Today we're gonna talk about genomics and proteomics
genomics and proteomics is simply the study at the genome or the study of the
proteome
so the genome is a complete set of genes and all the other genetic material in an
organism
and a proteome is simply the complete set of proteins that are made
by an organism
let's start off by talking about genomics
so the human genome is made up of 46 chromosomes
so it consists of 22 pairs of autosomes
so we've got chromosome 1 two pairs chromosome 2
two pairs chromosome 3 three pairs - two pairs just kidding
and on down through chromosome 22
and then we've got one pair of sex chromosomes
either 2 X's for female
or an X & Y for male another thing that we knew before we did the human genome
project is we had about
3 billion nucleotide base pairs so that's three billion A G C T all
mixed together
so what do we still need to learn
what we didn't know is what order all those A, C, T, G
were in
so if you look at three letter CRAB
if put him in this order they spell CRAB if you rearrange them they spell BRAC
if your arrange them to the spell
RABC so they all spell very different words
that have very different meaning same thing with those A, G, C, and Ts we
needed to know the right
order of all those letters kind of like reading a book
if you jumble up the words or jumble up the letters it's going to have a completely different
meaning
and so we've also of been able to figure out
out that sometimes a change in a single letter
can be the difference between a disease or health and so that order that sequence
is very very important another thing that we didn't know was how many genes
we had
so some researchers were thinking a hundred thousand genes
some researchers on the low end were thinking maybe fifty thousand genes
are but we had no idea how many we had
and we had no idea where in the genome they were
chromosome one chromosome 7 X chromosome
we still had to figure that out but before the human genome project
it would take about ten or more years
to sequence and study a single gene one
gene in this was a very slow and a very expensive process
and because of this being slow and expensive
it would take a very long time to develop new drugs new therapies to treat
diseases
so with the human genome project
they had about 20 government-funded researchers
research centers in about six countries working together
and also a private company Celera
to do this project and their goal was to develop
cheaper faster technology to sequence the genome
and they wanted the sequence the entire genome
in about 10 years so not one gene in 10 years
but the entire genome and they
also wanted to learn the location of every single gene
they wanted to know the sequence and order of every single nucleotide
every single A G C T and they wanted to make this information public
available for anybody to use and look at
so that people could advance science much more quickly and so that people
could advance
medicine much more quickly by having all this information
at their fingertips through the internet now
the old method for doing sequencing across a gene or across a chromosome is
using the method called chromosome walking so you start off with the probe
which I've got shown in red and then you sequence a little bit at the DNA
and then you stop and then you generate a new probe
and then you sequence a little bit of the DNA and then you stop and you create a new probe
and
you create a new probe sequence that DNA new probe sequence that DNA and so on
and so you constantly are repeating this process repeating this process repeating
this process
now the advantages when you're done walking across that gene or walking across
that chromosome
you know where all of those pieces go where all those pieces go
you know the order of all of those nucleotides all the way across that region
now the disadvantage is because you have to stop
each time and make a new probe
stop each time make a new probe so this chromosome walking can take a long time
to complete
so the new method
is the shotgun sequencing and this method was proposed by Craig Venter
from Celera Genomics so he said let's put that
other method on the table and try this new method
so what he wanted to do is he wanted to cut the entire genome into little pieces
chop it all up, all the way across those three billion
nucleotides and then he wanted to sequence
all those individual pieces and then last
he wanted to use a computer to assemble all these puzzle piece
so imagine doing 1000 piece puzzle
with no picture on the box that's kinda difficult now imagine
taking 46 individual puzzle
or 1000 piece puzzles and putting them
altogether mixing them up and trying to do all
all those puzzles at one time same kind of thing with this method
so the disadvantage of doing shotgun sequencing is you have no idea
what order these pieces came in but
the advantage was even with that disadvantage
with faster because you could plug all the sequences into a computer
and let the computer try this piece try this piece try this piece
and figure the puzzle out so you can see here this piece has an AAT
we're gonna match up with this piece down here that has an AAT
this piece over here GCCT
this piece down here has a GCCT and so on and the computer
while you go home and sleep while you go home and have lunch or something like that
the computers constantly working trying different puzzle pieces out
until we were able to figure out the entire sequence across
across a gene across the genome
now in 2003 they
finally finished the human genome project they completed it
to about 99.999 percent
that's pretty good and again they came up with that same number about
3 billion nucleotide
pairs now of that entire genome
they figured out that we had only about 21 thousand genes
that's not a hundred thousand that's not 50,000 they were guessing
21 thousand genes and that makes up only about 1.5 percent of our genome
far fewer than they expected now one reason for this
it's because of RNA splicing where you can have one gene
but you can have more than one gene product or more than one protein made
from that gene
now the rest of the DNA is non-coding
doesn't make polypeptide doesn't make RNA products
and so for that reason some times scientists call this junk DNA
now again junk DNA doesn't code for RNA or polypeptides
but some of it is quite useful about 25 percent of our genome
is DNA that codes for introns in gene regulatory sequences
so this affects how genes are turned on how genes are turned off
and other regulation so that's quite important we also have some junk DNA
where we have repetitive DNA sequences
that are important for chromosome structure so we've got telomeres and
centromeres
telomeres sit kind of on the ends of these chromosomes
and every time a cell would divide
these telomeres protect the genes on the inside of that
chromosome so if you didn't have any telomeres
when you would do cellular replication and make a new cell
and replicate that DNA, the ends of that chromosome
will get shorter and shorter and shorter untill we
start losing important parts of the gene and so by having those telomeres that
repetitive DNA on the
ends of the chromosome it protects that DNA that important stuff in the middle
now we also have repetitive DNA in centromeres
and this repetitive DNA is important for cell division
so when you undergo cell division it's important that you have
those centromeres where they can attach to the mitotic spindle
and separate to the proper side of each new daughter cell
if you don't have the centromeres that DNA is just going to be hanging free
not knowing which direction to go how to separate or how to divide
so again those centromeres even though it's just repetitive DNA
are still also very important for the structure of DNA
and then we've also got some interesting elements that are called transposable
elements or jumping genes
so it allows a gene to move from one place in the chromosome to another place
or perhaps even on it entirely different chromosome
in this is a field that people are starting to
look into right now and understand the utility of
that also we're still learning what
other sequences do so we've got some other junk DNA out there
we have no idea what it does is it important
or is it just simply holding the place
between genes we don't know yet
so future direction so we've been able to sequence the genome we're done right
not quite so one thing that we need to figure out is how genes are regulated
how they are turned on maybe turned on a little bit
turned on a lot full blast also we need to understand what products they make
what RNA and what polypeptides and again
some of those genes can make more than one product and also we need to know how
those products act
so what do the polypeptide do in the cell believe it or not we've got some genes
we know the sequence of the gene we can estimate what that protein product is
but we have no idea what its doing in the cell is it something useful
just hangin out no idea also
some of these proteins and polypeptides can interact with other proteins
and they can form complexes or they can interfere with the
activity of another protein we still have to figure that out
and then also we want to know how these products are regulated over time
under various conditions
so that brings us to the field of proteomics so we know that genes make
polypeptides and all the proteins that are found in an organism are called the
proteome
now the challenge with proteomics is that it's much more complicated than genomics
so with genomics we needed to know the A G C T sequence
in the entire genome with proteomics
we need to know all of the individual amino acid sequences
but there's more to it than just knowing that individual sequence
so again we know that genes can make multiple polypeptide products
so which ones are made in which cells gotta figure that out
proteomics again different cell types
can have a different set of proteins so our liver cells make
different materials than our brain cells our brain cells make different materials
than our muscle cells
we gotta figure that out so we have to analyze each and every cell type in our
body
also proteins have a unique three-dimensional shape
so just knowing the individual sequences those amino acid
is not enough we need to know how these guys fold
what domains are present in that particular protein to figure out how it
can interact with other stuff
also the amounts of proteins can vary from cell to cell
or even within the exact same cell type so as you age
what proteins that cell makes varies whether you've eaten a meal
whether you're under high temperature low temperature under stress whether
you've exercised
all these things influence how much of a protein is made
in any particular cell and then also proteins can be modified
so protein can be phosphorylated where you put a phosphate group on it
it could be ubiquitinated it can be acetylated in all of these modifications
effect the activity of a protein so again we might know the individual amino acid
sequence
we may have figured out its three-dimensional shape
but then when you start making these modifications it affects the activity of that
particular protein
so again the field of proteomics even though it's older
than the field of genomics since we got started in the nineteen fifties and early with this
it's still so new to us we still have so much that we're trying to explore and understand