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Question about metabolism and some chemical things?

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Question about metabolism and some chemical things?

Postby Doowally » Tue Mar 15, 2011 12:42 pm

Hello!

Can someone please really simply explain all of this ATP business?

I'm going to retake my secondary school final exam in biology and want to get my best results. Back when I was still in school I just milked my exams and didn't think about my future much.

I have my biology books and the information but I have trouble understanding it. I'm reading about metabolism at the minute and the "energy storing" is quite a problematic business for me. I'm really interested in biology and I do realise it's tightly wound with chemistry but the latter just does my head in.

So if anyone can explain ATP, GTP, CTP, UTP, TTP, NAD and other likes of these I'd be really grateful! Just what each of them is used for in the body, what is their main purpose.

There's more stuff I want to ask but I have no idea what these things are called in English so...
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Postby JackBean » Tue Mar 15, 2011 2:11 pm

ATP is used for building the DNA. It is also the main energy currency of the cell, you can find it everywhere.
other NTPs are used for DNA as well. And they are equivalents of ATP, so they can be used sometimes instead of it. Like GTP is often used by GTPases or in Kreb's cycle.
NAD and FAD are electron carriers or electron acceptors (depends on point of view), they are used by the dehydrogenases etc.
http://www.biolib.cz/en/main/

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Re: Question about metabolism and some chemical things?

Postby Doowally » Tue Mar 15, 2011 7:17 pm

Ugh. Okay I think I understood something. I'll write it down as I understand it and would you be so nice please and correct me if I'm wrong. And bear in mind English is not my native language so I don't know exactly what some things ar called.

Anyway, my question is about glucose disintegration (?). In my book it says there are three stages to it. glucolysis, citric acid cycle, and oxidative phosphorylation. (if the words are not right, I hope you get my point).
I understand that the first stage results in CH3COCOOH molecules and the synthesis of ATP.

Then the disintegration (?) of CH3COCOOH and then the NAD comes in. Where does it come from, where is it before that? Is it always in the cell or what? And what does it do? As I understand it does something with the 4 H molecules but I don't understand why or what the purpose is.

Then in the second stage the disintegration (?) of CH3COCOOH continues and and the NAD "combines" with H atoms. It says the CO2 molecules "extract". Where do they go?

And then in the third stage the synthesis of ATP molecules continues. And the rest I don't understand at all. Then by the end of it there's 38 ATP molecules. ???
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Re: Question about metabolism and some chemical things?

Postby sharstar25 » Fri Mar 18, 2011 9:39 pm

The first stage: glycolysis. This is where glucose undergoes many different enzyme-catalyzed reactions, and at the end of this process you have a net gain of 2 ATP molecules, as well as your end product - 2 molecules of pyruvate, CH3COCOO (no H there). (Glucose was a 6-carbon chain and now you have 2x 3-carbon chains - still 6 C atoms)


(Keep in mind there are 2 pyruvate molecules going through the same process at the same time.)

(NAD is involved in the next two steps i'll talk about - i'll go into more depth about NAD in a minute.)


The Pyruvate actually undergoes another transformation before entering the citric acid cycle, where the pyruvate is bound to an enzyme called Coenzyme A - this gives you Acetyl CoA which can then enter the citric acid cycle.
(In the first step of the citric acid cycle the CoA unattaches and is reused with other pyruvate molecules)


The 2nd stage: citric acid cycle. Your carbon molecules go through a series of reactions which produce 2 ATP molecules and 8 NADH molecules among other things.


Now, about those NAD molecules. They react with the carbon chains and strip off H atoms in order for the carbon chains to form new molecules. When NAD carries H, it becomes NADH - this is your NAD combining with H (The NADH is important in oxidative phosporylation.)
This happens 3 times per pyruvate molecule in the citric acid cycle (6 NAD --> 6 NADH) and once in that ministep I mentioned when pyruvate forms Acetyl CoA. So you have a grand total of 8 NADH molecules produced.

Eventually (during oxidative phosphorylation) the molecule will be restored to NAD, which then goes back into the citric acid cycle. It is recycled in the cell, going between these stages of cell respiration.

The CO2 is expelled from the cell, goes into the bloodstream, and we breathe it out. The citric acid cycle doesn't need all the carbons and oxygens left over from the new molecules it's been making, so it gets rid of them as CO2.


Finally, the synthesis of the rest of the ATP (32 or 34 molecules here, plus the 2 from glycolysis and the 2 from the citric acid cycle, gives 36 or 38 ATP) through oxidative phosphorylation.
This process is in 2 steps - the electron transport chain (ETC) and then actual oxidative phosphorylation - and it happens on the inner mitochondrial membrane, where there are many proteins.

Those ever-important NADH molecules come into play in the ETC. They release their load to a protein on the membrane (turning back into NAD).
Remember that hydrogen is 1 proton (H+) and 1 electron (e-).
The e- and H+ are separated, and some energy from the e- is used to "power" the membrane protein. This protein then "pumps" one H+ outside the membrane. The e- is passed on to more proteins, doing the same thing, and H+ collects outside the membrane until the e- energy is reduced enough for oxygen to take 2 e- out of the ETC, take 2 H+ from inside the cell and make water.
Now, the water taking in the e- is all good, but now we have a higher concentration of H+ outside the membrane than inside. This forms a concentration gradient. Remember that with concentration gradients, things always flow from where there's a high concentration to where there's a low one.
Also remember that H+ are charged, and so the membrane won't let them back through on their own. The only way H+ can get to that nice low concentration inside is to go through another protein channel. This protein is called ATP synthase because it makes ATP. When H+ flows through this protein, a "turbine" starts spinning in the protein, and this action combines two molecules to make ATP. Because there is a constant flow from this H+ buildup, ATP is constantly being made. That's why all of a sudden in this step you get 24 ATP molecules.


I'm sorry i know you wanted it explained simply but this was the best i could do. hope it helps. please ask me questions if you have any! :)
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Postby JackBean » Sun Mar 20, 2011 11:03 am

Doowally: you should read some real biochemical book, which really discribes what's going on
http://www.biolib.cz/en/main/

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Re: Question about metabolism and some chemical things?

Postby Stroodle » Sun Mar 20, 2011 12:19 pm

If you're more of a visual learner (like I am) watch some youtube videos with animations. I did this for so many things in high school bio (I still do it now in biomed) and got really good marks.
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Postby JackBean » Sun Mar 20, 2011 1:01 pm

I would prefer pictures in the books with additional explanatory text ;) And I'm visual learner as well
http://www.biolib.cz/en/main/

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Postby Doowally » Wed Apr 27, 2011 7:34 pm

Thanks, sharstar25, for the long explanation. I went throught the ATP business with my stepmother and I think we got it. :D
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