Noncovalent Bonds

Discussion in 'Health and medical' started by TomHendricks474, Feb 26, 2004.

  1. "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.
     
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  2. R Norman

    R Norman Guest

    On Thu, 26 Feb 2004 06:37:39 +0000 (UTC), [email protected]
    (TomHendricks474) wrote:

    >"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.
     
  3. << 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.
     
  4. I have never read such crap 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.
     
  5. R Norman

    R Norman Guest

    On Fri, 27 Feb 2004 16:41:01 +0000 (UTC), [email protected]
    (TomHendricks474) wrote:

    >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).
     
  6. 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
    AIP Home Page © 2004 American Institute of Physics One Physics Ellipse, College Park, MD 20740-3843
    Email: [email protected] Phone: 301-209-3100; Fax: 301-209-0843
     
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