Amino Acids- Metabolism

Just had a look at the dot points for this. Urggghhhh, I think this is the point where I looked at the lecture schedule to see how many more lectures we had on proteins and amino acids and groaned when I saw how many more there were.

Know the nitrogen cycle and and that the two major routes for the assimilation of nitrogen involve reduction of NO2 or N2, using complexes of enzymes in which complex electron transfer pathways occur, that both result in the formation of NH4 +.

The nitrogen cycle is, simply put, a series of reactions in which nitrogen can be converted into different forms, including NO2, NO3-, N2 and NH4+. NH4+ is the form in which we take nitrogen into our bodies, and it can be formed through the aerobic process of nitrate assimilation from NO3- to NO2 by nitrate reductase and then to NH4+ via nitrite reductase, or through the anaerobic processes of denitrification of NO3- to N2 and then nitrogen fixation from N2 to NH4+. (These processes are carried out by other organisms, not by us.) Of these routes, nitrogen assimilation is the most common.

Know that NADH and NADPH are reducing agents that supply electrons in a number of reactions.

I *think* NADH and NADPH help supply some of the electrons for the assimilation of nitrogen into the body. NADH also helps with ATP synthesis, while NADPH helps with synthesis reactions in the body. I'll probably go into these in more detail in a later post.

Know details of the three major reactions used in biology for NH3/NH4 + assimilation.

Urgh I hate having to learn details as my memory is not that great- I'd much rather just learn general principles and be able to apply them to any situation. Nevertheless, here are the three major reactions:

1. Carbamoyl-phosphate synthetase

In this reaction, NH4+, bicarbonate and ATP react to form carbamoyl phosphate and ADP. It starts with bicarbonate becoming phosphorylated by ATP. Ammonia then nucleophilically attacks the carbon atom in bicarbonate, displacing the phosphate group to form carbamate. Carbamate can then be phosphorylated by another molecule of ATP to form carbamoyl-phosphate, which can then enter the urea cycle to produce urea.

2. Glutamate dehydrogenase

In this reaction, NH4+ and alpha-ketoglutarate are reduced by NADPH to form glutamate. NH4+ first replaces the ketone group of alpha-ketoglutarate to form an intermediate with an H2N+ group, which is then reduced by NADPH to form the H3N+ group of glutamate.

3. Glutamine synthetase

In this reaction, NH4+, glutamate and ATP form glutamine and ADP. First, glutamate is phosphorylated by ATP to form a gamma-glutamyl phosphate intermediate. NH4+ then nucleophilically attacks gamma-glutamyl phosphate, releasing the phosphate group and forming glutamine.

Know the difference between an essential and non-essential amino acid (you do not have to learn which amino acids fall into each category).

In a nutshell, non-essential amino acids can be synthesised by us, whereas essential amino acids must be taken up in the diet.

Understand that amino acids are synthesised from metabolic precursors which are components of glycolysis, the TCA cycle and pentose phosphate pathway, that have other major roles in cellular metabolism (no need to learn details of the intermediates and which intermediates give rise to which amino acids). 

Hehe, this is something that I think that I shut out of my mind because I got overwhelmed by the diagram. The dot point is pretty self-explanatory, but I'll just give a quick recap over what the processes mentioned are. Glycolysis is the process in which glucose is broken down to produce some ATP as well as pyruvate. Pyruvate then enters the citric acid cycle (a.k.a. the TCA cycle) in which electrons are released and picked up by NADH to power the synthesis of ATP (that's not exactly how it works- as I mentioned earlier, that's a topic for another post). The pentose phosphate pathway is a sort of "side pathway" of glycolysis in which 5-carbon sugars (pentoses) and NADPH are produced. I reckon that it's pretty neat that intermediates in these pathways can also be used to produce amino acids.

Know details of the transamination reactions.

Urgh this is another "know details of these reactions" dot points again. Transamination reactions are reactions in which amino groups are transferred from one molecule to another. They are used in the synthesis of many amino acids, in which an amino group is transferred from glutamate to the ketone group of an alpha-keto acid (basically an amino acid with a ketone group instead of an amino group and hydrogen).

Transamination reactions are catalysed by the pyridoxal coenzyme complex. The attached coenzyme, pyridoxal phosphate, essentially picks up the amino group from glutamate and transfers it on to the alpha-keto acid. I think there are more steps involved in this, but this is the extent of what appears on the slides so I hope that this is all that we have to know.

Understand that amino acids are categorised as glucogenic or ketogenic and know the definition of these terms (no need to learn the specifics of which amino acids fall into which category nor the specifics of metabolites that they give rise to).

The terms glucogenic and ketogenic are related to the catabolism (breakdown) of amino acids. Glucogenic amino acids will break down to form intermediates in the synthesis of glucose, whereas ketogenic amino acids will break down to form intermediates (generally acetoacetate or acetyl CoA) in the synthesis of fatty acids or ketone bodies.

Understand the reasons for the different modes of excretion of nitrogen derived from amino acid catabolism.

There are three ways that nitrogen can be excreted: as ammonia (NH3), as urea or as uric acid. The method used depends on the organism: fish and some aquatic animals excrete nitrogen as ammonia, birds and some reptiles excrete it as uric acid, whereas we (and many other terrestrial animals) excrete it as urea. Ammonia is very toxic and requires lots of water for it to be removed quickly and safely, which is probably why this mode of excretion is only seen in aquatic animals. Urea is not as toxic, but is very soluble in water so it takes plenty of water with it when it is excreted. Uric acid, on the other hand, can be excreted as a paste (bird poo...) with minimal water loss. (I wonder why we don't use uric acid then? Seems like we could save water that way, but maybe there's more to the story.)

Have a basic understanding of how the urea cycle operates, especially the importance of the transamination reactions, glutamate dehydrogenase and carbamoyl phosphate synthetase in feeding nitrogen into the cycle. You should know the overall reaction for the urea cycle.

The urea cycle is the cycle in which nitrogen from NH4+ and aspartate forms urea, which is later excreted. NH4+ is first converted into carbamoyl phosphate through the carbamoyl phosphate synthetase reaction, covered earlier in this post. Carbamoyl phosphate then reacts with ornithine to form citrulline, which then reacts with arginine to form arginosuccinate. Arginosuccinate can then be broken down into arginine and fumarate. Arginine can be hydrolysed to form urea and ornithine (the latter of which can then react with carbamoyl phosphate to start the cycle over). Fumarate, on the other hand, can be hydrolysed to form malate, which can then be converted to oxaloacetate via malate dehydrogenase, releasing electrons which can be picked up by NAD+ to form NADH. Oxaloacetate can then undergo transamination to reform aspartate.

The overall reaction is as follows:

NH4+ + HCO3- + aspartate --> urea + fumarate