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

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Presentation transcript:

Friday, 18 November 2015 Welcome to Integrated Bioinformatics Metabolic Modeling

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

What Drives Glycolysis? C O e - pair

What Drives Glycolysis? C O e - pair

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

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?

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?

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?

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

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?

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

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

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...

Problem Set

How do you know when you’re done?

I think, therefore I am Rene Descartes

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

How do you know when you’re done?

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

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...?

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?

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

Investigate!