Regulation of Metabolic Pathways. 1. Metabolic pathways 2. Basic enzyme kinetics 3. Metabolic pathway regulation
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1 Regulation of Metabolic Pathways 1. Metabolic pathways 2. Basic enzyme kinetics 3. Metabolic pathway regulation
2 Basic Functions of Metabolic Pathways
3 Classification of Reactions! Fueling reactions (catabolic pathways)» Produce precursor metabolites needed for biosynthesis» Generate energy (ATP) for cellular functions» Produce reducing power (NAPDH) for biosynthesis! Biosynthetic reactions (biosynthetic pathways)» Produce building blocks for macromolecular synthesis» Produce coenzymes & signaling molecules! Polymerization reactions» Form macromolecules from building blocks! Assembly reactions» Chemical modifications of macromolecules to form cellular structures (cell wall, membranes)
4
5 Membrane Transport Processes! Free diffusion» Species transported down concentration gradient» Transport driven by chemical potential difference! Facilitated diffusion» Species transported down concentration gradient» Specific carrier or transmembrane protein involved! Active transport» Species can be transported up concentration gradient» Specific proteins or permeases involved
6 ! Basic functions Catabolic Pathways» Generate energy & reducing power» Produce precursors for biosynthesis! Participating pathways» Glycolytic pathway» Pentose phosphate pathway (PPP)» Fermentative pathways» Tricarboxylic acid (TCA) cycle» Anaplerotic pathways» Pathways involved in catabolism of fats, organic acids & amino acids
7 Glycolytic Pathway! Also called the Embden-Meyerhof-Parnas (EMP) pathway! Converts glucose to pyruvate! Generates ATP & NADH! Glucose + 2 NAD+ + 2 ADP + 2 Pi " 2 pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H20! Also produces three precursors for biosynthesis» Glyceraldehyde 3-phosphate (G3P)» 3-phoshoglycerate (3-PG)» Phosphoenolpyruvate (PEP)
8
9 Simplified Picture of Glycolytic Pathway
10 Pentose Phosphate Pathway (PPP)! Converts G6P to NAPDH & two precursors for biosynthesis» Ribose-5-phosphate (R5P)» Erythrose-4-phosphate (E4P)! Also produces glycolytic intermediates F6P & G3P! Relative flux through EMP & PPP varies» Energy & reducing power requirements» Need for precursor metabolites! PPP stoichiometry depends on extent carbon is recycled back to EMP
11 Oxidative PPP
12 Non-Oxidative PPP
13 Overall PPP
14 ! Fermentation Fermentative Pathways» Occurs under oxygen limited conditions» Pyruvate converted into metabolic products (lactic acid, acetic acid, ethanol)! Bacteria» Several different metabolic products formed» Mixed acid fermentation! Yeasts» Ethanol is the main metabolic product» Alcohol fermentation» Limited acetate & succinate also formed
15 Yeast Fermentation
16 TCA Cycle! Also called the citric acid cycle or Krebs cycle! Completely oxidizes pyruvate to produce ATP via oxidative phosphorylation! Location» Bacteria occurs in cytosol» Yeast occurs in mitochondria! Stoichiometry» Pyruvate + CoA + NAD " Acetyl-CoA + CO2 + NADH + H+» Acetyl-CoA + 3 NAD + FAD + GDP + Pi + 2H20 " 2 CO2 + 3 NADH + FADH2 + GTP + 2H+ + CoA
17 TCA Cycle in Yeast
18 Simplified Picture of TCA Cycle
19 Oxidative Phosphorylation in Yeast! Basic functions» Regenerate NAD+ for glycolysis» Generate ATP for biosynthesis! Basic mechanism» Electrons are transported from NADH & FADH through the electron transport chain to oxygen» Electron transport causes protons to be released into the intermembrane space» These electrons can be transported back into mitochondrial matrix by a proton conducting ATP-synthase» The detailed mechanistic steps are not completely understood! Theoretical yields» P/O ratio: 3 ATP/NADH & 2 ATP/FADH» Overall: 15 ATP/pyruvate» Actual yields are lower due to incomplete coupling of the oxidative & phosphorylation processes
20 Oxidative Phosphorylation
21 Biosynthetic Pathways! Generate 12 precursor metabolites needed for cellular synthesis! Amino acid biosynthesis» Forms 20 common amino acids» Well characterized in bacteria & yeast» Consumes considerable energy & reducing power! Biosynthesis of other building blocks» Nucleotides " RNA & DNA» Fatty acids " lipids» UDP-glucose " storage carbohydrates» Also consume energy & reducing power
22
23 Metabolic Pathway Regulation! Basic concepts» Pathways must be regulated to compensate for changes in nutrient availability & cellular demands» Regulated variables include concentrations of substrate, enzyme, product & special regulatory molecules» Regulation implemented over a very wide range of time scales (15 orders of magnitude)! Present focus» Regulation of enzyme activity at relatively short time scales» Best understood form of metabolic regulation
24 Hierarchy of Regulatory Mechanisms
25 Time Scale of Regulatory Mechanisms
26 Enzyme Regulation! Regulation of enzyme activity» Achieved at the metabolic level» Feedback inhibition & activation of enzyme activity by pathway substrate/products or global metabolites (ATP, NADH)» Fast responses (second time scale)! Regulation of enzyme concentration» Achieved at the gene level» Repression & induction of enzyme synthesis» Slow responses (hour time scale)» Focus of lecture on signal transduction networks
27 Michaelis-Menten Kinetics
28 Reversible Inhibition! Substrate inhibition» Rate inhibited by high substrate concentrations v " K max 2 m! S! S / K i! Competitive inhibition v» Inhibitor competes with substrate for enzymatic active sites v " K S vmaxs (1! I / K m i )! S! Non-competitive inhibition» Inhibitor reversibly binds to enzyme on non-active regulatory vmax sites S v " 1! I / Ki Km! S! Uncompetitive inhibition» Inhibitor v reversibly binds to max S enzyme-substrate v " complex 1! I / K Km 1! I / K i! i S
29 Allosteric Enzymes! Cooperativity» Binding to one vacant site induces altered affinities for remaining vacant sites» Homotrophic only substrate involved» Heterotrophic involve substrate & regulator! Allosteric enzymes» Exhibit cooperativity» Composed of multiple catalyic & regulatory subunits» Characterized by sigmoidal velocity curves» Allow large change in reaction rate for small changes in substrate concentration» Facilitate regulation of metabolic pathways where the substrate concentrations exhibit small variations
30 Cooperative Binding! Types of cooperative effects» Positive binding of first molecule activates binding of second molecule» Negative binding of first molecule inhibits binding of second molecule Hill equation n " vmaxs v " K! S number of n n sites
31 Glycolytic Pathway
32 Regulation of EMP & PPP in Yeast! Glycolytic (EMP) pathway» Hexokinase: inhibited by G6P (product inhibition)» Phosphofructokinase Inhibited by ATP & citrate (signals overabundance of TCA cycle intermediates) Activated by AMP & ADP (signal lack of available energy) Activated by ammonia, phosphate & fructose-2,6- bisphosphate (regulatory molecule)» Pyruvate kinase: inhibited by ATP & acetyl-coa! Pentose phosphate pathway» Glucose-6-phosphate dehydrogenase: activity regulated by NAPDH/NADP+ ratio
33 Glycolytic Regulation in Yeast
34 Phosphofructokinase (PFK) Regulation! PFK is a complex allosteric enzyme» Inhibited by ATP» Activated by fructose-2,6-bisphosphate (F-2,6-P)» F-2,6-P formed by phosphorylation of F6P by ATP! Cooperativity» ATP binding decreases affinity for F6P (substrate)» F-2,6-P binding causes large increase in F6P affinity» Glycolytic flux stimulated by F-2,6-P & inhibited by ATP! Regulatory effects» Allows PFK to increase activity in response to increasing F6P concentration» High energy levels suppress PFK activity
35 TCA Cycle in Yeast
36 Regulation of the TCA Cycle in Yeast! Citrate synthase» Weakly inhibited by NADH/NAD+ ratio! Isocitrate dehydrogenase» Strongly inhibited by NADH/NAD+ ratio» Activated by AMP» Inhibited by ATP! Alpha-ketoglutarate dehydrogenase» Weakly inhibited by NADH/NAD+ ratio
37 Regulation at the Gene Level
38 Summary! Metabolic pathways» Classified according to their function» Focused on yeast central carbon metabolism! Metabolic pathway regulation» Essential to control metabolic function» Implemented over a wide range of time scales» Focused on short-term regulation of enzymatic activities» Can involve complex mechanisms! Implications» Complexity necessitates integrative approaches» Metabolic pathway modeling & analysis
39 References! G. H. Braus, Aromatic Amino Biosynthesis in the Yeast Saccharomyces cerevisiae: a Model System for the Regulation of a Eukaroytic Biosynthetic Pathway, Microbiological Reviews, 55, (1991).! J. Nielsen & J. Villadsen, Bioreaction Engineering Principles, Plenum Press, New York, NY (1994).! M. L. Shuler & F. Kargi, Bioprocess Engineering: Basic Concepts, 2 nd edition, Prentice Hall, Englewood Cliffs, NJ (2002).! G. N. Stephanopoulos, A. A. Aristidou & J. Nielsen, Metabolic Engineering: Principles and Methodologies, Academic Press, New York, NY (1998).
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