Peptide chains with ER sequences

[lexia925]

I have been given 5 peptide chains with ER sequencs. I am supposed to draw the chain as it would be associated with the ER. But I don't understand by looking at one with just an N-terminal and Er signal how it should be positioned. How can you tell just by the presence (or absence of) an ER signal and stop transfer which end the N-terminal is and which is the C- terminal?

 

[greisen]

Could you please expand on the ER - what is ER?

 

[iansmith]

Have you look at a chapter on endoplasmic reticulum from a cell biology book.

This is an example,
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=reticulum&rid=mboc4.section.2202

Some figures that may help
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.2212
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.2215
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.2224
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.2225

 

[lexia925]

What we're supposed to do is figure out how to draw the protien on either side of the ER depending on if there is an ER signal or a stop transfer signal on it. Thats where i get lost.

 

[iansmith]

Look carefully at this picture

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.2224

there a signal peptide and a stop signal - What happen to the peptide?

Look a these two figures now
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.2225
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.2212

Different location of the signal peptide results in different events.

Also compare these figures
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.2225
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.2224
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.2227

Same kind of results but there two differences - Can you spot the differences?

Just to summarize question you need to ask when analyzing your peptide and the figures:
1. Is a ER signal peptide present?
2. If so, where is the signal peptide located (N-terminus, COOH-terminus or inside the peptide)?
3. If so, how many ER signa are present? Tell you how many transmembrane domain will be integrate in the membrane.
4. Is a stop transfer signal sequence present? Tell you if the protein will be integrated in the membrane
5. If so, how many stop transfer signal sequence and where the signal sequence located?