So now, let’s take a
look at how the ribosome
actually goes about
the elongation cycle.
This happens in a fairly cyclic way.
But before we get into
how the cycle works,
let’s look at some specific details
of how things move through these sites.
So we have the A, P, and E sites.
Here, we are looking at the
A-site and the P-site.
We have a tRNA holding onto
an amino acid in the P-site,
which I call the
polypeptide site, right?
And then we have a new tRNA arriving
in the arrival site, the A-site.
That tRNA in the A-site is going
to get the polypeptide chain
from the tRNA in the P-site.
So the tRNA in the P-site will
pass its polypeptide chain
onto the top of the amino acid
on the tRNA in the arrival site.
little bit confusing, but
you’ll be with me here shortly.
This tRNA that’s in the P-site
is going to pass the polypeptide
chain, the one on the A-site,
but not only that, it’s very specific
about the way that it binds it on there.
We’re going to take the carboxyl end of the
first amino acid, which came from P-site,
and stick it to the amino end of
the newly arriving amino acid
such that chain grows
in a direction
where the front of the
chain is the amino end
and the end of the chain we’re adding
on to essentially the carboxyl terminus
through a little bit of a roundabout way
of passing the chain over to the A-site.
When the ribosome translocates as
we’ll see in the elongation cycle,
then we will have the polypeptide chain
right back into the polypeptide or P-site.
So let’s look at that part of the story.
We have this elongation cycle.
Naturally, we are going to have
some other factors involved.
We’ll call them elongation factors.
Specifically in this case,
it’s elongation factor Tu,
And we have to use some energy, in
this case, in the form of 2 GTPs.
So we begin the cycle.
We have the formylmethionine
in the P-site.
We have a newly arrived tRNA with
the next amino acid in the A-site.
What happens now is we will invest a little
bit of energy using an elongation factor.
The elongation factor helps cleave the GTP
and release some energy in order
to help the polypeptide chain
move from the tRNA in the P-site
over to the tRNA in the A-site.
So it simply passes its chain to
the guy sitting in the A-site.
Then, some magic happens.
The chain is on the
tRNA in the A-site
and we have a little bit more energy
because something has to happen.
Elongation factor comes in again.
It helps us cleave some
energy from the GTP molecule
and that energy is used to
help the ribosome move along,
translocate along the
messenger RNA strand.
So once that ribosome translocates,
we will end up with an empty A-site
because the tRNA from the A-site
has now been moved
into the P-site.
So those guys stay put
on the messenger RNA.
After all, they are hydrogen-bonded to it,
with the codon and anticodon pairing.
So the polypeptide chain
is just back in the P-site
and the guy who was in the E-site
is going to get kicked out.
So the guy in the E-site gets kicked out
as the polypeptide chain
moves back to the P-site.
The whole cycle can repeat.
We’re going to have someone
arrive in the A-site,
the polypeptide chain
gets passed to the A-site
and the ribosome translocates
and so on and so forth.
So it’s a cyclic fashion of arrival, drop
off an amino acid, transfer it to A,
kick the guy out of the exit
site, so on and so forth,
adding amino acids to the chain, and
growing it towards the carboxyl terminus.
So spend some time thinking about that
and perhaps diagramming what
happens – pen on paper again –
what happens as the ribosome
translocates which way
is the messenger RNA moving
or the ribosome moving
in order to accomplish the
goals of growing this chain.
Again, peptidyl transferase is the enzyme
that’s involved in helping this transfer
of the polypeptide
chain from P to A,
ribosome translocates, and we’re
back in the P or polypeptide site.
Pretty exciting cycle, right?
So one little thing, we were alluding
to earlier the idea of wobble pairing.
So we have tRNAs that are associated
with specific amino acids.
But you’ll recall from our lesson where
we learned about the genetic code
that some amino acids can be
coded for by multiple codes.
You’ll notice in this figure,
the messenger RNA on the normal pairing
matches the third position nucleotide
on the anticodon of the tRNA.
However, in wobble pairing, we have kind
of an odd pairing going on in there.
G is not supposed to pair with U.
But in this case, it can because the rules
about pairing of codons and anticodons
in the third position seem to
be a little bit less stringent,
which allows for identical tRNAs
carrying their amino acid
to bind to less identical triplet
sequences on the messenger RNA.
So that is the nature of wobble
pairing and it can be the basis
when it’s not supposed to happen of some
mutations in the function of proteins,
but for this case, let’s
just call it normal.