lecture 1: plant biochemistry: general introduction
TRANSCRIPT
2/21/2012
1
Lecture 1: Plant Biochemistry: Lecture 1: Plant Biochemistry: General IntroductionGeneral Introduction
S.M. S.M. SitompulSitompul
http://smtom.lecture.ub.ac.id/Password: sm11tom
These are my rulesThese are my rules Come on time (Come on time ( 10’) 10’)
with a proper dresswith a proper dress 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 (75lecture and exam (75--99%)99%)
These are my These are my philosophiesphilosophies
•• Turn your enemies to Turn your enemies to be your friendsbe your friends
•• Turn your useless time Turn your useless time to be useful timeto be useful time
•• Make big problems to Make big problems to be small problemsbe small problems
•• Simplify the systems or Simplify the systems or problemsproblems
1.1. English PresentationEnglish Presentation Everyone has to make English PresentationEveryone has to make English Presentation
2.2. DictionaryDictionary Take your English dictionary every time I give my Take your English dictionary every time I give my
lecturelecture3.3. My DictionaryMy Dictionary Buy a writing book (100Buy a writing book (100--pages) and name it pages) and name it MY MY
DICTIONARYDICTIONARY Write down all English words with Indonesian Write down all English words with Indonesian
meanings that you do not know yetmeanings that you do not know yet4.4. Study GroupsStudy Groups Organize your study group, 5 member eachOrganize your study group, 5 member each
STRUCTURAL TASKSTRUCTURAL TASK
2/21/2012
2
EXAMPLEEXAMPLEThe effect of temperature on The effect of temperature on UreaseUrease ActivityActivity
SitiSitiAbstractAbstract
1.1. IntroductionIntroduction what is it about (General description)what is it about (General description) What is the problemWhat is the problem what is its importancewhat is its importance
2. 2. UreaseUrease Activity Activity 3. Conclusion3. Conclusion4. References (3 references at least)4. References (3 references at least)
http://www.dina.dk/efita-conf/program/papers.htm
STRUCTURAL TASK
5.5. PaperPaper Write a paper about Write a paper about Plant BiochemistryPlant Biochemistry
Take from published papers in Journal (internet)Take from published papers in Journal (internet) Max. 3 pages (single space)Max. 3 pages (single space)
CompetencyCompetency
Students on completion of this course would be ableStudents on completion of this course would be able
1.1. to explain plant biochemistry to explain plant biochemistry
2.2. to identify the basic molecules which make up to identify the basic molecules which make up plantplant
3.3. to describe the way in which chemical to describe 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
4.4. to describe the process of pant life on a chemical to describe the process of pant life on a chemical level level
5.5. to initiate ways from the standpoint of to initiate ways from the standpoint of biochemistry to improve the growth of plants or to biochemistry to improve the growth of plants or to solve problems in plant growthsolve problems in plant growth
LECTURE FLOWLECTURE FLOW
CompetencyCompetency1.1. Definition Definition 2.2. Course PlanCourse Plan Subjects Subjects ReferencesReferences
3.3. Introduction Introduction Basic PrincipleBasic Principle BiomoleculesBiomolecules What Is Biochemistry Used For?What Is Biochemistry Used For? The Core of Plant BiochemistryThe Core of Plant Biochemistry Breakthroughs In BiochemistryBreakthroughs In Biochemistry
4.4. Examples of BiochemistryExamples of Biochemistry
2/21/2012
3
1. Definition1. Definition
What is Plant Biochemistry ?What is Plant Biochemistry ?Plant Biochemistry, or the chemistry of living plants, isPlant Biochemistry, or the chemistry of living plants, is1.1. the study of the chemistry of living things (types, the study of the chemistry of living things (types,
structures & reactions)structures & reactions)2.2. the study of the process of plant life on a chemical the study of the process of plant life on a chemical
levellevel3.3. the study of the study of molecular basis of plant life molecular basis of plant life or or
the study of the way in which chemical components the study of the way in which chemical components are synthesized and utilized by plants in the life are synthesized and utilized by plants in the life process (growth & development).process (growth & development).
2. COURSE PLAN2. 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 , P.K., 1976. Outlines of
Biochemistry. John Wiley & Sons, New York.Biochemistry. 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 , L., 1975. Biochemistry. W.H. Freeman and Company, San FranciscoCompany, San Francisco
4.4. 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, , C.W., Bull, W.E. and Bowman, N.S., 1963. Fundamentals of College Chemistry. A N.S., 1963. Fundamentals of College Chemistry. A Harper International edition, Harper & Row, NY, Harper International edition, Harper & Row, NY, Evanston & London and John Evanston & London and John WeatherhillWeatherhill, Inc., Tokyo, Inc., Tokyo
2/21/2012
4
1. Basic Principle
• Living organisms, whether they are plants, animals or microbes, are made up basically of the same chemical components
• Biochemical Reactions
3. INTRODUCTION3. INTRODUCTION
Urease catalyzes the hydrolysis of urea
Urease from jack beans (Canavaliaensiformis) was the first enzyme ever purified and crystallised, an achievement of James B. Sumner in 1926 who earned a Nobel Prize in Chemistry in 1946
C O + 3 H2O Urease
H2N
H2N
2NH4++OH-+HCO3
-
2.2. BiomoleculesBiomoleculesWhat are Types of Molecules studied in Biochemistry?What are Types of Molecules studied in 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 principally based on Biochemical molecules are principally based on carbon.carbon.
2/21/2012
5
protein complex
protein subunit
amino acid
membrane
phospholipid
fatty acid
cell wall
cellulose
glucose
chromosome
DNA
nucleotidemonomer
polymer
supramolecularstructure
lipids proteinscarbo nucleic acids
cell wall
cellulose
glucosemonomer
polymer
supramolecularstructure
• Cellulose is the major structural material of plants. Wood is largely cellulose, and cotton is almost pure cellulose.
membrane
phospholipid
fatty acidmonomer
polymer
supramolecularstructure
2/21/2012
6
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 temperature
Derived 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
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
monomer
polymer
supramolecularstructure Enzyme complex
protein subunit
amino acid
2/21/2012
7
chromatin
DNA
nucleotidemonomer
polymer
supramolecularstructure
3.3. Importance of Plant BiochemistryImportance of Plant Biochemistry
What Is Biochemistry Used For?What Is Biochemistry Used For?1.1. Biochemistry is used to learn about the Biochemistry is used to learn about the biological biological
processesprocesses which take place in cells and organisms. which take place in cells and organisms. 2.2. Biochemistry may be used Biochemistry may be used to study the properties of to study the properties of
biological moleculesbiological molecules, for a variety of purposes. For , for a variety of purposes. For example, a biochemist may study the characteristics example, a biochemist may study the characteristics of of the keratin in hair so that a shampoo may be the keratin in hair so that a shampoo may be developed that enhances curliness or softnessdeveloped that 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 a example, a biochemist may use a certain lipid as a food additive. food additive.
4.4. Alternatively, a biochemist might find a substitute Alternatively, a biochemist might find a substitute for a usual for a usual biomoleculebiomolecule. For example, . For example, biochemists help to develop artificial sweeteners. biochemists help to develop artificial 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 biochemistry. machinery falls within the realm of biochemistry.
4.4. The core of plant biochemistryThe core of plant biochemistryThe core of biochemistry is The core of biochemistry is the conversion of the conversion of substrates to products substrates to products through through biochemical biochemical reactionsreactions which catalyzed by which catalyzed by enzymesenzymes in most in most cases. cases.
2/21/2012
8
Isolation and IdentificationIsolation and Identification1.1. Biochemistry is firstly concerned with the Biochemistry is firstly concerned with the isolation isolation
and and identificationidentification of all of all different substances different substances which which make up plant and animal organismsmake up plant and animal organisms
A living organism is composed of more than just A living organism is composed of more than just fasts, carbohydrates and protein. Hundreds of other fasts, carbohydrates and protein. Hundreds of other substances are necessary to the proper functioning substances are necessary to the proper functioning of the organismsof the organisms
Chemical ChangesChemical Changes2.2. Secondly, biochemistry is concerned with Secondly, biochemistry is concerned with all all
chemical changes chemical changes which take place in the cells to which take place in the cells to provide for energy, growth, reproduction, and aging.provide for energy, growth, reproduction, and aging.
Protoplasm is an aqueous solution of certain Protoplasm is an aqueous solution of certain substances with other substances with other colloidallycolloidally dispersed dispersed substances substances
PLAN
T BIO
CHEM
ISTRY
PLAN
T BIO
CHEM
ISTRY
5. 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
2/21/2012
9
• Two polynucleotides associate to form a double helix
• Genetic information is carried by the sequence of base pairs
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
Sel telur dengan inti dari induk yang berkembang menjadi anak domba yang sama dengan induknya
Sel induk
Sel telur
2/21/2012
10
How Dolly was cloned?How Dolly was cloned?
2/21/2012
11
4. EXAMPLES OF 4. EXAMPLES OF PLANT PLANT
BIOCHEMISTRYBIOCHEMISTRY
a. a-Amylase
b. Cellulose
2/21/2012
12
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
d. d. GugurGugur DaunDaun PerusakanPerusakan dindingdinding selsel
padapada lapisanlapisan absisiabsisioleholeh aktivitasaktivitas enzimenzimCellulaseCellulase dandanPolygalacturonasePolygalacturonase
SintesisSintesis keduakedua enzimenzimtersebuttersebut terhambatterhambatjikajika kadarkadar hormonhormontumbuhtumbuh auxinauxin cukupcukuptinggitinggi
Auxin
Ethylene
Cellulase/Polygalacturonase
• Transpor auxin dari tempat pembentukan pada bagian ujung daun ke lapisan absisi dihambat oleh hormon ethylene
2/21/2012
13
e. The Narcotic Analgesicse. The Narcotic Analgesics Narcotics block the transmission of the Narcotics block the transmission of the
nerve signal across nerve gaps, [the nerve signal across nerve gaps, [the minor analgesics blocked prostaglandin minor analgesics blocked prostaglandin synthesis]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))
MorphineMorphine:: 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.
2/21/2012
14
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).
2/21/2012
15
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 (>Lower emissions, High flash point (>300300F), SaferF), Safer
Biodegradable, Essentially nonBiodegradable, Essentially non--toxic.toxic.
Chemically, biodiesel molecules are monoChemically, biodiesel molecules are mono--alkyl esters alkyl esters
produced usually from triglyceride estersproduced usually from triglyceride esters
Biodiesel SamplesBiodiesel Samples
Chemistry of TriglyceridesChemistry of Triglycerides Biodiesel is made from the combination of a triglyceride Biodiesel is made from the combination of a triglyceride
with a with a monohydroxymonohydroxy alcohol (i.e. methanol, ethanol…). alcohol (i.e. methanol, 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:
2/21/2012
16
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 Individual step of TransesterificationTransesterificationFirst 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
PenyakitPenyakit encokencok (gout) yang (gout) yang mengakibatkanmengakibatkanradangradang padapada persendianpersendian adalahadalah akibatakibat
akumulasiakumulasi asamasam uraturat RadangRadang sendisendi dipicudipicu
oleholeh presipitasipresipitasi kristalkristaluraturat natriumnatrium ((sodium sodium urateurate crystalscrystals))
PenyakitPenyakit GinjalGinjal dapatdapatjugajuga terjaditerjadi karenakarenadeposisideposisi kristalkristal uraturatdalamdalam organ organ tersebutersebu
2/21/2012
17