In the past few days, I had to switch classes. I had to drop
Biology, but I have picked up Biochemistry to take its place, which is vital to my
degree program.
I bring this up because, seeing as how I want to have parallels
between this blog and what I am learning in academia with an emphasis on the chemical, I view this as a more chemical outlook on biology,
which is logical, seeing as how the name of the course is
“Biochemistry”.
With that in mind, let me begin with the meat of the blog.
For those of you pre-medical students reading this blog who are
taking organic chemistry and wondering why you need to take organic
chemistry, this blog entry is one of many examples of why pre-meds
need chemistry. There are also reasons why you should take physics,
but that will be for future blog entries.
All of us are made of chemicals. Stomach acid is a mixture of acids
which are used for reacting with the food and drink we consume, to
produce compounds which our intestines can absorb for rebuilding
muscles and organs, add numbers to blood cells, and all sorts of
other fun stuff, including producing the energy we need in order to
perform activities filled with awesome. There is the haemoglobin in
the blood which carries the oxygen we breathe to the muscles and
organs so that said oxygen can react to build up those parts of our
bodies. For those of us capable of seeing this blog to read it,
there are photosynthetic chemicals in the back of our eyes which
reacts chemically in the presence of photons, thusly producing the
sensation of light.
All of us have heard of deoxyribonucleic acid, better known as DNA.
This is the chemical which dictates all of these chemical reactions,
and so many more of them. In fact, all of the chemical reactions you
can think of, as well as everything that makes you who you are, is
determined by the particular order of the four bases in your DNA.
The DNA has a back-bone of a polymer of a sugar-phosphate compound.
The compound is a chain of alternating and groups. For each ,
there is a base bound to it. As you may very well know, there are
four bases in DNA which make up two base pairs. These bases are
typically represented by the letters A, C, G, and T, which stand for
adenine, cytosone, guanine, and thymine, respectively.
In order to understand the structure of DNA to better understand how
the human body works, you need to understand how DNA functions
chemically. Biological knowledge of DNA is nearly meaningless unless
you have the chemical knowledge, and the reciprocal is also true.
These two view-points are complimentary to one another.
We are all familiar with the double-helix shape of DNA. This is
brought on by the increased stability it brings to the double-strain.
Notice that the DNA is always depicted as bound by two “paths”,
for lack of a better word. These two paths represent the above
mentioned sugar-phosphate polymers. These also represent one unit of
DNA. The DNA is really two separate strains of DNA which are bound
to each other through non-conventional means. Hence the reason for
the word “double” in the term “double-helix”.
In order to understand the non-conventional means of the connectivity
between these two strings, there are some chemical concepts you need
to know, namely the following:
- Chemical Bulkiness:
The size of the groups depends on which bases connect to which. As anyone who has taken biology in high school should remember, the base A connects with the base T, and the G base connects to the C base. There is no other combination of base pairs.
This is because if there were any other combinations possible, then the width of the DNA chain would vary, which is biologically and chemically inefficient. The more variation in width of the molecule, the more potential chemical energy there is, which means the more likely it is to dissociate. Size is brought up because adenine and guanine are bicyclic compounds (compounds with two rings in them) while cytosine and thymine are monocyclic systems (compounds with one ring in them). A monocyclic compound connecting to a bicyclic compound ensures a relatively constant width. - Hydrogen Bonding:
When there is a compound where hydrogen is bound to an atom with sufficiently higher electronegativity then itself, it has the tendency to want to share its one single-bond with another highly electronegative atom from a different compound.
For instance, the adenine has an amine group (a group analogous to ammonia, where one of the hydrogens is replaced by an organic compound) bound to it. The hydrogen is bound to a nitrogen, a compound of sufficiently higher electronegativity for this purpose. Thymine has a carboxyl group (a carbon-oxygen double bond). The hydrogen goes through a weird bonding with the oxygen atom, while still bound to the nitrogen.
This occurs because the hydrogen atom has a sufficient partial positive charge on it and the oxygen has a sufficient negative charge on it. This hydrogen bonding is an electromagnetic attraction. The concept of “opposites attract” comes from this concept. Opposite charges attract each other. The positive charge of the hydrogen and the negative charge on the oxygen are attracted to each other. - Van der Waals Attractions:
The electron cloud around an atom is always moving, because the electrons themselves are always moving. This means that, for any given moment, there is a very small but very useful separation of charge within a neutral atom. When this atom comes close to another atom, there is an induced charge separation caused by electron repulsion. This creates two atoms which have a small electrostatic attraction to one another. - The hydrophilic effect.
A hydrophilic compound is one which repels water, like a tarp or a rain coat is hydrophilic. When a hydrophilic substance is in the presence of water, it has the tendancy to combine with other molecules of the same type, which explains why gasoline and water separates. Gasoline is hydrophilic, hating water.
These four concepts combined explain why the two strands of DNA comes
together. Hydrogen bonding between two bases of complimentary size
attract them to each other. At the distance of this hydrogen
bonding, the van der Waals attraction is at it's strongest,
strengthening the attraction. Since the DNA is in water in its
natural environment and is hydrophilic, they come together very
readily to do all of this.
How DNA stores genetic information is also a chemical process. The
DNA writes the information for proteins and cells and every aspect of
the body of the living organism. The proteins are “written” by
the protein getting to the appropriate part of the DNA strand and
going through a chemical reaction with that part of the DNA as a
catalyst. This is now the template for all future proteins. This
process occurs with everything genetic in nature. This concept I
will go in to further detail in a future blog.
As for this weeks prompt, I have a good one. I have encountered a
sizable number of pre-medical students taking organic chemistry, and
all of them have asked me the same question: “How am I ever going
to use this?” They ask me this question expecting me to answer it
for them. I do not know their particular plans for the future. I do
not know if they're going into surgical or medical, or what specialty
they plan to go into. So I cannot adaquetly answer this question for
them.
My prompt for you all is this: whenever you feel compelled to ask
this question to somebody regarding any material, instead of asking
that person, you should ask yourself that very question, with the
intent of answering it for yourself. Nobody knows what your plans
are better then you, so you are the person best qualified to answer
that question for yourself.
Let's take my case for example. My plan is to go into environmental
chemistry. What use is biochemistry to me? Well, upon me
contemplating, I realize that my plan involves saving the human
species by saving this planet. If I do not understand how the
biological system of humans work, then how can I hope to achieve that
goal? So biochemistry is vital in my study of environmental studies.
This, of course, is a drastically abridged version of that
mentality, but I hope you see the point.
Until next time, have a great week and don't forget to be awesome.
-K. “Alan” Eister Δαβ
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