Protein modifications | Biomolecules | MCAT | Khan Academy
- Articles, Blog

Protein modifications | Biomolecules | MCAT | Khan Academy

– [Voiceover] After a
polypeptide chain is formed, it’s going to be folded into its secondary and tertiary structure
into a very specific 3D conformation or shape. And at this point, we can
start calling it a protein. But, this protein may not be ready to carry out its function just yet. There might be some additional
protein modifications that need to be made to this protein before it can be functional. And those are called
protein modifications. There are two different types
of protein modifications. The first type is co-translational modification. And that means that these are modifications or changes
that happen to the protein, or actually to the polypeptide while it’s being translated. Let’s say we have the ribosome right here and we have a polypeptide
that’s being formed. So these changes are going to happen while the polypeptide is being formed. An example of a
co-translational modification is acetylation. And what happens during acetylation is, the first amino acid in the polypeptide, which is usually methionine,
is going to be removed. And in its place we put an acetyl group. Let’s just draw an acetyl group. And acetylation happens to 80-90% of eukaryotic proteins. But the significance of this modification is not known very well, we’re actually trying to figure out what the purpose of this modification is. The other type of protein
modification that happens is post-translational modification. And actually, most protein modifications fall into this category, and the examples we’re going to discuss in this video are all
post-translational modifications. And those modifications
happen after translation. Many post-translational modifications happen in the endoplasmic reticulum and the Golgi apparatus,
but not all of them. Let’s go through some examples. So the first
post-translational modification I want to talk about is glycosylation. Glycosylation, you can look at the word. The prefix “glyco” tells us that it has something to do with a carbohydrate. And so glycosylation is the adding of a carbohydrate to a protein. And most of the proteins in
this video are all in green. And glycosylation usually
happens to proteins that end up being embedded
in the cell membrane. So you can see here we
have a cell membrane and this protein embedded in it, and then there are these
carbohydrate groups attached. So here’s a carbohydrate group attached, and here’s another one. Glycosylation helps to identify
different types of cells. And one very common example
of where we use glycosylation is in the A, B, O blood groups. Let’s take four different red blood cells, and let’s just say that each
one of these red blood cells belongs to a different person. Red blood cells have these proteins embedded in their surface. And these proteins are
going to have, many times, different carbohydrate
groups attached to them. So let’s say that this
person right here has this particular carbohydrate
group attached to it. That makes him blood type A. Let’s say that this person has a different type of carbohydrate
attached to the protein. Let’s say it looks something like that. That makes them blood type B. Let’s say that this person has both of those carbohydrates attached to his red blood cells. That would make him blood type AB. And let’s say that this last person does not have any
carbohydrates of this category attached to the proteins
on his red blood cells, and so that makes him blood type O. So here’s a very common example of how glycosylation is used
in the identification of different types of cells. Let’s go on to a different type of post-translational modification
that’s pretty similar, and that is lipidation. Lipidation is when we
add a lipid to a protein, also a protein that’s going to be attached to the cell membrane. And this lipid we’re looking at is actually an example of a GPI anchor. And GPI anchors are
lipids that help to attach or tether proteins to the cell membrane. And just to give you an idea of maybe why this would be necessary. To quickly review the
structure of the cell membrane. We have these hydrophilic heads. That means that they are polar. And then we have, inside, these hydrophobic tails, and that means that they are non-polar. And so the protein has both
polar and non-polar parts on it, and maybe it just doesn’t attach well to the hydrophilic portion
of the cell membrane. So this GPI anchor, a
lipid, kind of plunges into the lipid or hydrophobic
part of the cell membrane. And we know that substances
that are similar, like substances that are both hydrophobic, attach very well to each other. So this lipid, which is
hydrophobic, attaches very well to the inner part of the cell membrane that is also hydrophobic. And so that’s how it helps to attach the protein to the cell membrane. Both glycosylation and lipidation usually do occur in the
endoplasmic reticulum, or in the Golgi apparatus. Let’s move on to some
protein modifications that have more to do with the activity or the function of the enzyme and less with the structure. So one very, very common
protein modification I want to discuss is phosphorylation. Phosphorylation is basically the adding of a phosphate group to a
protein or to an enzyme. Phosphorylation comes along
with dephosphorylation, is when you remove a phosphate group from the enzyme or the protein. I’m just going to make a
little bit of room over here. And so, what you’re looking
at is this schematic diagram of the sodium-potassium pump that’s found in basically
every animal cell. And another name for the
sodium-potassium pump, which is the enzyme
that you’re looking at, is the Na+ /K+ -ATPase. And so, this enzyme or protein, the sodium-potassium
pump, is responsible for maintaining the proper
osmolarity of sodium ions and potassium ions in and out of the cell. And so, let’s see how phosphorylation regulates this protein. And again, the proteins
that you’re looking at, they really all represent one protein. It’s just, we’re going through the motions of the changes that happen
to this one protein. It’s not like we’re looking at six different proteins in the membrane. So here’s our first step. And when you look at this enzyme, you can see that there
are three receptor sites for a particular ion,
this is the sodium ion. Represented by these dark blue circles. And then there are two receptor sites that look kind of more squarish, and those are receptor sites
for the potassium ions, and those are represented
by these light blue squares. So those are the potassium ions. And so, back to the first step, and what’s happening here. The sodium ions will attach to the receptor sites on the enzyme. And just to clarify, this
is the intracellular space, so this is basically the cytoplasm. And so these sodium ions are
coming from the cytoplasm. And then out here is
the extracellular space, the outside of the cell. Back to our first step. So the sodium ions attach
to the receptor site. When the receptor sites are full, it’s going to cause something to happen. It’s going to cause an ATP molecule, adenosine triphosphate,
to break down into ADP, adenosine diphosphate, plus phosphate. And then this phosphate will attach itself to the protein, and
that is phosphorylation. And so when this protein
gets phosphorylated, when the phosphate
group is attached to it, it causes there to be some sort of change in the conformation of the protein. And that change in
conformation causes the protein to turn itself around by 180 degrees and face the outside of the cell. That’s what you’re looking
at right over here. So our protein is still phosphorylated. I know I drew it in a different place, but just keep in mind that there’s still a phosphate
group attached to that protein. And then the protein
releases the sodium ions into the extracellular space. So the next step is number four. And again, we are still phosphorylated, there’s still a phosphate
group attached to our protein. And so in the next
step, the potassium ions on the outside of the cells
will attach themselves to the protein on the receptor sites. Take note, there are three
receptor sites for sodium but only two for potassium. When the potassium
receptor sites are full, it’s going to cause a
different change to happen. This phosphate group
is going to be removed. And that is called dephosphorylation. That phosphate group ends up
in the inside of the cell, and it gets recycled in some other way. And when this protein is dephosphorylated, when that protein is removed, it’s going to cause a different change in the conformation of the protein. And that change in conformation
causes the protein now to turn around again by 180 degrees and it faces the inside of the cell. So that’s our fifth step, you can see the protein is facing
the inside of the cell. And in the last step, the potassium ions are released into the inside part of the cell. And then we’re back to our first step. And so you can see that
the phosphorylation and dephosphorylation basically regulates the activity of this protein. And the end result that
we’re trying to get to is that we want there to be, on the outside of the cell, a rather high concentration of sodium, and a rather low
concentration of potassium. And on the inside of the
cell we want there to be a rather low concentration of sodium, and a relatively high
concentration of potassium. That’s accomplished by the fact that for every three
sodiums that are pumped out, two potassiums are pumped in. And so here’s an example,
a very common example of how phosphorylation
regulates a protein. And this doesn’t happen just
in the sodium-potassium pump, it happens in many, many
enzymes and proteins in our bodies and in cells. Let’s move on to two other
protein modifications that also have to do
with regulating an enzyme or something similar to that. So the next protein modification I want to talk about is methylation. And in particular, the methylation of certain proteins called histones. And those are these green
circles that you’re looking at. Histones are these proteins
around which DNA wraps itself. So they’re found in the chromosomes, and they help to package DNA in a very tight and organized manner. And sometimes histones are methylated, so let’s put some methyl
groups on our histones. Methylating and demethylating histones helps to turn certain genes on and off. And so here’s another example of, a protein modification
helps to regulate activity, but in this case we’re regulating the activity of genes
as opposed to proteins. Another protein modification I want to bring up is proteolysis. And by looking at this word, “proteo” means protein and “lysis” means to break something down,
or to cut something. Proteolysis is sometimes to take a protein and activate
it, we need to cut it. And in fact, the insulin
has to be cut twice before it’s activated. So let’s cut this protein twice. You may have actually
heard of the term zymogen. A zymogen is an inactive
form of an enzyme. And sometimes the way
to activate a zymogen is by cutting it, and that’s proteolysis. There’s one more protein
modification I want to discuss. And that is, sometimes we add a protein, ubiquitin, to another protein. So that protein I just added is ubiquitin. And this process is called ubiquitination. And what ubiquitination does is, it basically marks this green protein for degradation, or for breakdown. So within a short while
of being ubiquinated, this protein is going to be destroyed and the different parts
are going to be recycled. Let’s just quickly review the post-translational
modifications that we discussed. So we talked about
glycosylation and lipidation. Those are two protein modifications that generally happen
to proteins that end up being embedded in the cell membrane. So glycosylation was the
adding of a carbohydrate group which helps to identify certain cells, and lipidation is when you
add a lipid to a protein, and that generally helps
to anchor a protein to the cell membrane. Then we talked about phosphorylation, methylation and proteolysis. And these all had to do with activating or deactivating an enzyme or genes. So phosphorylation, we brought the example of
the sodium-potassium pump, which is basically regulated with phosphorylation
and dephosphorylation. Then we spoke about methylation, which basically helps to turn on or turn off certain genes. And proteolysis is a way in which many enzymes are activated. And the last
post-translational modification we talked about was ubiquitination. And ubiquitination marks
a protein for degradation, and then the various parts are recycled.

About James Carlton

Read All Posts By James Carlton

13 thoughts on “Protein modifications | Biomolecules | MCAT | Khan Academy

Leave a Reply

Your email address will not be published. Required fields are marked *