In class this week we are discussing genes alleles homologous genes between species and pseudogenes. In order to organize my thoughts (to the extent that I can), I sketched out this diagram to model the flow of information from DNA into proteins and tie this together with the idea that DNA undergoes mutations from time to time and that these mutations are the source of new alleles in the population.
1.Recall the central dogma
DNA –> RNA –> Protein
Information flows from the DNA out of the nucleus giving rise to proteins that make up the body and do its work. For EVERY gene, you have two alleles, one from mom, one from dad. We tend to only talk about the ones that give us distinct traits that we can see from the outside, but every gene these.
2. Mutations are altered forms leading to altered function
All genes are subject to mutations. Mutations may change the protein that the gene encodes or not. In cases when it does change the protein, we may see a change in function (Form dictates Function). Once we have two different versions of a gene that remain for any period of time, we call these forms alleles of the gene.
3. Interaction of Alleles
Mutations result in these new alleles that may function differently. This may manifest in a form of dominance. If one allele codes for a protein and a second suffered a mutation such that no protein is made, we may look for the protein and say that the form that makes the protein is dominant because one copy should be sufficient to get it made.
4. How can Alleles become Pseudogenes?
Sometimes, genes mutate into a nonfunctional allele that has no impact on the organism (e.g. vitamin C synthesis is not required when the animal eats sufficient vitamin C) in this case, there will be no selective pressure against the non-functional allele resulting in more mutations occurring without consequence. Over time, these alleles can be made completely non-functional. Pseudogenes are the remnants of these old genes that we can find in the DNA, but that are no longer functional due to an accumulation of mutations. (Only if both copies are mutated and there is no functional copy of the gene in the population do we can this a pseudogene).
5. Speciation and Relationships
As time passes, and speciation occurs, we can still see similarities between the genes of the descendent species, whether these are functional, or sometimes even when they are non-functional. My analyzing the similarities between shared genes, it is possible to infer some relationships between species and even quantitate these relationships in a way that can be used to construct a phylogenetic tree.
DownHouseSoftware 
ratabago
February 14, 2014 at 1:25 am
I’m going to put on my grumpy old pedant’s hat, and pick on your version of the central dogma. The version you are using is the version first published in 1965 by Watson in The Molecular Biology of the Gene, and is rather problematic. For one thing, it is completely overthrown by reverse transcriptase (and lots of other things). I feel the more useful version is Crick’s 1957/1958 original. This makes the point that “once (sequential) information has passed into protein it cannot get out again“. The arrow between DNA and RNA should be bi-directional, and there should be a circular path from RNA to RNA. And the idea that it only applies to sequential information is kind of important. Every few years or so Watson’s version results in someone who wants to be famous erroneously announcing to a press conference that the central dogma is dead. It’s as depressing as watching ENCODE members continually telling press conferences that until the last decade no one suspected a role for noncoding DNA.
Allele is another problematic word. It is so commonly used to mean alternate forms of a gene that it is easy to forget its wider meaning of any alternate sequence at a locus. An oversight I’m frequently guilty of.
If you would like a more detailed look at the two alternate forms of the central dogma, Larry Moran has a good one: http://sandwalk.blogspot.com.au/2007/01/central-dogma-of-molecular-biology.html
downhousesoftware
February 14, 2014 at 10:36 am
Ratabago, you are absolutely correct. To be honest, I have always used the central dogma as I presented it above because it was very clean and should be added to as we discussed more detailed systems that stray from this simplified flow of information. Part of me wants to defend its use because I am aware of the shortcomings that it has and I discuss those in my conversations in class, while asking them to use the central dogma as a scaffolding to build around.
However, I do want to equip my students with the best model possible. And I’m glad that you pointed this out and directed me to the sand walk page.
I struggle with a very similar dilemma when I teach immunology to my Microbiology students. I focus almost exclusively on immune reactions directed against protein antigens, but as I speak on that topic, there is always the gnawing voice in my head that screams, “but you’re over-simplifying!”
If you have found any online lectures that present the Crick model effectively, please let me know. I’d love to see how others talk about this in a way that answers these criticisms well.
Thanks again for being a good critic, Ratabago. A friend that gives one a pass on sub-par work or ideas is not being true.