Lecture 1- Metabolism: Basic Concepts and Design Chem 454: Regulatory Mechanisms in Biochemistry University of Wisconsin-Eau Claire 1 Introduction Questions we will focus on this semester: How does a cell extract energy and reducing power from its environment? How does a cell synthesize the building blocks of its macromolecules and the then the macromolecules themselves? How are these processes integrated and regulated? 2 2 Living organisms require an input of free energy to meet various needs: For mechanical work Introduction For active transport of molecules and ions For synthesis of biomolecules 3 3 Living organisms require an input of free energy Phototrophs Use energy from the sun to convert energy-poor molecules into energy rich molecules Chemotrophs Introduction btain energy by oxidizing the energy-rich molecules made by the phototrophs 4 4
Introduction Reduced molecules are energy-rich xidized molecules are energy-poor 5 5 Energy from photosynthesis or the oxidation of fuels can be transformed into an unequal distribution of ions across a biological membrane. The ion gradient can be used for xidative phosphorylation to make ATP Active transport across membranes Nerve transmission Introduction 6 6 Ion gradients: Introductions 7 See Chapter 2.3.3 7 Metabolism Metabolism is composed of many coupled interconnecting reactions 8 8
Metabolism 9 9 Metabolism Classes of metabolic pathways: Catabolic pathways Those that convert energy into biologically useful forms Fuels (carbohydrates, fats) C 2 + H 2 + useful energy Anabolic pathways Those that require an input of energy Useful energy + small molecules complex molecules 10 10 11 Metabolism Basic concepts of metabolism include: Thermodynamically unfavorable reactions can be driven by favorable reactions. ATP is the universal currency of free energy. ATP hydrolysis drives metabolism by shifting the equilibrium constant of coupled reactions. There is a structural basis for the high phosphoryl transfer potential of ATP. The phosphoryl transfer potential is an important form of cellular energy transformation. 11 Thermodynamics Thermodynamically unfavorable reactions can be driven by favorable reactions. Free energy change for a reactions: A + B Æ C + D Ê DG = DG 0' + RT lná C Ë A [ ][ D] [ ][ B] ˆ 12 12
Thermodyamics Coupling unfavorable reactions with favorable ones A B + C DG o' = +5 kcal mol -1 B Æ D DG o' = -8 kcal mol -1 A Æ C + D DG o' = -3 kcal mol -1 13 13 ATP ATP is the universal currency of free energy 14 14 Hydrolysis of ATP: ATP ATP + H 2 ADP + P i DG o ' = -7.3 kcal mol -1 ATP + H 2 AMP + PP i DG o ' = -10.9 kcal mol -1 15 15 ATP Hydrolysis ATP hydrolysis drives metabolism by shifting the equilibrium of coupled reactions 16 16
17 ATP Hydrolysis Problem: Under standard conditions, the free energy for the hydrolysis of L-glycerol phosphate to form glycerol and inorganic phosphate is -2.2 kcal/ mol. Calculate the factor by which the equilibrium ratio for the concentration of L- glycerol phosphate to glycerol is increased when ATP is used as the phosphoryl donor for the formation L-glycerol phosphate in place of inorganic phosphate. Do this calculation for liver where the concentrations for ATP, ADP and P i are 3.5 mm, 1.8 mm and 5.0 mm, respectively. 17 Phosphoryl transfer is a common means of energy coupling Molecular motors Muscle contraction Ion pumps ATP Hydrolysis 18 18 Structural basis for high transfer potential Compare: Phosphoryl Transfer ATP + H 2 ADP + P i DG o ' = -7.3 kcal mol -1 Glycerol 3-phosphate + H 2 Glycerol + P i DG o ' = -2.2 kcal mol -1 19 19 Phosphoryl Transfer Phosphate ester vs Phosphate anhydride CH 2 H CH H CH 2 P Adenosine P P P Glycerol 3-phosphate Adenosine triphosphate (ATP Y CH 2 P P P X P 20 Phosphate ester Phosphate anhydryde 20
Phosphoryl Transfer Stabilization of orthophosphate resonance stabilization electrostatic repulsion hydration 21 21 Stabilization of rthophosphate Resonance stabilization rthophosphate Pyrophosphate 22 22 Phosphoryl Transfer and Energy Transfer There are other molelcules with favorable phosphoryl transferase energies 23 23 Phosphoryl Transfer In terms of energy for phosphoryl transfer, ATP is intermediate: 24 24
Question: Phosphoryl Transfer What information do the G o data given in Table 14.1 provide about the relative rates of hydrolysis of pyrophospate and acetyl phosphate? 25 25 Phosphoryl Transfer Creatine phosphate is used to generate ATP in the short term: 26 26 Cellular Energy The oxidation of Carbon fuels is an important source of cellular energy 27 27 Cellular Energy The oxidation of Carbon fuels is an important source of cellular energy 28 28
Cellular Energy High phosphoryl transfer potential compounds can couple carbon oxidation to ATP synthesis. Ion gradients across membranes provide an important form of cellular energy The extraction of energy from foodstuffs occurs in stages. 29 29 Coupling oxidation to ATP synthesis High phosphoryl transfer potential compounds can couple carbon oxidation to ATP synthesis. Example from glycolysis: C H CH H + NAD + + H P C P CH H + NADH + H + CH 2 P CH 2 P 30 Glyceraldehyde 3-phosphate 1,3-Bisphosphoglycerate 30 Coupling oxidation to ATP synthesis In the next step ATP is harvested from the high energy phosphate intermediate. C P C H CH H + ADP CH 2 P 1,3-Bisphosphoglycerate CH H + ATP CH 2 P 3-Phosphoglycerate 31 31 Ion Gradients Ion gradients across membranes provide an important form of cellular energy 32 32
Cellular Energy Ion gradients across membranes can be used to synthesize ATP 33 33 Cellular Energy Extraction of energy from foodstuffs is carried out in stages: 34 34 Recurring Motifs in Metabolism Activated carriers exemplify the modular design and economy of metabolism. Key reactions are reiterated throughout metabolism. Metabolic processes are regulated in three principle way. 35 35 36 Activated Carriers ATP is an activated carrier of phosphate groups ther examples include: Activated carriers of electrons in oxidation reactions Activated carriers of electrons in reductive biosynthesis Activated carriers of two-carbon fragments 36
Activated carriers of electrons in catabolism NAD + (Nicotinamide Adenine Dinucleotide) 37 37 Activated carriers of electrons in catabolism FAD (Flavin Adenine Dinucleotide) 38 38 Activated carriers of electrons in catabolism Reduction of isoalloxazine ring of FAD 39 39 Activated carriers of electrons in biosynthesis NADPH (Nicotinamide Adenine Dinucleotide) 40 40
Activated carriers of acyl groups Coenzyme A is a carrier of Acyl groups 41 41 Activated Carriers ther common activated carriers: 42 42 Key Reactions There are six basic reactions in metabolism: 43 43 Metabolic motifs Key Reactions 44 44
Metabolic Regulation Metabolic processes are regulated in different ways: Enzyme levels (Genetic control) Enzyme activity (Allosteric control) Accessiblity of substrates to the enzyme (Competitive inhibition) 45 45 Metabolic Regulation Degradative and biosynthesis pathways are usually distinct Compartmentalization Allosteric control 46 46 Metabolic Regulation The energy charge [ ATP] + Energy Charge = 1 2[ ADP] [ ATP] + [ ADP] + [ AMP] 47 47