VCE Biology Question Thread

[alondouek]

Hi, can someone please explain the relationship between the structure and function of the extracellular matrix?

Because I understand its structure, that it consists of long flexible fibres embedded in a glycoprotein and glycolipid matrix but I am unsure of how this relates to its function?

Thankyou 

The extracellular matrix (let's call it the ECM for brevity) is composed of a multitude of components so it stands to reason that there are many associated functions, including:

 - structural support for the cell
 - regulation of intracellular communication
 - tissue barriers

among others. The ECM also has a role in the regulation of growth and in wound healing.

[That Other Guy]

I'm unsure of whether or not the specifics of this are extraneous to the study design, but how exactly does pH denature a protein? Does it pertain to the release of hydrogen ions and their subsequent bonding with certain amino acids? I could only see this as a feasible deduction if amino acids were polar...
Furthermore, if this is the case, then do some amino acids only exist within certain environments? For example, enzymes produced in the stomach would surely be resilient to denaturation in low pH levels, and yet others would not. Hence, would it be plausible to suggest that only non-polar amino acids form the polypeptides of proteins existing in highly acidic environments?
Are any amino acids polar?

I am theorizing here, but I would appreciate some clarity!

[masonruc]

I'm unsure of whether or not the specifics of this are extraneous to the study design, but how exactly does pH denature a protein? Does it pertain to the release of hydrogen ions and their subsequent bonding with certain amino acids? I could only see this as a feasible deduction if amino acids were polar...
Furthermore, if this is the case, then do some amino acids only exist within certain environments? For example, enzymes produced in the stomach would surely be resilient to denaturation in low pH levels, and yet others would not. Hence, would it be plausible to suggest that only non-polar amino acids form the polypeptides of proteins existing in highly acidic environments?
Are any amino acids polar?

I am theorizing here, but I would appreciate some clarity!

Omg slow down way to in depth for bio. All you need to know is that enzymes (proteins) work in an optimal pH enviro anything outside that optimal will have an effect on the structure of the protein. Hence the shape will alter and it will no longer be able to perform it's function.

[That Other Guy]

Omg slow down way to in depth for bio. All you need to know is that enzymes (proteins) work in an optimal pH enviro anything outside that optimal will have an effect on the structure of the protein. Hence the shape will alter and it will no longer be able to perform it's function.

Hahaha, I know that I probably jumped in the deep end... but I hate learning something without having a holistic explanation or model to at least satisfy my temporarily. I don't even know if my question was realistic or not. But thanks anyway!

[alondouek]

I'm unsure of whether or not the specifics of this are extraneous to the study design, but how exactly does pH denature a protein? Does it pertain to the release of hydrogen ions and their subsequent bonding with certain amino acids? I could only see this as a feasible deduction if amino acids were polar...
Furthermore, if this is the case, then do some amino acids only exist within certain environments? For example, enzymes produced in the stomach would surely be resilient to denaturation in low pH levels, and yet others would not. Hence, would it be plausible to suggest that only non-polar amino acids form the polypeptides of proteins existing in highly acidic environments?
Are any amino acids polar?

I am theorizing here, but I would appreciate some clarity!

Denaturation itself is a result of a change in the protein from a stable conformation to an unstable one. Different proteins have different preferred pH ranges, and when they are subjected to a pH that is not within their preferred range they reflect the change in their environment and alter in some way. Because tertiary and quaternary proteins are folded in a very specific way (so as to allow for specificity to a substrate), changes to the protein structure through denaturation ultimately affect or negate the function of that protein.

For example, if I were to place an enzyme in a lower-than-preferred pH, there are more H⁺ ions available. Some of the amino acids that make up this protein are polar (i.e. having a clear separation of electrical charge in the molecule); therefore the negative areas of the polar amino acids attract H⁺ ions, which then has an effect on the ability of the enzyme to hold its regular state (that is, it is unstable). The enzyme is said to be denatured, as it can no longer perform its regular function, being interaction with its specific substrate.

Hope that helped!

[That Other Guy]

Denaturation itself is a result of a change in the protein from a stable conformation to an unstable one. Different proteins have different preferred pH ranges, and when they are subjected to a pH that is not within their preferred range they reflect the change in their environment and alter in some way. Because tertiary and quaternary proteins are folded in a very specific way (so as to allow for specificity to a substrate), changes to the protein structure through denaturation ultimately affect or negate the function of that protein.

For example, if I were to place an enzyme in a lower-than-preferred pH, there are more H⁺ ions available. Some of the amino acids that make up this protein are polar (i.e. having a clear separation of electrical charge in the molecule); therefore the negative areas of the polar amino acids attract H⁺ ions, which then has an effect on the ability of the enzyme to hold its regular state (that is, it is unstable). The enzyme is said to be denatured, as it can no longer perform its regular function, being interaction with its specific substrate.

Hope that helped!

Yes, this was a major help! Logically, I assumed that some amino acids were polar, but I wasn't sure. In regards to enzymes in, for instance, the stomach, does the sequencing/composition of the protein allow for more resilience? Would it therefore be non-polar?

[alondouek]

In regards to enzymes in, for instance, the stomach, does the sequencing/composition of the protein allow for more resilience? Would it therefore be non-polar?

In short, yes. This is also beyond the VCE biology course, but some enzymes have inactive precursors called zymogens. In the stomach, our main proteolytic (breaks down proteins) enzyme is pepsin, but it is not synthesised by the body as pepsin. Instead, certain cells in the stomach (called 'chief cells') synthesize an inactive form of pepsin called pepsinogen. Pepsinogen is activated by the HCl in the stomach, thereby converting it into pepsin which can then fulfil its proteolytic role. How enzymes - in this example pepsin and pepsinogen - act in an environment is always at heart due to their amino-acid sequence.

How enzymes behave is a lot more complicated than a simple question of polarity; there are many, many factors that allow for them to act as they do as part of a biological system.

[That Other Guy]

In short, yes. This is also beyond the VCE biology course, but some enzymes have inactive precursors called zymogens. In the stomach, our main proteolytic (breaks down proteins) enzyme is pepsin, but it is not synthesised by the body as pepsin. Instead, certain cells in the stomach (called 'chief cells') synthesize an inactive form of pepsin called pepsinogen. Pepsinogen is activated by the HCl in the stomach, thereby converting it into pepsin which can then fulfil its proteolytic role. How enzymes - in this example pepsin and pepsinogen - act in an environment is always at heart due to their amino-acid sequence.

How enzymes behave is a lot more complicated than a simple question of polarity; there are many, many factors that allow for them to act as they do as part of a biological system.

I have heard about inactive protein and their activation, but never understood their application. Although this is all very interesting, I'll try not to think about it too much; I'll probably end up referencing it in some way and lose marks.

[MM1]

I'll probably end up referencing it in some way and lose marks.

Wait, are marks deducted if we reference information out of the scope of VCE Biol?!

[psyxwar]

Wait, are marks deducted if we reference information out of the scope of VCE Biol?!

nope, but if you reference information that is incorrect you will be penalised. It's good to learn stuff beyond the course, but don't do it for the sake of improving your biology mark; do it for the sake of learning (because honestly, there are better ways to invest time than reading about content irrelevant to the course if all you want to do is succeed in the subject)

[That Other Guy]

Wait, are marks deducted if we reference information out of the scope of VCE Biol?!

I'm not sure... but in the case of my protein question, if I explained all of that in an answer that required the simple answer of 'Proteins become denatured when the pH is beyond or below its optimum range.' Then surely I would lose marks... right? I haven't done a 3/4 subject before, so I have no idea.

[grannysmith]

I'm not certain on this, but I think they may take off marks if it seems you're trying to further justify a correct response?

[alondouek]

Wait, are marks deducted if we reference information out of the scope of VCE Biol?!

No haha, you'll never be deducted for knowing more than necessary.

However, markers do like to take off marks for waffling and for not answering the question. One of the main techniques my teacher taught me and I teach those I tutor is to answer the question 1) efficiently, 2) briefly and 3) correctly

[vox nihili]

Wait, are marks deducted if we reference information out of the scope of VCE Biol?!

You won't be deducted. But if you give an answer that's out of the scope, without referencing the answer that is in the scope of the course, you will lose marks.

[grannysmith]

Would it be correct/sufficient to say that cholesterol helps maintain the fluid mosaic model of the cell membrane?