plant biochemistry lecture 1: general introduction · · 2016-03-30meanings that you do not know...
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Plant BiochemistryLecture 1: General Introduction
http://smtom.lecture.ub.ac.id/Password:
Science without religion is lame,religion without science is blind.--Albert Einstein
Balasubramanian & Ponnuraj, 2010
The conversion of substratesto products throughbiochemical reactions whichcatalyzed by enzymes
Catalase
These are my rules Come on time ( 10’)
with a proper dress Get into the lecture
room, don’t hangaround
Use English in mylecture and exam (75-99%)
These are myphilosophies
• Turn your enemies tobe your friends
• Turn your useless timeto be useful time
• Make big problems tobe small problems
• Simplify the systems orproblems
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STRUCTURED TASK
1. English Presentation Every student has to make English
Presentation2. Dictionary Take your English dictionary every time I give my
lecture3. My Dictionary Buy a writing book (100-pages) and name it MY
DICTIONARY Write down all English words with Indonesian
meanings that you do not know yet
4. Literature Study Every student has to undertake literature
study to obtain more and detail informationas to the lecture materials
5. Study Groups Organize your study group, 5 member each
to discuss the lecture materials6. Paper (NO COVER) Write a paper about Plant Biochemistry or a summary
of a published papers in international Journal(internet)
One (1) page only, (single space) arranged in severalparagraphs (4-5 sentences/ paragraph), font (TimesNew Roman 12)
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EXAMPLE UreaseSiti
Paragraf 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. Kesimpulan
References (3 at least for paper, and 1 for a summary,international)
http://www.dina.dk/efita-conf/program/papers.htm
PAPER TOPICSENZYMES1. Catalase2. Amylase3. Urease4. Sucrase5. Cellulase6. Lipase7. Lactase8. Pectinase9. Phytase10. Pectinase11. Xylanase
12. Maltase13. Papain14. Bromelain15. Trypsin16. Supetoxide
dismutase17. Ascorbate
peroxidase18. Alanine
aminotrasferase19. Nitrite
reductase
20. Nitrate reductase21. Glutamine
synthetase22. Glutamate
synthase23. Glutamate
dehydrogenase24. Glutaminase25. Asparagine
synthase26. Arginine
deiminse27. Ficin
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28. Dextrase29. Pectinase30. Actinidin
COMPOUNDSChemical Structure, Functionand Synthesis31. Cathecin32. Theaflavins33. Capsaicinoids34. Berberine35. Capsidiol36. Hyoscyamine
37. Codeine38. Rishitin39. Jasmonic acid40. Anthraquinones41. Diosgenin42. Rosmarinic acid43. Saponin44. Scopoletin45. Anthocyanin46. Kinobeon47. Methoxymellein48. Salidroside49. Shikonin
LEARNING OUTCOMESStudents, after mastering materials of the presentlecture, should be able
1. to explain plant biochemistry in general
2. to identify the basic molecules which make upplant
3. to describe the way in which chemicalcomponents are synthesized and utilized byplants in the life process
4. to describe the process of pant life on a chemicallevel
5. to initiate ways from the standpoint ofbiochemistry to improve the growth of plants or tosolve problems in plant growth
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LECTURE OUTLINE
SUMMARYLEARNING OUTCOMESSTRUCTURED TASKCOURSE PLANREFERENCES
I. INRODUCTION1. Definition2. Basic Principle
II. BIOMOLECULES1. Carbohydrates2. Lipids
3. Proteins4. Nucleic acids
III. BICHEMISTRYIMPORTANCE1. Biochemistry Use2. The Core of Plant
BiochemistryIV. BREAKTHROUGHS IN
BIOCHEMISTRY1. Enzyme and DNA2. Genetic Engineering
Examples of Biochemistry
COURSE PLANNO. TOPICS Subject1. INTRODUCTION2. ENZYME I Introduction
3. ENZYME II Kinetics
4. ENZYME II Mechanism & Inhibitor
5. CARBOHYDRATE I Introduction
6. CARBOHYDRATE II Classification
7. METABOLIC ENERGY8. MID SMESTER EXAM9. LIPID
10. AMINO ACIDS11. BIOLOGICAL N FIXATION12. NUCLEIC ACID RNA and DNA
13. PROTEIN SYNTHESIS I Genome and gen
14. PROTEIN SYNTHESIS II Transcription and Translation
15. SECONDARY METABOLITES16. END SMESTER EXAM
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REFERENCES1. Berg, J.M., Tymoczko, J.L. and Stryer, L., 2002. Biochemistry.
5th edition: W.H. Freeman and Co,. New York2. Buchanan, B.B., Gruissem, W. and Jones, R.L., 2000.
Biochemistry and Molecular Biology of Plants. AmericanSociety of Plant Biologists
3. Conn, E.E. & Stumpf, P.K., 1976. Outlines of Biochemistry.John Wiley & Sons, New York.
4. Goodwin, T.W. & Mercer, E.I., 1990. Introduction to PlantBiochemistry. Pergamon Press, Oxford.
5. Stryer, L., 1975. Biochemistry. W.H. Freeman and Company,San Francisco
6. Wood, W.B., Wilson, J.H., Benbow, R.M., & Hood, L. E., 1981.Biochemistry A Problems Approach.
I. INTRODUCTION1. Definition
What is Plant Biochemistry ?1. Biochemistry is the study of molecular basis of
life (Stryer, 1975)2. Biochemistry is the study of the way in which
chemical 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).
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2. Basic Principle• Living organisms, whether they are plants, animals
or 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.
• 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 1946
Balasubramanian & Ponnuraj, 2010
Urease
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II. BIOMOLECULESWhat are Types of Molecules studied in Biochemistry? The principal types of biological molecules, or
biomolecules are: carbohydrates lipids proteins nucleic acids
Many of these molecules are complex moleculescalled polymers which are made up of monomersubunits
Biochemical molecules are principally based oncarbon.
monomer
polymer
supramolecularstructure
lipids proteinscarbo nucleic acids
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monomer
polymer
supramolecularstructure
• Cellulose is the majorstructural material of plants.Wood is largely cellulose,and cotton is almost purecellulose.
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, where
their 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.
One Fatty Acid
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monomer
polymer
supramolecularstructure
Description Saturated Fats Unsaturated Fats
Definition:Saturated fats are fats with asingle bond between thecarbon atoms of the fatty acids
Unsaturated fats are fats withone or more double bondsbetween the fatty acids
Health:
Excessive consumption is notgood because of theirassociation withatherosclerosis and heartdiseases.
Unsaturated fats areconsidered good to eat if youare watching your cholesterol
Cholesterol:Saturated fats increase LDL(bad cholesterol) and decreasethe HDL
Unsaturated fats increase HDL(good cholesterol) anddecrease LDL
Form: Solid at room temperature Liquid at room temperature
Derived from: Mostly from animal products Plants
Hydrocarbonchain:
contains only single bondsbetween carbon atoms, nodouble bonds (ex: stearic acis)
contains one or more doublebonds between carbon atoms-monounsaturated -polyunsaturated
Commonlyfound in:
Butter, coconut oil, breast milk,meat
Avocado, soybean oil, canolaoil, olive oil
Life: These are long lasting and donot get spoiled quickly These get spoiled quickly
Recommendedconsumption:
Not more than 10% of totalcalories per day.
Not more than 30% of totalcalories per day
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SaturatedFormula Common Name Melting Point
CH3(CH2)10CO2H lauric acid 45 ºCCH3(CH2)12CO2H myristic acid 55 ºCCH3(CH2)14CO2H palmitic acid 63 ºCCH3(CH2)16CO2H stearic acid 69 ºCCH3(CH2)18CO2H arachidic acid 76 ºC
UnsaturatedFormula Common Name Melting Point
CH3(CH2)5CH=CH(CH2)7CO2H palmitoleic acid 0 ºCCH3(CH2)7CH=CH(CH2)7CO2H oleic acid 13 ºCCH3(CH2)4CH=CHCH2CH=CH
(CH2)7CO2Hlinoleic acid -5 ºC
CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7CO2H
linolenic acid -11 ºC
CH3(CH2)4(CH=CHCH2)4(CH2)2CO2H
arachidonic acid -49 ºC
lipids
Omega-3 and Omega-6 Fatty Acids
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Cis and Trans Bonds
monomer
polymer
supramolecularstructure Enzyme complex
protein subunit
amino acid
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monomer
polymer
supramolecularstructure
III. THE IMPORTANCE OFBIOCHEMISTRY
1. Biochemistry UseWhat Is Biochemistry Used For?1. Biochemistry is used to learn about the biological
processes which take place in cells and organisms.2. Biochemistry may be used to study the properties
of biological molecules, for a variety of purposes.- For example, a biochemist may study the characteristics
of the keratin in hair so that a shampoo may be developedthat enhances curliness or softness.
3. Biochemists find uses for biomolecules.- For example, a biochemist may use a certain lipid as a
food additive.
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4. 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 isolation
and identification of all different substances whichmake up plant and animal organisms- A living organism is composed of more than just
fasts, carbohydrates and protein. Hundreds ofother substances are necessary to the properfunctioning of the organisms
2. Chemical Changes Secondly, biochemistry is concerned with all chemical
changes which take place in the cells to provide forenergy, growth, reproduction, and aging.- Protoplasm is an aqueous solution of certain
substances with other colloidally dispersedsubstances
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http://manet.illinois.edu/pathways.php
Chemical Changes:Metabolism
(146 pathways)1. Carbohydrate Metabolism (17)2. Energy Metabolism (8)3. Lipid Metabolism (14)4. Nucleotide Metabolism (2)5. Amino Acid Metabolism (16)6. Metabolism of Other Amino
Acids (9)7. Glycan Biosynthesis and Metabolism
(18)8. Biosynthesis of Polyketides and
Nonribosomal Peptides (9)9. Metabolism of Cofactors and Vitamins
(11)10. Biosynthesis of Secondary
Metabolites (21)11. Biodegradation of Xenobiotics (21)
1
102
3
8
6
9
7
4
5
11
PLAN
T BIOC
HEMI
STRY
Assume 10 reactions/pathway (glycolysis has 11reactions), then 146 x 10 = 1460 reactions/cell
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IV. BREAKTHROUGHS INBIOCHEMISTRY
1. Enzyme and DNA Two notable breakthroughs in the history of
biochemistry1. Discovery of the role of enzymes as catalysts2. Identification of nucleic acids as information
molecules Flow of information: from nucleic acids to
proteins
At 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 pairs
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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.
2. Genetic Engineering and Cloning
Cloning of African violets:1. Take a leaf from a plant2. Immerse the stalk in
water- Roots start to form
after a week3. Pot the plant- A new plant is
produced
The new plant isgenetically identicalto the parental plant
The color of theflowers are thesame
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Sel telur dengan inti dari induk yang berkembangmenjadi anak domba yang sama dengan induknya
How Dolly was cloned?
How Dolly was cloned?
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EXAMPLES OF PLANTBIOCHEMISTRY
1. Gugur Daun Perusakan dinding sel
pada lapisan absisioleh aktivitas enzimCellulase danPolygalacturonase
Sintesis kedua enzimtersebut terhambatjika kadar hormontumbuh auxin cukuptinggi
• Transpor auxin dari tempat ujung daun (tempatsintesis) ke lapisan absisi dihambat ethylene
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2. 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 the
poppy Papaver somniferum, Afghanistan spring 066100 tons alone.
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Morphine goes to receptors (opiate receptors) whichcontrol passage of Ca2+ and K + through channels, which inturn control acetylcholine (nerve transmitter) flow across
synapses.
DEPRESSES RESPIRATORY SYSTEM - usual overdoseeffect; some euphoria - plus is addictive
Komunikasi 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.
Cytochrome A3 catalyzes O2 H2OBlocks ability of mitochondria to use O2O2 saturation may be normal
Poisoning can occur throughpercutaneous absorption and inhalation.
Degree of symptoms depends onseverity of exposure.
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AntidoteSpecific antidotes available
1. 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 rhodanese
d. 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).
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e. 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 esters
produced usually from triglyceride esters
Biodiesel Samples
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Chemistry of Triglycerides Biodiesel is made from the combination of a triglyceride
with a monohydroxy alcohol (i.e. methanol, ethanol…). What is a triglyceride? Made from a combination of
glycerol and three fatty acids:
Transesterification
R1, 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.)
While actually a multi-step process, the overallreaction looks like this:
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Individual 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.
f. Penyakit encok (gout) yang mengakibatkanradang pada persendian adalah akibat akumulasi
asam urat
Radang sendi dipicuoleh presipitasi kristalurat natrium (sodiumurate crystals)
Penyakit Ginjal dapatjuga terjadi karenadeposisi kristal uratdalam organ tersebu
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ADENIUM OBESUM ' CHERRY'Grafted Desert RoseFamily : ApocynaceaeOrigin : East AfricaSize : 5'Light Requirements : Full Sun/LightShadeWater Requirements : Keep DryMin. Temp. : 35°Flower : Year Round
c. PIGMENT
Pigment Class Compound Type Colors
Porphyrin chlorophyll green
Carotenoid carotene andlycopenexanthophyll
yellow, orange, redyellow
Flavonoid flavoneflavonolanthocyanin
yellowyellow
red, blue, purple,magenta