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Foundations Part II > Turnover of Biological Macromolecules > Flashcards

Flashcards in Turnover of Biological Macromolecules Deck (30):

What happens to a cell if it is too packed

It will lyse


What is an important molecule that have to be degraded in the cell and there are various redundant mechanism for that

RNA, degraded by RANses.


What are RNAses? What are their types?

They are in the family of hydrolases, they require a metallic cofactor and they have 2 types:

1. Exonucleases
2. Endonucleases


What are exosomes

They are a ring like structure associated with degrading mRNA and either degrading or maturing rRNA and tRNA


What kind of activity they have

They are phosphorylytic enzyme, substitute a PO4 group instead of water to cleave something, they have both endonucleases and exonucleases activity


What kind of malformation can there be that may stall protein synthesis in the translation process

There can be malformations like RNA hair pin structures can form


What happens when the ribosomes encounter these malformation

Protein synthesis stops


How does a cell deal with these malformation

An endonuclease enzyme is recruited that cuts the mRNA from the middle. Then XRNA1 comes in to chew the mRNA from the 5' end and exosome chews it from the 3' end.


What is this process called

No go RNA decay (NGD)


Explain NGD, NMD and NSD

In nonsense mediated decay, the cell identifies the stop codon being placed too early, comes in. Endonuclease comes in to cut the mRNA in half, XRNA1 eats from the 5' end and exosome eats from the 3' end.

In nonstop decay, the polyA chain is tackled by the ribsomoes which shouldnt be exposed to them, the cell identifies this as having no stop codon, and the cell recruits exosome to chew this up


Explain the role regulatory RNA in the cell. Where are they placed inside the cell after becoming inactive or nonfunctional.

There are 2 types of regulatory RNAs:
miRNA and siRNAs.

They combine with normal RNA, making them inactive by dimerizing with them, these are then placed in P bodies which are structures without a cell membrane (theyre not sturcture but just a place in the cytosol)


How are these regulatory structures degraded

By exo and endonucleases.

Natural RNA have lower affinity for these enzyme, they have to be decapped, their poly A tail have to be removed and then they are chewed up


When does a cell needs to change its proteins?

When the cell changes cycle


Which proteins are degraded by a protesome and which ones are degraded by lysosomes

The one with short half lives are degraded by proteosomes, the one with longer are degraded by lysosomes


How does a lysosome digest proteins

There are 2 processes involved with this, the first one being autophagy which is the lysosome eats whatever comes in its way, the second one invplved chaperone mediated autophagy which is every selective


What degrades the proteins inside the lysosome

What is the order of this degradation

Cathepsin proteases, there is no specific order, single amino acids or dipeptide molecules are the product of these enzymes.


Does cathepsins give us an lysosomal storage disease



Is the ubiquitin tag conserved by the proteosome?



Does the location and the number of ubiquitin tag matter

Yes, there has to be a specific number of ubiquitin tags and they have to be at a certain number of places so that the protein can be transferred to the proteosome. We know that ubqiuitin tag has to be on certian numbered lysine residues of the protein for the protein to go to the proteosome


What is the least number of tags we need for proteosome

4 ubiquitin tags are needed


What are the defining features of proteosome

It is huge, it has specific enzymes for specific residues


What are the specific enzymes in the proteosomes

Chemotrypsin is for aromatic whereas trypsin is for basic


How are the products of proteosome important

Soemtime as long as 25 aa residues are left behind which are needed for immune system recognition


How is the mechanism know for prtoesome applied in medicine

It is used in the treatment of cancer


What is the function of oligosaccharides in the ER

To make glycolipids or glycoproteins


How are glycolipid or glycoproteins degraded

PNGase cuts the glycoproteins into oligosaccharide and proteins which are then taken to the lysosome for degradation.

Often times PNGase are found next to proteosomes


Disease associated with glycoproteins breakdown

Gaucher disease


What leads to lysosomal disease

Build of oligosacchardies, leads to necrosis of the cell as cell cannot degrade oligosaccharides in the lysosomes.


What happens to the glycoproteins that are not degraded via the lysosome

Cathepins chew them up


What disease is associated with the condition when cells cannot degrade membranes

Sphingomyelin deficiency disease or Nickman's Pick A and B. The cell cannot break the phosphoric acid bond. The phospholipases to break this bond are defective or completely missing.

This disease has poor prognosis.