Preparation for the FINAL EXAMA general review session with the instructor will be held on Wed., March 16, from 3 - 5 PM in 108 PH; I will try to make myself available as much as possible during the rest of the week. Chapter 1414.4 (p. 543) Gluconeogenesis; where does it deviate from being the reverse of glycolysis... 14.5 (p.549 - 552) The pentose phosphate pathway Chapter 1616.2 (p.606) - The TAC cycle; you should be able to relate it to other interconversions (e.g amino acid metabolism, the urea cycle, fatty acid oxidation and biosynthesis)Chapter 1717.2 Oxidation of fatty acids; the physiology is interesting, but we really start on the bottom of p. 634 with activation and transport into mitochondria (know the role of carnitine, but not its structural formula) know some general principles about complete oxidation of poly-unsaturated fatty acids and odd-number fattyacids, but not the detailed reactions (isomerizatins to move double bonds around, reductions to change two double bonds into one) dealing with propionyl-CoA requires cobalamin (containing cobalt) as a co-factor long chain fatty acid degradation in peroxisomes (generation of hydrogen peroxide) skip pages 648 - 650 (top)17.3 (p. 650) ketone bodies (Fig. 17.18: structures and reactions via HMG-CoA); under what conditions are they particularly relevant? structure of fat and phospholipids; the general function of lipasesChapter 18 18.1 Transaminations and the role of pyridoxal phosphate ammonia from glutamate in the liver 18.2 The urea cycle (p. 634) Chapter 1919.1 The electron transport chain: complexes, mobile carriers, proton pumps understanding of the role of hemes and iron-sulfur centersno need to memorize the Q cycle oxidative phosphorylation chemiosmotic hypothesis; the nature of the electrochemical gradient (two components for the proton-motive force)ATP synthase (overall structure, orientation in the membrane) from Table 19-4 you should understand the following inhibitors (their targets and their effect on electron transport and OXPHOS):cyanide, antimycin A, rotenone, dinitrophenol (DNP), atractyloside, oligomycin understand how Oxygen consumption is measured with an oxygen electrode as a function of time; the need for various substrates (including ADP and inorganic phosphate)uncouplers and thermoregulation (thermogenin (alias UCP)) the role of the adenine nucleotide and phosphate translocasesstop after p. 71819.6 (p. 723) Photosynthesis light reactions; recognize chlorophyll or other pigments, but no need to memorize structural formulae skip sections on bacteria, but concentrate on the "Z-scheme" in higher plants; know the components (generalnames) of the electron pathway in photosystems I and II (where are the quinones, where are the chlorophylls, the Fe-S centers, the heme/cytochrome, the ferredoxin, plastocyanin, flavin-containing oxidoreductase, oxygen evolving complex, why manganese ion,.... ) the antenna complex and the role of accessory pigmentsexciton transfer and photo-oxidationcompartmentalization of the chloroplast and its significance: where do reactions take place and where is the proton gradient comparison of ATP synthesis in chloroplasts and mitochondriacyclic photophosphorylation Chapter 20 dark reactions in photosynthesis p. 746 understand the Calvin cycle with intermediates and utilization of ATP and NADPH note parallel reactions with those shown in Fig. 15-15simplified form of aldolase and transketolase reactions (as shown in class) with no need to memorize the precise structural formulae of 4 carbon or 7 carbon intermediates (i.e. the correct stereochemical position of OH and H in the linear representation of the sugar intermediates) or the various isomers of the pentoses (except ribulose 1,5 bisphosphate) net reactions some general ideas about coordination/control of light and dark reactions (what does thioredoxin do?)photorespiration and the glycolate pathway: no detailed pathway, but understand that three subcellular organelles are involved; what is the net reaction?C3 vs C4 plants: how to increase the CO2 concentration in bundle sheath cells; role of mesophyll cell; the C4 pathway and its costs (ATP, NADPH). stop on p. 771, but pay attention to Fig. 20.26 in comparison to Fig. 15-21 and 15-15.22Chapter 21 synthesis of fatty acids the general role of biotin in acetyl-CoA carboxylase the reactions of fatty acid synthase (the distinction between the two important SH groups in the enzyme up to p. 798 (with no details on further elongation or desaturase reactions ) 21.4 (p. 816 - 817): biosynthesis of cholesterol, steroids, isoprenoids from acetyl-CoA to mevalonate; skip the details to activated isoprenes (p. 817) know the general possible fates of isopentenyl-pyrophosphate (Fig. 21-48): cholesterol and steroid synthesis synthesis of ubiquinone (used in mitochondria) synthesis of dolichol (used in synthesis of glycoproteinssynthesis of various vitamins what are chylomicrons, HDL, LDL, and VLDL (very general)structures to recognize: thiamine pyrophosphate, NADPH, ubiquinone, FAD, biotin, pyridoxal phosphate, CoA, schematic of acyl carrier protein, vit. B12, ubiquinone structures to remember: most of the molecules in the various cycles and pathways (except the disposal of glycolate);cholestrol and cholesteryl estersno need to remember intermediates/transition states in the enzyme catalysis in most reactions; remember cholesterol and esters of fatty acids and cholesterol THAT'S
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