GENERAL INTRODUCTION

LECTURE I :

Intestinal Ca2+-binding protein!

INTRODUCTION

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

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

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 organ Level– Leaves, Stems & Roots

• Organel Level– Chloroplasts, Mitochondria, Nucleus

etc.

• Molecular Level– Enzymes, Carbohydrates, Energy

Molecules, etc

What is Plant Biochemsitry ?

• 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 & 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• 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.

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 PRINCIPLELiving 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

1. Discovery of the role of enzymes as catalysts

2. Identification of nucleic acids as information molecules

Two notable breakthroughs in the history of biochemistry

Flow of information: from nucleic acids to proteins

DNA RNA Protein

COURSE SUBJECTS

1. ENZYME2. CARBOHYDRAT

E3. METABOLIC

ENERGY4. NITROGEN5. BIOLOGICAL

NITROGEN FIXATION

6. LIPID7. NUCLEIC ACID 8. PROTEIN 9. SECONDARY

METABOLITES

REFERENCES1. 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 dengan inti dari induk yang berkembang menjadi anak domba yang sama dengan induknya

Sel induk

Sel telur

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

A C

OH

B

OH

OH

2

1

3

5

6

4

O+

ANTHOCYANIDIN

ANTHOCYANIDIN Substituents Color Pelargonidin 4’-OH Orange-red Cyanidin 3’-OH,4’-OH Purplish red Delphinidin 3’-OH,4’-OH,5’-OH Bluish purple Peonidin 3’-OCH3,4’-OH Rosy red Petunidin 3’-O CH3,4’-OH,5’-

O CH3 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 asam 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 NitriteCYTOCHROME

Oxyhemoglobin Methemoglobin OXIDASE

CNRhodanase Cyano-methemoglobin

Sodium Thiosulfate

Thiocyanate Kidneys

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

Fatty AcidAlcoholGlycerin

Vegetable Oil

BiodieselFA

FAFA

FA

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:

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

CH2OOR1 catalyst CH2OH| |CHOOR2 + 3CH3OH 3CH3OORx + CHOH| |CH2OOR3 CH2OHTriglyceride 3 Methanols Biodiesel 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 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

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 (glukose adalah residu dari amylum)