Class Notes (808,294)
Canada (493,118)
Biology (2,220)
BIO120H1 (1,171)
Lecture 10

BIO240 Lecture 10

8 Pages
Unlock Document

University of Toronto St. George
Jennifer Harris

Lecture 10 Protein Folding & Degradation - In the past lectures we’ve looked at going from DNA to protein - Now we address the question why cells don’t explode from the protein, we look at the proteome and he wants to ask how we get rid of the proteins in the proteome - In the remainder of today’s lecture, we will cover protein folding with molecular chaperones, something we’ve heard about before and he wants to look at protein degradation, the proteosome and ubiquitin. - Short readings today but at the end of last lecture, the handout in the last lecture had the accurate readings, pay attention to the handout. He made a booboo for the lecture but the handout is accurate. - He has just said wow that’s a lot of protein, why don’t his cells explode? - Let’s consider for a moment, where that protein came from as it came off of the ribosome. - Let’s take a look as just a reminder, at translation. We see the peptide bond being made starting with methionine in eucaryotes and the formation of a peptide bond within the large subunit of the ribosome and the transfer that occurs from one tRNA to another. - There is a movie playing capturing the elongation of the peptide strand very slowly. All of this should be looking fairly familiar, the same is true on the next slide, the multistep process involved in making polypeptides, the process of translation and away we go. - This is a very simple multistep process involving the migration of the tRNAs from multiple active sites within the ribosomal complex. - We want to focus on what's happening to that protein as it comes off from the ribosome. - We know that a number of things must happen to it, we know that as it emerges from the ribosome it enters its life within the cell, that it has to be folded, that there may be association with cofactors there may be some form of covalent modifications of the proteins, intra and intermolecular interactions that can occur, assembly into multi-protein complexes etc. - Eventually we have a 3D structure that performs a function in the cell. Nascent polypeptide chain enters cell from ribosome  Folding and cofactor binding (non-covalent interactions)  covalent modification by glycosylation, phosphorylation, acetylation, etc  binding to other protein subunits  mature functional protein - The way you can think of a molten globule is the way the name implies, like a bead of wax dripping off a candle or lava from a volcano. - It's something that is very malleable, flexible in its shape but it's not yet assumed its final shape and that is captured in the textbook. - You see the transition in the slide. - The beginning of this folding of the molten globule begins right on the ribosome. Co-translational folding - As the protein rises from the ribosome during the process of translation, folding occurs and this is called co-translational folding. - Folding occurs as the protein emerges from the ribosome. - The problem is that not all proteins are folded properly, most are, most proteins will assume the leftmost route (going downwards). - It is the on-pathway folding meaning it is on the route towards a properly folded protein, it starts its life as a molten globule and eventually through thermodynamically driven interactions between the components of the molecules, between the AA R groups, you end up with a protein in its final properly folded form. - Every now and then you get folding that occurs off of this pathway, where misfolding has occurred, and it turns out that the cell has mechanisms to recognize these improperly folded proteins and get them back onto the properly folding pathway route again. - You have every now and then, proteins that misfold that can’t be refolded back to a properly folded state. - The bottom line is the cell has mechanisms that ensure a misfolded protein gets back onto the pathway towards correct folding but if it is completely irrecoverable, it gets trashed.  Heat shock protein 70 - Here is one of the mechanisms that get things back onto the properly folded pathway or to ensure they are on the pathway to begin with and that they fold properly, this is the role played by molecular chaperones. - An example of a molecular protein is heat shock protein 70, HSP 70 (remember not HSP90 which is an inhibitor). - The heat shock protein component of this is misleading, the name came about because in studies where people were originally looking at the proteome and this is some of the earliest proteomic work ever done, what they did was take a look at the differences of protein content and normal cells and those treated with heat. Those cells treated with heat created an abundance of a lot of these proteins which were, at that point in time named heat shock proteins because they were created in response to heat shock. - It turns out that these proteins are actually made every day and used every femptosecond of every day to ensure that proteins fold properly but they get expressed on much higher levels during heat shock because it is more likely for a protein to be misfolded when higher heat is present. - The thermodynamics changes so to protect the cells from the heat, the cell ensures that these molecular chaperones are there to make sure the folding process goes correctly, but they’re still there every minute of every day to ensure that the proteins in your cells are folded properly, this HSP 70. - We met HSP 90 earlier which is a chaperone which ensures that proteins stay outside in the cytoplasm and we saw that with the glucocorticoid receptor, yet another example of the chaperones that ensure proteins do what they do. - HSP 70 it binds to short stretches of hydrophobic amino acids in this instance and as he already said, it was named based on its appearance after heat shock. It turns out that different organelles have different HSP 70s but they all fulfill a similar role, recognizing hydrophobic patches and in an energy dependent fashion involving the hydrolysis of ATP, ensures that the protein folds into a proper shape on the basis of thermodynamic properties, it ensures that the protein is properly folded.  Barrel - like - Another kind of heat shock protein which is a molecular chaperone is heat shock protein 60 (HSP60) sometimes called TCP – 1 or GroEL. - Again it is named due to its abundant expression after heat shock but again this is also functioning every moment of every day. - In an energy dependent fashion, it folds misfolded proteins properly.  Through hydrophobic interaction - Here is how HSP 60 functions. You have a misfolded protein called a client protein, if this client protein has hydrophobic patches exposed, it's wrong in the aqueous environment within the cell. If you have a hydrophobic patch on the outside of this protein (trust me it's hydrophobic even though he says aqueous), it indicates that it is misfolded. - Sometimes the misfolded protein is fed in by heat shock proteins. - In a reaction that involves physical movement of the barrel structure itself causes the thermodynamic properties within the barrel to change and causes the protein to refolded and hopefully cause the protein to refold into a properly folded state. - What you’ve done is that you’ve taken what you knew was misfolded and there is a good chance that it's going to get properly folded. We will now see a movie - This movie captures what we’ve talked about in the last couple of slides, starting with HSP70 and moving on to HSP60. - There is a properly folded protein where we see hydrophobic amino acids are properly found in the interior of the structure. We see the two types of chaperones, starting with HSP70 bound to ATP, then we have proper co-translational folding where as hydrophobic amino acids emerge from the ribosome, they are protected by HSP70 which by now are involving the hydrolysis of ATP to ADP. An exchange with ATP, the chaperone will let loose and the protein will fold into its properly folded configuration, that’s example number 1. - Let’s take a look at HSP60, there we see barrel-like structure, the misfolded protein is being fed in and we see the hydrophobic patches interacting with the surface of the barrel, the barrel changes shape and out comes a nicely folded protein. - What he wants to do in the next lecture is talk about what happens to proteins when they aren’t properly folded, how do we get rid of the trash. Let’s see what happens to incompletely folded forms and digested in the proteasome. **Lecture 10 Ends Here** **Lecture 11 Starts Here** - Last lecture: we’ve taken a look at the elaboration of the central dogma & we’ve got ourselves as far as protein. We’ve talked about the proteome, how one analyzes individual proteins & determines their function within the proteome & what we started talking about in the last lecture was how proteins fold to give rise to appropriate structures & we started to consider what happens when we focus on that proteome, what happens when things don’t fold properly, when they don’t function properly, how do we get rid of that protein? - These are the pathways that proteins may assume as they are post-transcriptionally folded off of the ribosome & find their way to their function in an eucaryotic cell. - So the 1 part of the pathway is that proteins are correctly folded without help. - The 2 part of the pathway involves the role of the molecular chaperone HSP60 & HSP70 in the folding of proteins. - The final pathway is what happens to proteins that are incompletely folded or completely off the folding pathway & they are described as irretrievable errors/mistakes – these are digested in the proteasome, they are put in the equivalence of the cellular garbage can. - Thi
More Less

Related notes for BIO120H1

Log In


Don't have an account?

Join OneClass

Access over 10 million pages of study
documents for 1.3 million courses.

Sign up

Join to view


By registering, I agree to the Terms and Privacy Policies
Already have an account?
Just a few more details

So we can recommend you notes for your school.

Reset Password

Please enter below the email address you registered with and we will send you a link to reset your password.

Add your courses

Get notes from the top students in your class.