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As seen under a polarization microscope,enter image description here the A-Band in skeletal muscle fibres is so named because it is anisotropic in its refractive index which is a characteristic of orderly crystalline structure. On the other hand, the I-Band is so named because of its isotropic nature, as far as its refractive index is considered, which is characteristic of Amorphous substances or substances which lack long-range order. Both are filamentous (as opposed to globular) in the sarcomere (Actin is present as F-Actin).

But then why this difference in the characteristics of refractive index, which is indicative of order (i.e crystalline or amorphous?) in their molecular structure?

Moreover, is the H-Band anisotropic?

If not, then the anisotropy of the remaining part of A-Band must be a consequence of the relative arrangement of Actin and Myosin which are independently isotropic, and hence cannot give a possible isotropic arrangement.

If yes, then that indicates that the myosin filaments are anisotropic in themselves and actin filaments are isotropic. But, in the region of their overlapping (A-Band minus H-Band), the overlap is between an anisotropic (myosin) and an isotropic (actin) component which shouldn't be anisotropic because the randomness of actin filaments (i.e. its isotropicity) should make the entire configuration isotropic?

I am sorry if I am wrong in my understanding of isotropic and anisotropic characteristics, or if my question sounds too "physics-related", but this has been bothering me for quite some while now.

Here is a directly related question I asked on physics.se. It partly solves the problem of possible arrangement of isotropic elements to generate anisotropy.

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I am not sure if the "biochemistry" tag applies here. Please edit the tags if it doesn't. –  Satwik Pasani Oct 18 '13 at 17:30
    
refractive index is not just a property of an amorphous material. Crystalline solids also have refractive index but it may vary with different planes. And i dont think the A-band is in crystalline form. The anisotropy refers to polarization effects. You cannot deduce that myosin conributes to anisotropy. It is a property of a material as a whole (even same substances can exhibit different optical properties in different structural forms) –  WYSIWYG Oct 19 '13 at 5:02
    
@WYSIWYG I know refractive index is not the property of amorphous substances. I meant isotropic refractive index is a property of amorphous substances. And I was just saying, that normally, crystalline substances have anisotropic refractive index. Therefore, I wanted to know what property of the molecular structure of actin and myosin contributes to such a division of isotropic and anisotropic bands in the sarcomere –  Satwik Pasani Oct 19 '13 at 5:06
    
I am not sure about this but if you just take different sections and see how the 2D arrangement looks like then the A-Band region will look different in different sections (x-y and x-z planes). This may be the reason for the observed anisotropy. –  WYSIWYG Oct 21 '13 at 3:15
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This is sort of technical answer, but I hope its helpful I hope.

All these bands in the sarcomere are anisotropic. Isotropy would imply that the structure/properties of something is equally ordered or coherent in all 3 directions. The sarcomere has definite structure along its longer axis so the H band is anisotropic.

Since the H band is a small structure compared to the actin and myosin components of the sarcomere, much of the signal that one measures via diffraction or polarization experiments is from those two fibers and less information would be discernible from the anchoring portion (H band) of the myosin filament.

In the case of the A and H bands, which are identified by electron microscopy, the structure along the sarcomere axis is not very strong - they are thin sections of the sarcomere and tend to function structurally to connect the actin and myosin axes.

Because of this the information that you might get from A and H band segment studies will be that 'these bands are not very ordered along the axis of the sarcomere'. That's not a lot of information, and we know this from other experiments. But it is information nonetheless because they have some spatial organization.

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