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We have confirmed our prediction.
that is the question.
And the answer is simple, millions.
Today we will take a look at one.
I promise it's new, it's not a repetation
like the sine, line, alu or erv insertions
that the youtube is flooded with.
Protein kinase a is an enzyme
which catalyses the phosphorelation of a downstream target peptide.
PKA has two catalytic subunits and two regulatory ones.
Being activated by cAMP the catalytic subunits
phosphorelate the target peptide in the threonine or serine residue.
All PKA catalytic subunits have a motif called glycine lead.
This motif holds the ATP in a fixed position during catalyzation.
The consensus sequence of the glycine lead is GXGXXGXV
where G is glycine, V valine and X any amino acid.
Notice, the theory of evolution has a scope to make predictions here.
Firstly, although all the x residues are free to be any amino acid,
as organisms share common ancestors
there should be a tendency of those X residues to be homologous
in closely related organisms
and gradually diversified in the distantly related ones.
Secondly, even if the closely related organisms share common X residues in their glycine leads,
as it is possible for one amino acid to be coded by up to six codons-
the codons coding those X residues will be homologous in closely related organisms
and gradually diversified in the distantly related ones.
How can we confirm these predictions?
The first prediction can be confirmed using bioinformatic tool homologene
and the second one using BLAST.
Ok, so let's start.
We need to go to the NCBI website to do the Homologene.
So, type in www.pubmed.com.
Here we are.
Choose the Homologene database and type in your query term,
which is protein kinase A catalytic subunit.
Here is the result.
Notice the order.
Human, dog, cow, mouse, rat, chichen, zebrafish, wall cress, wall cress again and finally rice.
So, let's take a look at the multiple alignment.
Here it is and the glycine lead should be somewhere here.
We need to scan to find out where it is.
grv nope, ghy nope, gdt nope, gvgtfgkv yes.
We have found it, it's here.
These eight residues are the glycine lead, GXGXXGXV.
Notice here, the Homologene result accurately confirms the predictions we made.
We human along with two other eutherian mammals, mouse and rat;
one amniot, chicken and another gnathan zebra fish share a common glycine lead.
Composed of sequence GVGTFGKV.
In the viridiplantae we see the first amino acid substitution
as the wall cress glycine lead contains leucine instead of valine.
In the second wall cress there is another substitution
where lycine is changed into arginine.
The other viridiplantae rice shares the same glycine lead with the first wall cress.
So, the findings exactly fit with the orediction of the theory of evolution.#
Now let's do the BLAST.
Let's go to the gene database.
Here is the report.
So, this one- protein kinase A cAMP dependant catalytic beta *** sapiens,
that one sounds nice. So, let's take a look.
Here it is. We need to scroll down.
This is the refseq section
which lists all the isoforms of a gene
and their respective mRNA and protein products.
So, I'm choosing the isoform one and let's take a look at the protein.
Scroll down, here is the sequence.
So, the glycine lead should be somewhere here.
Let's try to find out where it is.
gfa nope, gta nope, gtgsfgrv yes.
We have found it, it's just here.
So, where it starts from? 60, 70, 80, 90, 98.
So, in the protein chain the glycine lead starts from the 98th amino acid.
Just remember that.
Now, let's take a look at the mRNA.
Scroll down.
CDS, that's what I'm looking for.
Here is the translate.
And it's telling me it starts from the 94th nucleotide.
So, scroll down, in the 94th nucleotide we should find the start codon.
So, 60 70 80 90 1234 yes we have found it,
ATG which codes for methionine.
So, the translation starts here and the glycine lead should be somewhere here.
We need to calculate to find out where it is.
So.......
In the protein chain we have seen the glycine lead starting from the 98th residue.
So, (98-1)x3= 291. And there are 94 nucleotide before the start codon.
So, let's add 94 nucleotides, 291+94= 385 nucleotide.
SO, the glycine lead should start from the 385th nucleotide.
360, 70, 80, 12345 Yes GGA, this codon codes for glycine.
So, we have seen the glycine lead starting from here.
Now I'm gonna do the BLAST.
I'm gonna do the protein BLAST first.
So, scroll up, click here.
THis is the query form.
That's the accession.
Make sure the database is correct.
So, I'm doing a protein BLAST. It's NR. Yes correct.
Select a target organism.I'm choosing chimpanzee.
So, let's do the BLAST.
Here is the result.
Found quiet a lot of target sequences.
Let's take a look at the first one.
cAMP dependant protein kinase, catalytic, beta, pan troglodytes.That's right.
And we know that the glycine lead starts from the 98th nucleotide.
SO, it should be somewhere here, yes it's here.GTGSFGRV.
Notice, this query sequence aligns accurately with the target sequence.
There is no substitution or anything like that.
Now let's do the nucleotide blast.
Scroll up, click here.
Choose the appropriate database.
I'm doing an mRNA so I'm choosing that.
Target organism chimpanzee. And BLAST.
There is the result.
Notice here, there are quiet less results in number than the protein BLAST.
It's because in protein there are 20 options for a single position
as there are 20 residues. But, in nucleotide there are only 4.
That's why in bioinformatics when we are doing sequence searches protein is preferable.
SO, let's take a look- pan troglodytes, similar to protein kinase, cAMP dependant, catalytic, beta
Right.
And we know that the glycine lead starts from the 385th nucleotide.
SO, it should be somewhere here, starting with the GGA codon.
Here it is. yes.
SO, it should be the glycine lead.
That is the glycine lead sequence.
And notice all the nucleotides allign properly with the target sequence.
Now what I'm gonna do is- I'm gonna do BLAST in two oter organisms.
I'm gonna do it in mouse and zebra fish, both protein and mRNA.
Then I'm gonna post a screen-shot of those and we will analyze the data.
Now let's analyze the data.
All glycine lead residues are identical in human, chimpanzee, mouse and zebra fish.
However, the codons coding those residues vary.
Human and chimpanzee share all the identical codons.
Mouse and human share 5 identical codons out of 8.
Human and zebra fish share only 1 identical codon.
So, the pattern predicted by the theory of evolution is evident here.
We have confirmed our prediction.