Questions on Antibody Structure

Most of these questions can be answered by referring to the images at http://www.umass.edu/microbio/chime/antibody/index.htm. It will also be helpful to refer to the appropriate chapter of a textbook of immunology.

These questions will help you focus your tour of antibody structure. It is recommended that you print this page and write your answers. Have your answers checked by your instructor.

    Ig Domain

  1. How many beta sheets are there in an Ig domain? How many beta strands are there in each sheet?

  2. Is there a beta strand which is not in a sheet? How many amino acids are in this strand?

  3. Are adjacent beta strands (in the sheets) parallel or antiparallel? (In the cartoon representation, the arrow begins at the amino N-terminus of the strand, and points to the carboxy C-terminus [arrowhead].)

  4. What two types of bonds are largely responsible for holding the two sheets together?

    Fab:Lysozyme

  5. There appears to be a hole in the middle of the spacefilled Fab. In reality, what would fill this hole?

  6. What kinds of bonds hold the heavy chain fragment to the light chain fragment in the Fab?

  7. What kinds of bonds hold the antigen (lysozyme) to the antibody?

  8. How many CDR's are there in the paratope? (The paratope is the site on Ab to which the Ag epitope binds.)

  9. Draw a map of the paratope showing the relative positions of the CDR's.

  10. Which CDR's are most variable? Where do these CDR's lie in the paratope?

  11. How many of the epitope-contact atoms in the paratope are not in the CDR's?

  12. How many amino acids of lysozyme are in contact with the Fab? How many separate blocks of sequential amino acids are in the epitope?

  13. Are all (or most) of the CDR's involved in contact with the epitope?

    F(ab')2

  14. What holds together the two arms of F(ab')2?

  15. What kind of chemical bond does pepsin break when it makes F(ab')2?

  16. Are the two light chains covalently linked to each other with disulfide bonds? The two heavy chains?

  17. What are the light chains covalently linked to?

  18. Where are the majority of disulfide bonds in IgG, and what do they link together?

    Whole IgG

  19. How many polypeptide chains make up an IgG molecule?

  20. Which domains have carbohydrate attached? How might this carbohydrate contribute to the function of these domains?

  21. What is the function of the thinnest part of the IgG molecule?

  22. What important feature of antibody function is not visible in these images?

    Comparisons between moieties

  23. How many immunoglobulin domains are there:

    1. In IgG?

    2. In F(ab')2?

    3. In Fc?

    4. In Fab?

    5. In Fv?

  24. How many variable domains are there in each of the above structures?

  25. In IgG, how many pairs of Ig domains are there? How many of these pairs are not directly attached to each other, side to side? Why aren't they?

  26. What are the approximate dimensions of a single Ig domain? (Hint: use the distance reporting mode available from the utility menu. It reports in Angstroms.) What about the nose-to-tail distance for a whole IgG molecule?

  27. What is the largest distance between contact atoms in the CDR's?

  28. A lymphocyte is about 10 micrometers in diameter. How many Angstroms is this? What is the approximate ratio of the diameter of a B lymphocyte to the diameter of its Ig receptor?

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