Biochemistry for Chemists
GENERAL OBJECTIVES:
1. Understand the phenomenon of intermediary metabolism
2. Understand the pathways of carbohydrate, protein and lipid metabolism
3. Understand proteins
4. Understand enzymes
Intermediary metabolism
1.1 Explain that metabolism in a living cell constitutes catabolic (breakdown) and anabolic (synthesis) processes which occur simultaneously.
1.2 Explain intermediary metabolism as the interchange ability of derivatives (metabolites) of carbohydrates, proteins and fats (lipids) via reactions mediated by appropriate enzymes and coupled by relevant coenzymes/cofactors.
1.3 Illustrate and explain intermediary metabolism by simple schematic diagrams
1.4 Illustrate the central role of acetyl CoA in intermediary metabolism.
1.5 Describe how the energy for cellular metabolism is derived from the break down of acetyl COA
1.6 Explain how the energy from 1.5 above is captured in the form of ATP (adenosine triphosphate) which is reversible.
1.7 Describe ATP as the universal energy currency in biological systems.
1.8 Explain how energy released from the degradation of some substrates may be utilized in the formation of other cellular components
1.9 Explain that the sum total of breakdown of carbohydrates, fats and proteins is a chain reaction involving transfer of reactions which lead to the final products of cellular respiration (CO2 + H2O) and ATP.
1.10 Describe the ATP cycle and explain how ATP forms the energy currency in biological system.
Nutrient metabolism
2.1 List the enzymes and products of digestion of carbohydrate.
2.2 Explain the term substrate level phosphorylation.
2.3 Define glycolysis as the pathway of breakdown of phosphorylated sugars to provide energy and lactate.
2.4 Describe the glycolytic pathway and the conversion of pyruvate to acetyl COA.
2.5 List the key enzymes of glycolysis.
2.6 Identify the steps that consume or yield energy in the glycolytic pathway.
2.7 Deduce the net energy yield of this glycolytic pathway.
2.8 Distinguish between aerobic and anaerobic glycolysis.
2.9 Describe the alternative pathway of glucose oxidation (pentose phosphate pathway/hexose monophosphate shunt)
2.10 State the biochemical importance of 2.9 above.
2.11 Describe glucogenesis, gluconeogenesis, glycogenesis and glycogenolysis.
2.12 Describe the Cori cycle.
2.13 Explain Pasteur effect.
2.14 Define oxidation of fatty acids.
2.15 Describe the processes occurring in fatty acid oxidation (activation dehydrogenation, hydration, further dehydrogenation and Thiaclastic cleavage).
2.16 Explain how all reactions of boxidation of fatty acid are reversible.
2.17 Explain how fatty acids undergo activation in the cytosol and enters the mitochondrion where it undergoes boxidation.
2.18 Describe the b -oxidation of fatty acids to acetyl COA.
2.19 Explain that the acetyl COA produced in fatty acid oxidation enters the TCA cycle for further degradation.
2.20 Describe the oxidation Via propionic acid of branched and odd-numbered fatty acids.
2.21 Explain that FADH2 and NADH + H+ produced in fatty acid oxidation are also oxidized through the electron transport system of the mitochondria eventually by molecular oxygen.
2.22 Compare the energy yield when one mole each of saturated and unsaturated fatty acids of equal chain length are completely oxidized.
2.23 Describe the formation and metabolism of ketone bodies (acetone, acetoacetate and p-hydroxy butyrate).
2.24 Describe the biosynthesis of fatty acids.
2.25 Describe the two pathways of fatty acid biosynthesis (cytoplasmic, mitochondrial)
2.26 Explain that the cytoplasmic pathway is the major pathway of fatty acid synthesis.
2.27 Describe the biosynthesis of triglycerides and phosphatides (phospholipids).
2.28 Describe the biosynthesis of sterols from cholesterol.
2.29 List the enzymes and products of protein digestion.
2.30 Explain how amino acids can be a source of cellular energy (surplus amino acids).
2.31 Explain how the carbon skeleton of amino acids are either converted into fatty acids and glucose or oxidized via the TCA cycle.
2.32 Explain the terms: ketogenic and glucogenic amino acids.
2.33 List ketogenic and glucogenic amino acids.
2.34 Explain transamination and oxidative deamination.
2.35 Write chemical equations to illustrate the process in 2.37 above.
2.36 Describe the formation of urea (urea cycle).
3.1 Know the structures of the common amino acids
3.2 Understand that amino acids are linked by peptide bonds to give polypeptide chains
3.3 Know that proteins consist of one or more polypeptide chains
3.4 Know the common conventions and be able to use shortened nomenclature to give the sequence of a polypeptide chain 3.4 Know the common techniques used to purify proteins
3.5 Know an experimental technique for sequence determination based upon degradation
3.6 Understand that the 3D shape of a protein may be obtained from single crystal X-ray diffraction experiments
3.7 Know the local folding (conformations) motifs for polypeptide chains
3.8 Understand primary, secondary, tertiary and quaternary structure.
3.9 Understand that the shape and function of the protein is defined by its primary sequence
3.10 Be familiar with models of some simple proteins (e.g. albumin, ribonuclease, etc) and relate structure with function.
4.1 Describe the distinctive features of enzymes e.g. active site specifically etc.
4.2 Explain enzymes specificity as the basis of classification.
4.3 Explain and determine enzymatic catalysis measurement by the rate of disappearance of substrate or formation of products.
4.4 Determine the effect of activators and inhibitors experimentally.
4.5 Define enzyme activity and specific enzyme activity in international units (I>U) and S>I unit.
4.6 Explain methods of enzyme assay.
4.7 Carry out enzymatic assay of a coloured substrate e.g. 4 nitropheny/phosphate by acid or alkaline phosphate.
4.8 Describe the assay for enzyme activity for a turbid substrate like milk e.g. xanthine oxidase in milk.
4.9 Explain coupled enzyme assays.
4.10 Explain how an enzyme reversibly combines first with its substrate to form an enzyme substrate complex.
4.11 Explain why the process of product formation from 4.10 above is a slow process.
4.12 Explain the term Rapid Equilibrium in the above example
4.13 Explain steady state and Pre-steady state.
4.14 Explain and determine enzymecatalysed reactions measurement under initial rate (Vo) conditions
4.15 Derive the Michealis-Menten equation from the expression:
E + Sk1k2 ESk3k4 E+P
4.16 Explain the Kinetic constant, Km, Vmax, Kcat.
4.17 Explain the physiological significance of Km.
4.18 Describe the determination of Km and Vmax by using line weaver Buck plots.
4.19 Show that Km and Vmax can also determined by Eddie-Hoffsted plots.
4.20 Carry out calculations/plots based on 2.17-2.20 above.
4.21 Relate recognition of substrate to the structure (shape and electronic nature) of the substrate and the complementary structure of the active site on the protein surface of the enzyme.
4.22 Relate catalysis to the preferential binding of the enzyme to the transition state for the reaction in preference to substrates or products.
4.23 Show the above preferential binding by relating it to structural diagrams, curly arrow mechanisms, and Energy diagrams.
4.24 Define cofactors, activators, coenzymes and prosthetic groups.
4.25 Explain how the rate of enzymatic catalysis can be affected by the presence of cofactors and inhibitors.
4.26 Define reversible inhibitors.
4.27 Distinguish 2.26 above using the line Weaver-Buck plots.
4.28 Distinguish between competitive, non uncompetitive inhibitors.
4.29 Describe transition state analogues as reversible inhibitors and relate this to chemical structure.
4.30 Discuss some transition state analogues that inhibit enzymes (e.g. pepstatin inhibition of pepsin and other carboxyl proteases) and relate the structure of the inhibitor to the transition state in the catalysed reaction