First Follow-Up to How to Easily Memorize the Chart for All 22 Amino Acids, including the Three-letter and One-Letter Symbols, and All Nine “Essential” Ones, with My Pentasyllables Method.
Better than the original article. Contains the chart and additional tips.
Introduction.
This article is about how to relatively easily memorize the names, three-letter symbols, one-letter symbols, and which of the five types it is, for each of the twenty-two proteinogenic amino acids, and retain these facts for life. These fundamental facts are all in the chart of the twenty-one amino acids and the image about pyrrolysine below it. Pyrrolysine is to be understood to be to right of proline in the “Special Cases” section of the chart. I could have left it out, but I like to be thorough, and I included it for the sake of completeness. Your ordinary memory will have no trouble recalling that it is the only proteinogenic amino acid that is not found in the human body. Strictly speaking it is not found being used as a proteinogenic amino acid by the human body, although there may be traces of it in an individual’s body due to having accidentally ingested some of it. Pyrrolysin is in fact quite commonly found in small quantities in ordinary fresh water. Once in the body, I imagine it could be used as a source of energy. But I digress. And I nitpick.
Here’s a link to a Wikipedia article that explains what amino acids are, that I think is excellent. It has been accorded “Good Article (GA) status by Wikipedia. https://en.wikipedia.org/wiki/Amino_acid.
Here’s the mnemonic for the 22 amino acids as a single line of four pentasyllables, both above and below the chart, for easy comparison with the chart. Since pyrrolysine is a special case I added it in my mnemonic to the “Special Cases” section of the chart, to the right of proline. I put some data about it from Wikipedia below the chart, but please think of it as to the right of proline in the chart.
AVILM FYW Ile Trp, stag STNQ Asn Gln, CUGP Sec Pyl O, ahl RHK ag DE done.
AVILM FYW Ile Trp, stag STNQ Asn Gln, CUGP Sec Pyl O, ahl RHK ag DE done.
Each of the twenty-two proteinogenic amino acids has a name, for example, “tryptophan”, a three-letter symbol, in this case, “Trp”, and a one-letter symbol, in this case “W”. One-letter symbols should only be used for comparing long sequences of amino acids, because otherwise confusion with symbols of chemical elements could result. For example, “W” is also the symbol for tungsten. “HCN” and “H-C-N” could mean “histidine-cysteine-asparagine”, which is a short sequence of amino acids, or it could mean “hydrogen cyanide”, which is a highly lethal poisonous gas. On the other hand, “His-Cys-Asn” is unambiguous, and is therefore preferred.
Here’s a summary of all the parts of the mnemonic for the twenty-two amino acids and how I use them.
Irregular three-letter symbols, and twenty irregular one-letter symbols are recalled with the following four lines of five syllables each. This allows you to recall or deduce sixty-six items in total: twenty-two names, twenty-two three-letter symbols, and twenty-two one-letter symbols. All that with a mnemonic that is just twenty syllables long. And that’s not to mention the fact that the positions on the chart are also encoded in the mnemonic, with each line containing only the amino acids of one part of the chart. For example, the first pentasyllable contains all eight of the amino acids that have hydrophobic side chains. Furthermore, the position within the hydrophobes section is indicated by the position in the hydrophobes line, indicates the complexity of the side chain because, within the hydrophobes section, complexity always increases as you go from left to right. This also gives you big reminder of the molecular structure of the amino acid (meaning the position of each and every atom in the molecule) as there is usually a single small change that causes the increase between successive hydrophobes.
All twenty-two one-letter symbols can be seen in the following four pentasyllables. Also shown are the five irregular three-letter symbols, and the initial letters of those names that I found difficult to recall together with a few other initial letters of names, to complete syllables of the mnemonic.
The rules are that a word in all uppercase is a string of one-letter symbols of amino acids, while a word has only the first letter in uppercase is a three-letter symbol for an amino acid, and lastly, a word in lowercase is a string of initial letters of names of amino acids, except for the word “done” which is just the English word “done”, added to make the line contain five syllables, and which just means “finished”, because the mnemonic is finished.
AVILM FYW Ile Trp, (“hydrophobic” because “a film of oil is hydrophobic”)
stag STNQ Asn Gln, (“polar uncharged” because “the stag is near the north pole and never charged another stag)
CUGP Sec Pyl O, (“special cases” because “special” contains “sec”)
ahl RHK ag DE done. (“ahl ruck” is “positive thinking”, and “I’m done here” is a “negative thing to say”.)
Using the mnemonic.
“AVILM FYW” is the set of eight hydrophobic amino acids’ one letter symbols, and “AVILM” is additionally the initial letters of the names of the first hydrophobes. Strictly speaking, it’s only the side chains of the amino acids that are hydrophobic, polar uncharged, special cases, positively charged, or negatively charged, and not the whole amino acid.
Anyway, I can recall that “AVILM” is the initial letters of alanine, valine, isoleucine, leucine, and methionine. I can also recall that “FYW” is the set of one-letter symbols of phenylalanine, tyrosine, and tryptophan. I heard once that “F” was chosen as the one-letter symbol for phenylalanine because “P” had already been assigned to proline, and ph” makes an “F” sound, “Y” stands for tyrosine because it contains a “Y”, and “W” is tryptophan because the big snowman shape on the end of the side chain of tryptophan calls to mind the shape of a “W”. Or maybe vice versa. It was very thoughtful of them, don’t you think? The three-letter symbols for the eight hydrophobes are all regular except for “Ile” and “Trp” is what the last part of the first pentasyllable is saying. I can thus recall that “Ile” means isoleucine and “Trp” refers to tryptophan, while alanine is easy because it is just “Ala”, which is just the first three letters. Don’t forget to have each three-letter start with a capital letter, with the rest in lower case. Similarly, valine is “Val”, leucine is “Leu”, methionine is “Met”, phenylalanine is “Phe”, and lastly, tyrosine is “Tyr”. Look at that, will you? Twenty-four items recalled and/or deduced using only five mnemonic syllables. Eight names, eight three-letter symbols, and eight one-letter symbols.
You should have no problem using the rest of the mnemonic as it should be self-explanatory now, but I’ll go through the next pentasyllable anyway. It’s “stag STNQ Asn Gln” which I pronounce as a pentasyllable as follows. “stag stunk ass’n guln”. “stag” is all lower case so it’s the initials of the polar uncharged side chain amino acids. I can recall serine, threonine, asparagine, and glutamine. “STNQ” is a string made of the symbols of serine, threonine, asparagine, and glutamine. I find it convenient to have two ways of recalling the names of the amino acids of this quartet because I find asparagine and glutamine tend to otherwise get confused in my mind with arginine, aspartic acid, and glutamic acid. The “N” of “STNQ” reminds me that it’s asparagine because aspartic acid has no “N” in it. This was, I heard once, built in by the people that chose the symbols, decades ago. Brilliant. This in turn reminds me that it’s glutamine and not glutamic acid, because I can recall easily that aspartic acid and glutamic acid are together in their own other section that they have to themselves, just the two of them. “Q” sounds like “glue” but both “glutamine” and “glutamic acid” have that sound in them, so “Q” is tough to learn.
You absolutely could not have any problem using the rest of the mnemonic, but I’ll go through it anyway. The next section is the “Special Cases” section of weird and wonderful amino acids, and its pentasyllable is “CUGP Sec Pyl O”, pronounced “cug-puh sek pile oh” or maybe “kug pee sek pillow”. “CUGP” is the set of one-letter symbols for cysteine (not to be confused with cystine), selenocysteine, glycine, and proline. “Sec” is the three-letter symbol for selenocysteine, and last but not least is “Pyl”, the three-letter symbol for pyrrolysine, the little-known proteinogenic amino acid discovered in bacteria in a lake in 2002. Finally there is “O” which is the one-letter symbol for pyrrolysine. Whenever I memorize any list, I always include every controversial case, because I figure I can easily use my ordinary memory and logic later to recall that something is controversial, because controversy is fascinating. It’s also great fun when other people don’t know about the controversial cases. I’m sure there are many biology PhD’s who have never heard of pyrrolysine. Great: I can tell them about it. It’s hard to spell, too. Another plus, if you can spell it.
Next up are the five electrically charged acids. First, three positive ones, and then two negative ones. The pentasyllable is “ahl RHK ag DE done”. “ahl” is arginine, histidine, and lysine and “RHK” is their symbols respectively. It is said that “R” was chosen for sounding like “ar” of “arginine”, and that “K” is the one-letter symbol of lysine because “k” comes directly before “l” in the alphabet. I remember it by thinking that “lysine” is close to “lye” which I believe is another name for potassium hydroxide (more often for sodium hydroxide in modern times, according to Wikipedia), and the symbol for potassium is “K”. On to “ag DE done”. “ag” is the initials of aspartic acid and glutamic acid. “DE” are the one-letter symbols for those two. It is said that the “t” of “aspartic” sounds like a “D” sound in American English (“asparDic acid”) which makes sense. In some accent, glutamic acid might be referred to as “glutamiEk acid”. Also, “E” is straight after “D” in the alphabet. And with the word “done” we are done.
Suggested pronunciation.
A vilm few I’ll turp,
stag stunk ass’n guln,
cugpuh sec pile oh,
ah’ll ruck ag de. Done.
Another mnemonic, this one only for the one-letter symbols of the nine essential amino acids.
One-letter symbols of the nine “essential” amino acids.
VILM FW T H K
vilm fwuh tee aitch kay
Easy to recall “VILM FW” because it’s all the hydrophobic ones except “A” and “Y”, ie except alanine and tyrosine.
