THE KNOW LIST: BIS103 FINAL EXAM
General:
The final exam will focus on material after the second midterm (about 60%) and the rest cumulative. Questions
on more recent material will be more detailed than those addressing material covered in midterms 1 and 2.
Structures, be able to recognize from name and structure:
See Structure Know List
Pathways to know the reaction steps of and overall role in metabolism
 Anaerobic glycolysis (Lactate/Ethanol fermentation pathways)
 Aerobic glycolysis
 Catabolism of glycerol
 Gluconeogenesis
 Glycogen (starch) synthesis and breakdown
 Breakdown of CHO other than glucose
 AA breakdown (Ala, Gly, Ser, Glu, Gln, Asp, Asn) and synthesis
 TAG and fatty acid breakdown and synthesis
 PPP
 ETC (mitochondria and photosynthesis)
Other things to know
 Concept of pathway cooperation, common pathway intermediates, and opposing pathway reactions.
 Gibbs (standard) free energy, equilibrium, Keq, Q. Know how to use G, G0’, E0’ (as concepts of
reaction coupling and predictions of direction; I will NOT ask calculation questions).
 Pathways that utilize GLC and pathways that utilize acetyl-CoA.
 Role of co-factor covered in class, e.g. give example and/or recognize reaction that uses co-factors.
 Roles and general reaction steps of PPP, which parts flux under what conditions?
 Ketogenesis: When and where does it occur? Why are ketone bodies important?
 Distinguish
between
substrate-level
phosphorylation,
oxidative
phosphorylation
(ETC),
photophosphorylation (Photosynthesis).
 Know reactions (not exact mechanism) of complexes of respiratory electron transport (ETC, complexes IIV), reaction of ATP synthase (F0 and F1 domain major functions, rotation, beta-subunit conformational
changes).
 Understand the function/impact of uncouplers in/on the ETC and ATP formation.
 Overall role of the Calvin cycle, RUBISCO reaction (do not memorize pathway or products of Calvin
cycle).
 Compare mitochondrial and plastidial ETC and ATP synthesis, PPP and Calvin cycle.
 Concept of the proton motif force.
 Aminotransferase reactions, use of alpha-KG as universal amino acceptor, Glu as universal donor, role of
PLP, especially amino acid aminotransferase reactions, deamination.
 N removal in different organisms: NH3 in aquatics, uric acid in birds, and urea in terrestrial animals.
 Role and principle of urea cycle (not the structures).
 Know the comparison of net yields of ATP and NADH and FADH2 for glycolysis, TCA cycle, betaoxidation.
 Understand concept of metabolic shuttles for moving electrons or co-factors between compartments.
 Subcellular locations in animals for glycolysis, gluconeogenesis, TCA cycle, FA synthesis, beta-oxidation,
photosynthesis (light reactions and Calvin cycle).
 Names of compartments of mitochondria and chloroplasts and what reaction and pathways happen where.
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Fates of acetyl-coA in animals vs. plants; no net CHO synthesis from FA in animals, but glyoxylate cycle
allows net synthesis of CHO from FA in plants, fungi.
Differences in protein, amino acid metabolism between plants and animals.
Activation of metabolites, adding good leaving groups (thioester, acyl phosphate, enolic phosphate,
acetylation, phosphorylation, high energy compounds etc.); what are common “activated intermediates” in
CHO synthesis, FA synthesis?
Idea and examples of reciprocal regulation, complete vs. partial futile cycling and why futile cycling is
useful?
Types of enzyme regulation, changing specific activity (allosteric regulation, covalent modification).
Enzyme regulation (Why? How? Which?), Properties of physiologically reversible enzymes.
KPIEs, why are these KPIEs, at beginning of pathway, at branch points.
What are common allosteric regulators? Relationship to pathways? What do F2,6bisP and cAMP do?
Mammalian integration of anabolic and catabolic carbohydrate, lipid, and protein metabolism and the role of
hormones and cellular conditions. E.g. Changes in energy sources during fasting or well-fed states in
humans.
Hormonal integration of metabolism, roles of glucagon, insulin and adrenaline.
Common enzymes to know the name and reaction:
 Phosphofructokinase (PFK-1)
 Fructose-1,6-bisphosphatase
 Phosphofructokinase-2 (PFK-2)/Fructose-2,6-bisphosphatase (bifunctional enzyme)
 Glycogen (starch) phosphorylase a, b forms
 Pyruvate dehydrogenase (PDH)
 Lactate dehydrogenase
 Gluco(hexo)kinase
 Pyruvate kinase
 Pyruvate carboxylase
 Glycogen synthase
 Protein kinase A
 Adenylate cyclase
 Lipase
 ETC: Complex I, Complex II (succinate dehydrogenase), Complex III, Complex IV
 ATP synthase
 RuBISCO
 Protease/proteinase
 Glu dehydrogenase
 Serine hydroxymethyl transferase
 Nitrate reductase
 Nitrogenase
 GLN synthetase
 Glutamate Oxoglutarate Amino Transferase (GOGAT)
General enzyme reaction to know:
 Kinase
 Phosphatase
 Ketolisomerase
 Transketolase
 Aminotransferase/Transaminase
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Amino acid hydroxylase
Demaninase
Dehydrogenase
Isomerase
Transferase
Hydrolase
Lyase
Ligase
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