Psyxwar's Biology 3/4 Question Thread

[psyxwar]

It's good to know more detail, at times. That probably is too much. That cleavage is made by a protein called FtsZ, which constricts it. In animal cells, it's actin I believe. Something you'll encounter in Uni biol as a key difference, though not relevant to this.

As for your quick question. Short answer is no. I know this is at conflict with my previous statement about the FtsZ, but sometimes knowing too much is not a good thing. The exams are marked in relevance to the course. For example, if you use a method in Specialist maths, that you've learned externally...perhaps it's something in Uni, you may very well get a mark for the right answer, though, the marking scheme does not provide for anything that is not part of the prescribed course. Often, extra information can be beneficial in the multiple choice questions (particularly as the difficulty of the science gets greater and things become less "up for interpretation"), however, in short answer questions, you will not be rewarded for giving an answer that is outside of the course. Biology in particular. The marking schemes look for very specific statements, very specific pieces of information. You are guaranteed that these pieces of information are part of the course; it will not suffice to look for them in your extra knowledge!

Having said that though, it is important to have a genuine interest, but, if you can't learn to switch between the two; that is, learn the course and learn what isn't in it, then you're best to stop yourself going too far out of bounds!

Yeah I definitely agree with you with how knowing too much can be detrimental at the VCE level... learnt from first hand experience, lol.

Would two different sequences located on the same gene locus on homologous chromosomes coding for the same protein be considered different alleles? eg. 2 different sequences that both code for say the A antigen on RBCs

Also, what is a good definition of the genome for VCE? TSFX says that it's the complete genetic code of a cell/ organism, including extrachromosomal DNA, but other sources say it's just the haploid complement of genetic material in a cell/ organism.

[Russ]

Epitote is the portion of the antigen expressed on cells that initiates the immunogenic response. Antigen is anything that initiates an immunogenic response. Is this correct?

Antigen can be a little annoying to define. I've had a look at a few sources previously and they all have slightly different ways of defining exactly what it is.

Briefly; the definition of an antigen as something that provokes an immune response is not actually 100% correct. It's a generally accurate simplification that is very useful though. Many antigens are immunogenic but it's not accurate to say that "an epitope is an antigen". If you put just an epitope into the body, you would not get an immune response.

[Yacoubb]

Yeah I definitely agree with you with how knowing too much can be detrimental at the VCE level... learnt from first hand experience, lol.

Would two different sequences located on the same gene locus on homologous chromosomes coding for the same protein be considered different alleles? eg. 2 different sequences that both code for say the A antigen on RBCs

Also, what is a good definition of the genome for VCE? TSFX says that it's the complete genetic code of a cell/ organism, including extrachromosomal DNA, but other sources say it's just the haploid complement of genetic material in a cell/ organism.

That's good

Plus what's your question? I don't understand you're question? But I think I get part of it, so here it goes:

If the genotype for the A antigen is homozygous, then the alleles are the same on the homologous chromosomes. However, if the genotype is heterozygous, then the alleles for the A antigen on RBC would be different.

[vox nihili]

Briefly; the definition of an antigen as something that provokes an immune response is not actually 100% correct. It's a generally accurate simplification that is very useful though. Many antigens are immunogenic but it's not accurate to say that "an epitope is an antigen". If you put just an epitope into the body, you would not get an immune response.

An epitope is just an expressed antigen essentially, right?

[psyxwar]

That's good

Plus what's your question? I don't understand you're question? But I think I get part of it, so here it goes:

If the genotype for the A antigen is homozygous, then the alleles are the same on the homologous chromosomes. However, if the genotype is heterozygous, then the alleles for the A antigen on RBC would be different.

That's just what TSFX says though; I haven't seen it like that anywhere else

As in, are different variations of the Ia allele considered alleles in themselves? Different variations of a gene that end up coding for the same protein, but are still different.

[vox nihili]

That's just what TSFX says though; I haven't seen it like that anywhere else

As in, are different variations of the Ia allele considered alleles in themselves? Different variations of a gene that end up coding for the same protein, but are still different.

Strictly speaking yes, though in most applications they'd be grouped, because most of the time the point of interest in the genes is the protein they produce.

[Russ]

An epitope is just an expressed antigen essentially, right?

An expressed antigen? An epitope is just a small sequence on an antigen that has a particular conformation or sequence that is recognised by the antibody

[vox nihili]

An expressed antigen? An epitope is just a small sequence on an antigen that has a particular conformation or sequence that is recognised by the antibody

Well it is the portion of the antigen that is retained after the lysozymes have had at it, and is subsequently presented on the MHC molecules. More broadly though, yeah, the portion that is recognised by an antibody or cell.

[Russ]

Well yes, but the above was pointing out that you can't just replace "antigen" with "epitope". An antigen has epitopes, which by themselves are not antigens.

[vox nihili]

Well yes, but the above was pointing out that you can't just replace "antigen" with "epitope". An antigen has epitopes, which by themselves are not antigens.

Makes sense. That was my initial understanding of it, but I think I got myself confused a bit. My Biology dictionary says under epitope "see antigen", so obviously they're not too fussed by the difference haha!

[psyxwar]

Why does DNA polymerase require a primer but RNA polymerase does not?

[Yacoubb]

Why does DNA polymerase require a primer but RNA polymerase does not?

Its because DNA polymerase, can only add DNA nucleotides to an existing DNA strand. Thus, a primer is required to add the DNA nucleotides to the complementary strand in the 3' direction. RNA polymerase is capable of adding RNA nucleotides from scratch. So, no primer is needed.

DNA polymerases add nucleotides to the 3′ end of a polynucleotide chain. The polymerase catalyzes the nucleophilic attack of the 3′-hydroxyl group terminus of the polynucleotide chain on the α-phosphate group of the nucleoside triphosphate to be added. To initiate this reaction, DNA polymerases require a primer with a free 3′-hydroxyl group already base-paired to the template. They cannot start from scratch by adding nucleotides to a free single-stranded DNA template. RNA polymerase, in contrast, can initiate RNA synthesis without a primer.

http://www.ncbi.nlm.nih.gov/books/NBK22374/ <- good link

[vox nihili]

Why does DNA polymerase require a primer but RNA polymerase does not?

There's a section of DNA (one per gene in eukaryotes) called the promoter. RNA polymerase runs along DNA until it sees the promoter and binds to it. Part of the promoter is a site called the initiator site, that's where it starts. The lack of primer may have toe do something with the fact that there is no association between the strands. Quite honestly, I've just looked at my Biol textbook for Uni, and whilst it makes the point that there needn't be any primers, it doesn't explain why. I have a genetics textbook somewhere though, so I'll have a squiz at that in a tic!

[psyxwar]

"Because DNApol needs a free 3' hydroxyl group to add its nucleotide too. Its active site isn't capable of initiating polymerization itself.

The active site of RNApol is capable of initiating polymerization at a promoter sequence. The difference in the two, is in the geometry and nature of their active sites."

Yeah, it seems to be due to the nature of the enzymes themselves and the actual process they catalyse. So DNA polymerase doesn't actually recognise promoters?

[vox nihili]

"Because DNApol needs a free 3' hydroxyl group to add its nucleotide too. Its active site isn't capable of initiating polymerization itself.

The active site of RNApol is capable of initiating polymerization at a promoter sequence. The difference in the two, is in the geometry and nature of their active sites."

Yeah, it seems to be due to the nature of the enzymes themselves and the actual process they catalyse. So DNA polymerase doesn't actually recognise promoters?

Yeah, that does seem to be the case. What I've just read in the textbook seems to suggest that it does indeed have to do with the different machinery of the enzymes. In actual truth, RNA polymerases use a variety of 'extra molecules' to determine the location of the promoter, whereas DNA polymerase just uses primers. Little bit easier I guess!