regrades need to be typed and turned in next tuesday after class

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

X-ray structure of a protein-conducting channel

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

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BACKGROUND

-how secreted proteins are made-very ordered and controlled

EndoplasmicReticulum

Sec61/SecY

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

Mutations Made point mutations in genes of the

subunit to strengthen crystal contact

Hypothesis Proposed a mechanism of the channel

where it opens for polypeptide translocation by displacement of a PLUG

How is this plug unlocked The plug is removed so translocation

can occur from the Signal Sequence that is on the polypeptide

Model from Experimental Work

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Immune System

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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

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

Antibodies

-important for binding antigen so that it may be neutralized andtaken up by cells that eat (macrophage)

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

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

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

Cell Membranes

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What is in a cell membrane

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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

Basic Unit of the bilayer

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Links hydrophillic part to hydrophobic

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

How do proteins fit into all this?

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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

Kyte-Doolittle plot

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-tells you if you protein of interest crosses the membrane-number of peaks tells you how many times it crosses