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Forces Affecting Conformation in Biological Molecules
We now turn our attention to the various forces that affect biomolecules, stabilizing or destabilizing their various conformations Wherever there is a force, you should think of energy as well The stronger a particular force is, the larger is the energy difference associated with a movement with or against that force Therefore all of these forces affect the energy state of the biomolecules It is important to understand that biomolecules run the gamut from molecules that are made up of only a few atoms, to relatively enormous macromolecules that are made up of literally thousands or tens of thousands of atoms As a result, particularly in the larger molecules, it is possible that many different forces can come into play at the same time All of the forces we will speak about are electronic in nature (ie, they ultimately involve the interaction of positive and/or negative charges) These forces manifest themselves in a large variety of ways and we classify them as different forces in order to categorize them according to their different behavior
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B i o p h y s i c s D e mys tifie D
CHAPTER OBJECTIVES
In this chapter, you will
Learn the forces that influence the conformation of biomolecules Learn the relative strengths of these forces Understand the conditions under which each force becomes significant Learn to calculate the value of various forces in biomolecules
chapter 6 F o r c e s A F F e c t i n g c o n F o r m At i o n i n B i o L o g i c A L m o L e c U L e s
Chemical Bonds
Molecules are atoms connected together The bonds that connect atoms together in molecules are called chemical bonds There are, however, many types of bonds and forces that influence the exact location of the atoms within a molecule, and so influence the conformation (shape) of the molecule These we will discuss later in this chapter But we need to first understand chemical bonds, since chemical bonds provide the primary structure of molecules A chemical bond between two atoms always involves one or more of the outer electrons of the atoms These outermost electrons that participate in chemical bonding are called valence electrons There are two main types of chemical bond: A covalent bond occurs when one or more of the valence electrons from each atom are shared between the two atoms An ionic bond occurs when one or more of the valence electrons are completely stripped away from an atom and are donated to the neighboring atom Just as a reminder (you ve probably heard this before in an introductory chemistry or physics course) a couple of points to keep in mind: First, we think of electrons orbiting the nucleus as kind of an electron cloud One possible reason for this is because, from our perspective, each electron moves so fast and orbits the nucleus in so many different directions that even in the simplest atom, hydrogen, the single electron orbiting the nucleus can be thought of as a cloud of negative charge buzzing about From a quantum mechanical point of view, we say that the cloud represents the probability of finding the electron at a given point in space The denser the cloud at any given point, the higher the probability of finding the electron at that point at any moment in time From a colloquial point of view, we say the electron, in its buzzing about, on average spends more time where the cloud is dense and on average spends less time where cloud is thin The other point to keep in mind is that the electrons orbit the nucleus in layers called orbitals, with various numbers of electrons in each orbital As we mentioned, it is the outermost electron cloud that participates in chemical bonding, with one or more of its electrons
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