In chemistry, when one claims that two are interacting, what is being implied is that in some manner those substances are touching. In , what this means is that the substance or substances that are being acted upon are physically touching the catalyst. In doing so, the substances are being manipulated in some way chemically. This, again in terms of chemistry, generally means that chemical bonds are being broken and/or formed. Almost every chemical reaction that goes on in your body occurs both in association with catalysts and because of the presence of these catalysts.
In biology, catalysts usually consist of proteins, that is, as enzymes. For this reason and more, a good place to start towards understanding how could possibly function – that is, are not simply – is to understand proteins. As the title of this section is intended to suggest, at their basis proteins consist of chemical strings, that is, "strings" such as one sees with . A protein is quite a bit more complicated than a spaghetti noodle, however, as we will now consider.
The first step towards decoding what proteins are all about involves a bit of . These words, at a minimum, include amino acid and polypeptide. Indeed, we can describe a hierarchy that begins at one end with amino acid, progresses through the concept of polypeptide, and then up to protein, where none of these words are completely synonymous. In other words, amino acids make up polypeptides which, in turn, make up proteins.
With regard to the amino acids making up proteins, a useful is that letters (amino acids) make up words (polypeptides) which in turn make up sentences (proteins). This analogy can be continued, with sentences making up paragraphs () that, along with figures and tables, make up sections of chapters (cells), which in turn combine into chapters (tissues), and so on. The one major caveat with this analogy, however, is that proteins can consist of either individual polypeptides or of multiple polypeptides, which in turn can be either the same or different types. That is, "sentences" in this scheme – the analog of proteins where polypeptides are the words – can consist of single words ("Yes!"), repeats of a single word ("No, no, no, no, no!"), or multiple words with or without repeating ("I can't really think of a good example here, a lapse for which I apologize."). Note also the punctuation which, for the sake of completeness, we can think of as the non-amino acid aspects found in association with many proteins (protein cofactors).
In the there are 26 letters, and well over forty symbols if we also include numbers along with such things as commas and quotation marks. These symbols can be combined in all sorts of ways, but only some of those ways make sense, either in terms of how English words are constructed (their structure; you don't want too many consonants in a row) or what English words formally exist (their meaning or function). So too, for proteins we can use the terms structure (shape or conformation) and function. Contrasting the English language, proteins, consist, however, of "only" 20 "letters" (that is, amino acids; more formally, these would be "typically translated amino acids"). Despite this apparent relative lack of diversity, the potential variety of polypeptide "words" actually is much greater than that of English words because of a combination of polypeptides being much longer (e.g., hundreds of amino acids long) and there being much more room for "slop" in their "spelling".
Just as it is possible to get across meaning despite incompetent typing or spelling skills – perhaps particularly when emailing, IMing, texting, etc. – so too proteins can be quite tolerant of "misspellings" (in structure) while still conveying meaning (function). In fact, this tolerance for a certain degree of slop in protein structure, while still maintaining basic protein functions, is an important component of what can be described as the of organisms: Too low tolerance for structural modification would severely curtail the ability of organisms to "experiment" with slight variations in genotype and phenotype. , by contrast, tend to have much less tolerance for random change and as a consequence are much less "" (as any knows, it can take hours or even much longer to locate simple errors that can so easily throw off thousands of lines of ). So too can have much less tolerance for misspellings in formal writing assignments than you might be able to get away with in written communication with friends and family, providing for much greater "looseness" in your interactions with the latter than might be possible in your relationship with the former. Slop thus can be a good thing, at least when not overdone or used inappropriately.
Just as individual letters have different meanings, in particular representing different sounds, so too do amino acids have different meanings. Differences in meanings with amino acids, though, are chemical. Thus, while we might pronounce the letter O as "Oh", so too an amino acid, such as (of or fame), will invariantly convey the chemical "sound" of "acidic" (in fact, glutamate is the simplest of the ). Other amino acids are basic (sucking up rather than giving off the acidic hydrogen ions, H+) and/or are what is known as polar (meaning that they have rather than the charges of acidic or basic amino acids). They can also, instead, be nonpolar (do not readily in water). These different chemistries mean that were you to march along a polypeptide chain, recalling that these are molecule, then you would encounter different chemistries at every amino acid step, just as you encounter different retail shops and restaurants as you walk along a .
These different chemistries – and this is crucial to your understanding of proteins – both interact with each other and with other things and do so in chemically different ways. For example, negatively charged amino acids (which are acidic) will interact with positively charged amino acids (which are basic) while nonpolar amino acids preferentially interact with each other but not with charged or partially charged (polar) amino acids. It is as though couples were pairing off at high school dances, only in some instances opposites attract (opposite charges) while in other cases it is similarities that drive the associations (nonpolar interactions).