1. Regrades need to be typed and turned in next TUESDAY after class

2. X-ray structure of a protein- conducting channel

3. Secreted Proteins Have a special sequence on them called a signal sequence, which directs them to Endoplasmic Reticulum Ribosome brings the half made protein to ER membrane where it must be thread through the membrane Sec61 is one of these channels that funnels the protein through to the inside of the ER

4. BACKGROUND -how secreted proteins are made -very ordered and controlled Endoplasmic Reticulum Sec61/SecY

5. Study Show importance of Sec61/SecY for protein translocation into ER Use M.jannaschii to determine by X-ray crystollography at 3.2 A Determine the process of how translocation is carried out

6. Mutations Made point mutations in genes of the  subunit to strengthen crystal contact

7. Hypothesis Proposed a mechanism of the channel where it opens for polypeptide translocation by displacement of a PLUG

8. How is this plug unlocked The plug is removed so translocation can occur from the Signal Sequence that is on the polypeptide

9. Model from Experimental Work

10. Immune System

11. Immune Cells Need to be able to present bad guys to cells that can get rid of them Therefore evolution has created a set of specially designed proteins for this

12. MHC class 1 and class 2 MHC1 on all cells. Binds proteins that are degraded from inside cell and presents them for monitoring MHC2 present mostly on antigen presenting cells so OVERALL IDEA, these are great for binding a variety of proteins in order to display on surface

13. Antibodies -important for binding antigen so that it may be neutralized and taken up by cells that eat (macrophage)

14. Made By B cells Two chains: heavy and light Both have variable and constant regions Variable regions will bind to antigen Change in 1 amino acid of the sequence is enough for the antibody to be specific for another antigen

15. How do we get such wide diversity in the body of antibody Have rearrangements of genes Heavy variable chain is encoded by V, D, J Light chain is encoded by V and J

16. OVERALL PIC Rearrangement is going to give us the ability to produce a lot of different antibody in case we come across a antigen of that type

17. Cell Membranes

18. What is in a cell membrane

19. What processes occur across a cell membrane Pinocytosis- cell drinking Endocytosis-cell taking up specific molecules via the molecule binding to a specific membrane protein Then you have passive diffusion, facilitated diffusion, and active transport

20. Basic Unit of the bilayer Links hydrophillic part to hydrophobic

21. The phospholipid has double character -has two parts: Water loving polar head and water hating hydrophobic tail -this is termed an Amphipathic Molecule -when you through in water by itself, it will energetically surround where the heads interact with each other and the tails are hidden from the water and interact with each other - this is called a micelle

22. How do proteins fit into all this?

23. Membrane Proteins need to be designed in a way that allows them to energetically exist in the membrane while still being able to carry out their functions

24. Kyte-Doolittle plot -tells you if you protein of interest crosses the membrane -number of peaks tells you how many times it crosses