1. Friday, 18 November 2015 Welcome to Integrated Bioinformatics Metabolic Modeling

4. I'm confused about whether glycolysis adds the H or removes it from NADH+

5. What Drives Glycolysis? C O e - pair

6. What Drives Glycolysis? C O e - pair

7. What Drives Glycolysis? C O e - pair glucose O OHOH HOHO OHOH OHOH OHOH O OHOH pyruvate O ATP O OHOH pyruvate O

8. O OHOH O Gla3P O OHOH O O O NAD+ NADH O OHOH O O ADP ATP Gla 3-P dehydrogenase 3-P-glycerate (3PG) What Drives Glycolysis?

9. O OHOH O Gla3P O OHOH O O O NAD+ NADH O OHOH O O ADP ATP Gla 3-P dehydrogenase 3-P-glycerate (3PG) What Drives Glycolysis?

10. O OHOH O Gla3P O OHOH O O O NAD+ NADH O OHOH O O ADP ATP Gla 3-P dehydrogenase 3-P-glycerate (3PG) What Drives Glycolysis?

11. I'm confused about whether glycolysis adds the H or removes it from NADH+

12. O OHOH O Gla3P O OHOH O O O NAD+ NADH O OHOH O O ADP ATP Gla 3-P dehydrogenase 3-P-glycerate (3PG) What Drives Glycolysis?

13. My hunch was that reaction 12 is needed... NADH NAD+ O O OHOH DHAP O OHOH Glycerol-3P OHOH

14. My hunch was that reaction 12 is needed... since I'm not modeling Glo3p (since we don't care about any of the steps that come after it) I need to leave out one of the Ks

15. Eisenthal & Cornish-Bowden (1998) O O OHOH DHAP O OHOH Glycerol-3P OHOH NADH NAD+ My hunch was that reaction 12 is needed... since I'm not modeling Glo3p (since we don't care about any of the steps that come after it) I need to leave out one of the Ks...

17. Problem Set

19. How do you know when you’re done?

20. I think, therefore I am Rene Descartes

21. How do you know when you’re done? I am, therefore I’m at steady state Trypanosome

22. How do you know when you’re done?

23. New Prediction external glucose fructose bisphosphate Metabolic model How to get there? SQ4. Consider the metabolite fructose-bis- phosphate (FBP)... a. Identify where in glycolysis it appears.

24. New Prediction external glucose fructose bisphosphate Metabolic model How to get there? ? SQ4b. Thinking of glycolysis as the flow of water through a hose with valves controlled by enzymes along the way, where is the obstruction...?

25. New Prediction external glucose fructose bisphosphate Metabolic model How to get there? ? SQ4c. If there is an obstruction at that point, what metabolite(s) would you expect to accumulate? What not?

26. New Prediction external glucose fructose bisphosphate Metabolic model ? What do you predict about other metabolites? How to get there?

27. Investigate!