The Biological Question Thread

[Russ]

What do you mean "all these normal alleles"? If you're referring to the 4 used to plate onto the microarray, they've been artificially synthesised and supplied to whoever is doing the investigation.

The DNA colour is determined by its fluorescence. So if it anneals with the dna already in the plate, it will remain and thus show a colour. The idea is that they've put all 4 possible mutations of that base onto the microarray. Then they've added the "normal" DNA and the daughter's DNA to each field. If it matches, it binds and thus is not washed away and will fluoresce.

So the daughter's DNA will only fluoresce based on what she got from her parents - if normal, green and if mutated, red. You're not actually "staining" the DNA.

[stonecold]

What do you mean "all these normal alleles"? If you're referring to the 4 used to plate onto the microarray, they've been artificially synthesised and supplied to whoever is doing the investigation.

The DNA colour is determined by its fluorescence. So if it anneals with the dna already in the plate, it will remain and thus show a colour. The idea is that they've put all 4 possible mutations of that base onto the microarray. Then they've added the "normal" DNA and the daughter's DNA to each field. If it matches, it binds and thus is not washed away and will fluoresce.

So the daughter's DNA will only fluoresce based on what she got from her parents - if normal, green and if mutated, red. You're not actually "staining" the DNA.

So the probes won't fluoresce if DNA doesn't bind to them?

Isn't that what they have said though?  Normal DNA is labelled green, and cancer person DNA is labelled red?

I am used to the other way around, where you label the DNA, and then it can hybridise with the probes, and then only labelled DNA will remain.

[Russ]

So the probes won't fluoresce if DNA doesn't bind to them?

Nope, because then they're washed away and aren't retained in the well, so there's nothing there that's been tagged.

They're labelling the probe because if they labelled the DNA then every well would produce a colour when inspected. This way if it doesn't bind, there'll be no colour.

[stonecold]

What I don't get is these 'normal' alleles that have been fluoresced to appear green right?
I'm guessing they've been made in the lab?

They will hybridise with the normal DNA chips.

Why can't the red ones do that?

The cancer persons DNA has been fluoresced red.  What if they have the normal allele?

They don't have to have a mutant allele, as mentioned in the stem.  'Only 60%'

I don't get what the colours are for either.  VCAA's explanation has me confused...

And sorry, in the question it says the solutions with the DNA are labelled.

[Russ]

Ah okay, 60%. I skimmed it and just assumed it was saying p53 is always there, since it's such a major factor.

Okay, the cancer person's DNA will fluoresce red always (because it's been labelled red). If they have the mutant allele, you will see the red in one of the other wells (ie NOT the normal allele well). If they don't have a p53 mutation, you will see the red in the far left well...although it'd be mixed with green to make...some other colour.

So the red tagged DNA can bind any of them, depends on whether the cancer patient has the mutation or not. In the question, however, since the red fluorescence is in the 3rd well, the patient has the mutation.

The question does suck though, i doubt they'll make this mistake again.

[cypriottiger]

i didnt really find a problem in this question, lost a mark by stating the probe as a RNA strand instead of DNA, damn u primers!
what is it that you guys dont understand? (sorry but i really cbf reading through previous posts)

[sillysmile]

okay, so what do you think the answer to the following question (from stav 2007) is?



Turner's Syndrome is an example of chromosomal aneuploidy, i.e. a variation in chromosome number. In the case of Turner's Syndrome the individual has only one X chromosome

Q12
A person with the turner genotype would phenotypically be:

A. male as males have one X chromosome
B. female as there is no Y chromosome
C. unisexual being phenotypically uncertain regarding gender
D. normal female as only one X chromosome is ever activated in a cell

[masonnnn]

i'd say c as the others are somewhat referring to genotype where as the question says phenotypically.
though i could be wrong, don't know x&y chromosomes in that much detail so i guess one of the others could be correct.

[sillysmile]

i'd say c as the others are somewhat referring to genotype where as the question says phenotypically.
though i could be wrong, don't know x&y chromosomes in that much detail so i guess one of the others could be correct.

I thought C too, but apparently the answer is B

[stonecold]

Ah okay, 60%. I skimmed it and just assumed it was saying p53 is always there, since it's such a major factor.

Okay, the cancer person's DNA will fluoresce red always (because it's been labelled red). If they have the mutant allele, you will see the red in one of the other wells (ie NOT the normal allele well). If they don't have a p53 mutation, you will see the red in the far left well...although it'd be mixed with green to make...some other colour.

So the red tagged DNA can bind any of them, depends on whether the cancer patient has the mutation or not. In the question, however, since the red fluorescence is in the 3rd well, the patient has the mutation.

The question does suck though, i doubt they'll make this mistake again.

Thanks Russ.  This is what I thought.  Wouldn't that make their answer to the last question wrong as well, because I said the daughters alleles would appear whatever colour they stained them?

My understanding of DNA probes/microarray chips was that every allele in the wells is a probe and is known.  Labelled DNA from the source, is then added to the DNA chip, and if the person has an present allele on the chip, it will hybridize, and become stuck to that particular probe.  Then, the chip is rinsed, and all DNA which has not hybridized get washed away.  Then, whichever probes fluoresce, are known to have come from the source DNA.

[stonecold]

i'd say c as the others are somewhat referring to genotype where as the question says phenotypically.
though i could be wrong, don't know x&y chromosomes in that much detail so i guess one of the others could be correct.

I thought C too, but apparently the answer is B

Yeah, it is B.

My teacher told me this. 

Y chromosome = male
No Y chromosome = female

So XXY is male and XXX is female etc.

[matt123]

i'd say c as the others are somewhat referring to genotype where as the question says phenotypically.
though i could be wrong, don't know x&y chromosomes in that much detail so i guess one of the others could be correct.

I thought C too, but apparently the answer is B

Yeah, it is B.

My teacher told me this. 

Y chromosome = male
No Y chromosome = female

So XXY is male and XXX is female etc.

I dont get how the answer is B.

If you only have 1 x chromosome for turner .. how can it be in a female? .. xxx = 3 x chromosomes??

what obvious thing am i missing here?

[stonecold]

i'd say c as the others are somewhat referring to genotype where as the question says phenotypically.
though i could be wrong, don't know x&y chromosomes in that much detail so i guess one of the others could be correct.

I thought C too, but apparently the answer is B

Yeah, it is B.

My teacher told me this. 

Y chromosome = male
No Y chromosome = female

So XXY is male and XXX is female etc.

I dont get how the answer is B.

If you only have 1 x chromosome for turner .. how can it be in a female? .. xxx = 3 x chromosomes??

what obvious thing am i missing here?

What I just said.

SRY gene, which makes someone male, is on the Y chromosome.  No Y chsm, no SRY gene, no male.  Simple really.

[Russ]

Because the Y chromosome pretty much only encodes genes for making you "male".
If you don't have it, you will be phenotypically female.

Wouldn't that make their answer to the last question wrong as well, because I said the daughters alleles would appear whatever colour they stained them?

Yeah that's what I thought as well. I suspect that they've made a mistake, because I cannot see how you can reconcile the two pieces of information. They probably wrote the questions first (to assess XYZ dot points of the study design) and then provided appropriate background information. Unfortunately, in the background information was the fact about the 60% penetrance and it all got confused. I think what you would expect to see if the girl has the mutation is a green well and a red well and 2 black wells. If she doesn't, you'd see 3 black wells and a brown? well. I suppose if you used the appropriate technique you could observe the individual light emissions, but yeah...don't like that question.

that, or i've gotten horribly confused somewhere

[sillysmile]

i'd say c as the others are somewhat referring to genotype where as the question says phenotypically.
though i could be wrong, don't know x&y chromosomes in that much detail so i guess one of the others could be correct.

I thought C too, but apparently the answer is B

Yeah, it is B.

My teacher told me this. 

Y chromosome = male
No Y chromosome = female

So XXY is male and XXX is female etc.

I dont get how the answer is B.

If you only have 1 x chromosome for turner .. how can it be in a female? .. xxx = 3 x chromosomes??

what obvious thing am i missing here?

What I just said.

SRY gene, which makes someone male, is on the Y chromosome.  No Y chsm, no SRY gene, no male.  Simple really.

that is simple, thanks