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I'm having little trouble studying general relativity or quantum field theory, but remembering all the amino acids and being able to think about them is something that's completely, utterly and absolutely, defeated me...

How do I think about the amino acids, without any memorization, and be able to 'derive' all the names, all the categories they fit into, and their important properties? Memorizing some crazy mnemonic is of no help when it says nothing about the amino acids, I can't memorize it without meaning that explains a lot of things. I ultimately just want to be able to read Albert's Molecular Cell Biology and appreciate it, but I can't without conquering this little issue!

On a side note regarding memorization tricks: is there a mnemonic scheme for the amino acids analogous to the thermodynamical Zhao square, (which gives all the info you need about basic thermo by drawing lines and squares)?

Any help is greatly appreciated, thank you.

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Sorry, but I don't understand your question. Can you please make this more precise? –  Chris Jun 16 at 19:04
    
This question appears to be off-topic because it is about memorization techniques - maybe academia.SE might be suitable? –  fileunderwater Jun 16 at 21:18
    
My post explicitly says "without any memorization", the entire purpose of the post is that I'm asking for a way to derive all of the properties of the amino acids in a consistent non-memorization way. Said differently: How would you explain the amino acids and all their important properties (for biology on the level of Albert's) to someone in a way that they can reconstruct what you say. e.g. in physics you can derive the entire theory of electromagnetism by postulating an action principle, using one idea and some obvious rules. Apologies if that wasn't completely clear. –  bolbteppa Jun 16 at 21:37
    
I have amended my response to your question however the short answer, to the best of my knowledge, is that it is not possible since thats not how AA nomenclature works. –  Bez Jun 16 at 21:55
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Amino acids have different side chains.If you remember the side chains of each amino acids, and know enough chemistry, you can easily derive almost all the properties of the amino acid. –  biogirl Jun 17 at 15:06

2 Answers 2

I'm sure there are lots of ways of handling this, but there are only 20 of them (more or less). I really wanted to figure out how the amino acids resulted in the resulting protein structure. So I started to break them down into categories. The categories cannot draw boundaries exactly since one amino acid might belong to several categories in a unique way, but it starts to give you a sense of what the sidechains do.

Aliphatic : G A L I V M P
Aromatic : F Y W H
Polarizable : F Y W H M C R
Polar: S T Q N D E K C
Small: A S T G C
Large : F Y W H R K
Strong Structural variation: P G

you still have to memorize them eventually, but you can make it easier to put them in categories and in these groups its easier to bring them to mind.

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The question is slightly unclear but will do my best to answer it. I'm not a purist as a biochemist and I can tell you when it comes to biology, there are just certain information you have to memorise and one such instance is AA names. You can drive the AA full chemical name (and its properties such as charge, hydrophilic/hydrophobicity) from its molecular structure but such an approach is far far harder than to remember simple names such as A = alanine, S = serine, P = proline etc! There are some odd ones like Y, which is tyrosine but again the only reason they chose letter Y (second letter in tyrosine) was because (the first) letter T was used for threonine. If you want information on AA and their properties look at this page (http://www.bio.davidson.edu/biology/aatable.html), but I'm curious as to why you need to know individual AA properties. I don't suggest it is not important but AA property makes more sense in terms of its context in a protein sequence as it interacts with other AA properties and within a 3D protein structure.

Saying that AA names taken at face value do not make sense since it is not telling information about their property, although true, is broadly similar to saying protein names taken at face value do not make sense, again kind of true, because they do not say anything about their function (not true all the time but mostly true). To me this is the wrong way of looking at it. The designations for AA names were made as they were easier to memorise/refer to (and consequently become aware of their properties e.g. Y is capable of becoming phosphorylated) just as it is easier to refer to protein by its name and not its full AA sequence.

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Are you telling me that if I derive the molecular structure I can derive all the info on this massive list, as in - if I can picture the structure of Alanine A in my head I'll immediately know a massive amount of info about A? Judging from this page books.google.ie/… the molecular structure of Ethylene can be determined by a quantum mechanical variational calculation, can the same thing be done for all 20 amino acids and if I did that would I be able to derive all those properties from knowing the molecular structures? –  bolbteppa Jun 16 at 23:57
    
I do not know much about QM to comment on it but in general, if you know molecular structure of a (complex) molecule and your chemistry is good enough to know what each part entails in terms of its properties towards the entire structure, then yes, you will know many properties of a molecule. That is how people know if a molecule is for example polar or non polar etc. Obviously the more complex a molecule gets, the harder the tasks becomes, which is why we not only use wet experimentations but also computer simulations. –  Bez Jun 17 at 9:44

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