Principles of Biochemistry: Course Overview and Evaluation Methods

1. (Semester 1 -2017/18) BCH 3000 PRINSIP BIOKIMIA Dr. Syahida Ahmad Jabatan Biokimia Fakulti Bioteknologi & Sains Biomolekul Email: syahida@upm.edu.my H/P: 010-4009727 1

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3. Course Evaluation Principle of Biochemistry (BCH3000) (Semester 2 -2016/17) 3

4. Exam Mid Term Mid Term = 40% - 13-15 October 2017 Topics covered in test Introduction to Biochemistry Carbohydrates Amino Acids& Proteins Lipids Membranes Nucleicacids Enzymology 4

5. Format Exam Mid Term Mid Term = 40% - 13-15 October 2017 Types of Questions Duration – 3 hours Multiple choice – 80 questions (1 mark each) Short Answers - Choose 4 out of 8 questions ; 5 marks each Total Marks = 100 5 5

6. Course Evaluation Final Examination = 40% Topics covered in exam Carbohydrate metabolism Photosynthesis Lipid metabolism Protein & amino acid metabolism Nucleic acid metabolism Hormones Integration & control of metabolism 6

7. Course Evaluation SCL (Student Centered Learning = 10%) In this exercise, each student is required to produce a model of an oligopeptide using materials from the environment. The model should be able to demonstrate clearly the structural configuration of the oligopeptide. The student will be asked to present the model and explain the structural configuration. 7

8. Course Evaluation SCL (Student Centered Learning) = 10% Model Requirements The student must design and produce a model of an oligopeptide All amino acids must be different from one another and of different group Materials used must be from the environment. No model kit will be allowed. This is also not computer modeling The model should clearly show the structure of the amino acid Student will be asked to explain their respective models 8

9. Course Evaluation SCL (Student Centered Learning = 10% • Week 7 – Submit Oligopeptide Model via email • Week 13/14 – Presentation on the Model • Place – Biotech 2, UPM Serdang • Date – please inform when you are available • Evaluation by a panel 9

10. Course Evaluation ASSIGNMENT (10%) TOPICS Only 2 assignments are required Assignments can be submitted any time but not later that week 8. Assignments can be sent directly to me via e-mail, preferably in pdf formats 10

11. Course Evaluation ASSIGNMENT TOPICS (10%) How is knowledge in Biochemistry important in Human Ecology? (Compulsory) Diabetes mellitus is a group of metabolic disorders of carbohydrate. Describe in detail the statement. (Carbohydrate metabolism) In your own words, describe how carbohydrate, lipid and protein metabolism are interrelated. (Integration of metabolism) 11

12. Sinopsis This course encompasses the main biomolecule components in biochemistry. Metabolism involving the anabolism and catabolism of major biomolecules are also explained. 12

13. Learning Outcome • Membezakan struktur dan fungsi biomolekul yang terdapat dalam sistem biologi (C4) • Menyatakan pelbagai proses metabolisme yang utama (P2) • Menerangkan tindakbalas biokimia (A3) • Menyelesaikan masalah dalam metabolisme biomolekul dengan menggunakan maklumat dari pelbagai sumber (CTPS, LL) 13

14. Brief Lecture Contents • Introduction-Biochemistry? Contributions? Important life components • Carbohydrates – Classification–mono , di, polysaccharides – Structure–configuration & stereochemistry; reactions – glucose and other sugars • Amino acid & protein – biological roles, structure, classification, reactions, analysis. Peptides – primary, secondary, tertiary and quaternary structures • Lipid – functions & distribution, characteristics of fatty acids-saturated & unsaturated f/acids. Structures & characteristics of triacylglycerols, phospholipids, sphingolipids, terpenes & steroids 14

15. Brief Lecture Contents • Nucleic acids – components – purines, pyrimidines. Structure, reactions & importance of nucleosides, nucleotides & polynucleotides. DNA, RNA – structure, functions & types • Enzymology – Classification, naming, active sites. Enzyme kinetics. Factors affecting enzyme activity- enzyme & substrate concentration, pH, temperature . Substrate specificity – single & multiple substrate. Enzyme inhibitors – competitive, con-competitive, uncompetitive. Control of enzyme reactions – product inhibition, Isoenzymes, multienzyme system and allosteric enzymes 15

16. Brief Lecture Contents • Carbohydrate metabolism – Metabolic energy cycle – Bioenergetics: ATP other high energy compounds. Storage & energy transfer. Glycolysis & fermentation. Electron transport system. Compartmentation & mitochondria. Phosphorylation & production of ATP. Anaplerotic reactions. Glyoxylate cycle. Gluconeogenesis. Pentose phosphate pathway. Integration and control. • Photosynthesis – Fixation of CO2 during photosynthesis. Chlorophyll, components of photosynthesis. Photosystem I & II. Photophosphorylation. Calvin cycle. Hatch-Slack cycle. 16

17. Brief Lecture Contents • Lipid metabolism – Lipid oxidation- Enzymes involved, energy production. Oxidation of saturated & branched fatty acids. Formation of ketone bodies. Lipid biosynthesis –mitochondrial system and extra-mitochondrial. Cycle & enzymes involved. Synthesis of saturated & unsaturated fatty acids. Cholesterol synthesis & control. • Protein & amino acid metabolism – Degradation of amino acids- transamination, deamination, decarboxylation. Cycle involved- intermediates for the TCA cycle. Ammonia and urea metabolism. Biosynthesis of amino acids- role in the metabolism of porphyrin and nucleic acids. Nitrogen fixation. 17

18. Brief Lecture Contents • Nucleic acid metabolism – synthesis of mononucleotides – purines, pyrimidines – cycle and enzymes involved; control. Biosynthesis of ribo & deoxyribonucleotides. Characteristics of genetic materials – chromosomes. Genetic code, base sequence. DNA replication. DNA repair. Protein synthesis – ribosome, co-factor involved & phase of synthesis. Inhibition and control of synthesis. • Membrane Biochemistry – Modification & structure. Model for membrane structure. Transport mechanism across membrane – passive & active transport. 18

19. Brief Lecture Contents • Hormones- Introduction to plant & animal hormones. Reactions & control of endocrine hormones. Hormone reactions at the molecular level. • Integration & control of metabolism. Relationship between carbohydrate, lipid and protein metabolism. 19

20. Why study biochemistry? • Part of curriculum • Explain a lot of the controversies in the news at the moment. • Stem cell study • Cloning of the human being • Diseases (defect in metabolism) • GM (genetically modified)food and organisms 20

21. BIOCHEMISTRY: A PROLOGUE Biochemistry = the chemistry of life. •  bridges the gap between chemistry (the study of the structures and interactions of atoms and molecules) and biology (the study of the structures and interactions of cells and organisms). • Since living things are composed of inanimate molecules, life, at its most basic level, is a biochemical phenomenon. Inert; not living; not lively 21

22. Living organisms • diverse in their macroscopic properties • BUT remarkable similarity in their biochemistry that provides a unifying theme with which to study them. • For example, hereditary information is encoded and expressed in an almost identical manner in all cellular life • the series of biochemical reactions= metabolic pathways, as well as the structures of the enzymes that catalyze them are, for many basic processes, are nearly identical from organism to organism. 22

23.  This strongly suggests that all known life forms are descended from a single primordial ancestor in which these biochemical features first developed 23

24. Although biochemistry is a highly diverse field, it is largely concerned with a limited number of interrelated issues. These are • What are the chemical and three-dimensional structures of biological molecules and assemblies, how do they form these structures, and how do their properties vary with them? • How do proteins work?- what are the molecular mechanisms of enzymatic catalysis, how do receptors recognize and bind specific molecules, and what are the intramolecular and intermolecular mechanisms by which receptors transmit information concerning their binding states? 24

25. How is genetic information expressed and how is it transmitted to future cell generations? • How are biological molecules and assemblies synthesized? • What are the control mechanisms that coordinate the myriads of biochemical reactions that take place in cells and in organisms? • How do cells and organisms grow, differentiate, and re­produce? 25

26. History of Biochemistry • fairly new field of science -the 20th century • first landmark of biochemistry - Friedrich Wohler (1828) synthesized the organic compound urea from the inorganic compound ammonium cyanate • building blocks of life were the same as those of non-living things • The role of enzymes as catalyst - Buchner showed that a process of biochemistry, catalysis, could occur independently from living cells (enzymes in yeast extracts and fermentation) 26

27. History of Biochemistry • Fischer developed the lock and key model (enzyme as rigid lock, substrate as key) A modified version of this model (induced fit) is still used today • The second part of the 20th century saw advances in structural biology especially the structure of proteins • The first protein structures were determined by John C. Kendrew and Max Perutz in the 1950s and 1960s. • Now have determined the structures of more than 1000 proteins. 27

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29. History of Biochemistry • The role of nucleic acid as information molecules • In 1944 Oswald Avery et al extracted DNA from a toxic strain of a bacteria and when added to a nontoxic strain resulted in the bacteria being transformed into a virulent strain. • Watson and Crick (1950) deduced the 3D structure of DNA. • Crick predicted that information encoded in DNA is transcribed to ribonucleic acid and then translated to protein. • This unidirectional information flow is referred to as the central dogma of molecular biology 29

32. BIOLOGICAL STRUCTURES Living things are enormously complex. • simple E. coli cell contains some 3 to 6 thousand different compounds, most of which are unique to E. coli ; Homo sapiens (human beings), may contain 100,000 different types of molecules, although only a minor fraction of them have been characterized. •  biochemical understanding of any organism would be a hopelessly difficult task ??  No !!!! - Why ???? 32

33. Living things have an underlying regularity that derives from their being constructed in a hierarchical manner. Multicellular organisms Organizations of organs Tissues Cells Subcellular organelles Supramolecular assemblies of macromolecules 33

34. An example of hierarchical organization of biological structures 34

35. The cell is the basic unit of life Cells are classified as eukaryotes or prokaryotes 1. Prokaryotes (bacteria) • Ubiquitous, no nucleus, only approx 1000 genes 2. Eukaryotes (plants, animals, fungi and protists) • Membrane bound nucleus, 1000 fold greater in volume. 35

36. An animal cell 36

37. A plant cell 37

38. What makes a living thing? 38

39. The Chemical Elements of Life • Only six nonmetallic elements make up 97% of the weight of most organisms – carbon, oxygen, hydrogen, nitrogen, phosphorous and sulfur. • All form stable covalent bonds. • here are also 5 common ions found in all organisms: - Calcium (Ca2+), Potassium (K+) Sodium (Na+), Magnesium (Mg2+), Chloride (Cl-) • Water is a major component of cells. • Altogether, a total of 29 different elements are commonly found in living organisms. 39

40. Brown – important elementspurple – essential ionsdark blue – more common trace elementslight blue – less common trace elements 40

41. Organic compounds • Most of the solid material of cell consists of carbon-containing compounds (organic compounds). • The organic compounds of interest is shown 41

42. Functional Groups • These organic compounds have own specific functional groups 42

43. The elements of life are assembled into molecules with common structures and patterns – how ?? – via linkages (bonds) 43

44. Water Properties • All living cells depend on water for their existence. • Metabolic machinery of cells has to operate in an aqueous environment • Water molecule – polar • Water molecule is V-shaped with an angle of 104.5O 44

45. Noncovalent Interactions in Biomolecules There are 4 types of noncovalent interactions. • Charge-charge interactions • Electrostatic interactions between two charged particles e.g. NaCl • The strongest noncovalent forces • Also responsible for mutual repulsion of similarly charged ionic groups 45

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47. 2. Hydrogen bonds • A type of electrostatic interaction which occurs in many macromolecules • Among the strongest noncovalent forces in biological systems • Strong enough to confer structural stability but weak enough to be readily broken. • Can form when a hydrogen covalently bonded to a strong electronegative atom, such as nitrogen, oxygen and sulfur 47

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49. Hydrogen bonding 49

50. 3. Van der Waals Forces • Weak intermolecular forces produced between all neutral atoms by transient electrostatic interactions • Have attractive and repulsive components • forces that exist between MOLECULES of the same substance 50