GENERAL INTRODUCTION

1. GENERAL INTRODUCTION LECTURE I : Intestinal Ca2+-binding protein!

2. 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

3. 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

4. THE BUILDING ELEMENTS OF LIFE • Plant organ Level • Leaves, Stems & Roots • Organel Level • Chloroplasts, Mitochondria, Nucleus etc. • Molecular Level • Enzymes, Carbohydrates, Energy Molecules, etc

8. 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).

9. 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.

10. 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.

11. The Core of Plant Biochemsitry • IsolationandIdentification • Biochemistry is firstly concerned with theisolationandidentificationof 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

12. 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

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

14. Breakthroughs in Biochemistry Two notable breakthroughs in the history of biochemistry • Discovery of the role of enzymes as catalysts • Identification of nucleic acids as information molecules Flow of information: from nucleic acids to proteins DNA RNA Protein

15. ENZYME CARBOHYDRATE METABOLIC ENERGY NITROGEN BIOLOGICAL NITROGEN FIXATION LIPID NUCLEIC ACID PROTEIN SECONDARY METABOLITES COURSE SUBJECTS

16. REFERENCES • Conn, E.E. & Stumpf, P.K., 1976. Outlines of Biochemistry. John Wiley & Sons, New York. • Goodwin, T.W. & Mercer, E.I., Introduction to Plant Biochemistry. Pergamon Press, Oxford. • Stryer, L., 1975. Biochemistry. W.H. Freeman and Company, San Francisco • Wood, W.B., Wilson, J.H., Benbow, R.M., & Hood, L. E., 1981. Biochemistry A Problems Approach. • 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

17. Examples of Plant Biochemistry

18. 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

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

20. How Dolly was cloned?

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

23. ADENIUM OBESUM ' CHERRY' Grafted Desert Rose Family : Apocynaceae Origin : East Africa Size : 5' Light Requirements : Full Sun/Light Shade Water Requirements : Keep DryMin. Temp. : 35° Flower : Year Round

26. Sex & Genetics The traits inherited from both parents are determined by genes in DNA

27. Genetic Inheritance & DNA

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

29. 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

30. Auxin Ethylene Cellulase/Polygalacturonase Gugur daun • Perusakan dinding sel pada lapisan absisi oleh aktivitas enzim CellulasedanPolygalacturonase • Sintesis kedua enzim tersebut terhambat jika kadar hormon tumbuh auxin cukup tinggi • Transpor auxin dari tempat pembentukan pada bagian ujung daun ke lapisan absisi dihambat oleh hormon ethylene

31. 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)

32. Morphine: Opium [est. ~ 10,000 tons] extracted from the poppy Papaver somniferum, Afghanistan spring 06 6100 tons alone.

33. 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

34. 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.

35. Sodium Nitrite CYTOCHROME Oxyhemoglobin Methemoglobin OXIDASE CN Rhodanase Cyano-methemoglobin Sodium Thiosulfate Thiocyanate Kidneys Cyanide Poisoning • Antidote • Nitrites and Sodium Thiosulfate

36. Fatty Acid Alcohol Glycerin 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 FA FA FA Biodiesel Vegetable Oil

37. Biodiesel Samples

38. 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:

39. TransesterificationWhile actually a multi-step process, the overall reaction looks like this: CH2OOR1 catalyst CH2OH |  | CHOOR2 + 3CH3OH  3CH3OORx + CHOH | | CH2OOR3 CH2OH Triglyceride 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.)

40. 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

41. NOTES TO REMEMBER

42. Functional groups in biochemistry • Functionalgroups - 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-)

43. Fig 1.2 (a) General formulas

44. Fig 1.2(b) General Formulas

45. Fig 1.2 (c) General Formulas

46. 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)