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Quiz #4/5. Quiz #4/5. #4: Glycolysis (Tuesday, Feb 20 th ) #5: TCA cycle (Monday, Mar 5 th ) Pathways are in the books Quiz will have the entire pathway: All cofactors will be present Random intermediate and enzymes removed You fill in the missing names
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Quiz #4/5 • #4: Glycolysis (Tuesday, Feb 20th) • #5: TCA cycle (Monday, Mar 5th) • Pathways are in the books • Quiz will have the entire pathway: • All cofactors will be present • Random intermediate and enzymes removed • You fill in the missing names • Draw the structure for 1 intermediate • Indicated by a larger box
Effects of pH on Enzyme Activity • Protonation state of side chains • Variation in protein structure • Substrate binding • catalysis • Ionization of substrate • Substrate binding
Temperature Protein unfolding
Control of Enzyme Availability Principles of Genetic Regulation
Types of Enzymes“Control of Gene Expression” • Constitutive Enzymes: e.g. glycolytic enzymes and gluconeogenic enzymes • Inducible Enzymes: e.g. b-galactosidase • Repressible Enzymes: e.g. ten enzymes of histidine biosynthesis
Negative Regulators[Bind to operators or upstream repression sequences (URS)]
Positive Regulators[Bind to promoters, enhancers or upstream activation sequences (UAS)]
Regulation of Enzyme Catalytic Activity Covalent Modification Allosteric Enzymes
Principles Governing Controls of Enzyme Catalytic Activity • Regulatory Enzymes • Enzyme catalyzing committed, rate-limiting step (often first step) • Thermodynamically highly favorable reaction • Outcomes of Regulation • Feedback inhibition (fbi) of biosynthetic pathways • Modulation of metabolic flux
Protein Modification(Phosphorylation/Dephosphorylation) Page 390
Non-covalent Modification Effectors or Ligands Positive: activators Negative: inhibitors
Allosteric Enzymes(Modulation of Enzyme Catalytic Activity) • Substrate Binding • Catalytic Rate • Both
Glycogen Phosphorylase Figure 12-16
Rationale for Regulation Efficiency and Flexibility
Biological Efficiency • Biosynthesis • Synthesize precursors not available in diet • Cease synthesis when precursors become available in diet (pre-existing enzymes) • Produce precursors and macromolecules at appropriate rates • Catabolism • Degrade most appropriate nutrients at appropriate rates
Biological Flexibility • Adaptaton to Dietary Changes • Need for biosynthetic products • Catabolism of new nutrients • Control of pre-existing enzymes • Metabolic Flux • Rates of metabolism reflecting needs for energy and macromolecular synthesis
Control Mechanisms • Control of Enzyme Availability • Induction/repression • Control of Enzyme Activity • Covalent/Non-covalent • Control of Substrate Availability
Types of Regulation • Specific: pathway’s substrate or product • General: needs for C or N sources or growth rates (e.g. energy charge)
Signals Mediating Regulation Availability of Substrates or Products (Ligands) Regulatory Proteins
Mechanisms of Complex Feedback Inhibition • Cumulative: sum of individual inhibitions • Concerted: both end products required for inhibition • Isoenzyme: two enzymes, each inhibitable by different end product
Cumulative Feedback Inhibition D E D D E E A A B B C C A B C F F G G F G
Concerted Feedback Inhibition D E D D E E A A B B C C A B C F F G G F G
Isozymes D E D E A B C A B C F G F G D E A B C F G
Modulation of Metabolic Flux Energy Charge
Energy Charge(Daniel Atkinson) Steady-State E.C. = 0.93 ATP, ADP and AMP = Regulatory Ligands
Energy Charge Anabolic pathways (Biosynthesis) Catabolic Pathways (Degradation) Produce ATP Activated Low EC (AMP) Inhibited Hig EC (ATP) • Require ATP • Activated • High EC (ATP) • Inhibited • Low EC (AMP)