Metabolism: Basic concepts Hand-out for the CBT version November 2011 This module is based on 'Biochemistry' by Berg, Tymoczko and Stryer, seventh edition (2011), Chapter 15: Metabolism: Basic Concepts and Design. Coupled, interconnecting reactions 1. There are a number of major purposes of living organisms that require a constant input of free energy. Which of the following functions are a purpose of metabolism? o Extract chemical energy from substances obtained from the external environment o Form and degrade the biomolecules of the cell o Convert exogenous foodstuffs into building blocks and precursors of macromolecules o Equilibrate extracellular substances and the biomolecules of the cell o Assemble the building-block molecules into macromolecules 2. The reaction A B has a G of -12.5 kj/mol (-3.0 kcal/mol). A. When will this reaction proceed spontaneously? B. Does the equilibrium constant favour the formation of B over the formation of A? C. Could the equilibrium constant be calculated if the initial concentrations of A and B were known? D. Will the value of G ' also be negative?
ATP as universal currency 3. ATP is the universal currency of energy in biological systems. Why is ATP compared to currency? 4. Glucose 1-phosphate is converted to fructose 6-phosphate in two successive reactions: 1. Glucose-1-P glucose-6-p Gº' = -7.1 kj/mol 2. Glucose-6-P fructose-6-p Gº' = -1.7 kj/mol What is the Gº' for the overall reaction? 5. Consider the reaction: PEP (phosphoenolpyruvate) + ADP + P pyruvate + ATP Gº' = -31.4 kj/mol Calculate Gº' for the hydrolysis of PEP. 6. Inside cells, the DG value for the hydrolysis of ATP to ADP + P i is approximately -50 kj/mol. You know: Gº' = -30.5 kj/mol, R = 0.0083 kj/mol K, T = 310 ºK A. Calculate the value of ln([adp][p i ]/[ATP]) B. Calculate the approximate ratio of [ATP] to [ADP][P i ] found in cells at 37º C. [ATP] : [ADP][P i ] =
7. A. Two reactions involve metabolites found in the same sub-cellular compartment. Are these reactions coupled? B. One reactions forms an ionic gradient across a membrane. This drives another reaction that uses the gradient to render it exergonic. Are these reactions coupled? C. Two reactions share a common intermediate. Could it be that these reactions are coupled? D. In one reaction, a protein is activated by binding another molecule or by being covalently modified. This provides energy to drive a second reaction. Are these reactions coupled? 8. A. How many phosphoanhydride bonds does ATP contain? B. How many phosphate ester bonds does ATP contain? C. To what part of the molecule of ATP is the triphosphate bonded by this phosphate ester bond? D. What is the name of the nitrogenous base of ATP? E. The active form of ATP is usually in a complex with a metal ion. Which one is this usually?
9. ATP has a high-phosphate group-transfer potential. Which of the following factors contributes to this? o Increase in the electrostatic repulsion of oxygens on hydrolysis of ATP o Greater resonance stabilization of ADP and P i than of ATP o Interaction of the terminal phosphoryl group with the ribose group in ADP o Formation of a salt bridge between the base amino group and the negative charges of the phosphate oxygens in ATP 10. Which of the following are high-energy compounds (capable of substrate level ADPphosphorylation)? o glycerol 3-phosphate o adenosine diphosphate o glucose 6-phosphate o 1,3-biphosphoglycerate 11. ATP falls in the middle of the list of compounds having high phosphate group-transfer potentials. Why is this advantageous for energy coupling during metabolism? 12. The following questions are about the phosphoryl transfer potential of a human skeletal muscle. A. For how long can the ATP of muscle tissue sustain contraction? B. Which compound serves as a phosphoryl reservoir that replenishes the ATP pool? C. For how long can the creatine phosphate support the contraction? D. What can you say about the standard free energy change of hydrolysis for the phosphoguanidino group of creatine phosphate? Indicate on this bar if the change is positive or negative, and large or small. E. Which compound is required to turn creatine into creatine-phosphate?
Oxidation of carbon fuels 13. The following questions are about the ATP-ADP cycle in biological systems. A. What can drive ATP synthesis? B. What does the oxidation of fuel molecules form? C. Is it true that ATP hydrolysis is used to drive reactions that require an input of free energy? 14. There are three phases of catabolism that generate energy from foodstuffs. Write the characteristics next to the correct phase. Phase I Phase II Phase III
Recurring motifs 15. The following questions all deal with the reduction of NAD +. A. Is NAD + a flavin nucleotide? B. Is NAD + the major electron acceptor or donor used in fuel metabolism? C. Does NAD + contain ATP as part of its structure? D. What part of NAD + accepts a hydride ion during reduction? o adenine group o phosphate group o nicotinamide ring o sugar group closest to adenine 16. What happens during the reduction of FAD? 17. Four cofactors are listed below. These cofactors are also activated carriers. In the leftmost column of the table, several structural features and properties are listed. Match these features and properties to the correct cofactors. Phosphoanhydride bond ATP FAD NAD + CoA Ribose group Sulphur atom Adenine group Nicotinamide ring Phosphate transfer Acyl group transfer Isoalloxazine ring Electron transfer
Question 18 18. Conversions involving ATP and NADH + H + release large amounts of free energy. These are released by the transfer of the phosphate group from ATP to H 2 O, and the transfer of electrons from NADH + H + to O 2. Therefore these cofactors are activated carriers of phosphate and protons/electrons respectively. However, both molecules are relatively stable in the presence of H 2 O and O 2. How is this possible? 19. Write after the following coenzymes the group that is transferred by the coenzyme. CoA ATP Biotin NADPH Thiamine phosphate 20. What water-soluble vitamin forms part of the structure of CoA? 21. Enzymes are given functional names; for example, "isomerisation" is catalyzed by "isomerase". What would be the enzyme name for the following reaction types? Ligation: Hydrolysis: Group transfer: Oxidation: 22. The biochemical pathway for the catabolism of a molecule is almost never the same as the pathway for the biosynthesis for that molecule. What can be the reason?
23. By which way(s) is metabolism regulated? 24. The following questions are about the energy charge, an index for the energy status of a cell. A. Is this the same as the phosphorylation potential? B. What are the minimum and maximum values for the energy charge, and when are they reached? C. Between what values does the energy charge of most cells range?