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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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a. a-Amylase

b. Cellulose

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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

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https://d194ekacf8mn8t.cloudfront.net/content/femsre/27/2-3/239/F2.large.jpg

Model of urease activation. Synthesis of active urease requires theformation of a complex between the (UreABC)3 urease apoprotein andUreDFG.