LECTURE I :

GENERAL
INTRODUCTION

Intestinal Ca2+-binding protein!

Welcome to the Course of

Plant Biochemistry

Coordinator : Prof. Dr. S.M. Sitompul

These are the rules of

biochemistry course
I always come on time
( 10) with a proper
dress
Get into the lecture
room, dont hang
around
I use English in my
Power Point (50-50%)

These are the important

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 (KISS)

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

Poverty
Unemployment
Environmental Degradation
Catastrophes (Flood & Drought)
Diseases (Avian Flu)
Food Shortage/Starvation

HOW TO SOLVE THE PROBLEMS ?

It is important first to understand living
systems (how the system works)
the chemical elements which make up plant
body
the function of each element in the life process
the interaction between elements in the life
process

A better understanding of living systems

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

THE BUILDING ELEMENTS OF

LIFE
Plant Level
Leaves, Stems & Roots

Organ Level
Chloroplasts, Mitochondria, Nucleus etc.

Molecular Level
Enzymes, Carbohydrates, Energy
Molecules, etc

What is Plant Biochemistry ?

Definition.
Biochemistry is the study of the process of

plant life on a chemical level

Plant Biochemistry, or the chemistry of living

plants, is the study of molecular basis of
plant life or the study of the way in which

chemical components are synthesized and

utilized by plants in the life process (growth
and development)

ABSTRACT
The core of biochemistry is the conversion of

substrates to be products through biochemical

reactions which catalyzed by enzymes in most

cases.
Therefore, the course of plant biochemistry is
started with the discussion of enzymes which is

then followed by carbohydrate metabolism,

energy molecule metabolism, nitrogen
metabolism (amino acids), lipid metabolism,
nucleic acid metabolism, protein synthesis, and
the synthesis of secondary metabolites.

Objectives and Competency of

Plant Biochemistry Course
Objectives
The main objectives of this course is to
consolidate the knowledge of students on the

basic molecules of plant life, and to increase their

understanding on the metabolism of the basic
molecules.

Competency
Students taking this course would be competent in

describing the life of plants from the standpoint of

biochemistry which competency could be used to
initiate ways to improve the growth of plants or to
solve problems in plant growth agriculture.

The Core of Plant Biochemsitry

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 fats,

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

BASIC PRINCIPLE
Living organisms, whether they are
plants, animals or microbes, are
made up basically of the same
chemical components
Biochemical Reactions
SUBSTRACT(S) + ENZYME

PRODUCT(S)

Breakthroughs in Biochemistry
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

DNA

RNA

Protein

COURSE SUBJECTS
1.
2.
3.
4.

INTRODUCTION
ENZYME
CARBOHYDRATE
METABOLIC
ENERGY
5. NITROGEN

6. BIOLOGICAL N
FIXATION
7. LIPID
8. NUCLEIC ACID
9. PROTEIN
10. SECONDARY
METABOLITES

REFERENCES
1. Conn, E.E. & Stumpf, P.K., 1976. Outlines of
Biochemistry. John Wiley & Sons, New York.
2. Goodwin, T.W. & Mercer, E.I.,???. Introduction to
Plant Biochemistry. Pergamon Press, Oxford.
3. Stryer, L., 1975. Biochemistry. W.H. Freeman and
Company, San Francisco
4. Wood, W.B., Wilson, J.H., Benbow, R.M., & Hood, L.
E., 1981. Biochemistry A Problems Approach.
5. Wood, J.H, Keehan, C.W., Bull, W.E. and Bowman,
N.S., 1963. Fundamentals of College Chemistry. A
Harper International edition, Harper & Row, NY,
Evanston & London and John Weatherhill, Inc.,
Tokyo

Examples of Plant
Biochemistry

What is Cloning?
Cloning is to make a genetically
identical organism through non-sexual
means.
Cloning of African violets:
Take a leaf from a plant
Immerse the stalk in
water

What is Cloning?
Roots start to form after a week
Pot the plant
A new plant
is produced

How Dolly was cloned?

Sel telur

Sel
induk

Sel telur dengan inti dari induk yang

berkembang menjadi anak domba
yang sama dengan induknya

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

3
2
+
O

OH
A

4
B

5
6

C
OH

OH
ANTHOCYANIDIN

ANTHOCYANIDIN
Pelargonidin
Cyanidin
Delphinidin
Peonidin
Petunidin

Substituents
4-OH
3-OH,4-OH
3-OH,4-OH,5-OH
3-OCH3,4-OH
3-O CH3,4-OH,5O CH3

Color
Orange-red
Purplish red
Bluish purple
Rosy red
Purple

Sex & Genetics

The traits inherited from both parents are

determined by genes in DNA

Genetic Inheritance & DNA

Short segment of a
DNA molecule
Two polynucleotides
associate to form a
double helix
Genetic information is
carried by the sequence
of base pairs

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 tersebut

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

Auxin

Ethylene

Cellulase/Polygalacturonase

Transpor auxin dari tempat pembentukan pada

bagian ujung daun ke lapisan absisi dihambat
oleh hormon ethylene

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.

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

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.

Cyanide Poisoning
Antidote
Nitrites and Sodium Thiosulfate
Sodium Nitrite
Oxyhemoglobin

Rhodanase

Methemoglobin

Cyano-methemoglobin

Sodium Thiosulfate
Thiocyanate

Kidneys

CYTOCHROME
OXIDASE
CN

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

FA

Fatty Acid
Alcohol
Glycerin

FA

FA

FA

Biodiesel

Vegetable Oil

Biodiesel Samples

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:

CH2OOR1
catalyst
|

CHOOR2 + 3CH3OH 3CH3OORx

|
CH2OOR3

Triglyceride

3 Methanols

Biodiesel

CH2OH
|
+ CHOH
|
CH2OH

Glycerin

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.)

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.
H O
| |
HCOR1
|
HCOOR2
|
HCOR3
| |
H O

H
|
+ HCONa
|
H

+H2O

Triglyceride + Methoxide + H2O

H
|
HCO
H O
|
| |
CHOOR2 + HCOR1 + NaOH
|
|
HCOR3
H
| |
H O

Diglyceride + Biodiesel + NaOH

NOTES TO REMEMBER

Functional groups in biochemistry

Functional groups - specific parts of molecules
involved in biochemical reactions
Figure 1.2 shows the general formulas of:
(a) Organic compounds

(b) Functional groups

(c) Linkages common in biochemistry

(R represents an alkyl group (CH3CH2)n-)

Fig 1.2 (a) General formulas

Fig 1.2(b) General Formulas

Fig 1.2 (c) General Formulas

Many Important Biomolecules are

Polymers
Biopolymers - macromolecules created by
joining many smaller organic molecules
(monomers)
Condensation reactions join monomers
(H2O is removed in the process)
Residue - each monomer in a chain