Need explanation for Short Tandem Repeats and Hypervariable regions

[lanvins]

Can someone explain Short Tandem Repeats and Hypervariable regions for me? And tell why one is better then the other?

Also, why is the fact that mtDNA mutates rapidly a good thing?

Thanks

[JL_91]

I am not sure if Hypervariable regions are the same thing as Variable Nucleotide Tandem Repeats (VNTRs)? I will base my answer on the assumption that they are.

Short Tandem Repeats (STRs) and VNTRs are basically sections of non-coding DNA that are repeated many times; STRs have a repeat sequence of 2-5 bases, and VNTRs more than 5 bases. The repeats are present in all members of the human population, but each individual has their own unique number of repeats. Therefore STRs and VNTRs are used in DNA profiling, since people can be identified on the basis of differences in the length of their DNA repeats. I don't think STRs are necessarily 'better' than VNTRs, or vice versa.

To answer your 2nd question - the advantage of the rapid mutation rate of mtDNA is that it is highly useful to make comparisons between animals of the same species, or species that are moderately or closely related, in order to establish evolutionary relationships. mtDNA mutates at a steady rate, so it acts as a 'molecular clock'. The greater the number of base pairs difference between two samples from two species, the longer they have been separated as different species. Compare this method of establishing evolutionary trees to using skulls and other bones, for example. Anatomical features change very slowly, so it is more difficult to correctly establish evolutionary timelines using them as evidence. Example: hominin evolution. Many of what we have now established as distinct 'early human species' have the same, or similar, prominent brow ridge, large teeth and prominent facial profile; however they are grouped as being different species. This shows you just how much easier it is to use something that changes rapidly, as your tool for evolutionary comparison.

[Stephanie]

well thats a pretty good answer to your questions

I think we have to be careful when talking about mtDNA and how rapidly it changes because mtDNA mutates at a fairly slow or steady rate its the D-loop part of mtDNA that mutates rapidly... ive seen a few nasty multiple choice questions about that

[JL_91]

Yes, we do have to be careful about that. We talk about things changing 'rapidly', but I think it's only 'rapid' in relation to things like the anatomical features I mentioned in my first reply. Also note that mtDNA has a higher (but again, not necessarily 'HIGH') rate of substitution mutations as compared to nuclear DNA.

[bturville]

mtDNA mutates at a fairly slow or steady rate its the D-loop part of mtDNA that mutates rapidly...

Thats very important to keep in mind. I think there was a question about that on the exam I did last year.

[NE2000]

mtDNA mutates at a fairly slow or steady rate its the D-loop part of mtDNA that mutates rapidly...

Thats very important to keep in mind. I think there was a question about that on the exam I did last year.

Yes, but they gave everyone the mark for that question. But anyway, parts of mtDNA do indeed mutate very slowly. The D-loop, which is a non-coding region, mutates rapidly; and you'll find non-coding regions including introns tend to do that anyway. Although because there are so many mitochondria, many mutations aren't carried to the next generation. And mutating rapidly isn't necessarily good for comparative biochemistry, because it only is worthwhile up to a certain genetic distance, after which the differences are too great.

[bucket]

uhm, mtDNA does mutate much more quickly than nuclear DNA right?

[shinny]

I think we have to be careful when talking about mtDNA and how rapidly it changes because mtDNA mutates at a fairly slow or steady rate its the D-loop part of mtDNA that mutates rapidly... ive seen a few nasty multiple choice questions about that

...what she said. Not many people pick up on this...so yeh, I think mtDNA actually mutates slower. It's just the D-loop that mutates alot faster.

[NE2000]

But VCAA's explanation was they didn't mean to say "mutate" they meant to say "changes slower"

[shinny]

"All students were awarded one mark for this question. The intended answer was option C; however, the wording of this option was ambiguous and should have been ‘changes more slowly than nuclear DNA’."

Hmm. Wonder how that's ambiguous =S Perhaps you could interpret it as they physically mutate slower or something, rather than they mutate less over a certain period of time. iunno x_x Swear you could just do that question by a process of elimination anyway, the others are clearly wrong =P

[NE2000]

Yeah that's what I did when I was going through last year's paper