The Acids of Life

To begin, I would like to thank my biochemistry Professor, MaryKay Orgill, Ph. D., for fact checking this post, despite her busy schedule, and despite today being her birthday. Happy birthday Captain!

Before I begin my topic today, I want to clear up some confusion the general population has about homonyms. The confusion is that the general use of a word is perceived to also be the scientific use of the same word. With the exception of the vast majority of astronomical terms (because astronomy, for the most part, has the capacity to be an exception), this is not true. These are homonyms, which are words in English which are spelled the same, sound the same, and have different definitions. In engineering, the term moment means to apply a force in a circular fashion, not a general short period of time. In biology, a Calorie is a specific unit of energy in chemical reactions, not merely something you have to consume. In chemistry, reactions are transfer of electrons and changing of energy, not what a response to a statement.

I say this because todays blog with be on the topic of nucleic acids, which are the acidic structures of proteins.

It is my understanding that most people perceive acid as something which “dissolves everything”, or react heavily with everything. (Just as a side note here, the word “dissolve" here is used in the common context; the chemical meaning of dissolve is very different then this common usage, but I'll save that for a future blog.) The definition of acid is far different from this in it's scientific definition. Yes, under the definition, there are some more extreme acids which “dissolve everything”. There are also more extreme alkalies which “dissolve everything”. More often then not, though, acids and alkalies are much more mild.

There are three types of acid, but for this purpose, I speak of Brønstead-Lowry acids, which are those molecules which can react with alkali compounds. Acidity, in this context, is the measure of how easily a hydrogen atom of an acid can transfer from the acid to the alkali in this way. So this is really a measure of the strength of how strongly the hydrogen is attached to the acid.

Proteins are vital for all aspects of a biological life. This is because they are capable of performing a wide variety of tasks, including but not limited to transportation of molecules from one area of the body to another (as in hemoglobin with oxygen), provide mechanical support (such as muscles), and transmit nerve impulses (as with nerve endings on the skin). There are four key reasons why proteins can take up so many functions:

1. Proteins are polymers of amino acids. Most amino acids are moderately weak in their acidic nature.
2. Proteins have a lot of functional groups. Functional groups are groups of atoms within a molecule which we deem as important to chemical reactions. What we deem as important and why will come in a later blog.
3. Proteins can interact with one another and other big molecules to form assemblies. This is kind of like a snowball going down hill will pick up snow on the way down.
4. Depending on the order of amino acids, proteins can range from quite rigid to quite flexible. This determines the purpose of the protein. The α-keratin protein in your hair is rigid, while the hemoglobin protein needs to be flexible so that it can readily hold on to and release oxygen molecules.

As mentioned before, the protein is a polymer of amino acids. There are 20 amino acids commonly found in proteins, and the order which they are placed in the protein determines their shape, which determines the physical and chemical properties.

The base-chain (the string of atoms which are linear in configuration and which all amino acids have in common) has an ammonium ion on one side and an acetate ion group on the other. This is used to connect to one another at the ends, where the NH3 side loses 2 hydrogens and the COO side loses an oxygen.  The nitrogen binds to the carbon. This process also forms a full carbon-oxygen double-bond, where there used to be a bond somewhere between single and double bonds. This process of stringing the amino acids together turns a moderately strong acid into a non-reactive acid, and allows the full functionality of proteins. This also creates a water molecule for every two amino acids that come together in this fashion.

Amino acids can do this little trick because the COO side, in it's basic state, is as alkali as the ammonia side in it's acidic state is acidic. This produces a long chain we call proteins. The chain produced depends on which amino acids are available in the general vicinity, steric hindrance brought about by the side chains, and charge of side chains. The size cause electron repulsion, and opposite charges attract, while the same charge detract.

This is the basics of how proteins are formed. I hope you have learned something, including why it is wrong to assume the common use of a word is the same as scientific use of the same word.

My prompt for my readers, as always, relates to this blog, and relates to my native English speaking readers. Consider all of the vocabulary you use in your day-to-day life which you use in more then one context. In each case, consider how its definition might be different based upon the contexts which you use it. There are many examples of this in both written and spoken word.

A good example in both is the word dough. Depending on context, it could be used as the main ingredient of dough-nuts or as a slang term for money. There is a distinct difference here.

In spoken word alone, a good example are the trio “to”, “two”, and “too”. The first is the directional word, the second is the number, and the third is “as well”. Verbally, they all sound exactly the same, but you know which one is used based on context.

A good written word example is read (present tense) and read (past tense). The prior is pronounced like the last name of the present Senate Majority Leader, and the latter has the pronunciation of the color, but both are spelled the same. In written word, the only way to differentiate between which tense it is would be to determine the tense of the sentence it is used.

There are many more examples of this, and use this as your means to reason out why the common usage of terms are different than the scientific definition of terms in the English Language.

Until next week, have fun. Learn. And don't forget to be awesome.

-K. “Alan” Eister Δαβ

References:
Bronsted-Lowry Acid Definition:
Chemistry: The Central Science; by Theodore L. Brown, H. Eugene LeMay, Jr., Bruce E. Bursten, and Catherine J. Murphy; page 668
Everything else: 
Biochemistry 7th edition; by Jeremy M. Berg, John L. Tymoczko and Lubert Stryer; copyright 2012; ISBN-13: 9787429229364; chapter 2: Protein Composition and Structure;