Digital Biology Friday: The importance of being aerobic

If we compare sections 1, 2, and 3, we see that section 2 matches very well in a number of different samples, and that there are differences between the sequences in sections 1 and 3.

We also learn something about the people who did the experiment.

At first it appears somewhat odd that there are many matching sequences that are all shorter than the genome and all the same length.

What's up with that?

It turns out that information doesn't have anything to do with the fraction of the genome that matches our query. These short segments are PCR products. They're the same size because the PCR reactions were all done with the same primers. Part of the goal of these experiments was to characterize the genetic diversity of the great apes and see how the different species are related. It's cheaper to do this with shorter bits of DNA than sequencing entire mitochondrial genomes, and thus, we have lots of PCR data.

But why are the sequences in section 2 so similar and the sequences in sections 1 and 3, so different?

A likely explanation is that there is a reason why the sequences in section 2 don't show much (or any) change and why the the sequences in section 3 are free to do so.

To understand the reason for the differences, I looked at the blastn results to learn if a gene mapped to section 2 and the identity of that gene. You can see how to do that here.

The gene in section 2 codes for NADH dehydrogenase subunit 5.

NADH dehydrogenase subunit 5 is a protein that works with 41 other proteins, in a huge complex (respiratory complex I) to help us carry out aerobic respiration. Aerobic respiration is a good thing because we get way more energy from our glucose than we would otherwise (38 molecules of ATP per 1 molecule of glucose, in fact, as opposed to 2).

You've probably seen those 3 dimensional puzzles that require many different pieces to fit together in a certain way. If I took one of those puzzle pieces and damaged it somehow so that the shape changed a little, what do you think would happen to the puzzle?

Since the NADH dehydrogenase subunit 5 protein has to interact with so many other parts, we can predict that mutations that change the amino acid sequence of NADH dehydrogenase subunit 5 would probably have harmful effects, and those effects would most likely limit the ability of individuals with these mutations to reproduce.

In fact, this is correct. Mutations in this gene are harmful and do cause serious disease (1).

1. Nishigaki, Y.; Marti, R.; Hirano, M. :
ND5 is a hot-spot for multiple atypical mitochondrial DNA deletions in mitochondrial neurogastrointestinal encephalomyopathy. Hum. Molec. Genet. 13: 91-101, 2004.

technorati tags: ,
, , , ,

Copyright Geospiza, Inc.

More like this

There's lots of cool stuff coming out in the speciation literature. The Questionable Authority has posted on two recent studies on sympatric speciation (see here and here). Nature, which published the two sympatric speciation papers, has a summary available here. I am of the opinion that most…
Want to learn more about Parkinson's disease? See why a single nucleotide mutation messes up the function of a protein? I have a short activity that uses Cn3D (a molecular viewing program from the NCBI) to look at a protein that seems to be involved in a rare form of Parkinson's disease and I…
In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions. We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and…
I've stood at the periphery of the dichloroacetate (DCA) story mostly because my attention has been needed elsewhere as of late. However, I was very interested in the blogosphere attention given to the Cancer Cell paper from a group led by Dr Evangelos Michelakis at the University of Alberta in…