Gedentag und vielkommen sele Rook und yetzt die Eriste klauzer Frager.
Velke uni professor hat das Schönster arbeit simmer.
Und wie ferschbrocken oder Beidrot probere isch auf English und nacht daim nach sie die
forläzungen geherdhaben maken wir eine Stikprober. Beforzugensie forläzungen auf Deutsch oder auf
English. So now I'm going to talk about three special amino acids in terms of their geometry.
So I'm not talking chemistry, hydrophobic, hydrophilic, charged polar, I'm talking about
geometry right now. And there are three special amino acids. The first of these is proline.
If you like flat pictures, look up here. But let's look at this nice, slightly livelier picture.
So here's the backbone of the protein. So it goes nitrogen, alpha carbon, carbonyl carbon.
But look more carefully, alpha carbon, beta, gamma, delta. And then the side chain,
this is the side chain, comes back and it is covalently bonded to the nitrogen here.
So this is not a normal side chain which goes off into space. This comes back and this puts some
serious geometric restrictions on a proline. First thing is proline does not have two rotatable
angles. So V and C, oder auf English, phi and psi. Proline has only got one rotatable angle,
this one here, which is the psi angle, oder psi. So proline's geometry is going to be very different.
So to make that clear, consider the Ramachandran plot. Down in the corner, I have all amino acids.
That's a beta fault letter, beta strand, or a beta sheet residues here, alpha helix here,
something else over here. Now look at proline. The phi angle is always within this region here,
and C can rotate relatively freely. So these are the only angles that a proline residue can reach.
And if this was an interactive lecture, you might say, what are these points up here?
And I would say, I think those are errors in the protein data bank, because chemically,
they are pretty much impossible. Right, so proline, I mean, what's the consequence of this?
It means that if you have a proline at a certain position in a protein, and it mutates,
it's very likely that the protein structure will change, which is probably going to be deadly,
but not always. So prolines are not completely conserved on the evolutionary time scale,
by no means at all. You can substitute a proline with many residues, which will land in this region.
But there are some substitutions which will be forbidden. If the angle at a certain site
was to move over here, you would be dead. The protein would not fold anymore.
And remember, is Schubertreiber ambition, I exaggerate a little bit when I say you will be
dead. If your protein function requires an angle here, your protein folding, I should say,
then it has to be conserved. My favorite amino acid is actually glycine. And I am not just
saying that, because I have to give protein lectures. There's a good reason for this.
Let us look at glycine. Here is a set of three glycines in a row. And if you look closely,
so nitrogen, alpha carbon, carbonol carbon, look at the alpha carbon. There's no real side chain
here. There is just a proton. So proton here and a proton there. There is nothing else there.
This is geometrically important. It means that glycine can adopt confirmations which no other
amino acid can reach. And why? Look at the size of this side chain here. This representation,
so now you have to look at the screen. This representation here is roughly the volume
of the atoms. It tells us how big things are. So if you look at an oxygen here, you can see,
for example, a little bump. If you look at this carbon here, the alpha carbon, there is almost
no bump that's bigger than the carbon would be anyway. Protons are really, really small.
Or protons attached to carbons like this are really, really small. If you were, for example,
to replace this proton here by an alanine side chain, you can see the bump is much bigger.
And you get collisions between these atoms and some of the neighbors in certain geometries.
So this will have an evolutionary consequence, which is interesting.
So remember the plot for all amino acids here, the Ramachandran plot. So here's the phi angle
and here's the psi angle, or phi and c. Now contrast that with the same angles
just for glycine residues here. So for all residues, this area here is forbidden. For glycine,
roughly 50% of glycine residues are in this region on the right-hand side here,
and roughly 50% are in the places normal amino acids can get to.
And now we have the explanation, who were these points in the Ramachandran plot?
These points here, when I showed all amino acids, are these ones here.
So when you look at all amino acids, the guys here are nearly all glycines. When we zoom in
on glycines, we also see these other regions here, which were these rather faint or a thinner cloud
of points. So glycine can adopt geometry that is not possible for the other amino acids.
And what's the evolutionary consequence? If you have a glycine here and you have a mutation
to almost any other amino acid, the mutant protein will have an angle on this side of the plot,
because you can't fit the other amino acids in on this side. So if your protein folding,
an angle depends on the chain direction going like this, then you have a mutation,
and it has to go like that. That means your protein folds completely differently
and probably doesn't work anymore. So if you have an enzyme where that happens,
you have a mutation away from a glycine, your enzyme doesn't fold, and if that protein was
important to you or your metabolism, you die, you don't get to make babies. So numerically
half of the glycines in proteins are rather boring. You can substitute these glycines here
and the protein might still work. At the same time, half the glycines in proteins,
the ones over here, if you mutate there, you die. So when you look at the conservation,
the evolutionary conservation of amino acids, half of the glycines are extremely important.
Of course, you don't know this when you look at the sequence level. When you're just doing a
sequence alignment, you do not have structural information. So you cannot tell if you have a
boring glycine or a really important glycine. And this feature you can really see in alignments.
So for example, there's a glycine in a common protein like hemoglobin that is pretty much
conserved across every animal on Earth because hemoglobin is just a collection of helices.
And if a special glycine mutates, the helices can't fold in the correct way.
So I find glycine, although it doesn't do any biochemistry, it only has protons here,
is to me the most fun amino acid. And if you ever look at a sequence alignment and you see
an incredibly conserved glycine, it's usually due to structural properties of the protein.
And it usually means that in the structure, this glycine is over here. Okay, so that was
a lot said about the smallest of the amino acids. The last special amino acid is cysteine.
Okay, so why is cysteine really important? Look at a piece of protein. Here's a bit of
a root grout, a bit of backbone. I should go from N-terminus, I should go up the page.
So N-C-alpha carbonyl carbon, N-C-alpha carbonyl carbon. If you look at a cysteine here,
it goes alpha carbon, beta carbon, gamma sulfur. So this is a sulfur atom here,
or if you want to speak German, you could say it's a T-ol group, a thiol group. So S-H.
Here's another bit of the backbone, also going up the page. So here's one amino acid.
Here's an alpha carbon, beta carbon, and a cysteine residue. So a gamma sulfur here.
This gamma sulfur and this gamma sulfur can form a covalent bond.
So you end up with a structure that looks like this. So alpha, beta, gamma. And here's the gamma
sulfur from this part of the protein. So that would be known as an oxidation reaction going
from this side to that side because the sulfur here goes from a more reduced state to an oxidized
state. But that's chemistry. I was going to talk about geometry. What this means is that a protein
chain can go up all over the place, come down, and be covalently connected here.
So if you want to talk topology, that changes the topology, the hard connections within a protein.
It has certain consequences. There are some proteins which fold up.
So you have a protein. It's rather large. It folds up. This bond is formed. And then other parts of
the protein are chopped off. So you go from a pre-protein to a final protein. When the other
parts of the protein are chopped off, this, without the disulfide bond here, the protein
would not be stable. So disulfide bonds stabilize certain protein conformations.
And I think at the start, I didn't mention the word. The name of this is a disulfide bond.
And obviously, an amino, a cysteine in a disulfide bond tends to be more conserved
than a reduced cysteine. And the reason for that is this is geometrically rather different to that.
And if you mutate this residue, you can't form the disulfide bond. So again,
your protein structure would change. Don't forget, of the cysteine residues,
not all cysteine residues form these disulfide bonds. Biochemistry is absolutely full of cysteine
residues, which are open like this one over here. And these guys, then cysteine behaves
like a middle hydrophobic residue. You find it in the middle of beta sheets relatively often.
And there is a saying amongst the biochemists that in the main part of an animal cell,
you have reducing conditions. So the disulfide bonds are not formed under normal conditions.
But that's a wild generalization. Not that I'm a real biochemist,
but it depends on what organelle you're looking at. And there are plenty of proteins
that are secreted from cells and then get to form disulfide bridges.
So let us summarize, which means let me summarize so far. Proteins are just polymers.
You could be more specific and say they are heteropolymers. Not all the building blocks
are the same. There are 20 kinds of building block. Don't forget that secondary structure
is really a property of just the backbone. It's the backbone that forms the hydrogen bonds that
make alpha helices and beta strands. And this property of the backbone doesn't depend on the
kind of amino acid. So alpha helices and beta strands are not very specific to certain kinds
of amino acids. It's the side chains, however, that do determine the secondary structure
in the sense that a protein folds up, hydrophobic residues come together,
and then each atom has the choice. Is it going to be in a lower energy configuration
if we have an alpha helix here or a beta strand? So it's the overall protein shape that determines
do we end up with alpha helices and beta strands at certain sites. And this is a property of the
side chain. Don't forget the special amino acids, so cysteine because it can form disulfide bridges,
glycine because it can visit the forbidden regions of the Ramachandran plot, and proline
has this very restricted geometry. Proline cannot be a hydrogen bond donor.
Proline can only form one hydrogen bond. So the other amino acids can form two
hydrogen bonds of the backbone, and that means the proline makes a mess of secondary structure,
and you can go so far as to say the proline can never be part of a perfectly regular alpha helix
because it cannot donate into a hydrogen bond. So proline breaks alpha helices.
It also breaks beta strands to a slight amount, but actually the strand can still form.
It's just not going to be as stable. And let me leave you with a last evolutionary thought.
What is the number of possible sequences you could have for a chain of length n?
So let's say n is 80, 8, 0, which is a very small protein. The number of possible sequences
of length 80 is 20 times 20 times 20, and so on. So 20 to the 80th power, which would be
larger than the number of protons in the universe. And here's the evolutionary thought.
What that means to me is it is absolutely clear that on the evolutionary timescale
we have not visited even a small fraction of protein sequences. You could say
that life on Earth proteins are trapped in one little region of the set of possible
protein sequences. So there could be radically different proteins which would fold and work,
but you will never find them on the evolutionary timescale.
Now just some formalities. This I don't want to talk about, but you do have to learn
amino acid nomenclature. So amino acids have got long names, which we tend to use. They have
three letter names which are rather readable, and then they have one letter names which are
not so readable. So A stands for alanine. That's clear. Would you have guessed if you had not heard
biochemistry lectures that D stands for aspartate? There is no logic there. Do not worry about it,
and do not stay up at night asking yourself why an epsilon, a Y is used for tyrosine, for example.
You will get gray hair if you spend too much time on that. That's the way the world works.
Convention, when you write down a sequence, is you always write from the N terminal end to the C
terminal end, and you need that convention so that if I see a sequence that goes E, F, G, I know
that E is at the N terminal end, and it's the same idea as when you talk to a nucleotide person,
they always write 5 prime to 3 prime. You need these conventions to save space, and so we all
agree on a description. Tiny bit more nomenclature. You will see the terms as well as secondary
structure. There are, of course, other kinds of structure. Primary structure is a term I will not
use. It just means the sequence of amino acids, so the primary structure of some protein might start
ACDF. The reason I do not use this term is just why say primary structure when I can say
the sequence of amino acids. So I think it's clearer to say what something is.
Secondary structure is a useful term because if I say to use secondary structure,
you know that I'm probably talking about alpha helices and beta strands and maybe a few more.
And I'm talking about the structure as defined by the hydrogen bond pattern of the backbone.
Tertiary structure is okay as a term. It says how did the secondary, it's the overall
fold of a protein. If you like, you could say it's how the secondary structure units fold up.
But again, it's not a term I use very often because if I know how the protein folds up,
I probably am talking about the coordinates of a protein. So it's not a nasty word, but to me,
I do not use it very much. So if these terms, I would say secondary structure is important.