So RNA has many functions and some of
these functions include the following.
Obviously, we have discussed in other
presentations, the synthesis of proteins
and this includes the various
most common types of RNA: the transfer RNA,
the ribosomal RNA and the messenger RNA.
RNA, as I noted, is the genetic material
for certain RNA containing viruses.
RNA has been found to catalyze
reactions in some cases and this
type of the RNA has the name of a ribozyme.
RNA is also, more recently described
as, being able to control
gene expression and these
tiny little RNAs called miRNA
and siRNA participate in a process
we described as RNA interference.
And last RNAs participate in the
processing of yet even another RNAs.
And these are called small nucleolar
RNAs or snoRNAs, as we shall see.
Now RNA of course has a structure
that comes from the nucleotides
comprising it and the nucleotides
are ribonucleotides, A,U,C, and G.
The RNA strands are a little bit
different from DNA strands and the
RNAs are usually present in a single stranded form,
although, some viruses have a double stranded nature.
The single stranded form of RNA
can pair with itself in many cases.
And one of the reasons this is more commonly
happening with RNA than it is with
for example a single stranded DNA,
is that in RNA a base pair between G and U
is somewhat stable. A GT base
pair in DNA is not stable.
Watson and Crick were credited with discovering the B form of
DNA which you can see on the right side of this slide.
Rosalind Franklin whose data they borrowed discovered
the A form of DNA that you see on the left.
Now the reason I am showing you these two slides is that
RNA also has some specific configurations that it makes.
The A form of DNA and the B form of DNA, though
they look very similar are not the same.
The B form of DNA you see in the bases aligned and
what's look like a stereotype fashion on the right.
But in the A form those
bases are not flat.
Now turns out that the
A form of DNA is also the
form that DNA-RNA duplexes form
and it's also the form that RNA-RNA
duplexes form. So for our purposes
the A form will be the more relevant structure to be thinking
about with respect to the structure of RNA when it is in a duplex.
Now I wanna illustrate one of the common types of
self paring things that RNA molecules can do
and this depends on the sequences of course.
So we see on the screen a sequence
of a single strand of RNA.
Now the bases in this RNA
actually are able to
form complementary pairs with each other and you can see
this in the red nucleotides that I have marked here.
What happens with this RNA is that these
nucleotides can find each other very readily
and when they do they form what's
called a stem-loop structure.
This stem-loop structure arises
from the fact that there is
an invert repeat of those nucleotides.
And that invert repeat of those nucleotides allows
for a pairing structure such as we see.
We call this structure a stem-loop and
it's sometimes also called a hairpin.
A stem-loop has obviously a loop at
the top and a stem at the bottom.
Now we see this self-pairing nature of
RNA in many different forms of RNA.
Here is actually a ribozyme, a catalytic
RNA, and you can see that it has
extensive sets of structures or
base pairings within itself.
These types of base pairings are
referred to as secondary structures.
So the stem-loops are examples that we
can see very simply in this figure
and we can also see that there are
stems that have mismatches within them.
So it's not like everything
is perfectly paired and
not like everything has to be perfectly
paired in order to give this structure.
There are also unpaired regions
within a molecule, as you can see here.
And last there are stems that have
bulges and bulges arise where there
portions that pair and then inserts, as you can see in the
bottom sequence, that don't fit into the overall structure.
Now we have seen before
in another presentation
that the various ribosomal RNAs
have secondary structure
as well and these of course arise from
the self pairing that you see here.
It's though that these secondary
structures of the small ribosomal RNAs
are important for the binding of proteins
in the ribosome and to give those
proteins and the structure that
the ribosome ultimately has.
Now we also have seen in another
presentation the structure of transfer RNAs
and the transfer RNAs have this internal base
pairing sequence that we have seen here.
In last we have also seen the larger ribosomal RNAs whose
sequence is so large we can't show you
the individual nucleotides very clearly. But in the
figure on the right you can get an idea of all the
stems and stem-loops and mismatches and so
forth that are appearing in that molecule.