What is the question they were trying to answer, and what were their overall conclusions

Write a one page  literature review of your figure ( FIGURE ASSIGNED 6 d-g)

Abstract:  What is the question they were trying to answer, and what were their overall conclusions

Introduction: Introduce, briefly, the endomembrane system and how proteins move back and forth. Describe the importance of the KDEL sequence. What is the question they are trying to answer in your figure? How does this question relate to the larger context of the whole paper?

Body: What technique are they using? Briefly describe the technique. For each experiment tell me specifically what the variables are from that technique for that experiment (so which antibody are they using, and how did they prepare the samples) . How can that particular antibody or preparation help them to answer their question. What were their observations? What do they see?

Conclusions: What do they conclude from this figure or part of a figure?

This description, must be IN YOUR OWN WORDS.  Focus, on the parts of the signaling cascade that they are trying to understand.

Assignment 3: Cell Biology

For this assignment we will be looking an article from 2008 that describes a signaling event that is stimulated by an increase in ER to golgi traffic. Below are your instructions for the assignment and a reading guide to help you through the paper. A table of figure assignments can be found in the assignment on Canvas.

The Assignment:

Read the introduction and discussion of the paper to get some idea of what they are talking about. Then look specifically at the figure or part of a figure that you were assigned (see the canvas assignment page). Write a one page literature review of your figure ( FIGURE ASSIGNED 6 d-g) . This should include:

Abstract: What is the question they were trying to answer, and what were their overall conclusions

Introduction: Introduce, briefly, the endomembrane system and how proteins move back and forth. Describe the importance of the KDEL sequence. What is the question they are trying to answer in your figure? How does this question relate to the larger context of the whole paper?

Body: What technique are they using? Briefly describe the technique. For each experiment tell me specifically what the variables are from that technique for that experiment (so which antibody are they using, and how did they prepare the samples) . How can that particular antibody or preparation help them to answer their question. What were their observations? What do they see?

Conclusions: What do they conclude from this figure or part of a figure?

This description, must be IN YOUR OWN WORDS. Focus, on the parts of the signaling cascade that they are trying to understand.

Background: Below is some background material that may help you understand the paper.

The authors are investigating the interactions between the ER and golgi, and how these two organelles coordinate to allow for the movement of proteins down the secretory pathway.

They are using cultured cells that either normally secrete a particular protein like procollagen-I (PC-I), or they are transfecting their cells with DNA that causes them to express the vesicular stomatitis virus G glycoprotein (VSVG). Both of these proteins go through the standard secretory pathway, which is to say, they are produced in the RER, transported to the golgi, and then transported to the plasma membrane and released from the cell.

In these papers they are interested in how the ER and Golgi coordinate levels of trafficking. Thus, they would like to create a situation where there is a sudden increase in the levels of trafficking from the ER to the golgi. They do this by exploiting a curious property of their two secreted proteins, which is that these proteins do not fold correctly at slightly higher temperature. Thus, at the higher temperature these proteins are held up in the ER by protein chaperones, and they accumulate in the ER to very high levels. When the temperature is lowered at lot of this protein folds up correctly and is released to the golgi causing a sudden increase in ER to Golgi traffic. They are interested in what effect this increased traffic has on the Golgi, and how the golgi might sense that increase.

A few vocab words that might be helpful

KDEL – a sequence found in resident ER proteins that acts as a tag to cause them to be returned to the ER when they are incorrectly brought to the golgi. Literally the amino acids Lysine (K); Aspartic Acid (D); Glutamic Acid (E) and Leucine (L). If you see a protein name (STB for example) with the letters KDEL in supper script it means they took that protein, which does not normally have a KDEL, and attached a KDEL sequence to it. They do this for a few different proteins in this paper.

KDEL-R – a receptor that recognizes and binds to the KDEL sequence. This receptor also binds to adaptors for the COPI vesicles and helps to bring these ER residents back from the golgi. These papers define additional new roles for this protein.

Kinase – a type of enzyme that adds a phosphate onto other proteins. The addition of a phosphate is a signaling mechanism that causes a change in the activity, binding partners or localization of a protein. Phosphorylation most often occurs on the amino acids Serine, Threonine, and Tyrosine. In particular Tyrosine phosphorylation is associated with the activation of a variety of proteins including the Src family of kinases

p-Tyr – this is short hand for an antibody that recognizes a variety of proteins if they have a phosphate attached to the amino-acid tyrosine. Tyrosine phosphorylation is a frequent method for activating kinases. If you are not sure which kinase might be active, and you want to look generally at kinase activation, you can use this antibody to identify ALL proteins with a phosphorylated tyrosine residue.

SFK – Src family kinases – a group of related kinases (they all have some recognizable domains that are similar between the family members). These are often signaling kinases, they act in a variety of signaling pathways. They are themselves activated by the addition of a phosphate on one of their Tyrosine residues. The point of this paper is more about how the signaling pathway is activated, and less about what it actually does (or how it does it) after it is activated. We are going to talk about signaling pathways next week, so don’t worry too much about what is going on downstream of this activation.

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