BabcockHall

Do you know anything about the classification of aminoacids as ketogenic versus glucogenic? If you don't, this will be a very difficult problem. However, I can suggest a starting point: What do you think will be the fate of the carbon skeletons of aspartate?

Anomers are special in the sense that the alpha and beta configuration can slowly interconvert in a solution of free glucose. That is not true of most epimers. Of course, once the glucose is joined to another molecule, the rate interconversion slows down to essentially zero.

Yes, but cysteine is capable of quite a bit of chemistry apart from forming disulfide bonds.

CharonY, I agree. I would just like to add that proteins sometimes denature by unfolding, but sometimes the suffer covalent change, such as proteolysis. I think each protein has to be judged on a case-by-case basis.

There would not be any fatty acid synthesis, but rather fatty acids would be catabolized, some to carbon dioxide and some into ketone bodies. Some of the TAG stores in adipose and elsewhere would be turned into ketone bodies in the mitochondria of liver. These are water soluble, and heart muscle would be one tissue that would use them for energy. Some portion of the proteins would also become ketone bodies, because some amino acids are entirely ketogenic.

What chemical species would accept the electrons?

TAG = triacylglycerol = triglyceride. I am not sure whether or not this was clear from my previous comments. The main storage location for TAGs is in droplets within adipose tissue.

I wonder whether or not lactame should be lactam, but other than that I did not see any errors.

Let me clarify. When the liver produces a VLDL particle, the fatty acids are no longer free, but rather in the form of TAGs.

No, Each NADH has a pair of electrons to give (ultimately) to oxygen. The same is true of FADH2. To verify this you can assign oxidation numbers to the relevant carbon atoms in the molecules. The electrons go through the electron transport chain to oxygen. When they do, a protonmotive force (pmf) is built up, and this is the energy used for the synthesis of ATP. In other words, the electrons do not go to ATP. The protonmotive force is a type of electrochemical gradient. Peter Mitchell first proposed this was the driving force for synthesis of ATP, to the best of my knowledge.

The chemical shift of each peak tells about the environment of the atom, i.e. what functional group is nearby. The area of the peak is proportional to the the number of equivalent hydrogen atoms. The number of peaks is the number of groups of equivalent hydrogen atoms. If there is symmetry present, this can sometimes be inferred from the number of peaks versus the number of hydrogen atoms in the chemical formula. The splitting pattern gives an indication of the number of neighboring hydrogen atoms.

Pretty much, although there is one odd extra amino acid, selenocysteine, and some residues arise from posttranslational modification of existing amino acids. The genetic code is nearly universal, although I think that there are some minor exceptions in mitochondria. I think that there must be some differences in amino acid abundance among different organisms; otherwise, there would not be the problem of consuming a complete protein that vegetarians face.

For example, why do we need both leucine and isoleucine? Does anyone know of a good book or review article that discusses (or even speculates) on this question?

I am not an expert, but I have some ideas that could be explored. Dietary lipids (including fatty acids) might be packaged into chylomicrons (the fatty acids would be first converted into TAGs) for consumption by other tissues. However, if the fatty acids are being synthesized from other carbon sources such as glucose, that would take place in the liver. The the liver would package them as VLDL particles.

Twelve pairs of electrons is twenty four electrons. That is enough to reduce six molecules of O2.

I think that if you want to find kcat, you would need both an accurate protein concentration and knowledge that your enzyme was pure.

Are you reading at a single wavelength (280 nm), or are you taking spectra?

Consider a solution of glutamate at its pI (which I seem to recall is about 3.25). At this pH, the ammonium group has a one full (+) charge. The side chain carboxylic acid is mostly neutral, but a small percentage of the time it loses a proton. Therefore it has roughly a charge of 0.1(-). The carboxylic acid that is directly attached to the alpha carbon has a charge of roughly 0.9(-). Thus the positive and negative charges cancel out at this pH. These numbers all depend on one's choice of pKa values.

I would desalt a small portion of the ammonium sulfate precipitate quickly, and run an activity assay on that. Sometimes just centrifuging then removing the supernatant removes most of the ammonium sulfate, and sometimes a Penefsky column works well. I also think starting with a different purification method might be a good idea, as others have said. You might want to pick up Scopes' book and Clarence Suelter's book.

In general the nonesssential amino acids are produced by transaminations of glycolytic or TCA cycle intermediates, or a few extra reactions. The essential amino acids generally have longer pathways. The aspartate pathway and the aromatic amino acid pathway both have many steps.