Noncovalent Bonds

On Thu, 26 Feb 2004 06:37:39 +0000 (UTC), [email hidden]

(TomHendricks474) said:

"Without noncovalent bonds, such vital life activities as metabolic reactions, duplication of DNA,
and movement of materials within cells could not occur." Cell and Mole Bio, Karp

Knowing how key noncovalent bonds are to every aspect of life how could it begin with covalent
bonds instead? Doesn't it make sense that the origin of life was variants of noncovalent bonds?

And just a side note. To get variants to select from, you would have to have variant conditions in
the environment - correct? The alternative of never changing conditions would NOT produce variants.

Thus to get variants you would have to have an environment with variatable conditions - a
heat cycle.

The world of chemistry includes a whole range of chemical bonds: ionic, covalent, and a whole series
of weaker interactions. All of them play a role in living systems. They differ greatly in their bond
strength. The dynamics of life requires some parts -- structural components -- to have bonds
extremely stable to thermal agitation (kT or RT levels of energy). Other aspects are quite variable
and require smaller energies so that changes are possible -- conformation changes in proteins, for
example, or temporary binding of ligands to receptors. All the different bond types, ionic,
covalent, and weaker hydrogen bonding and the like play a vital role in cell processes.

I don't understand the need to say "life began with covalent bonds" or "life began with non-
covalent". Wouldn't it be better to simply assume that "life began with a suitable combination of a
variety of complex chemicals combining ionic, covalent, and other forms of bonds to allow relatively
stable structures to interact in a complex dynamical system"?

And the note of variation also doesn't make much sense. Variation originates in mutation --
inaccuracies in a copying mechanism so that offspring are not all identical to the parent or to each
other (without regard to whether the reproducing objects are molecules or organisms or systems). It
is not caused by variation in the environment. In addition, you don't need a "heat cycle" to produce
environmental change. Spatial variation will do.

<< I don't understand the need to say "life began with covalent bonds" or "life began with non-
covalent". Wouldn't it be better to simply assume that "life began with a suitable combination of a
variety of complex chemicals combining ionic, covalent, and other forms of bonds to allow relatively
stable structures to interact in a complex dynamical system"?

I think that is too vague a response in trying to understand the origin of life. I know that
covalent bonds would produce some molecules with stability. That I grant. But to get to the heart of
the origin, there must have been variants. How would you get variants from covalent bonds?

I don't think you can. Or , let me say this, you may have fluke examples, but noncovalent bonds
would be the more chemically selected of the two for their versatility and changeableness. It is
they that would daily come up with all kinds of variants. Then we don't have a single fluke event,
we have daily experiments for millions of years.

And because of that we should be looking at a scenario that begins with the production of monomers,
THEN begins the noncovalent bonds world or what I call the h-bond world (or maybe even the purine
world) - making numerous variants. And the best of those surviving a 2nd day etc. And the best of
that group of survivors, lasting 2 days longer than others etc. If we can break it down to one or
the other - either mostly covalent bonds or mostly noncovalent bonds, don't you see how just that
distinction opens up the door to the origin? IF I am correct, then we need to look at strands of RNA
and amino acids in a heat cycle and see how they connect up -if they do. I suggest some aspect of
these two will chemically help the other survive longer than molecules not connected up.

The heat cycle makes the h-bond variants out of the primordial sea of molecules, then the variants
lead to the next step. How can that not be the scenario?

RSN And the note of variation also doesn't make much sense. Variation originates in mutation...

TH Yes - so heat up variants to 100C and continually increase the heat for a billion years and see
what kind of variants you get - none. If you cool it down below 0C and continue cooling, what
variants do you get - we get hibernation of all chemical processes. We are only left with one
environment that will give us variants - a heat cycle
- a varying but cyclical enivronment.

How can one of the other scenarios work?

RSN -- inaccuracies in a copying mechanism

TH We are talking about a billion years apart in time. I'm asking how could any of this start in
either an environment that continually got hotter endlessly. Or the other extreme - got colder
endlessly. Every aspect of life is in the very very very narrow temp zf liquid water. What life
exists at absolute zero, or in the middle of a burning star? So lets Z** noncovalent bonds) would
respond to the cyclical heat cycle then. any other scenario might be interesting, but it won't have
anything to do with the OOL. Would it?

Best wishes, Tom

RSN In addition, you don't need a "heat cycle" to produce environmental change. Spatial variation
will do. TH Explain please.

I have never read such [censored] in my life! Without covalent bonds there would be no universe! A
covalent bond is a sharing of a pair of electrons. The bond can be nonpolar as when atoms share
electrons equally or polar when they don't. A hydrogen bond is based on covalent bonds. An ionic
bond is when an atom gains or loses electrons and acquires a net positive or negative charge. Water
is an example of hydrogen bonding and shows polarity. Life also depends on hydrophobic interactions
such as the thin oily membrane which separates the cell's watery surroundings and watery interior.

What the hell is a "non-covalent" bond? You mean ionic bond? Do yourself a favor Mr. Hendricks and
pick up a biology text and read about the different kinds of interactions instead of sounding like a
pretentious fool.

Michael Ragland

<< I don't understand the need to say "life began with covalent bonds" or "life began with non-
covalent". Wouldn't it be better to simply assume that "life began with a suitable combination of a
variety of complex chemicals combining ionic, covalent, and other forms of bonds to allow relatively
stable structures to interact in a complex dynamical system"?

I think that is too vague a response in trying to understand the origin of life. I know that
covalent bonds would produce some molecules with stability. That I grant. But to get to the heart of
the origin, there must have been variants. How would you get variants from covalent bonds?

I don't think you can. Or , let me say this, you may have fluke examples, but noncovalent bonds
would be the more chemically selected of the two for their versatility and changeableness. It is
they that would daily come up with all kinds of variants. Then we don't have a single fluke event,
we have daily experiments for millions of years.

And because of that we should be looking at a scenario that begins with the production of monomers,
THEN begins the noncovalent bonds world or what I call the h-bond world (or maybe even the purine
world) - making numerous variants. And the best of those surviving a 2nd day etc. And the best of
that group of survivors, lasting 2 days longer than others etc. If we can break it down to one or
the other - either mostly covalent bonds or mostly noncovalent bonds, don't you see how just that
distinction opens up the door to the origin? IF I am correct, then we need to look at strands of RNA
and amino acids in a heat cycle and see how they connect up -if they do. I suggest some aspect of
these two will chemically help the other survive longer than molecules not connected up.

The heat cycle makes the h-bond variants out of the primordial sea of molecules, then the variants
lead to the next step. How can that not be the scenario?

RSN And the note of variation also doesn't make much sense. Variation originates in mutation...

TH Yes - so heat up variants to 100C and continually increase the heat for a billion years and see
what kind of variants you get - none. If you cool it down below 0C and continue cooling, what
variants do you get - we get hibernation of all chemical processes. We are only left with one
environment that will give us variants - a heat cycle
- a varying but cyclical enivronment. How can one of the other scenarios work?

RSN  -- inaccuracies in a copying mechanism TH We are talking about a billion years apart in time.
I'm asking how could any of this start in either an environment that continually got hotter
endlessly. Or the other extreme - got colder endlessly. Every aspect of life is in the very very
very narrow temp zf liquid water. What life exists at absolute zero, or in the middle of a burning
star? So lets Z** noncovalent bonds) would respond to the cyclical heat cycle then. any other
scenario might be interesting, but it won't have anything to do with the OOL. Would it? Best wishes,
Tom RSN   In addition, you don't need a "heat cycle" to produce environmental change. Spatial
variation will do. TH Explain please.

On Fri, 27 Feb 2004 16:41:01 +0000 (UTC), [email hidden]

(TomHendricks474) said:

We are talking about a billion years apart in time. I'm asking how could any of this start in
either an environment that continually got hotter endlessly. Or the other extreme - got colder
endlessly. Every aspect of life is in the very very very narrow temp zf liquid water. What life
exists at absolute zero, or in the middle of a burning star? So lets Z** noncovalent bonds) would
respond to the cyclical heat cycle then. any other scenario might be interesting, but it won't have
anything to do with the OOL. Would it?

Best wishes, Tom

RSN In addition, you don't need a "heat cycle" to produce environmental change. Spatial variation
will do. TH Explain please.

I don't really follow your arguments about heat cycling, to be quite honest.

You seem to think that the alternatives are constant change towards increased temperature or
constant change towards decreased temperature. Since we know the temperature on the surface of the
earth has remained reasonably "constant" (water usually remains liquid), then there is a "heat
cycle". Also, somehow that heat cycle was necessary for the origin of life. I agree that a "constant
temperature" really means a fluctuating temperature, not absolute cnstancy, and that may consistute
a "cycle" but I don't see how that relates to the origin of life.

Further, you insist that environmental variablility be necessary to poduce variation in
organisms. I suggested spatial variability (the temperature here is not the same as the
temperature there) is just as variable as temporal variability (the temperature now is not the
same as the temperature earlier).

Hydrogen Bonds Have Covalent Properties

Experimenters have confirmed the controversial idea first proposed by Nobel Laureate Linus Pauling
in the 1930s that the rules of quantum mechanics cause the weak hydrogen bonds between H2O molecules
in ice get part of their identity from stronger covalent bonds within the H2O molecule. The figure
depicts the quantum-mechanical nature, or covalency, of the hydrogen bond between neighboring H2O
molecules in the ice structure. The basic unit of ice is the H2O molecule which is depicted here
using red balls for the oxygen atoms and white balls for the hydrogen atoms. The two relatively
strong electronic bonds that make up the H2O molecule itself are represented in the figure by the
darker yellow clouds. While the intermolecular bonds, or hydrogen bonds, are primarily electrostatic
in nature, in which the molecules are attracted by means of separated electric charges, the
experimenters found that the bond is in part quantum mechanical, or covalent in nature, in which
electrons are spread out and shared between atoms. The quantum-mechanical or wavelike aspect of this
bond is depicted by the lighter yellow clouds. In water and ice the intermolecular interaction is
due primarily to the hydrogen bond. In ice, the hydrogen-bonded molecules are ordered in a regular
array to form a molecular crystal. Working at the European Synchrotron Radiation Facility (ESRF) in
Grenoble, France, the US-France-Canada research team designed an experiment which utilized the ultra-
intense x-rays that could be produced at the facility. With these x-rays, they studied the "Compton
scattering" that occurred when the x-ray photons ricocheted from ordinary ice. Named after physicist
Arthur Holly Compton, who won the Nobel Prize in 1927 for its discovery, Compton scattering occurs
when a photon impinges upon a material containing electrons. When an incoming photon (blue arrow),
produced by the synchrotron, strikes the ice sample, it transfers some of its energy of motion
(kinetic energy) to the electrons, and emerges from the material with a different direction and
lower energy (red arrow).

By studying the properties of many Compton-scattered photons, one can learn a great deal about the
properties of the electrons in a material. In particular, Compton scattering is uniquely able to
measure a solid's "ground-state electronic wavefunction," the complete quantum-mechanical
description of an electron in its lowest energy state. The ground-state wavefunction in ice
indicates that there is a quantum-mechanical overlap of the electrons on neighboring H2O molecules,
i.e., that the hydrogen bond is partly covalent. (Figure courtesy of Bell Labs/Lucent Technologies.
Thanks to Eric Isaacs of Bell Labs/Lucent Technologies for supplying much of the caption.)

This research is reported by E.D. Isaacs, A. Shukla, P.M. Platzman, D.R. Hamann, B. Barbiellini, and
C.A. Tulk in the 18 January 1999 issue of Physical Review Letters. Link to Physics News Preview: The
Secret Nature of Hydrogen Bonds Link to related Physics News Update item Click on Logo to Return to
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