VCE Biology Question Thread

[cosine]

first time asking a question and it might be a dumb one  but i still don't really understand a proteome, can you please explain it to me. thanks

Proteome is the collection of all the proteins within an organism's cells. We usually talk about single proteins and their importance in the metabolism, but infact, many protein functions are linked together. It's not like there is only one protein in the cell of an organism, instead, proteins interconnect and function together to achieve their function. Proteomics is the study of the collection of proteins in an organism.

[BakedDwarf]

first time asking a question and it might be a dumb one  but i still don't really understand a proteome, can you please explain it to me. thanks

Proteome is the complete set of proteins that are expressed by the genetic material.

Edit: beaten :S

[cosine]

If B cells have specific immunoglobulins on their surfaces, and these bind with their specific antigen on pathogens, is this how B cells recognise these foreign material? A few days ago I learnt that immune cells possess receptors on their surfaces that actually detect the MHC Class I markers of other cells and detect them as either self or non-self, is this the case with B cells? If so, then is this process different to when anitbodies on B cells bind with antigens?

[vox nihili]

Proteome is the collection of all the proteins within an organism's cells. We usually talk about single proteins and their importance in the metabolism, but infact, many protein functions are linked together. It's not like there is only one protein in the cell of an organism, instead, proteins interconnect and function together to achieve their function. Proteomics is the study of the collection of proteins in an organism.

Nice explanation

If B cells have specific immunoglobulins on their surfaces, and these bind with their specific antigen on pathogens, is this how B cells recognise these foreign material? A few days ago I learnt that immune cells possess receptors on their surfaces that actually detect the MHC Class I markers of other cells and detect them as either self or non-self, is this the case with B cells? If so, then is this process different to when anitbodies on B cells bind with antigens?

Your question is outside of the VCE course. B-cells do indeed express antibodies on their surface. These are IgM antibodies and they effectively function as a receptor. Indeed, the IgM antibody forms a complex with a number of other proteins, making the B-cell receptor (BCR). The BCR binds to free antigen (via the antibody) and, if it does bind, it causes the proliferation of the B-cell. The B-cell will then secrete antibodies with the same specificity as the IgM antibodies involved in the BCR.

This differs from T-cells because T-cells don't have the capacity to bind free antigen. Rather, they bind antigen that is presented in MHC class I or MHC class II molecules.

[Biology24123]

Nice explanation

Your question is outside of the VCE course. B-cells do indeed express antibodies on their surface. These are IgM antibodies and they effectively function as a receptor. Indeed, the IgM antibody forms a complex with a number of other proteins, making the B-cell receptor (BCR). The BCR binds to free antigen (via the antibody) and, if it does bind, it causes the proliferation of the B-cell. The B-cell will then secrete antibodies with the same specificity as the IgM antibodies involved in the BCR.

This differs from T-cells because T-cells don't have the capacity to bind free antigen. Rather, they bind antigen that is presented in MHC class I or MHC class II molecules.

A few things

B cells have to be activated by helper T cells before they proliferate
And I'm pretty sure cytotoxic T cells bind to free antigens

[cosine]

Thanks guys, apologies for being a menace but I really struggle with this topic and want to refine this; so do B cells recognise foreign material only when their specific immunoglobulins binds with the specific antigen found on a pathogen?

Also, how and I emphasise how, how are antigens recognised by phagocytes and other white blood cells involved in the non-specific second line of defence? I have a little understanding but unsure if this is correct. I think that certain receptors on these phagocytes bind with the MHC Class I molecules of the foreign particles and don't recognise them, hence engulfing the whole particle?

Quote wikipedia: The phagocytes move by a method called chemotaxis. When phagocytes come into contact with bacteria, the receptors on the phagocyte's surface will bind to them.

I got told earlier that we should just refer to the phagocytotic receptors as 'receptors', but do these receptors bind to the antigens of the pathogen? Is it simply what was said earlier that these receptors bind with MHC Class I markers of pathogens which display non-self antigens and hence the complex will lead to the engulfing of the pathogen?

[vox nihili]

A few things

B cells have to be activated by helper T cells before they proliferate
And I'm pretty sure cytotoxic T cells bind to free antigens

The first is correct, except for very rare cases. A T-cell with specificity to the same antigen must bind to an activated B-cell to allow the B-cell to proliferate properly.
The second is wrong. Cytotoxic T-cells bind to antigen expressed in MHC class I molecules. T-helper cells bind to MHC class II molecules.

Thanks guys, apologies for being a menace but I really struggle with this topic and want to refine this; so do B cells recognise foreign material only when their specific immunoglobulins binds with the specific antigen found on a pathogen?

Also, how and I emphasise how, how are antigens recognised by phagocytes and other white blood cells involved in the non-specific second line of defence? I have a little understanding but unsure if this is correct. I think that certain receptors on these phagocytes bind with the MHC Class I molecules of the foreign particles and don't recognise them, hence engulfing the whole particle?

Quote wikipedia: The phagocytes move by a method called chemotaxis. When phagocytes come into contact with bacteria, the receptors on the phagocyte's surface will bind to them.

I got told earlier that we should just refer to the phagocytotic receptors as 'receptors', but do these receptors bind to the antigens of the pathogen? Is it simply what was said earlier that these receptors bind with MHC Class I markers of pathogens which display non-self antigens and hence the complex will lead to the engulfing of the pathogen?

I just want to preface this next answer by saying that the VCE course is actually really poor on immunology. There are too many gaps in the course that make it impossible to get an appreciation of how things work. Nearly everything I've told you about immunology is outside of the course. Your textbook will serve as a good guide of what you actually need to know. The stuff I'm adding is so that you can synthesise a model in your head for how the immune system actually works.

Yes, you're right on the B-cells. They bind directly to free antigen (whether it be attached to a pathogen or floating around) and are subsequently activated by T-helper cells. How that happens is not important, but you do need to know that both do happen.

Not quite. Again, way out of the course: cells of the innate immune system express receptors called PRRs. These receptors bind to molecular motifs that are associated with pathogens (such as lipopolysaccharide, ssDNA or dsRNA—these are molecules not found in mammals, hence their association with invaders). That's how they are alerted to an infection.
How they actually clear the infection really depends on the particular molecular. The innate response is actually really carefully intertwined with the adaptive response. So, for instance, macrophages tend to gobble up bacteria that have been coated with antibodies first. I'm not going to go into these details though because it's too much and I'm not confident I know all of them!

I think my answer above answers your next question.

Just really want to stress this point:

MHC class I: expressed on all cells, present antigens from within the cell, are bound by cytotoxic T-cells ONLY
MHC class II: expressed on antigen presenting cells, present antigens from the extracellular environment (i.e. tissues), are bound by T-helper cells ONLY

[Biology24123]

The first is correct, except for very rare cases. A T-cell with specificity to the same antigen must bind to an activated B-cell to allow the B-cell to proliferate properly.
The second is wrong. Cytotoxic T-cells bind to antigen expressed in MHC class I molecules. T-helper cells bind to MHC class II molecules.

I just want to preface this next answer by saying that the VCE course is actually really poor on immunology. There are too many gaps in the course that make it impossible to get an appreciation of how things work. Nearly everything I've told you about immunology is outside of the course. Your textbook will serve as a good guide of what you actually need to know. The stuff I'm adding is so that you can synthesise a model in your head for how the immune system actually works.

Yes, you're right on the B-cells. They bind directly to free antigen (whether it be attached to a pathogen or floating around) and are subsequently activated by T-helper cells. How that happens is not important, but you do need to know that both do happen.

Not quite. Again, way out of the course: cells of the innate immune system express receptors called PRRs. These receptors bind to molecular motifs that are associated with pathogens (such as lipopolysaccharide, ssDNA or dsRNA—these are molecules not found in mammals, hence their association with invaders). That's how they are alerted to an infection.
How they actually clear the infection really depends on the particular molecular. The innate response is actually really carefully intertwined with the adaptive response. So, for instance, macrophages tend to gobble up bacteria that have been coated with antibodies first. I'm not going to go into these details though because it's too much and I'm not confident I know all of them!

I think my answer above answers your next question.

Just really want to stress this point:

MHC class I: expressed on all cells, present antigens from within the cell, are bound by cytotoxic T-cells ONLY
MHC class II: expressed on antigen presenting cells, present antigens from the extracellular environment (i.e. tissues), are bound by T-helper cells ONLY

Ok but how are specific cytotoxic T cells produced? T helper cells activate cytotoxic T cells to divide?

[tashhhaaa]

this isn't really a specific question but how should we be studying for Bio at this time of the year?

I realised I haven't finished my notes but I'm thinking it's pointless to continue. I've also forgotten a lot of the content and I'm not sure how to approach my study tbh

[Biology24123]

this isn't really a specific question but how should we be studying for Bio at this time of the year?

I realised I haven't finished my notes but I'm thinking it's pointless to continue. I've also forgotten a lot of the content and I'm not sure how to approach my study tbh

Do a practise exam and see what you don't know. Then see what topics you need to work on

[Biology24123]

Can someone give a definition of why genetic drift has a greater effect in small populations. I understand that random chance has a greater effect in small populations but how would you formulate that into a formal answer?

[vox nihili]

Ok but how are specific cytotoxic T cells produced? T helper cells activate cytotoxic T cells to divide?

Hmmmmm a good question. I'm not entirely sure. I'll check in with my friend tomorrow. I suspect that it's probably a combination of things and that T-helper cells are probably involved.

Can someone give a definition of why genetic drift has a greater effect in small populations. I understand that random chance has a greater effect in small populations but how would you formulate that into a formal answer?

I guess a way of doing it would be to acknowledge that an individual in a small population represents a greater percentage of the size of that population than someone in a large population and therefore, the loss of that individual represents a greater loss of genetic diversity in a smaller population than in a larger one.

With that said, that's still really stuffy and convoluted but it would be enough to get the marks. It's actually quite difficult to define, so yet another good question actually. Just as long as you can demonstrate you know why. You could even draw a diagram or actually do some basic maths.
In a population of four the loss of one person is a loss of 25% of the population, therefore big loss
in a population of 100, the loss of one person is a loss of 1% of the population, therefore small loss

[cosine]

The first is correct, except for very rare cases. A T-cell with specificity to the same antigen must bind to an activated B-cell to allow the B-cell to proliferate properly.
The second is wrong. Cytotoxic T-cells bind to antigen expressed in MHC class I molecules. T-helper cells bind to MHC class II molecules.

I just want to preface this next answer by saying that the VCE course is actually really poor on immunology. There are too many gaps in the course that make it impossible to get an appreciation of how things work. Nearly everything I've told you about immunology is outside of the course. Your textbook will serve as a good guide of what you actually need to know. The stuff I'm adding is so that you can synthesise a model in your head for how the immune system actually works.

Yes, you're right on the B-cells. They bind directly to free antigen (whether it be attached to a pathogen or floating around) and are subsequently activated by T-helper cells. How that happens is not important, but you do need to know that both do happen.

Not quite. Again, way out of the course: cells of the innate immune system express receptors called PRRs. These receptors bind to molecular motifs that are associated with pathogens (such as lipopolysaccharide, ssDNA or dsRNA—these are molecules not found in mammals, hence their association with invaders). That's how they are alerted to an infection.
How they actually clear the infection really depends on the particular molecular. The innate response is actually really carefully intertwined with the adaptive response. So, for instance, macrophages tend to gobble up bacteria that have been coated with antibodies first. I'm not going to go into these details though because it's too much and I'm not confident I know all of them!

I think my answer above answers your next question.

Just really want to stress this point:

MHC class I: expressed on all cells, present antigens from within the cell, are bound by cytotoxic T-cells ONLY
MHC class II: expressed on antigen presenting cells, present antigens from the extracellular environment (i.e. tissues), are bound by T-helper cells ONLY

I know, i think this is why I don't understand immunology that much because honestly every text book has a different perception of it...

What do you mean that MHC Class I are bound by cytotoxic T-cells only? Does this just mean that only Tc cells can bind to the MHC Class I receptors that are found on all nucleated cells?

And can you please give me a VCE explanation of how certain phagocytes, such as neutrophils or macrophages actually detect pathogens? I mean, im pretty sure our billions of phagocytes encounter many other cells, but how exactly do they recognise a foreign molecule?

Cheers.

[pi]

Just really want to stress this point:

MHC class I: expressed on all cells, present antigens from within the cell, are bound by cytotoxic T-cells ONLY
MHC class II: expressed on antigen presenting cells, present antigens from the extracellular environment (i.e. tissues), are bound by T-helper cells ONLY

Easy way to remember (or at least for idiots like me haha):
- MHC II + CD4T -> 2 x 4 = 8
- MHC I + CD8T -> 1 x 8 = 8

Always multiples to 8!

[vox nihili]

Easy way to remember (or at least for idiots like me haha):
- MHC II + CD4T -> 2 x 4 = 8
- MHC I + CD8T -> 1 x 8 = 8

Always multiples to 8!

That's really good! Using that from now on haha

I know, i think this is why I don't understand immunology that much because honestly every text book has a different perception of it...

What do you mean that MHC Class I are bound by cytotoxic T-cells only? Does this just mean that only Tc cells can bind to the MHC Class I receptors that are found on all nucleated cells?

And can you please give me a VCE explanation of how certain phagocytes, such as neutrophils or macrophages actually detect pathogens? I mean, im pretty sure our billions of phagocytes encounter many other cells, but how exactly do they recognise a foreign molecule?

Cheers.

Yes, that's right. Just remember that MHC molecules aren't receptors though. Cytotoxic T-cells are activated by class I, T-helper cells by class II.

Genuinely, I actually can't because it's not covered by the course. The very simple form of the explanation above is that phagocytes express receptors that allow them to detect pathogens.

How it actually happens is much the same, but the added detail is that these receptors bind molecules that only pathogens produce. So the presence of those molecules in the bloodstream is therefore indicative of infection. The phagocytes then launch a non-specific response to the pathogens, because they don't know from which particular pathogen the molecule comes.