Unit 1. Introduction and a Few Basics

BIOCHEMISTRY FOR CITIZENS

I present here a set of readings in biochemistry, at a level appropriate for those with little or no background in science. My main goal in these readings is to give you some background against which to think about how science is related to other forms of knowledge, particular the knowledge we obtain from literature, art, music, and religion.

I have good reasons for choosing the life sciences for this purpose. As the frontiers of life science have penetrated into living matter to the molecular level, as our knowledge of biomolecules and how they work has become more detailed and more powerful, life science has become incomprehensible to many non-scientists, particularly those with little knowledge of chemistry and physics. As a result, some of the most exciting developments in modern science go right over the heads of many otherwise informed and concerned citizens.

I believe that I can convey the excitement of this field to you, regardless of your background, as long as you are willing to apply yourself to some readings that begin at a very accessible level, and then gradually raise the level of your knowledge to what is required to understand the science that makes news today, and will affect your life tomorrow. Understanding modern science is important for voting citizens, medical patients, consumers, and anyone who looks with wonder at the world around them.

I hope you find these readings accessible, useful, interesting, and exciting.

A. We study chemistry because
many things we can see are caused by things we cannot see.

Water molecules in ice (1)

A simple example is the shape of a snowflake, which results from the unseen structure and properties of water molecules. The two atoms of hydrogen (white balls) in a water molecule are tightly linked to an oxygen atom (red) by covalent bonds, giving what a chemist knows as H20. Water is best pictured as bent H-O-H, as in the figure. As water freezes, the H-O-H molecules begin to stick to each other by way of weaker, non-covalent, bonds (dashed lines), each between a hydrogen of one water molecule and the oxygen of another. The strongest bonding occurs when rings of six molecules form and grow onto each other. This six-fold symmetry is preserved in the growing structure, and when it becomes large enough to be visible, we see the same symmetry in the snowflake. With the tools of chemistry, we can learn the structures of molecules, and figure out how they give rise to visible properties.

Snowflake, exhibiting the same six-fold
symmetry shown for water molecules in ice.
A 3-cm snowflake is about 10 million
times larger than a water molecule.

Scientists explore the material world, the purely physical world of objects and processes that any person can observe directly or experience indirectly by measurement with scientific tools. The product of scientific exploration is reliable knowledge—knowledge to give us understanding of the physical world, and guide our attempts to manage it, rather than be completely at its mercy.

You might be thinking that understanding why a snowflake has six arms is satisfying, but not really a milestone on the road to a fuller life. But understanding molecular causes can save lives. A loved one suffering from cancer is a victim of faulty molecular events that we can neither see, nor understand, nor repair, without the tools of chemistry.

Is the physical world all there is?

How is the physical world, that complex amalgam of objects external to the thinker (sometimes called third-person entities), related to human consciousness, and to feelings like pain, happiness, disappointment, and hope (first-person experiences)? How is it connected to human values like charity, love, tolerance, and honesty? How does a world composed of mindless atoms and molecules produce poetry, painting, and songs?

Even though cells and organisms are bewilderingly complex, scientists have amassed abundant and convincing evidence that life evolved to this level of complexity from simpler cells and organisms by the evolutionary process originally outlined by Charles Darwin: natural selection acting on random variation in heritable cell properties. We have every reason to believe that the first cells arose spontaneously from non-living matter, but it will be difficult to recreate this process in today’s cell-eat-cell world. It has been said that nothing in biology makes sense except in the light of evolution.

We cannot be sure yet whether life is common or rare in our universe. We have no reason to believe that we are alone, but plenty of reason to think that we might be separated from the nearest other life by vast distances and intervals of time. Earth’s atoms of carbon, nitrogen, oxygen, hydrogen, sulfur, and phosphorus are among a very tiny fraction of atoms lucky enough to be engaged with life. We are lucky to be made of them.

Most philosophers of science are strangers to scientific research, often strangers even to the undergraduate science laboratory. Not surprisingly, their work often is of little value or interest to scientists, and it is easy for non-scientists to overestimate the power of the philosophy of science to help them understand science. The best way to understand science is to do it. Next best is to learn about it from scientists. Philosophers who write about science, but have never done research, are too often whistling in the dark.

B. From cells to molecules

A cell and its organelles (3)

In sheer numbers, most of the living organisms on the earth consist of one cell, and they are invisibly small. Humans and other visible organisms are composed of many cells, each similar to one-celled organisms. Just as bicycles are made of components—wheels, gears, brakes, and seats—cells are made of components called organelles. Examples: the nucleus contains genes made of DNA, and mitochondria are the cell’s power plants.

When you ask what organelles are made of, you have reached the molecular level. The components of organelles are molecules of the four main classes of biochemicals: lipids, carbohydrates, proteins, and nucleic acids (below).

C. I do, I understand

Learning science is not an armchair activity. In a well-conceived teaching laboratory, students focus not on what scientists know, but on how they know it. And learning how scientists discover is the key to understanding science. No amount of absorbing science’s current models and ideas can give the insight that one gains from doing experiments, observing the results, and trying to figure out what they mean. Science’s current models come from such activities, and cannot be fully understood without understanding where models come from.

Shown below are models of four main types or classes of biomolecules: 1. carbohydrates (small segment of starch); 2. lipids (lecithin), the class that includes fats; proteins (small segment of a gene-regulating protein); and nucleic acids (DNA segment). In these models, the element carbon is white, oxygen red, nitrogen dark blue, hydrogen light blue. This type of image is called a ball-and-stick (B&S) model. For size comparison, a water molecule is the size of one of the oxygen atoms.

The four classes of biomolecules:
carbohydrate, lipid, protein, nucleic acid

As biomolecules go, these are small examples. Biomolecules are complicated machines.

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Citations

(1) Figure made using the program Jmol (http://jmol.sourceforge.net/) displaying an ice model (ICES-hex.pdb) produced by the Theoretical and Computational Biophysics Group, University of Illinois at Champagne-Urbana, copyright 1994 through 2012 by the University of Illinois Board of Trustees and others.

(2) http://en.wikipedia.org/wiki/File:Snowflake_-_Microphotograph_by_artgeek.jpg

(3) I can no longer find this image online.