Motors II; General Metabolism I

1. Motors II;General Metabolism I Andy HowardIntroductory Biochemistry, fall 2010 17 November 2010 Motors II; Metabolism I

2. Metabolism:the core of biochem • All of biology 402 will concern itself with the specific pathways of metabolism • Our purpose here is to arm you with the necessary weaponry • … but first, we need to explain the role of Ca2+ in muscle contraction Motors II; Metabolism I

3. Muscle Calcium Ca2+ receptors Troponin C and I Smooth muscle Metabolism Definitions Pathways Metabolism, continued Control Feedback Flux Phosphorylation Other PTMs Evolution What we’ll discuss Motors II; Metabolism I

4. Muscle Contraction Is Regulated by Ca2+ Ca2+ Channels and Pumps • Release of Ca2+ from the SR triggers contraction • Reuptake of Ca2+ into SR relaxes muscle • So how is calcium released in response to nerve impulses? • Answer has come from studies of antagonist molecules that block Ca2+ channel activity Motors II; Metabolism I

5. Ca2+ triggers contraction • Release of Ca2+ through voltage- or Ca2+-sensitive channel activates contraction • Pumps induce relaxation Motors II; Metabolism I

6. Dihydropyridine Receptor In t-tubules of heart and skeletal muscle • Nifedipine and other DHP-like molecules bind to the "DHP receptor" in t-tubules • In heart, DHP receptor is a voltage-gated Ca2+ channel • In skeletal muscle, DHP receptor is apparently a voltage-sensing protein and probably undergoes voltage-dependent conformational changes Motors II; Metabolism I

7. Ryanodine Receptor The "foot structure" in terminal cisternae of SR • Foot structure is a Ca2+ channel of unusual design • Conformation change or Ca2+ -channel activity of DHP receptor apparently gates the ryanodine receptor, opening and closing Ca2+ channels • Many details are yet to be elucidated! Motors II; Metabolism I

8. Ryanodine Receptor • Courtesy BBRI Motors II; Metabolism I

9. Muscle Contraction Is Regulated by Ca2+ Tropomyosin and troponins mediate the effects of Ca2+ • See Figure 16.24 • In absence of Ca2+, TnI binds to actin to keep myosin off • TnI and TnT interact with tropomyosin to keep tropomyosin away from the groove between adjacent actins • But Ca2+ binding changes all this! Motors II; Metabolism I

10. Ca2+ Turns on Contraction • Binding of Ca2+ to TnC increases binding of TnC to TnI, simultaneously decreasing the interaction of TnI with actin • This allows tropomyosin to slide down into the actin groove, exposing myosin-binding sites on actin and initiating contraction • Since troponin complex interacts only with every 7th actin, the conformational changes must be cooperative Motors II; Metabolism I

11. Thin & thick filaments • Changes that happen when Ca2+ binds to troponin C • Fig. 16.24 Motors II; Metabolism I

12. Binding of Ca2+ to Troponin C • Four sites for Ca2+ on TnC - I, II, III and IV • Sites I & II are N-terminal; III and IV on C term • Sites III and IV usually have Ca2+ bound • Sites I and II are empty in resting state • Rise of Ca2+ levels fills sites I and II • Conformation change facilitates binding of TnC to TnI Motors II; Metabolism I

13. 2 views of troponin C • Ribbon • Molecular graphic • Fig. 16.25 Motors II; Metabolism I

14. Smooth Muscle Contraction No troponin complex in smooth muscle • In smooth muscle, Ca2+ activates myosin light chain kinase (MLCK) which phosphorylates LC2, the regulatory light chain of myosin • Ca2+ effect is via calmodulin - a cousin of Troponin C Motors II; Metabolism I

15. Effect of hormones on smooth muscle • Hormones regulate contraction - epinephrine, a smooth muscle relaxer, activates adenylyl cyclase, making cAMP, which activates protein kinase, which phosphorylates MLCK, inactivating MLCK and relaxing muscle Motors II; Metabolism I

16. Smooth Muscle Effectors Useful drugs • Epinephrine (as Primatene) is an over-the-counter asthma drug, but it acts on heart as well as on lungs - a possible problem! • Albuterol is a more selective smooth muscle relaxer and acts more on lungs than heart • Albuterol is used to prevent premature labor • Oxytocin (pitocin) stimulates contraction of uterine smooth muscle, inducing labor Motors II; Metabolism I

17. Oxytocin structure • P.532 Motors II; Metabolism I

18. Metabolism • Almost ready to start the specifics(chapter 18) • Define it!Metabolism is the network of chemical reactions that occur in biological systems, including the ways in which they are controlled. • So it covers most of what we do here! Motors II; Metabolism I

19. Intermediary Metabolism • Metabolism involving small molecules • Describing it this way is a matter of perspective:Do the small molecules exist to give the proteins something to do, or do the proteins exist to get the metabolites interconverted? Motors II; Metabolism I

20. How similar are pathways in various organisms? • Enormous degree of similarity in the general metabolic approaches all the way from E.coli to elephants • Glycolysis arose prior to oxygenation of the atmosphere • This is considered strong evidence that all living organisms are derived from a common ancestor Motors II; Metabolism I

21. Anabolism and catabolism • Anabolism: synthesis of complex molecules from simpler ones • Generally energy-requiring • Involved in making small molecules and macromolecules • Catabolism: degradation of large molecules into simpler ones • Generally energy-yielding • All the sources had to come from somewhere Motors II; Metabolism I

22. Common metabolic themes • Maintenance of internal concentrations of ions, metabolites, & (? enzymes) • Extraction of energy from external sources • Pathways specified genetically • Organisms & cells interact with their environment • Constant degradation & synthesis of metabolites and macromolecules to produce steady state Motors II; Metabolism I

23. Metabolism and energy Motors II; Metabolism I

24. Metabolic classifications • Carbon sources • Autotrophs vs. heterotrophs • Atmospheric CO2 as a C source vs. otherwise-derived C sources • Energy sources • Phototrophs vs. chemotrophs • (Sun)light as source of energy vs. reduced organic compounds as a source of energy Motors II; Metabolism I

25. Fourway divisions (table 17.2) Motors II; Metabolism I

26. Another distinction: the organism and oxygen • Aerobes: use O2 as the ultimate electron acceptor in oxidation-reduction reactions • Anaerobes: don’t depend on O2 • Obligate: poisoned by O2 • Facultative: can switch hit Motors II; Metabolism I

27. Flow of energy • Sun is ultimate source of energy • Photoautotrophs drive synthesis of [reduced] organic compounds from atmospheric CO2 and water • Chemoheterotrophs use those compounds as energy sources & carbon; CO2 returned to atmosphere Motors II; Metabolism I

28. How to anabolism & catabolism interact? • Sometimes anabolism & catabolism occur simultaneously. • How do cells avoid futile cycling? • Just-in-time metabolism • Compartmentalization: • Anabolism often cytosolic • Catabolism often mitochondrial Motors II; Metabolism I

29. Pathway • A sequence of reactions such that the product of one is the substrate for the next • Similar to an organic synthesis scheme(but with better yields!) • May be: • Unbranched • Branched • Circular Motors II; Metabolism I

30. Catabolism stages • Stage 1: big nutrient macromolecules hydrolyzed into their building blocks • Stage 2: Building blocks degraded into limited set of simpler intermediates, notably acetyl CoA • Stage 3: Simple intermediates are fed to TCA cycle and oxidative phosphorylation Motors II; Metabolism I

31. Anabolism stages • Short list ofsimple precursors • These are elaboratedin characteristic ways to build monomerse.g.: transamination of -ketoacids to make -amino acids • Those are then polymerized to form proteins, polysaccharides, polynucleotides, etc. Motors II; Metabolism I

32. Some intermediates play two roles • Some metabolites play roles in both kinds of pathways • We describe them as amphibolic • Just recall that:catabolism is many down to few, anabolism is few up to many Motors II; Metabolism I

33. Differences between catabolic and anabolic pathways • Often they share many reactions, notably the ones that are nearly isoergic (Go ~ 0) • Reactions with Go < -20 kJ mol-1 are not reversible as is • Those must be replaced by (de)coupled reactions so that the oppositely-signed reactions aren’t unfeasible Motors II; Metabolism I

34. Other differences involve regulation • Generally control mechanisms influence catalysis in both directions • Therefore a controlling influence(e.g. an allosteric effector)will up- or down-regulate both directions • If that’s not what the cell needs, it will need asymmetric pathways or pathways involving different enzymes in the two directions Motors II; Metabolism I

35. ATP’s role • We’ve discussedits significance asan energy currency • It’s one of two energy-rich products of the conversion of light energy into chemical energy in phototrophs • ATP then provides drivers for almost everything else other than redox Motors II; Metabolism I

36. NAD’s role • NAD acts as asan electronacceptor via nettransfer of hydride ions,H:-, in catabolic reactions • Reduced substrates get oxidized in the process, and their reducing power ends up in NADH • Energy implied by that is used to make ATP (2.5 ATP/NAD) in oxidative phosphorylation Image courtesy Michigan Tech Biological Sciences Motors II; Metabolism I

37. NADPH’s role • Involved inanabolic redoxreactions • Reducing power in NADPH  NADP used to reduce some organic molecule • Involves hydride transfers again • NADPH regenerated in phototrophs via light-dependent reactions that pull electrons from water Motors II; Metabolism I

38. How do we study pathways? • Inhibitor studies • Mutagenesis • Isotopic traces (radio- or not) • NMR • Disruption of cells to examine which reactions take place in which organelle Motors II; Metabolism I

39. Why multistep pathways? • Limited reaction specificity of enzymes • Control of energy input and output: • Break big inputs into ATP-sized inputs • Break energy output into pieces that can be readily used elsewhere Motors II; Metabolism I

40. iClicker quiz question 1 A reaction A+B  C+D proceeds from left to right in the cytosol and from right to left in the mitochondrion. As written, it is probably • (a) a catabolic reaction • (b) an anabolic reaction • (c) an amphibolic reaction • (d) we don’t have enough information to answer. Motors II; Metabolism I