Kyle’s Section BIBC100 – Structural [email protected] Summer 2005 Problem Set #101. Describe the structural similarities between the constant and variable domains found in immunoglobulins. 2. What does CDR stand for? Where on an immunoglobulin protein is this region found?3. Where on the variable domains are the amino acid sequences found which have the highest degree of variability?4. What does the Major Histocompatability Complex (MHC) do? How does the structure of this protein allow it to do this?5. How does a T-cell receptor interact with an MHC?6. Name two receptor proteins that are members of the Receptor Tyrosine Kinase (RTK)superfamily. 7. What is the function of the enzymatic domain “tyrosine kinase”?8. Upon ligand binding, how do the tyrosine residues on the intracellular regions of tyrosine kinase receptors become phosphorylated?9. Certain cytosolic proteins will recognize these phosphorylated tyrosines. All of these proteins share the same domain which is responsible for this recognition. What is thisdomain called?10a. These proteins which have an SH2 domain, and therefore recognize phosphorylated tyrosine residues on tyrosine kinase receptors are 2nd messengers of a ___________ ____________ pathway. 10. What is a G protein-coupled receptor (GPCR)? How many transmembrane spanning alpha helices are found in a GPCR? 11. Give an example of a G protein-coupled receptor (GPCR).12. Name the cofactor found in both bovine rhodopsin and bacteriorhodopsin transmembrane proteins. What does this cofactor do?13. Name the ligand that binds to the Beta-adrenergic receptor’s binding site?14. What are the 4 steps of the H+ pumping mechanism found in bacteriorhodopsin?15. Name three steps that describe how an HIV virus infects a white blood cell.16. Which enzyme in HIV is responsible for transcribing a single stranded RNA into a double stranded DNA that can be integrated into the host cell’s genome?17. What do gag and Gag-pol do?18. What happens in the “maturation” stage of the HIV virus developmental cycle?19. Name the three enzymes in HIV that are responsible for replicating the viral genome and creating new viral particles. Also describe what they do.20. What does gp120 do for the HIV virus? Name the protein that it recognizes21. What is CCR5 and what does it do?22. What does gp41 do for the HIV virus?23. Describe the active site of the HIV protease. How would designing protease inhibitors be an effective strategy for fighting
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