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Plant Biochemistry
Lecture 1: General Introduction
Catalase

The conversion of substrates

to products through
biochemical reactions which
catalyzed by enzymes

Science without religion is lame,

religion without science is blind.
--Albert Einstein

Balasubramanian & Ponnuraj, 2010

These are my rules  These are my

 Come on time ( 10’) philosophies
with a proper dress • Turn your enemies to
 Get into the lecture be your friends
room, don’t hang • Turn your useless time
around to be useful time
 Use English in my • Make big problems to
lecture and exam (75- be small problems
99%) • Simplify the systems or
problems

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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 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 information
as to the lecture materials
5. Study Groups
 Organize your study group, 5 member each
to discuss the lecture materials
6. 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 several
paragraphs (4-5 sentences/ paragraph), font (Times
New Roman 12)

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EXAMPLE Urease
Siti
Paragraf 1. Uraikan informasi umum mengenai Urease
(kapan ditemukan & siapa penemunya, dimana terdapat
umumnya, dll)
Paragraf 2-3. Uraikan fungsi catalase khususnya pada
tanaman termasuk reaksi yang dikatalisis dan pengaruh faktor
lingkungan (mis. pH, temperatur, dll.)
Paragraf 4-5. Uraikan perkembangan hasil penelitian
tentang 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 TOPICS
ENZYMES 12. Maltase 20. Nitrate reductase
1. Catalase 13. Papain 21. Glutamine
2. Amylase Bromelain
14. synthetase
3. Urease Trypsin
15. 22. Glutamate
4. Sucrase 16. Supetoxide synthase
5. Cellulase dismutase 23. Glutamate
6. Lipase 17. Ascorbate dehydrogenase
7. Lactase peroxidase 24. Glutaminase
8. Pectinase 18. Alanine 25. Asparagine
9. Phytase
aminotrasferase synthase
10. Pectinase
19. Nitrite 26. Arginine
reductase deiminse
11. Xylanase
27. Ficin

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28. Dextrase 37. Codeine

29. Pectinase 38. Rishitin
30. Actinidin 39. Jasmonic acid
40. Anthraquinones
COMPOUNDS 41. Diosgenin
Chemical Structure, Function 42. Rosmarinic acid
and Synthesis 43. Saponin
31. Cathecin 44. Scopoletin
32. Theaflavins 45. Anthocyanin
33. Capsaicinoids 46. Kinobeon
34. Berberine 47. Methoxymellein
35. Capsidiol 48. Salidroside
36. Hyoscyamine 49. Shikonin

LEARNING OUTCOMES
Students, after mastering materials of the present
lecture, should be able
1. to explain plant biochemistry in general
2. to identify the basic molecules which make up
plant
3. to describe the way in which chemical
components are synthesized and utilized by
plants in the life process
4. to describe the process of pant life on a chemical
level
5. to initiate ways from the standpoint of
biochemistry to improve the growth of plants or to
solve problems in plant growth

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LECTURE OUTLINE
SUMMARY 3. Proteins
LEARNING OUTCOMES 4. Nucleic acids
STRUCTURED TASK
III. BICHEMISTRY
COURSE PLAN
REFERENCES
IMPORTANCE
1. Biochemistry Use
I. INRODUCTION 2. The Core of Plant
1. Definition Biochemistry
2. Basic Principle IV. BREAKTHROUGHS IN
BIOCHEMISTRY
II. BIOMOLECULES
1. Enzyme and DNA
1. Carbohydrates
2. Genetic Engineering
2. Lipids
Examples of Biochemistry

COURSE PLAN
NO. TOPICS Subject
1. INTRODUCTION
2. ENZYME I Introduction
3. ENZYME II Kinetics
4. ENZYME II Mechanism & Inhibitor
5. CARBOHYDRATE I Introduction
6. CARBOHYDRATE II Classification
7. METABOLIC ENERGY
8. MID SMESTER EXAM
9. LIPID
10. AMINO ACIDS
11. BIOLOGICAL N FIXATION
12. NUCLEIC ACID RNA and DNA
13. PROTEIN SYNTHESIS I Genome and gen
14. PROTEIN SYNTHESIS II Transcription and Translation
15. SECONDARY METABOLITES
16. END SMESTER EXAM

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REFERENCES
1. Berg, J.M., Tymoczko, J.L. and Stryer, L., 2002. Biochemistry.
5th edition: W.H. Freeman and Co,. New York
2. Buchanan, B.B., Gruissem, W. and Jones, R.L., 2000.
Biochemistry and Molecular Biology of Plants. American
Society 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 Plant
Biochemistry. 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. INTRODUCTION
1. 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 and
utilized by the organism in the life process
(Goodwin & Mercer, 1990).

Plant Biochemistry is the study of molecular basis of

plant life that includes the synthesis and utilization
of 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 same
chemical components
• The formation of compounds (biomolecules)
required in the living process of plants, from the
chemical components, occurs through biochemical
reactions catalyzed in most cases by enzymes
under genetic control and environmental influence.

• Enzymes, therefore, are crucial in the biochemical process

of plant life. For example, the break down of urea to be
ammonium occurs through a hydrolysis reaction catalyzed
by enzyme urease.

Urease

• Urease from jack beans (Canavalia

ensiformis) 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
Balasubramanian & Ponnuraj, 2010

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II. BIOMOLECULES
What 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 molecules

called polymers which are made up of monomer
subunits
 Biochemical molecules are principally based on
carbon.

carbo lipids proteins nucleic acids

monomer

polymer

supramolecular
structure

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monomer

polymer

supramolecular
structure

• Cellulose is the major

structural material of plants.
Wood is largely cellulose,
and cotton is almost pure
cellulose.

One Fatty Acid

 The “head” of the molecule is a carboxyl group

which is hydrophilic.
 The “tail” of a fatty acid is a long hydrocarbon
chain, making it hydrophobic.
 Fatty acids are the main component of soap, where
their tails are soluble in oily dirt and their heads are
soluble in water to emulsify and wash away the oily
dirt. However, when the head end is attached to
glycerol to form a fat, that whole molecule is
hydrophobic.

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monomer

polymer

supramolecular
structure

Description Saturated Fats Unsaturated Fats

Saturated fats are fats with a Unsaturated fats are fats with
Definition: single bond between the one or more double bonds
carbon atoms of the fatty acids between the fatty acids
Excessive consumption is not
good because of their Unsaturated fats are
Health: association with considered good to eat if you
atherosclerosis and heart are watching your cholesterol
diseases.
Saturated fats increase LDL Unsaturated fats increase HDL
Cholesterol: (bad cholesterol) and decrease (good cholesterol) and
the HDL decrease LDL
Form: Solid at room temperature Liquid at room temperature
Derived from: Mostly from animal products Plants
contains one or more double
contains only single bonds
Hydrocarbon bonds between carbon atoms
between carbon atoms, no
chain: double bonds (ex: stearic acis)
-monounsaturated -
polyunsaturated
Commonly Butter, coconut oil, breast milk, Avocado, soybean oil, canola
found in: meat oil, olive oil
These are long lasting and do
Life: not get spoiled quickly
These get spoiled quickly

Recommended Not more than 10% of total Not more than 30% of total
consumption: calories per day. calories per day

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lipids
Saturated
Formula Common Name Melting Point
CH3(CH2)10CO2H lauric acid 45 ºC
CH3(CH2)12CO2H myristic acid 55 ºC
CH3(CH2)14CO2H palmitic acid 63 ºC
CH3(CH2)16CO2H stearic acid 69 ºC
CH3(CH2)18CO2H arachidic acid 76 ºC
Unsaturated
Formula Common Name Melting Point
CH3(CH2)5CH=CH(CH2)7CO2H palmitoleic acid 0 ºC
CH3(CH2)7CH=CH(CH2)7CO2H oleic acid 13 ºC
CH3(CH2)4CH=CHCH2CH=CH
linoleic acid -5 ºC
(CH2)7CO2H
CH3CH2CH=CHCH2CH=CHC
linolenic acid -11 ºC
H2CH=CH(CH2)7CO2H
CH3(CH2)4(CH=CHCH2)4(CH2)
arachidonic acid -49 ºC
2CO2H

Omega-3 and Omega-6 Fatty Acids

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Cis and Trans Bonds

monomer amino acid

polymer protein subunit

supramolecular
structure Enzyme complex

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monomer

polymer

supramolecular
structure

III. THE IMPORTANCE OF

BIOCHEMISTRY
1. Biochemistry Use
What 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 developed
that 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 substitute

for a usual biomolecule. For example, biochemists
help to develop artificial sweeteners.
5. Biochemists can help cells to produce new
products. Gene therapy is within the realm of
biochemistry. The development of biological
machinery falls within the realm of biochemistry.

2. Molecular Characterization
The core of biochemistry is the characterization of
organismal life at molecular level including the
conversion mechanism of substrates to products
through biochemical reactions catalyzed by
enzymes under genetic control and environmental
influence.

1. Isolation and Identification

 Biochemistry is firstly concerned with the isolation
and identification of all different substances which
make up plant and animal organisms
- A living organism is composed of more than just
fasts, carbohydrates and protein. Hundreds of
other substances are necessary to the proper
functioning of the organisms

2. Chemical Changes
 Secondly, biochemistry is concerned with all chemical
changes which take place in the cells to provide for
energy, growth, reproduction, and aging.
- Protoplasm is an aqueous solution of certain
substances with other colloidally dispersed
substances

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Chemical Changes: 7 11
Metabolism
(146 pathways) 8 4
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 1
Acids (9)
7. Glycan Biosynthesis and Metabolism 6
(18) 3
8. Biosynthesis of Polyketides and
Nonribosomal Peptides (9)
9. Metabolism of Cofactors and Vitamins
5
(11)
10. Biosynthesis of Secondary
Metabolites (21)
11. Biodegradation of Xenobiotics (21) 9
2
10

http://manet.illinois.edu/pathways.php

Assume 10 reactions/pathway (glycolysis has 11

reactions), then 146 x 10 = 1460 reactions/cell
PLANT BIOCHEMISTRY

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IV. BREAKTHROUGHS IN
BIOCHEMISTRY
1. Enzyme and DNA
 Two notable breakthroughs in the history of
biochemistry
1. Discovery of the role of enzymes as catalysts
2. 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 within
hearing distance that we had found the secret of life. — James Watson

• Two polynucleotides
associate to form a
double helix
• Genetic information is
carried by the sequence
of base pairs

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2. Genetic Engineering and Cloning

 Advances in the study of genetics (DNA) have led to
the development of genetic engineering and cloning
 Genetic engineering is the manipulation of genes to
create purposefully versions of organisms
 Cloning is to make a genetically identical organism
through non-sexual means.
 Cloning of African violets:
1. Take a leaf from a plant
2. Immerse the stalk in
water
- Roots start to form
after a week
3. Pot the plant
- A new plant is
produced

The new plant is

genetically identical
to the parental plant

The color of the

flowers are the
same

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How Dolly was cloned?

Sel telur dengan inti dari induk yang berkembang

menjadi anak domba yang sama dengan induknya

How Dolly was cloned?

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EXAMPLES OF PLANT
BIOCHEMISTRY

1. Gugur Daun
 Perusakan dinding sel
pada lapisan absisi
oleh aktivitas enzim
Cellulase dan
Polygalacturonase
 Sintesis kedua enzim
tersebut terhambat
jika kadar hormon
tumbuh auxin cukup
tinggi

• Transpor auxin dari tempat ujung daun (tempat

sintesis) ke lapisan absisi dihambat ethylene

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2. The Narcotic Analgesics

 Narcotics block the transmission of the
nerve signal across nerve gaps, [the minor
analgesics blocked prostaglandin
synthesis]
 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 06
6100 tons alone.

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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.

c. Cyanide Poisoning
 Disrupts metabolism by inhibiting metal
containing enzymes, most notably,
cytochrome oxidase.
 Cytochrome A3 catalyzes O2  H2O
 Blocks ability of mitochondria to use O2
 O2 saturation may be normal
 Poisoning can occur through
percutaneous absorption and inhalation.
 Degree of symptoms depends on
severity of exposure.

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Antidote
Specific 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

d. Methanol Poisoning
 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).

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

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 determine the final properties of
the biodiesel (cetane number, cold flow properties, etc.)

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Individual step of Transesterification

First 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.

f. Penyakit encok (gout) yang mengakibatkan

radang pada persendian adalah akibat akumulasi
asam urat
 Radang sendi dipicu
oleh presipitasi kristal
urat natrium (sodium
urate crystals)
 Penyakit Ginjal dapat
juga terjadi karena
deposisi kristal urat
dalam organ tersebu

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a. a-Amylase

b. Cellulose

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c. PIGMENT ADENIUM OBESUM ' CHERRY'

Grafted Desert Rose
Family : Apocynaceae
Origin : East Africa
Size : 5'
Light Requirements : Full Sun/Light
Shade
Water Requirements : Keep Dry
Min. Temp. : 35°
Flower : Year Round

Pigment Class Compound Type Colors

Porphyrin chlorophyll green
Carotenoid carotene and yellow, orange, red
lycopene yellow
xanthophyll
Flavonoid flavone yellow
flavonol yellow
anthocyanin red, blue, purple,
magenta

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Model of urease activation. Synthesis of active urease requires the

formation of a complex between the (UreABC) 3 urease apoprotein and
UreDFG.
https://d194ekacf8mn8t.cloudfront.net/content/femsre/27/2-3/239/F2.large.jpg

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