VCE Biology Question Thread

[PhoenixxFire]

Sorry about my phrasing for the first question. I meant in the sense that the binding of coenzymes to the enzymes is temporary since they have weak bonds ,as opposed to prosthetic groups which are permanent in enzymes since they have really strong bonds with the enzyme.

In that case yep they're temporary, they'll disconnect after the reaction and be replaced with a new coenzyme

Also, congrats darkz! Somehow i missed the addition to your sig haha

Edit: @erutepa. Totally fine to include it, sometimes extra context helps with understanding things, just didn't want to confuse anyone else.

[Evolio]

Thank you darkz, PhoenixxFire and Erutepa!
By the way, a massive congratulations on your 50 for bio darkz!
 

[ssillyssnakes]

I hope that this isn't a dumb question - I have tried looking into it online but I've yet to find any answers that I properly understand - but what happens to the mRNA molecule after translation? Can it be reused by the cell whenever the protein it codes for is needed, or is it that one mRNA codes for only one copy of one protein and then is destroyed or something?

[PhoenixxFire]

I hope that this isn't a dumb question - I have tried looking into it online but I've yet to find any answers that I properly understand - but what happens to the mRNA molecule after translation? Can it be reused by the cell whenever the protein it codes for is needed, or is it that one mRNA codes for only one copy of one protein and then is destroyed or something?

No such thing as a dumb question! Please no one try and prove this wrong though lol

The one mRNA strand can be translated multiple times to produce multiple (identical) polypeptides. The poly A tail that is added during post-transcription modification helps the mRNA strand stay around for a bit. Eventually it gets broken down though - but I don't know exactly how that works (and you don't need to know the details).

[DBA-144]

I hope that this isn't a dumb question - I have tried looking into it online but I've yet to find any answers that I properly understand - but what happens to the mRNA molecule after translation? Can it be reused by the cell whenever the protein it codes for is needed, or is it that one mRNA codes for only one copy of one protein and then is destroyed or something?

Cell's don't want the mRNA strand to stick around for long- otherwise the cell will be wasting energy producing proteins it does not require. Therefore, what it does is that it adds a Poly-A tail to the 3' end during post-transcriptional modificaiton. Not only does this Poly-A tail provide the mRNA strand with stability, but this tail gets shorter and shorter every time a ribsome synthesises a polypeptide chain. So, eventually, the Poly-A cap is completely gone, and then it gets broken down by an enzyme or something (not sure quite how this bit happens). I am almost certain that this is carried out by a protein of some sort however.

Note here that the Poly-A tail is not very long (I believe it to be only about 250 adenine bases long), so it can still get used multiple times and not stick around for too long either. 

Hopefully this helps. Also happy to be proven wrong what do you mean there are no stupid questions @ PF?? of course we can prove it wrong lol

[Sine]

I hope that this isn't a dumb question - I have tried looking into it online but I've yet to find any answers that I properly understand - but what happens to the mRNA molecule after translation? Can it be reused by the cell whenever the protein it codes for is needed, or is it that one mRNA codes for only one copy of one protein and then is destroyed or something?

Prokaryotes - one time use as it is not stable hence degrades after 1 use
Eukaryotes - multiple time use - can be used multiple times as it is quite stable (has 3' polyA tail and 5' methyl guanosine cap)

[ssillyssnakes]

Cell's don't want the mRNA strand to stick around for long- otherwise the cell will be wasting energy producing proteins it does not require. Therefore, what it does is that it adds a Poly-A tail to the 3' end during post-transcriptional modificaiton. Not only does this Poly-A tail provide the mRNA strand with stability, but this tail gets shorter and shorter every time a ribsome synthesises a polypeptide chain. So, eventually, the Poly-A cap is completely gone, and then it gets broken down by an enzyme or something (not sure quite how this bit happens). I am almost certain that this is carried out by a protein of some sort however.

Note here that the Poly-A tail is not very long (I believe it to be only about 250 adenine bases long), so it can still get used multiple times and not stick around for too long either. 

Hopefully this helps. Also happy to be proven wrong what do you mean there are no stupid questions @ PF?? of course we can prove it wrong lol

Prokaryotes - one time use as it is not stable hence degrades after 1 use
Eukaryotes - multiple time use - can be used multiple times as it is quite stable (has 3' polyA tail and 5' methyl guanosine cap)

Okay so can the 3' poly A tail be varied in how many adenosine molecules it has, with some mRNA molecules purposefully having more? Because some proteins are going to be used by the cell more often and will need to be translated more often, will they have longer poly A tails, or is it the same general length to maintain stability and these proteins will have to just be transcribed more?

[Erutepa]

Okay so can the 3' poly A tail be varied in how many adenosine molecules it has, with some mRNA molecules purposefully having more? Because some proteins are going to be used by the cell more often and will need to be translated more often, will they have longer poly A tails, or is it the same general length to maintain stability and these proteins will have to just be transcribed more?

From some quick reading:
1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4163081/ (only breifly read)
2. https://en.wikipedia.org/wiki/Messenger_RNA
It seems that this is the case to a certain degree, however, it is a bit more complicated than what is simply stated:

the correlation was observed between longer poly(A) tails and increased protein expression at specific times in the circadian cycle.

Funnily enough, as seen in the Wikipedia article, poly-A tails may be added in prokaryotes to mRNA in order to facilitate degradation.
In addition to this, from the introduction on that first source, it can be seen that variation in the poly-A tail may serve multiple other cell functions.

All this being said, for the purpose of VCE biology, all that I think you will need to know is that a poly A tail is added to the 3' end of the mRNA during post-transcriptional modification to prevent degradation.
You shouldn't need to know why it prevents degradation or the relationship between longer tails and mRNA lifespan, but knowing more shouldn't hurt.

[ssillyssnakes]

From some quick reading:
1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4163081/ (only breifly read)
2. https://en.wikipedia.org/wiki/Messenger_RNA
It seems that this is the case to a certain degree, however, it is a bit more complicated than what is simply stated:Funnily enough, as seen in the Wikipedia article, poly-A tails may be added in prokaryotes to mRNA in order to facilitate degradation.
In addition to this, from the introduction on that first source, it can be seen that variation in the poly-A tail may serve multiple other cell functions.

All this being said, for the purpose of VCE biology, all that I think you will need to know is that a poly A tail is added to the 3' end of the mRNA during post-transcriptional modification to prevent degradation.
You shouldn't need to know why it prevents degradation or the relationship between longer tails and mRNA lifespan, but knowing more shouldn't hurt.

Thank you for that!

I read probably 1/2 of that study (got bored one it started discussing different methods of measuring polyA tail size ha) but that was really interesting. One part that was really interesting was that for some mRNA molecules, having shorter polyA tails could prevent enzymes from destroying the molecules because the long A tail could actually signal them and prevent the mRNA from 'sliding under the radar'. That's how I understood it at least. The relationship between the polyA tail size and developmental genes was quite interesting too, although I can't say I fully understood everything.

I figure that learning more that's outside of the curriculum isn't too bad, as long as it doesn't impact the knowledge required for the course

[PhoenixxFire]

I figure that learning more that's outside of the curriculum isn't too bad, as long as it doesn't impact the knowledge required for the course

Learning outside of the course certainly makes it more interesting - just make sure you’re familiar with the study design so you know what the parameters of the course are

[DBA-144]

This question is quite similar to the previous one.

How might prokaryotes modify their proteins and have functional diversity in their proteome?

The primary and secondary strucutres I understand, but how do proteins in prokaryotes get their 3D functional shape if there is no rough er to do this for them? How are proteins in prokaryotes modified, like how do they make speciliased proteins, such as RNA plymerase and carrier proteins?

Thanks. 

[vox nihili]

This question is quite similar to the previous one.

How might prokaryotes modify their proteins and have functional diversity in their proteome?

The primary and secondary strucutres I understand, but how do proteins in prokaryotes get their 3D functional shape if there is no rough er to do this for them? How are proteins in prokaryotes modified, like how do they make speciliased proteins, such as RNA plymerase and carrier proteins?

Thanks. 

How do proteins produced in free ribosomes (i.e. ribosomes not on the rough ER) get their shape in eukaryotes? Answer that first and see if that gets you any closer!



(most of the answer to this question is beyond VCE though tbh).

[DBA-144]

How do proteins produced in free ribosomes (i.e. ribosomes not on the rough ER) get their shape in eukaryotes? Answer that first and see if that gets you any closer!



(most of the answer to this question is beyond VCE though tbh).

I believe that they would get their primary and secondary structures forming naturally from the sequence of their amino acids, which is a result of the sequence of nucleotides in the mRNA strand, the secondary by Hydrogen bonding between closeby R groups and that the 3D functional shape would be from proteins in the cytosol that are specifically responsible for folding proteins into particular shapes, akin to what chaperone proteins do?

And this would be the same mechanism in prokaryotes?

[ssillyssnakes]

I believe that they would get their primary and secondary structures forming naturally from the sequence of their amino acids, which is a result of the sequence of nucleotides in the mRNA strand, the secondary by Hydrogen bonding between closeby R groups and that the 3D functional shape would be from proteins in the cytosol that are specifically responsible for folding proteins into particular shapes, akin to what chaperone proteins do?

And this would be the same mechanism in prokaryotes?

From my (basic) understanding, the tertiary structure doesnt require enzymes to bond parts of the protein together, the bonds can be naturally forming hydrophobic/hydrophilic bonds, for example. Secondary structure is the natural hydrogen bonding between areas of the polypeptide chain, while tertiary is all kinds of bonding that occurs within the secondary (I'm not sure if that makes much sense and if I'm super wrong here but oh well).

So I would guess that prokaryotic proteins could still develop tertiary structure and have specialised proteins, the reactions just wouldn't be catalysed by enzymes. I think this would mean there is no glycoproteins in prokaryotic cells, but I might be wrong on that

[Erutepa]

I believe that they would get their primary and secondary structures forming naturally from the sequence of their amino acids, which is a result of the sequence of nucleotides in the mRNA strand, the secondary by Hydrogen bonding between closeby R groups and that the 3D functional shape would be from proteins in the cytosol that are specifically responsible for folding proteins into particular shapes, akin to what chaperone proteins do?

And this would be the same mechanism in prokaryotes?

Secondary sticture results from hydrogen bonding between the regular repeating amino acid backbone and not the variable side chains. hydrogen bonds that form between side chains fall under the tertiary structure classification.

Protein chaperones do not determine the folding, but simply facilitate and help it along. The folding of the polypeptide is still determined by the sequence of amino acids and the properties of the variable side chains of that sequence.

This would be more or less the same in prokaryotes

This question is quite similar to the previous one.

How might prokaryotes modify their proteins and have functional diversity in their proteome?

The primary and secondary structures I understand, but how do proteins in prokaryotes get their 3D functional shape if there is no rough er to do this for them? How are proteins in prokaryotes modified, like how do they make speciliased proteins, such as RNA plymerase and carrier proteins?

Thanks. 

the rough ER does not give the protein its 3D shape, it rather contains proteins which can modify the protein by such mechanisms as cleavage or the addition of carbohydrate chains.
Here it is the case that protein cleavage (for example) can occur in the ER, but also in other places (like at the ribosome). As such, it can occur for proteins in prokaryotes and for proteins which aren't being secreted by eukaryotic cells.
 This is just from a brief read, so It may be incorrect in some ways.
You can read more about it here: https://www.ncbi.nlm.nih.gov/books/NBK9843/

Let it be known that a lot of this is all beyond the knowledge of VCE biology; all you need to know is that protein folding occurs determined by the sequence of amino acids and protein modification occurs. With protein modification like cleavage you only need to know it in terms of secreted proteins in the endomembrane system (i believe), and you do not need to know the precise enzymes or what not, just that the polypeptide chain is cleaved as part of producing the proteins functional 3d shape.