Saturday, September 24, 2016

God's Gift to Molecular Biology: the Hydrogen Bond

 alpha-helix showing hydrogen bonds
It has been recognized that hydrogen bonds restrain protein molecules to their native configurations, and I believe that as the methods of structural chemistry are further applied to physiological problems it will be found that the significance of the hydrogen bond for physiology is greater than that of any other single structural feature. 
--Linus Pauling, The Nature of the Chemical Bond 

The image at the right is a stick model of an alpha-helix structure, like that of DNA; the spiral configuration is held together by hydrogen bonds (see below), shown as yellow sticks (from Wikimedia Commons).


Much has been said of the Anthropic Coincidences, the special values of physical constants and force laws that enable a universe to support carbon-based life.   Even more remarkable, I believe, are the wonderful physical-chemical processes that sustain the life of living things, from the simplest one-celled organisms to us, all of which are made possible by hydrogen bonding.

In an early post, The Theology of Water, I discussed the marvelous and unusual properties of water, properties that stemmed from the nature of the hydrogen bond,  properties that enables an environment friendly to life as we know it on earth.    In this post I want to explore in more detail the nature of the hydrogen bond and its significance for molecular biology and physiology.   Hydrogen bonding plays a role in biochemical reactions, in anti-body mechanisms, and in all of molecular biology and, most importantly,  in how DNA acts as a blueprint for the synthesis of proteins.  A book would be needed to explore all this in detail, so I'll focus on the essentials--the basics of what a hydrogen bond is and its role in the structure of DNA.


Let's imagine God thinking in his design of nature, now I want chemistry to have not only strong interactions between atoms, but also gentle ones:  so that complicated structures can unfold and rewind easily, and so that big and small molecules can come together and join for reactions and go apart readily--Velcro or a zipper, not glue or nails.   What should I use?  I have it--a hydrogen bond.
(Note:  please don't criticize me for heresy here--I'm using a semi-literary device to make a point.   I know God holds an infinite number of thoughts and   plans simultaneously in His infinite mind.)

Here's the basic idea:  H (hydrogen) bonded to O (oxygen) as in H-O-H (water) shows a slight positive electrical charge;  :O, oxygen with a pair of unbonded (lone) electrons, shows a slight negative charge.   Similarly, :N (nitrogen), with a pair of lone electrons shows a slight negative charge, and N-H, hydrogen bonded to nitrogen, show a slight positive charge.     There is an electrical attraction between these small positive charges;  there is also, as nmr experiments have recently shown, a contribution from chemical bonding (sharing of electrons) to hydrogen bonding, so that it is more than simple electrostatic interaction.

In the figure below are shown the types of hydrogen bonds important in molecules of biological interest.

The single dashes represent single bonds;
The = signs, double bonds;
The - - -, hydrogen bonds;
The " : ", lone pair electrons;
Superscripts, delta plus and delta minus, small net positive and negative charges.

Hydrogen bonds energies are about 1/20 to 1/30 the value of ordinary covalent bonds, so the hydrogen bonds can be broken much more easily than covalent bonds; for example the O-H bond energy is about 430 kJoules/mole, whereas the O-H - - - :O   hydrogen bond energy is 21 kJoules / mole


Watson (or was it Crick?) in a moment of insight noticed that the bases (nitrogen containing molecules bound to sugar pieces in nucleotides such as DNA, RNA) matched each other by hydrogen bonding like pieces in a jig-saw puzzle.   They could thus stabilize a helical structure, by links across the spiral, as shown below.
Diagram: double helix of Chromosome CRUK 065
from Wikimedia Commons
  The base pairs are shown below:

Adenine(A)-Thymine(T) Base Pair
from Wikimedia Commons

Guanine(G)-Cytosine(C) Base Pair
from Wikimedia Commons

Adenine(A)-Uracil(U) Base Pair
from Wikimedia Commons

These bases are attached to sugar-type pieces, which in turn have phosphate groups on them that form the links between base units.   The hydrogen bonds linking base pairs are strong enough to hold together the two DNA strands in the spiral helix, but weak enough that they can be "unzipped" by mild chemical action, an enzyme RNA polymerase, which yields messenger RNA.


Before discussing the mechanism by which DNA enables protein synthesis, a few remarks about the bases as letters in a word,  words which  encode which  amino acids are used as building blocks in the protein.   In this process, a linear combination of three bases is used to encode which amino acid is put into a protein.   So we can regard the bases as letters and the combination of three bases as a three letter word; the three letter word is called a "codon".   There are four bases* so there are 4^3 = 64 possible codons.  There are 20 amino acids found in proteins, plus codons for beginning and ending protein synthesis, so that several codons may encode for incorporating the same amino acid, i.e. there is a redundan.   See here and here for tables showing specific codon / amino acid relations.


I'll give just a brief summary here of gene expression--transcription and translation.   More detailed accounts are given in the linked web sites and videos.
STEP 1: transcription--RNA polymerase unzips the double strand and attaches complementary bases to single strand RNA.   See  here and here**   Note that the RNA polymerase is a large protein, much bigger than the DNA strand.   Also note that one strand of the DNA serves as a "template"--bases complementary to bases in the template strand are linked, e.g. G to C,  C to G,  A to T,  U to A, and as they're linked they detach to yield mRNA (messenger RNA).   See the flash animation for a more detailed description of this process.
STEP 2: translation--mRNA leaves the cell nucleus, goes into the cytoplasm
where it attaches to a ribosome, where protein synthesis occurs.   In the process transfer RNA molecules are sent by the ribosome to attach specific amino acids, coded by the m-RNA, to form a protein.


The description is extremely concise--a lot is left out and I urge the reader to look at the recommended links, animations and explanations and to explore this fascinating subject.   Summarizing gene expression in one paragraph is  much like trying to do that for the Bible, Old and New Testaments.

What amazes me is that molecular biologists and those who deal with gene expression, and all the other wonders of molecular biology don't paraphrase Psalm 19A:  "DNA declares the glory of God, and gene expression shows forth the work of His hands..".     Certainly the hydrogen bond, which is a crucial element in these processes, neither too weak nor too strong, is a marvel in itself.
God's providence in molecular biology is as marvelous as it is in physics.

ADDED 25 September, 2016

One of the hymns at Mass today was "O Beauty Ever Ancient" by Roc O'Connor, S.J.  The hymn is taken from St. Augustine's Confessions.  The third verse struck me as a particularly apt close for this post:
"The created world is glorious, yet I could not see within,
see your loveliness behind all,
find the Giver in the gift."


*Note: uracil replaces thymine in the RNA and is encoded by the complement of thymine, adenine--see the section on gene expression.   The presumed explanation for this replacement is greater chemical stability of uracil compared to thymine.

**Note: scroll down to get to the animation and click on the arrow to start it.

Thursday, September 1, 2016

Internet Guidelines from The Rule of St Benedict

St.Benedict Writing his Rules
from Wikimedia Commons
“The prophet shows that, for the sake of silence, we are to abstain even from good talk. If this be so, how much more needful is it that we refrain from evil words, on account of the penalty of the sin..."

 "The fourth degree of humility is, that, if hard and distasteful things are commanded, nay, even though injuries are inflicted, he accept them with patience and even temper, and not grow weary or give up… ."

"The eleventh degree of humility is, that, when a monk speaketh, he speak gently and without laughter, humbly and with gravity, with few and sensible words, and that he be not loud of voice, as it is written: 'The wise man is known by the fewness of his words."

St. Benedict of Nursia,
The Rule of St. Benedict, Chapters 6 and 7.


In 2005 I became an Oblate of the Order of St. Benedict.   This is a "third order" composed of lay people;  one of the requirements  to be an oblate is that one studies and follows The Rule of St. Benedict, as it might apply to a non-monastic contemporary situation.   Other requirements are laid out in more detail elsewhere.   For this post, I'd like to focus on those aspects of The Rule that might apply to behavior on the internet.   

Before doing that, a bit of biography and a mea culpa (said in all seriousness) is in  order.    In my younger days I had a temper and an inability to take criticism.  Moreover, I did not suffer fools gladly, but used all  the resources of native wit to embarrass them and show them as foolish.   Along came the internet, and I served for a while as moderator for the Magis Faith and Reason Facebook webpage.    The snarky and vicious comments of evangelical atheists disturbed me greatly.  (I recall one comment made by a particularly vicious female on her web page, announcing the new Magis Facebook page: "fresh meat, guys.  Let's go kill them.")    My blood pressure and pulse rate would rise, my stomach would churn, when I read slanderous, nasty, irrational comments about the Church, the Magis Institute and my own articles.   So I  got out of that kitchen.  ("If you can't take the heat....")

This was a few years after I had become a Benedictine Oblate, but although I had studied the rules, I had not really taken them to heart.   It was only after mentoring prison inmates who were learning to be Benedictine Oblates and seeing how they used The Rule in reacting to unjust treatment, that I began to see that The Rule had to be a way of life, not just an object of study.   When the next occasion came to apply The Rule I was, if not altogether ready, more prepared.


Several weeks ago Ben Butera was kind enough to review my third ebook "Science versus the Church--'Truth Cannot Contradict Truth.' ", in a post, "Four Big Bangs?"   A commentator, "Anonymous",  really lambasted the book, or rather Chapter 4, in which I discussed the Church's dogma of Creatio ex Nihilo, creation of the universe by God from nothing, and several cosmological theories about the beginning (or non-beginning) of the universe.    In that chapter I tried to follow the proposition set forth in the preface of my book:
"That is the theme of this book: nothing that we know about the world from empirically verified scientific theories conflicts with Catholic teaching. Where there does appear to be a conflict, it arises from theories that are not verified by observation and that, in most cases, can never be so tested. As in many cosmology theories, theories about how (and whether) the universe came to be are untestable and lie in the domain of what might be best termed “mathematical metaphysics.” In short, there is no war between science and the Church." Robert Kurland, Science versus the Church--"Truth Cannot Contradict Truth."
However, according to "Anonymous", I failed miserably.  In attempting (not altogether successfully) to understand his/her criticisms, I tried to see whether I was misunderstood and how I could clarify misunderstandings.   When Anonymous insulted me by belittling my status as a Catholic physicist (I'm not sure whether as a physicist, or as  a Catholic or as the conjoined entity), I attempted to make a joke of it   This really infuriated Anonymous.  I guess that reaction validates the point made in the quote above about the 11th degree of humility--that the Benedictine should speak without laughter, something which is very difficult for me to do.  

At any rate, toward the end of this exchange it seemed, and I'll let the reader judge for himself / herself, that the tone of "Anonymous's" comments become less heated and more conciliatory, so perhaps acting by the Rules did have some effect.   There seemed to be more of a dialogue.


To give a general discussion of The Rule of St. Benedict would require much more space than a single post.  Much of it pertains to how monks in a community might best behave to follow Christ and to maintain the well-being and order of the community, but even the directions on how the steward best maintains the pantry and how and what the monks should eat and drink  are relevant for our times.  Web references and books are given below for those who would like to learn more.

I'm going to focus on those parts of The Rule that seem to me to be most important in our relations with those with whom we interact by comments on posts, our own and those of others.

1. Be mindful of the wounds of others.   We should remember that even the most hateful and spiteful commentator has some reason to behave that way and we should be careful not to hurt them more.   We should not try to belittle them, to shame them, or make them seem less, just to win an argument or make ourselves feel superior.   To quote Fr. Donald Raila, Director of Oblates at St. Vincent Archabbey:
"The Rule of St. Benedict is written for a community of wounded persons.  At the end of a series of precepts for dealing with wounded brothers, the abbot is enjoined to 'realize that he has undertaken care of the sick, not tyranny of the healthy.'   Therefore, 'he is to imitate the example of The Good Shepherd.' "Fr. Donald Raila, OSB, Lessons from Saint Benedict--Finding Joy in Daily Life.
In my replies to "Anonymous" I did not follow this precept as I should have.  In explaining that the physics of the "raisin loaf analogy" for the expanding universe was correct, I made a comment that this explanation followed from first year physics.   That was snarky, meant (albeit subconsciously) to belittle "Anonymous" and should not have been made.   And, as the first quote says "we are to refrain from evil words."

2.  I interpret the second quotation "on the fourth degree of humility" as telling us to listen to criticisms even though they seem to be not justified or based on false premises.   We should learn from them, and if they seem unintelligible, ask the person making that criticism to explain what premises or line of reasoning he/she is following.

3.  We should reflect carefully on criticisms, even when they're worded in a belligerent or belittling way, to determine whether there's substance to them and, if so, how we can use that criticism to make our points more clearly and correctly.

4.  One of the comments made by St. Benedict in the chapter on obedience has to do with accepting orders, just or unjust, without grumbling.   And that means both external and internal grumbling.   This can be translated to accepting justified criticism without grumbling, either external or internal.

5.  Finally, the last of the quotations above, "that he speak gently ...with few and sensible words" applies to comments and rebuttals.  There's an implication here that what we say should be instructive, not just empty chatter.  I'm not sure about the injunction to abstain from laughter--perhaps St. Benedict meant laughing at someone, rather than with,  and I am very often tempted to use humor to defuse anger (not always successfully, as pointed out above).

The rules above are just a few general ones that can be drawn from The Rule.   There may well be others, and if the reader can supply others, I'd be most grateful.  Also, I must confess that I have just begun to follow these rules, even though I've been a Benedictine Oblate for more than 10 years.   It takes conscious effort; it's very tempting to react in kind when someone is particularly nasty.  But following these rules and The Rule is an aid, a prosthesis, to help us live as a Christian.


Friday, August 12, 2016

iBook version of "Science versus the Church" now available.

Here's the video that opens the iBook version--NASA ESA montage of the Big Bang to Hubble.   It's also got other bells and whistles: scrolling sidebars, interactive image (neuron), image gallery (inventions and math of Hellenistic Greeks).

Here's the website for those of you with Macs and/or Ipads.

It took much more toil (some of it frustrating) to get this all working, but I think this is the future of eBooks.

Thanks for looking.

About Me

My photo

Retired, cranky, old physicist.   Convert to Catholicism in 1995.   Trying to show that there is no contradiction between what science tells us about the world and our Catholic faith.   Intermittent blogs and adult education classes to achieve this end (see   and

Extraordinary Minister of Communion volunteer to federal prison and hospital; lector, EOMC.
Sometime player of bass clarinet, alto clarinet, clarinet, bass, tenor bowed psaltery for parish instrumental group and local folk group.

And, finally, my motivation:
“It is also necessary—may God grant it!—that in providing others with books to read I myself should make progress, and that in trying to answer their questions I myself should find what I am seeking.
Therefore at the command of God our Lord and with his help, I have undertaken not so much to discourse with authority on matters known to me as to know them better by discoursing devoutly of them.”
St. Augustine of Hippo, The Trinity I,8.