Explain why proteins are degraded
Proteins are degraded for two main reasons. Firstly, anything non-functional gets degraded pretty quickly because some non-functional proteins can actually be somewhat harmful to the cell (if they act on the wrong substrate or whatever). Secondly, proteins that the cell doesn't currently need get degraded in order to free up some space for useful proteins.
Be able to describe the structure and function of lysosomes with respect to the degradation of proteins.
Lysosomes are small single-membrane organelles in the cell in which protein degradation takes place. They contain hydrolytic enzymes and have an acidic internal environment (~pH 5), maintained by an energy-guzzling H+ pump. This acidity unfolds the proteins to make them more susceptible to proteases, as well as affords said proteases the optimal environment in which to work. One benefit of these proteases functioning well at an acidic pH is that, if the lysosome ruptures, the proteases won't function so well at the pH in the rest of the cell and therefore won't go around eating everything else.
Be able to discuss cathepsins
One of the proteases found in lysosomes is cathepsins. They cleave peptide bonds within proteins.
Since I've just written a whole bunch of posts covering how proteins are made and all that, let's discuss that in relation to cathepsins. Cathepsins are synthesised on the endoplasmic reticulum (ER), and like many other proteins that are synthesised on the ER, they have a signalling sequence that is later cleaved. Other regions of interest in the cathepsin sequence are the Pro region, heavy chain and light chain, which will all get a mention in this story.
Alright, so cathepsins get synthesised on the ER. Aside from synthesis, several post-translational modifications take place here. Folding occurs, guided by the Pro region. Disulfide bonds also form, both within the heavy chain and between heavy and light chains. N-linked glycosylation with high-mannose glycans also occurs. (If you're confused by this terminology, please see my previous post about post-translational protein modifications.)
After synthesis on the ER, the cathepsin travels to the Golgi apparatus. Here, the mannose residues are phosphorylated to form mannose 6-phosphate, or m6p. This m6p is actually quite important, as it will eventually bind to a receptor on endosomes (lysosome precursors), which allows the cathepsin to be taken up into the endosome/lysosome.
But wait! It's not done being processed yet. Once in the endosome/lysosome, further modifications happen thanks to the acidic environment inside the lysosome. Some cleavage also occurs: the Pro region gets cleaved off, and the heavy and light chains get cleaved (though they are still joined by a disulfide bond). And the cathepsin is complete! Ta-da!
Be able to describe the role of lysosomes in autophagy
Know the different types of autophagy
Autophagy is the digestion of organelles and so forth in the cell. There are three main types of autophagy that involve lysosomes: macroautophagy, microautophagy and chaperone-mediated autophagy (CMA).
Macroautophagy
Macroautophagy involves the action of cytoplasmic phagophores, which are cup-shaped structures made up of lipids as well as ATG ("autophagy-related") proteins. These phagophores close off around the structures to be digested. When they close off, they are known as "autophagosomes." These autophagosomes fuse with the lysosomes, allowing them to release their contents into the lysosome, where they can be digested by the hydrolytic enzymes within the lysosome.
Microautophagy
Microautophagy has the same end result as macroautophagy, but it reaches its goal more directly. The lysosome simply digests anything that it wants to chew up via endocytosis. (You can read a bit more about endocytosis in an earlier post of mine.)
Chaperone-mediated autophagy (CMA)
Chaperone-mediated autophagy, as the name suggests, requires a chaperone protein. Usually this is a chaperone complex that includes our old friend hsp70 (which is also heavily involved in protein folding as discussed here and here). This chaperone complex binds to a consensus sequence that it recognises, and then docks to the LAMP-2A receptor (lysosome-associated membrane protein type 2A) located on the lysosomal membrane. This allows the protein to be degraded to be funnelled into the lysosome, where it can get degraded.
Know the structural characteristics of the proteasome
Proteasomes are made up of a cylindrical barrel, with caps at each end. Not really sure what else I'm meant to say here.
Be able to describe the binding sites for ubiquitin
The protein ubiquitin is a very useful tag for degradation, among other things. Its C-terminal can bind to lysine residues of target proteins, including Lys-48 of other ubiquitins. This allows proteins to be ubiquitinated in three main ways: monoubiquitination, in which a single ubiquitin is attached to a lysine on the target protein; multiubiquitination, in which multiple ubiquitins are attached to different lysine residues on the target protein; and polyubiquitination, in which an ubiquitin chain with ubiquitins attached C-terminal to Lys-48 is joined to a lysine residue on the target protein. (That was probably a horrible misuse of semicolons. Sorry, Grammar Nazis.) Usually it is polyubiquitin that is associated with protein destruction.
Be able to describe the ubiquination process
Ubiquitination requires the actions of three proteins, imaginatively named E1, E2 and E3. (They actually do have more interesting names: ubiquitin-activating enzyme, ubiquitin-carrier protein/ ubiquitin-conjugating enzyme and ubiquitin-protein ligase, respectively.) There are three steps, which are reasonably easy to remember because E1 is in the first step, E2 is in the second step and E3 is in the third step. Here's the process, in all its glory:
- The C-terminal of ubiquitin is joined to E1. This requires ATP.
- Ubiquitin is transferred to E2.
- E3 transfers ubiquitin to the target protein. (E3 is responsible for recognising the target protein.)
By now, you might have been wondering why I mentioned proteasomes and then randomly started rambling about ubiquitin. Well, the two are actually related. As I mentioned, ubiquitin is a useful tag for degradation. That degradation occurs in proteasomes.
The caps of the proteasomes are responsible for recognising ubiquitin chains. Once a polyubiquitinated protein arrives at the cap, deubiquitinase enzymes remove ubiquitin and release it so that it can go and slap a target on its next victim. In the cap, the protein is also unfolded and transferred to the barrel- a process that requires ATP (I guess the basic rule of thumb is that proteins don't like being unfolded, and require a fair bit of energy to do so). The cylinder of the proteasome is the protease bit that breaks down the protein into short peptides. These short peptides are released into the cytoplasm to be degraded by peptidases in the cytoplasm.
And that's it for the protein life cycle! Cool story, huh?
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