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Clarification of the Various Metabolic Pathways

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Clarification of the Various Metabolic Pathways

Postby seabreeze » Mon Apr 21, 2008 5:58 am

we've been studying several pathways in my intro biochem class, and individually, I understand the pathways pretty well and no all individual steps and enzymes and substrates involved.
But I'm rather unclear about how they all tie in together, so I was wondering if someone could help me out.
These are the ones we've studied so far:
glycogen synthesis (from starch)
glycogen breakdown (from hunger/fear via glucagon/epinephrine)
glycolysis
gluconeogenesis
TCA cycle
Electron Transport Chain
Oxidative Phosphorylation
ATP Synthesis Via Proton Gradient

Here's my understanding of it so far:
you use starch to form glycogen that you store, and during hunger or whatever, you break it down into energy?
glycolysis is used to generate ATP, and also the substrates for TCA cycle?
The TCA cycle is used mainly to generate reducing power
this reducing power is used in electron transport chain, which together with oxidative phosphorylation generate like -220 kj/mol of energy or something that's needed to synthesize ATP?
the protons pumped across IMM during electron transport are pumped back in, whose energies are used to release ATP in FoF1 ATP synthase

Can anyone confirm or correct me on this, and help me tie these pathways together? I'm really struggling conceptually with it :(

Thanks guys!
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Re: Clarification of the Various Metabolic Pathways

Postby blcr11 » Mon Apr 21, 2008 9:20 am

Glycogen and starch are both polymers of glucose. The only real difference between them is the average linear chain length and degree of [1,6] crosslinking. They serve the same purpose (warehousing glucose for use on demand, essentially) but starch is made by plants while glycogen is made by eukaryotes.

In eukaryotes, glucose is released on demand from glycogen in the form of glycogen-1-phosphate by the action of glycogen phosphorylase. The activity of this enzyme is regulated by its of phosphorylation state by a series of kinases/dephosphorylases ultimately connected to – among other things, but primarily adrenergic and hormone receptors and cyclic-AMP (not to be confused with ATP, very different things are cAMP and ATP, both serving very different purposes).

Glycogen-1-phosphate enters glycolysis directly. The endproduct of glycolysis is the 3-carbon unit, pyruvate, which enters the mitochondrion (in eukaryotes) where it is processed by the TCA cycle to produce reducing equivalents in the form of NADH, which in turn drive the electron transport cycle, producing ATP with the help of the natural EMF potentials of the cytochromes involved in the transport system and your friendly local proton gradient, which finally results in all those reducing equivalents being used to reduce oxygen to water (well, an oxygen radical and then a hydroperoxide, really, but ultimately it’s water).

…and a partridge in a pear tree.

I think that’s everything. I’ll take your word for it about the -220 kJ thing. I’d have to look that up to be sure. What is that, the heat of formation of ATP or something like that?
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Postby Darby » Mon Apr 21, 2008 5:29 pm

This may not help much, but it's impressive (you can click parts to enlarge):

http://www.expasy.ch/cgi-bin/show_thumbnails.pl
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Postby blcr11 » Mon Apr 21, 2008 7:21 pm

The Metabolic Pathways chart is impressive. Its one drawback for the uninitiated is that you have to have a pretty good idea which area to focus on or you will spend a lot of time just wandering around and, if you're on a slow connection, that will get tiresome real quickly. But I agree, it is a nifty chart. I especially like - and use - the fact that once you are looking at the part of the chart you want, the names of the enzymes are themselves active and you can link directly to the enzyme properties and from there to gene-specific information. It's like the enzyme world is your oyster.

I guess I should also point out that when I said "eukaryote" I meant eukaryotes other than plants, which are also eukaryotes. Bacteria don't make glycogen or starch. When they run out of one nutrient, they usually switch to whatever else is handy at the time, if they can, or die (or sporulate, in some cases), if they can't.
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