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I have asked a question on physics stackexchange, but was redirected here. I copy the entire question word for word. The original is here.

Let's, for example, take a ribosome. It is an enzyme that is in turn just a molecule that must follow the laws of physics.

Correct me if I'm wrong, but it can be looked upon as a molecular machine made up of several pieces. What exactly makes those pieces work together?

Why does the ribosome bind to a strand of RNA? Is it just the shape and electric charge or is it something more? Once the ribosome is bound to a piece of RNA, how does it move?

In a way, I'm looking for the "ghost in the machine". I'm interested in molecules in general, not just ribosomes. What is it that, on a level of single atoms, makes molecules "alive" - move, assemble a protein, etc. ?

PS. I'm having trouble phrasing my question, so if anything is not clear, please leave a comment and I will address it.

Edit 1: This is most definitely a physics question. I'm looking at the scale of several atoms.

Let me give a hypothetical example:

Imagine a strand of carbons. Also imagine that there exists a molecule that can move along this strand. How would it do it? What forces would move it along this strand? Is it electromagnetism? Would gravity be involved to a significant degree? What effect would shape have?

Does this make the question clearer?

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    $\begingroup$ Looking at the scale of atoms will not help understanding a molecular machine made of thousands of them. $\endgroup$
    – Chris ♦
    Jan 5, 2016 at 18:51
  • $\begingroup$ @Chris How should I try to understand molecular machinery? What topics, books, resources should I look for? $\endgroup$
    – Anton
    Jan 5, 2016 at 19:06
  • $\begingroup$ I agree with Chris, a lot of how enzymes process things is related to their structure and the charge or lack of charge in the active site. You also have to consider that ATP is used to catalyze many reactions, meaning you have to take a more macro look. I'd start with Biophysics. $\endgroup$
    – Nathan
    Jan 5, 2016 at 19:36
  • $\begingroup$ @Nathan do you have a suggestion for a resource to start? Maybe a textbook? $\endgroup$
    – Anton
    Jan 5, 2016 at 20:00
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    $\begingroup$ amazon.com/… $\endgroup$
    – Nathan
    Jan 5, 2016 at 20:06

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This question is waaaay too broad, but I'll give some short and simplified answers to the hypothetical you asked at the end. First, let's reformulate your example a little bit:

How does the ribosome move along a strand of RNA?

  • How would it do it?
    • By hydrolyzing GTP and somehow coupling the free energy associated with that reaction to forward motion. Keep in mind that both ribosome and RNA are constantly undergoing random-walk Brownian motion (ie jiggling), so it's more a matter of biasing the ribosome's motion in a particular direction than it is of moving the ribosome in the first place.
  • What forces would move it along this strand?
    • The current understanding of molecular biophysics, which is by no means complete, says that the primary driver of this sort of protein activity is electrostatic forces.
  • Is it electromagnetism?
    • There are no electric currents, per se, so magnetism does not play a role.
  • Would gravity be involved to a significant degree?
    • At these scales gravity does not have a significant effect.
  • What effect would shape have?
    • Shape has an enormous effect. One of the fundamental axioms of molecular biophysics is that function follows form. The 3D configuration of those electrostatic forces I mentioned is determined in turn by the 3D configuration of the involved macromolecules.

If you want to know (a lot) more about this specific question, and if you have access to journals, check out this review: How Should We Think About the Ribosome?

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  • $\begingroup$ You write "By hydrolyzing GTP and somehow coupling the free energy". When you say somehow, do you mean to say that it is very complex process or that humanity does not know? $\endgroup$
    – Anton
    Jan 6, 2016 at 3:26

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