Lecture 12: From Genome to Phenome
- So elaboration of the central dogma. Where are we?
- One of the things he hasn’t focused on in its relation to DNA, RNA and a protein is that
obviously there is cross-talk between the different pathways in terms of their regulation. In
fact the metabolome can feed back and modulate things like the RNA pool even the
regulation of the DNA chromatin structure itself. The interactome feeds back and so on.
Moreover things feed forward in those particular pools as well so there’s a lot of complexity.
- How does this fit into the big picture? He wants to see how one goes from all of this to the
phenome the physical thing you see in front of you and that is what we’re ultimately
interested in, how all of these things are integrated to give rise to the diversity of organisms
we see around us.
- We’re going to just recap everything covered in the past 11 lecture and talk about the
implications of this in giving rise to diversity of the phenome. Introduce concept of genetics
and briefly talk about science fiction and science fact.
- Over the term we’ve looked at this elaboration of the central dogma and we’ve talked about
the generation of the phenome. We’ve gone from genomes to phenomes. We’ve taken a look
at the various steps involved in generating an organism like ourselves.
- We started ourselves with the role of the transcriptome and deriving the variety of
transcripts that are present within the genome and we talked about how there were
differences not just between very different organisms and within organism between cell
- We talked about the role the epigenome plays in giving rise to differences in the
- For example, here gene B active in the 4 year old Malcolm Campbell and gene D inactive.
This changes dramatically as we go from the young chap to the ancient one on the right side.
- We talked about the sort of things influencing this and they are the transcription factors, the
gene specific transcription factors, the sequence specific transcription factors, the gene
regulatory proteins, all one and the same.
- This is what the transcriptome is going to look like and ultimately we’re going to create a
proteome and the proteome will give rise to these differences. - Finally, we looked at how the proteins interact in the interactome and how that is going to
give rise to those sort of differences.
- The one thing that he finds talking to students at the end of the course is the wow factor in
that all of these things give rise to differences in organisms, it's a wonder that we even get
organisms looking alike at all with the sheer number of steps for possible variations to occur.
- That begs the question, where do the differences come from? We know where the
differences come from because we missed out an important element in our consideration of
genome to phenome.
- We missed out on MENDEL.
- When he was at the monastery, he was sent off to solve a particular problem that the monks
were having problems with regards to organisms breeding true. The head of the monastery
was interested mainly in sheep growing nearby. Gregor was sent off to Vienna to study
subjects that might help him out in solving this problem so that to ensure that organisms
farmers were growing for particular reasons, sheep and their wool for instance, were always
bred true. The problem was that animals didn’t always breed true, breeding two perfectly
good sheep together could produce an offspring that had terrible wool production, why was
that? Why did in some pairings, some things work whereas other pairings failed?
- He was sent off to study with the best people like Dr. Doppler for studying physics
(Doppler effect guy). He studied lots of different subjects, brought that information back to
the Augustinian monastery and proceeded to plant particular plants: peas, garden peas.
- He published some astonishing results he learned about his garden peas at 1865 at the age of
43. In doing so he became the father of modern genetics.
- He was looking at these garden peas in the slide. He was looking at alternative traits or
alternate pairs of traits in garden peas. They are called antagonistic pairs like long and short
stems, green versus yellow pods and purple versus yellow flowers.
- He described these particular antagonistic pairs, he didn’t use the word genes but he called
the differences between them, alleles. These variant forms were called alleles. An allele is a
variant at a genetic locus. We will touch on the source briefly on the source of variation
between antagonistic pairs, the source of variations. - We will look at round versus wrinkled peas.
- We won’t look too much at dominant versus recessive traits except here, it turns out that the
dominant allele in this case is the round one. It gives rise to a functional starch branching
enzyme which converts unbranched starch to branched starch and this branched starch just
the way in which it retains water, allows for a nice round pea.
- The point he wants to make from this slide is that, that allele does something molecular, it
does something biochemical, it encodes an enzyme that does a particular job that gives rise to
a visible trait.
- The recessive allele is effectively nonfunctional, it has an inactive starch branching enzyme
and as a consequence, unbranched starch isn’t converted to branched starch so the water
retention properties of that results in a wrinkled pea.
- We not only have a molecular explanation for the trait but we have a molecular explanation
for the antagonistic pair, one enzyme is functional, the other is dysfunctional. That is the
source for these traits, the source of the variation that we see in nature, it's these simple
molecular explanations. It all comes back to what we learned and that it comes down to
things like gene expression and the elaboration of the central dogma, we will explore this
idea with alleles.
- Imagine that we have a normal functional gene, it has a promoter, which comprises of the
minimal promoter and the gene regulatory sequences, a coding sequence beginning with
ATG, finishing with TGA, an intron in the middle, they’re all labeled.
- In the process of transcription, we’re going to make the immature transcript first, that will
be processed to get rid of the intron, add the poly-A tail and the 5’ cap giving rise to mature
RNA and then through translation, that will be made into a nascent protein which folds
through co-translational folding to give rise to a nice folded protein in the bottom. That gives
rise to function.
- This is what we saw with Mendel’s round pea allele, let’s consider the sources of the
dysfunctional or non functional allele.
- There is our wild type allele and here what we do is change a single nucleotide in the coding
sequence and that produces a transcript that will get spliced and processed, and there is our
same nucleotide change and that will change a glycine to a glutamate residue. What may
happen as a consequence of that is at the end of that, perhaps the glycine was required for a
particular secondary structure for that enzyme, is that we may end up with an unhappy
protein at the end and no or altered function.
- Here we see that just by changing the nucleotide sequence and just changing something
we’ve learned about this term, (protein folding) we can ultimately change the function that
arises from that. There we have a misfolded protein and altered function.
- Here is another example where we introduce another nucleotide change that gives rise to a
premature stop codon which is nicely transcribed and processed and during translation, we’ll
end up with a truncated protein being made. There is the half frowny face and has altered
- We can keep doing this with many other examples as we can imagine.
- Here he has changed a stop codon into something that is not a stop codon. So now, we
create a transcript and translation proceeds where translation wouldn’t proceed normally
giving rise to an elongated protein which again, may have altered function, that would be
mutant allele 3. - Another example is that we alter the intron so that it is no longer spliced properly so we
have mis-splicing that occurs and as a consequence we get all sorts of crap produced, lots of
garbage without a function at all in the organism.
- Here we’re changing a nucleotide sequence in a gene regulatory region in the promoter and
what we end up with here is some sort of altered transcription, in his example it is no
transcription whatsoever so no RNA therefore no protein and no function.
- In the end, what we end up with is a bunch of different alleles and they are produced merely
on the basis of single nucleotide changes to DNA structure resulting through the central
dogma and the things we learned associated with the elaborated central dogma with varied
function at the end. All of these different steps we learned about over the course of the term
can give rise ultimately, to altered function and therefore the diversity of the organisms we
see around us.
- Some of us might be scratching our head and saying that can’t possibly be true for
everything we’ve covered and he would argue that everything we’ve covered can have some
sort of molecular variant that can give rise to different function.
Movie playing - This example is being presented in this movie.
- What we’re looking at is we’re going to ubiquinate that etaxin (not sure if this is what he
really said) molecule there. There’s our ubiquitin carrier enzyme, there is wild type etaxin
and that is a protein one needs to turn over in the cell, what happens is that the E2 E3 ligase
complex is going to come along and we’re going to get ubiquitination taking place of the
etaxin there’s polyubiquitination, that will go to the proteosome, the cap opens up on the
basis of perceiving the poly A signals and the cap feeds the protein into the core where the
proteases are. Of course what’s going to come out of the other end is poop that is the peptide
we see at the far end.
- Imagine if we were to mutate etaxin such that it no longer properly unfolded when it
interacted with the cap, there it is, it's going to just sit th