Conformation
Many of a macromolecule's fundamental characteristics are determined by that molecule's degree of polymerization, but the molecule's physical structure also makes a significant contribution to its macroscopic properties.
The terms configuration and conformation are frequently, and mistakenly, used interchangeably to describe the geometric structure of a macromolecule. More correctly, a macromolecule's configuration is that part of its structure that is determined by its chemical bonds. A macromolecule's configuration cannot be altered without breaking and reforming chemical bonds. Conformation, on the other hand, refers to structural effects that arise from the rotation of molecular segments about single bonds. But the two terms are related, as shown below.
There are two types of configurations: cis and trans. The cis configuration arises when substituent groups are located on the same side of a carbon-carbon double bond. The trans configuration describes substituents on opposite sides of the double bond. These structures cannot be changed by any physical means, e.g. rotation, short of breaking and reforming chemical bonds.
Stereoregularity is used to describe the configuration of macromolecular chains, in which three distinct structures are possible: In an isotactic configuration, all substituent groups are located on the same side of the macromolecular chain; the substituent groups of a syndiotactic polymer are located on alternating sides of the chain; and an atactic polymer has a random placement of substituent groups.
If two atoms are joined by a single bond, rotation may occur about the bond because there is no need to break the bond for it to occur, which is different from the case of a double bond. When an atom rotates about a single bond relative to the atom with which it is joined, there is an adjustment of torsional angle. If the two atoms are bonded to other atoms or groups, those configurations that vary in torsional angle are referred to as conformations. Because, in general, each conformation corresponds to a different set of interactions between neighboring atoms or molecular groups, different conformations usually correspond to different potential energy states for the molecule.
In the case of carbon-carbon single bonds in a macromolecule such as polyethylene, there are three possible conformations. The energy barriers separating these three conformational states are much greater than thermal energy fluctuations, so the time spent in each conformational state will be longer than the time of a thermal vibration.
Unlike polyethylene, a protein molecule contains many molecular groups that interact with each other, either on the same or on adjacent molecules. Interactions such as those between hydrogen bonds and amido-hydrogen atoms and carbonyl-oxygen atoms, forces between charged groups, and solvent-polymer effects may all contribute to the conformation of a protein molecule. Hydrogen bonding gives rise to two familiar protein conformations in biological systems: planar sheets and the alpha helix.X-ray diffraction has proven an important technique for determining the conformations of protein molecules.
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