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GENERAL INTRODUCTIONGENERAL INTRODUCTION

LECTURE 1 :LECTURE 1 :

http://lecture.ub.ac.id/smtomsm09tom1

These are my rulesThese are my rules Come on time (Come on time (

10’) with a proper 10’) with a proper dressdress

Get into the lecture Get into the lecture room, don’t hang room, don’t hang aroundaround

Use English in my Use English in my lecture and exam lecture and exam (75(75--99%)99%)

These are my philosophies

• Turn your enemies to be your friends

• Turn your useless time to be useful time

• Make big problems to be small problems

• Simplify the systems or problems

WWelcomeelcome to the course to the course of of Plant BiochemistryPlant Biochemistry

Objectives and CompetencyObjectives and CompetencyStudents on completion of this course Students on completion of this course would be ablewould be able

1.1. to identify the basic molecules which make to identify the basic molecules which make up plantup plant

2.2. to describe the way in which chemical to describe the way in which chemical components are synthesized and utilized components are synthesized and utilized by plants in the life processby plants in the life process

3.3. to describe the process of pant life on a to describe the process of pant life on a chemical level chemical level

4.4. to initiate ways from the standpoint of to initiate ways from the standpoint of biochemistry to improve the growth of biochemistry to improve the growth of plants or to solve problems in plant plants or to solve problems in plant growthgrowth

LECTURE FLOWLECTURE FLOW1.1. Introduction Introduction ((PendahuluanPendahuluan))2.2. DefinitionDefinition ((DefinisiDefinisi))

What is Plant Biochemistry ?What is Plant Biochemistry ? PrinsipPrinsip DasarDasar ((Basic PrincipleBasic Principle)) What are Types of Molecules studied in Biochemistry? What are Types of Molecules studied in Biochemistry?

((JenisJenis molekulmolekul)) What Is Biochemistry Used For? (What Is Biochemistry Used For? (KegunaanKegunaan BiokimiaBiokimia) ) The Core of Plant Biochemistry The Core of Plant Biochemistry ((IntiInti daridari BiokimiaBiokimia)) Breakthroughs In Biochemistry Breakthroughs In Biochemistry ((TerobosanTerobosan dalamdalam

BiokimiaBiokimia))3.3. Course Plan (Course Plan (RencanaRencana KuliahKuliah))

References (References (ReferensiReferensi))3.3. Examples of Biochemistry Examples of Biochemistry ((ContohContoh BiokimiaBiokimia))

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1. INTRODUCTION1. INTRODUCTIONHOW TO STUDYHOW TO STUDY1.1. ENGLISH PRESENTATIONENGLISH PRESENTATION2.2. STUDY MODEL: PCL (STUDY MODEL: PCL (PropagationPropagation--

Centered LearningCentered Learning) or SPARS () or SPARS (SelfSelf--Propagating and Regenerating SystemsPropagating and Regenerating Systems))i.i. Form Student Discussion Group (SDG) each of 5 Form Student Discussion Group (SDG) each of 5

membersmembersii.ii. Follow the procedure of PCL or SPARS Follow the procedure of PCL or SPARS

(http://lecture.ub.ac.id/smtom)(http://lecture.ub.ac.id/smtom)IM = INDIVIDU MAHASISWAD = DOSENKDM = KELOMPOK DISKUSI MAHASISWA

TRADISONAL (TCL)

PCL

IM DKDM

IM D

IM

IM

IM

IM

IM

PovertyPoverty UnemploymentUnemployment Environmental DegradationEnvironmental Degradation Catastrophes (Flood & Drought)Catastrophes (Flood & Drought) Diseases (Swine Flu: H1N1)Diseases (Swine Flu: H1N1) Food Shortage/Starvation Food Shortage/Starvation

(Kwashiorkor) (Kwashiorkor)

Do you want to solve problems of life ?, at what level ?

HOW TO SOLVE THE PROBLEMS ?HOW TO SOLVE THE PROBLEMS ? It is important first to understand living It is important first to understand living

systems (how the system works) systems (how the system works) the chemical elements the chemical elements which make up plant which make up plant

bodybody the function of each element in the life the function of each element in the life

processprocess the interaction between elements in the life the interaction between elements in the life

processprocess A better understanding of living systems A better understanding of living systems

would help to identify a problem in the life would help to identify a problem in the life process, and to initiate a way to solve the process, and to initiate a way to solve the problemproblem

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2. DEFINITION2. DEFINITIONa. What is Plant Biochemistry ?a. What is Plant Biochemistry ?Biochemistry, Plant Biochemistry (the Biochemistry, Plant Biochemistry (the chemistry of living plants) ischemistry of living plants) is1.1. the study of the chemistry of living things the study of the chemistry of living things

(types, structures & reactions)(types, structures & reactions)2.2. the study of the process of plant life on a the study of the process of plant life on a

chemical levelchemical level3.3. the study of molecular basis of plant lifethe study of molecular basis of plant life or or 4.4. the study of the way in which chemical the study of the way in which chemical

components are synthesized and utilized by components are synthesized and utilized by plants in the life processplants in the life process (growth & (growth & development).development).

b. Basic PrincipleLiving organisms, whether they are plants, animals or microbes, are made up basically of the same chemical components

Biochemical Reactions

c. What are Types of Molecules studied in c. What are Types of Molecules studied in Biochemistry?Biochemistry?

The principal types of biological molecules, or The principal types of biological molecules, or biomoleculesbiomolecules are: are: carbohydrates carbohydrates lipids lipids proteins proteins nucleic acids nucleic acids

Many of these molecules are complex molecules Many of these molecules are complex molecules called polymers which are made up of monomer called polymers which are made up of monomer subunitssubunits

Biochemical molecules are Biochemical molecules are pricinpallypricinpally based on based on carbon.carbon.

Cellulose

• Cellulose is a polymer of β-D-Glucose, which in contrast to starch, is oriented with -CH2OHgroups alternating above and below the plane of the cellulose molecule thus producing long, unbranched chains.

• The absence of side chains allows cellulose molecules to lie close together and form rigid structures.

• Cellulose is the major structural material of plants. Wood is largely cellulose, and cotton is almost pure cellulose.

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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

Description Saturated Fats Unsaturated Fats

Definition:Saturated fats are fats with a single bond between the carbon atoms of the fatty acids

Unsaturated fats are fats with one or more double bonds between the fatty acids

Health:

Excessive consumption is not good because of their association with atherosclerosis and heart diseases.

Unsaturated fats are considered good to eat if you are watching your cholesterol

Cholesterol:Saturated fats increase LDL (bad cholesterol) and decrease the HDL

Unsaturated fats increase HDL (good cholesterol) and decrease LDL

Form: Solid at room temperature Liquid at room temperatureDerived from: Mostly from animal products Plants

Hydrocarbon chain:

contains only single bonds between carbon atoms, no double bonds (ex: stearic acis)

contains one or more double bonds between carbon atoms -monounsaturated -polyunsaturated

Commonly found in:

Butter, coconut oil, breast milk, meat

Avocado, soybean oil, canola oil, olive oil

Life: These are long lasting and do not get spoiled quickly These get spoiled quickly

Recommended consumption:

Not more than 10% of total calories per day.

Not more than 30% of total calories per day

d. What Is Biochemistry Used For?d. What Is Biochemistry Used For?1.1. Biochemistry is used to learn about the Biochemistry is used to learn about the

biological processes which take place in cells biological processes which take place in cells and organisms. and organisms.

2.2. Biochemistry may be used to study the Biochemistry may be used to study the properties of biological molecules, for a variety properties of biological molecules, for a variety of purposes. For example, a biochemist may of purposes. For example, a biochemist may study the characteristics of the keratin in hair so study the characteristics of the keratin in hair so that a shampoo may be developed that that a shampoo may be developed that enhances curliness or softness. enhances curliness or softness.

3.3. Biochemists find uses for Biochemists find uses for biomoleculesbiomolecules. For . For example, a biochemist may use a certain lipid as example, a biochemist may use a certain lipid as a food additive. a food additive.

What Is Biochemistry Used For?What Is Biochemistry Used For?4.4. Alternatively, a biochemist might find a Alternatively, a biochemist might find a

substitute for a usual substitute for a usual biomoleculebiomolecule. For example, . For example, biochemists help to develop artificial biochemists help to develop artificial sweeteners. sweeteners.

5.5. Biochemists can help cells to produce new Biochemists can help cells to produce new products. Gene therapy is within the realm of products. Gene therapy is within the realm of biochemistry. The development of biological biochemistry. The development of biological machinery falls within the realm of machinery falls within the realm of biochemistry. biochemistry.

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e. The core of plant biochemistrye. The core of plant biochemistry1.1. The core of biochemistry is The core of biochemistry is the conversion of the conversion of

substrates to products substrates to products through through biochemical reactionsbiochemical reactionswhich catalyzed by which catalyzed by enzymesenzymes in most cases. in most cases.

2.2. Isolation and IdentificationIsolation and Identification Biochemistry is Biochemistry is firstly concerned with the firstly concerned with the

isolationisolation and and identificationidentification of of all different all different substances substances which which make up plant and animal make up plant and animal organismsorganisms

A living organism is composed of more than A living organism is composed of more than just fasts, carbohydrates and protein. just fasts, carbohydrates and protein. Hundreds of other substances are necessary Hundreds of other substances are necessary to the proper functioning of the organismsto the proper functioning of the organisms

2.2. Chemical ChangesChemical Changes Secondly, biochemistry is concerned Secondly, biochemistry is concerned

with all chemical changes which take with all chemical changes which take place in the cells to provide for energy, place in the cells to provide for energy, growth, reproduction, and aging.growth, reproduction, and aging.

Protoplasm is an aqueous solution of Protoplasm is an aqueous solution of certain substances with other certain substances with other colloidallycolloidally dispersed substances dispersed substances

PLAN

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PLAN

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f. Breakthroughs in BiochemistryTwo notable breakthroughs in the history of biochemistry 1. Discovery of the role of enzymes as

catalysts2. Identification of nucleic acids as information

molecules Flow of information: from nucleic acids to proteins

Short segment of a Short segment of a DNA moleculeDNA molecule

• Two polynucleotides associate to form a double helix

• Genetic information is carried by the sequence of base pairs

3. COURSE PLAN3. COURSE PLANNO. TOPICS WEEK1. INTRODUCTION 1

2. ENZYME 2-4

3. CARBOHYDRATE 5-6

4. METABOLIC ENERGY 7

MID SMESTER EXAM 8

5. LIPID 9-10

6. NITROGEN METABOLISM 11

7. BIOLOGICAL N FIXATION 12

8. AMINO ACIDS 13

9. NUCLEIC ACID 1410. PROTEIN 15

END SMESTER EXAM 16

REFERENCESREFERENCES1.1. Conn, E.E. & Conn, E.E. & StumpfStumpf, P.K., 1976. Outlines of Biochemistry. , P.K., 1976. Outlines of Biochemistry.

John Wiley & Sons, New York.John Wiley & Sons, New York.2.2. Goodwin, T.W. & Mercer, E.I., Introduction to Plant Goodwin, T.W. & Mercer, E.I., Introduction to Plant

Biochemistry. Biochemistry. PergamonPergamon Press, Oxford.Press, Oxford.3.3. StryerStryer, L., 1975. Biochemistry. W.H. Freeman and Company, , L., 1975. Biochemistry. W.H. Freeman and Company,

San FranciscoSan Francisco4.4. Wood, W.B., Wilson, J.H., Wood, W.B., Wilson, J.H., BenbowBenbow, R.M., & Hood, L. E., , R.M., & Hood, L. E.,

1981. Biochemistry A Problems Approach. 1981. Biochemistry A Problems Approach. 5.5. Wood, J.H, Wood, J.H, KeehanKeehan, C.W., Bull, W.E. and Bowman, N.S., , C.W., Bull, W.E. and Bowman, N.S.,

1963. Fundamentals of College Chemistry. A Harper 1963. Fundamentals of College Chemistry. A Harper International edition, Harper & Row, NY, Evanston & London International edition, Harper & Row, NY, Evanston & London and John and John WeatherhillWeatherhill, Inc., Tokyo, Inc., Tokyo

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4. EXAMPLES OF PLANT 4. EXAMPLES OF PLANT BIOCHEMISTRYBIOCHEMISTRY

a. a-Amylase

b. Cellulose

ADENIUM OBESUM ' CHERRY'Grafted Desert RoseFamily : ApocynaceaeOrigin : East AfricaSize : 5'Light Requirements : Full Sun/Light Shade Water Requirements : Keep DryMin. Temp. : 35°Flower : Year Round

c. PIGMENT

Pigment Class Compound Type Colors

Porphyrin chlorophyll green

Carotenoid carotene and lycopenexanthophyll

yellow, orange, red yellow

Flavonoid flavoneflavonolanthocyanin

yellow yellow

red, blue, purple, magenta

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d. d. GugurGugur DaunDaun Perusakan dinding sel Perusakan dinding sel

pada lapisan absisi oleh pada lapisan absisi oleh aktivitas enzim aktivitas enzim CellulaseCellulasedandan PolygalacturonasePolygalacturonase

Sintesis kedua enzim Sintesis kedua enzim tersebut terhambat jika tersebut terhambat jika kadar hormon tumbuh kadar hormon tumbuh auxin auxin cukup tinggi cukup tinggi

Auxin

Ethylene

Cellulase/Polygalacturonase

• Transpor auxin dari tempat pembentukan pada bagian ujung daun ke lapisan absisi dihambat oleh hormon ethylene

e. The Narcotic Analgesicse. The Narcotic Analgesics Narcotics block the transmission of the nerve signal Narcotics block the transmission of the nerve signal

across nerve gaps, [the minor analgesics blocked across nerve gaps, [the minor analgesics blocked prostaglandin synthesis]prostaglandin synthesis]

The more important ones:The more important ones: Morphine, codeine,Morphine, codeine, oxycodoneoxycodone (PERCODAN), (PERCODAN), hydromorphonehydromorphone

(DILAUDID), methadone, + heroin [ = not legal](DILAUDID), methadone, + heroin [ = not legal] meperidinemeperidine (DEMEROL), (DEMEROL), pentazocinepentazocine (TALWIN),(TALWIN), fentanylfentanyl (SUBLIMAZE), (SUBLIMAZE), buprenorphinebuprenorphine (BUPRENEX(BUPRENEX))

Morphine:Morphine: Opium [est. ~ 10,000 tons] extracted from the Opium [est. ~ 10,000 tons] extracted from the

poppy poppy PapaverPapaver somniferumsomniferum, Afghanistan spring 06 , Afghanistan spring 06 6100 tons alone.6100 tons alone.

Morphine goes to receptors (opiate receptors) which control passage of Ca2+ and K + through channels, which in turn control acetylcholine (nerve transmitter) flow across

synapses.

DEPRESSES RESPIRATORY SYSTEM - usual overdose effect; some euphoria - plus is addictive

Komunikasi saraf (neuron & nerve cells) antara satu dengan yang lain, atau dengan yang lain (kelenjar, otot & organ tubuh lain) terjadi melalui pelepasan zat, “neurotransmitters”, pada reseptor dari neuron atau organ bersangkutan. Suatu zat yang secara mengyakinkan berfungsi sebagai neurotransmitter adalah Acetylcholine.

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f. Cyanide Poisoningf. Cyanide Poisoning Disrupts metabolism by inhibiting metal Disrupts metabolism by inhibiting metal

containing enzymes, most notably, containing enzymes, most notably, cytochromecytochrome oxidaseoxidase..

CytochromeCytochrome AA33 catalyzes Ocatalyzes O2 2 HH22OOBlocks ability of mitochondria to use OBlocks ability of mitochondria to use O22OO22 saturation may be normalsaturation may be normal

Poisoning can occur through Poisoning can occur through percutaneouspercutaneous absorption and inhalation.absorption and inhalation.

Degree of symptoms depends on Degree of symptoms depends on severity of exposure.severity of exposure.

Sodium Nitrate injected

Oxyhemoglobin Metemoglobin

Cyano-methemoglobin (low toxicity)

Sodium Thiosulfate injected

Thiocyanate Kidneys

CN

Cytochrome oxidase

Rodonase

AntidoteSpecific antidotes available

1. Sodium nitrite reacts with hemoglobin to form methemoglobin that removes cyanide ions from various tissues to form cyanmethemoglobin (relatively low toxicity).

2. The function of Sodium thiosulfate is to convert cyanide to thiocyanate, by an hepatic enzyme known as rhodanese

g. g. MethanolMethanol PoisoningPoisoning Methanol itself has a relatively low degree of toxicity,

but it is metabolized to formic acid which is responsible for the acidosis and blindness that characterizes methanol poisoning.

The initial step in the metabolism of methanol occurs by the action of alcohol dehydrogenase (ADH).

h. What is Biodiesel?h. What is Biodiesel? Alternative fuel for diesel enginesAlternative fuel for diesel engines Made from vegetable oil or animal fat Made from vegetable oil or animal fat Meets health effect testing (CAA)Meets health effect testing (CAA) Lower emissions, High flash point (>300F), SaferLower emissions, High flash point (>300F), Safer Biodegradable, Essentially nonBiodegradable, Essentially non--toxic.toxic. Chemically, biodiesel molecules are monoChemically, biodiesel molecules are mono--alkyl alkyl

esters produced usually from triglyceride estersesters produced usually from triglyceride esters

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Biodiesel SamplesBiodiesel SamplesChemistry of TriglyceridesChemistry of Triglycerides

Biodiesel is made from the combination of a Biodiesel is made from the combination of a triglyceride with a triglyceride with a monohydroxymonohydroxy alcohol (i.e. methanol, alcohol (i.e. methanol, ethanol…). ethanol…).

What is a triglyceride? Made from a combination of What is a triglyceride? Made from a combination of glycerol and three fatty acids:glycerol and three fatty acids:

TransesterificationTransesterificationWhile actually a multiWhile actually a multi--step process, the overall reaction looks like this:step process, the overall reaction looks like this:

CH2OOR1 catalyst CH2OHCH2OOR1 catalyst CH2OH| | ||CHOOR2 + 3CH3OH CHOOR2 + 3CH3OH 3CH3OORx + CHOH3CH3OORx + CHOH| || |CH2OOR3 CH2OHCH2OOR3 CH2OHTriglyceride 3 Triglyceride 3 MethanolsMethanols Biodiesel GlycerinBiodiesel Glycerin

R1, R2, and R3 are fatty acid alkyl groups (could be different, or the R1, R2, and R3 are fatty acid alkyl groups (could be different, or the same), and depend on the type of oil. The fatty acids involved same), and depend on the type of oil. The fatty acids involved determine the final properties of the biodiesel (determine the final properties of the biodiesel (cetanecetane number, cold number, cold flow properties, etc.)flow properties, etc.)

Individual step of TransesterificationIndividual step of TransesterificationFirst step, triglyceride turned into diglyceride, methoxide (minus Na) joins freed FA to make biodiesel, Na joins OH from water (from methoxide formation) to make NaOH. Other H joins the diglyceride.

H O H| | |

HCOR1 H HCO H O| | | | |

HCOOR2 + HCONa +H2O CHOOR2 + HCOR1 + NaOH| | | |

HCOR3 H HCOR3 H| | | |H O H O

Triglyceride + Methoxide + H2O Diglyceride + Biodiesel + NaOH

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ii. What is Cloning?. What is Cloning? Cloning is to make a genetically identical Cloning is to make a genetically identical

organism through nonorganism through non--sexual means.sexual means. Cloning of Cloning of African violetsAfrican violets:: Take a leaf from a plantTake a leaf from a plant Immerse the stalk in waterImmerse the stalk in water

• Roots start to form after a week

• Pot the plant• A new plant is produced

How Dolly was cloned?How Dolly was cloned?

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Sel telur dengan inti dari induk yang berkembang menjadi anak domba yang sama dengan induknya

Sel induk

Sel telur

Penyakit encok (gout) yang mengakibatkan radang Penyakit encok (gout) yang mengakibatkan radang pada persendian adalah akibat akumulasi asam uratpada persendian adalah akibat akumulasi asam urat RadangRadang sendisendi dipicudipicu oleholeh

presipitasipresipitasi kristalkristal uraturatnatriumnatrium ((sodium sodium urateuratecrystalscrystals))

PenyakitPenyakit GinjalGinjal dapatdapatjugajuga terjaditerjadi karenakarenadeposisideposisi kristalkristal uraturatdalamdalam organ organ tersebutersebu