkanradang pada persendian adalah akibat akumulasiasam urat Radang sendi dipicuoleh presipitasi kristalurat natrium (sodiumurate crystals)Penyakit Ginjal dapatjuga terjadi karenadeposisi kristal uratdalam organ tersebu26
2/12/2016a. a-Amylaseb. Cellulose27
2/12/2016c. PIGMENTADENIUM OBESUM ' CHERRY'Grafted Desert RoseFamily : ApocynaceaeOrigin : East AfricaSize : 5'Light Requirements : Full Sun/LightShadeWater Requirements : Keep DryMin. Temp. : 35 Flower : Year RoundPigment ClassCompound ene andlycopenexanthophyllyellow, orange, yellowred, blue, purple,magenta28
2/12/2016Model of urease activation. Synthesis of active urease requires theformation of a complex between the (UreABC) 3 urease apoprotein ntent/femsre/27/2-3/239/F2.large.jpg29
2/12/2016 2 STRUCTURED TASK 1. English Presentation Every student has to make English Presentation 2. Dictionary Take your English dictionary every time I give my lecture 3. My Dictionary Buy a writing book (100-pages) and name it MY DICTIONARY Write down all Englis
Introduction of Chemical Reaction Engineering Introduction about Chemical Engineering 0:31:15 0:31:09. Lecture 14 Lecture 15 Lecture 16 Lecture 17 Lecture 18 Lecture 19 Lecture 20 Lecture 21 Lecture 22 Lecture 23 Lecture 24 Lecture 25 Lecture 26 Lecture 27 Lecture 28 Lecture
4. Plant Biochemistry 5. Clinical Biochemistry 6. Biomembranes & Cell Signaling 7. Bioenergetics 8. Research Planning & Report Writing (Eng-IV) 9. Nutritional Biochemistry 10. Bioinformatics 11. Industrial Biochemistry 12. Biotechnology 13. Immunology 14. Current Trends in Biochemistry
1. Fundamentals of Biochemistry by J.L. Jain 2. Biotechnology by B.D., Singh 3. Principles of Biochemistry by Lehninger, Nelson & Cox 4. Outlines of Biochemistry by Conn & Stumpf 5. Textbook of biochemistry by A VSS, Ramarao 6. An Introduction to Practical Biochemistry by D.T. Plummer 7. Laboratory Manual in Biochemistry by Jairaman
Lecture 1: A Beginner's Guide Lecture 2: Introduction to Programming Lecture 3: Introduction to C, structure of C programming Lecture 4: Elements of C Lecture 5: Variables, Statements, Expressions Lecture 6: Input-Output in C Lecture 7: Formatted Input-Output Lecture 8: Operators Lecture 9: Operators continued
Advancement to Candidacy Application pdf insert Biochemistry Year 3 10 Annual Ph.D. Thesis Committee Meeting Form (Years 3 – 5) 12 Biochemistry Year 4 14 Biochemistry Year 5 16 Biochemistry Year 6 18
Analytical Biochemistry (Textbook) Analytical Biochemistry, 2nd edition, by D.J. Holme and H. Peck, Longman, 1993 Available on Reserve. Physical Biochemistry (Textbook) Physical Biochemistry (2nd edition, 1982) D. Freifelder (QH 345.F72). This is a particularly good reference text for spectroscopy, centrifugation, electrophoresis, and other .
Department of Biochemistry - Website information 1. Department: Biochemistry 2. About Department The Department of Biochemistry was instituted as one of the departments of Sciences in the academic year 1998-1999. 3. Objective & Scope To enable the students to understand the concept of biochemistry regarding biomolecules
Department of Biochemistry Introduction: The dynamic department of Biochemistry is spear headed by our worthy principal Lt Gen Abdul Khaliq Naveed (HI) who is a pioneer in the field of medical biochemistry, chemical pathology and medical genetics. He is presiding over the national Society of Medical Biochemistry (SOMB).
