Molecular Biology Structure of Proteins

Hello, and welcome back to www.educator.com.0000

Remember, this is our molecular biology course.0003

Today, we are going to talk about the structure of proteins.0010

As an overview, we have to first talk about amino acids, since those are the monomers of proteins.0012

We will talk about the types of bonds in proteins called peptide bonds.0019

And then, importantly, we will talk about the big types of organization of structure.0024

We will mention protein folding and briefly talk about post-translational modifications.0030

Finally, we will end with protein classification and a short introduction on enzymes being biological catalyst,0036

just as we mentioned in the first lecture.0044

Amino acids, as I said, are the monomers that make up proteins.0050

This is the general structure of an amino acid right here on the left.0056

As we see here, we have a carboxylic acid group.0060

We have a carbon bound to that, which is our α carbon.0071

Then, bound to the α carbon is our amino group.0080

The carbon, its 3rd bond, the α carbon, it makes with a hydrogen.0087

And finally, its 4th bond is to something else, what we call an R group or a side chain.0092

The amino group, the hydrogen, and the carboxylic acid group, all attach to the α carbon,0104

is going to look the same in all of our amino acids.0110

The only difference is going to be in the R group.0112

Importantly, the acid dissociation constant of the amino group is at 9.1.0116

The acid dissociation constant of the carboxylic group is 2.3.0126

Those will come into play a little later.0131

Amino acids are going to make up proteins.0135

They do this by making peptide bonds also known as amide bonds.0139

The addition of amino acid 2 to amino acid 1 is catalyzed.0146

The type of reaction is called a condensation reaction, in which case we are pushing out water.0155

This right here is our water molecule that gets pushed out.0164

As we can see here, the N terminal, the N portion of amino acid 2 always comes in and0171

make its attachment, its bond to the C terminal portion of amino acid 1.0181

That is why we have amino acids following an N to C terminal orientation.0188

A protein is N to C, it is basically like saying N is the N terminal, amino acid is the 1st amino acid it is put in.0198

The C terminal amino acid is the last one that it is put in.0208

Here is a table of the 21 amino acids that we find in proteins.0216

Many of you may have learned that there are 20 amino acids found in proteins and that is very correct.0222

The one that makes the 21st is selenocysteine.0229

That is just a cysteine molecule that has a selenium group, instead of a sulfur group.0235

This is also been found to be incorporated into proteins.0247

These are all 20 amino acids that we incorporate into proteins.0250

There are many other types of amino acids that are not incorporated into proteins.0255

Our amino acids can be broken into multiple groups.0260

We have our charged amino acids, we have our positively charged or basic amino acids.0265

We have our negatively charged or acidic amino acids.0276

Only 5 of the 21 have any type of charge.0281

We have our uncharged amino acids, right here in group B.0287

We have in group D, our hydrophobic side chains.0294

These are the ones that are going to participate in our hydrophobic bond.0299

We have our special cases, as I said before, selenocysteine, is a kind of a special case.0303

cysteine is very special, and that sulfhydryl group right here, can participate in what are called disulfide bonds.0310

These are very important for the structure of proteins.0318

Glycine is special and that it is the simplest amino acid to where it is R group is only a hydrogen.0322

Proline is specific, is a special case, it actually has a secondary amide.0333

Its R group is not free, it comes back and bind to the amino group.0342

We will know this later, being able to call this a helix breaker.0348

When we talk about our amino acids, we need to know that our ionization will vary based on the environment, the pH.0358

We have our cation, a cation is just another way of saying a positively charged ion.0367

An anion is a negatively charged ion.0382

That is what we normally think of.0389

Our cation group is when we have our amino group being proteinated.0393

It has an extra charge right here, we have this extra positive charge because it has an extra hydrogen.0400

We still have the carboxyl group having its proton.0415

This can only happen when we are at a pH below the acid dissociation constant of that carboxylic acid group,0419

as well as below the amino group.0430

If you remember, the PKA, this is 2.3 and the PKA of this is 9.1.0433

When this is below 2.3, the pH is below 2.3, we are in the cation form.0449

When we increase our pH, pass that 2.3, we are going to start getting into what is called the zwitterion form.0470

This is going to exist between the PKA of our carboxlic acid group and the PKA of our amino group.0481

This is when our pH is between 9.1 and 2.3.0491

This is when we are going to see a zwitterions form.0511

What that means is that the carboxylic acid, if we see over here, it no longer has its H over here.0520

Now it has a partial negative charge, right.0528

We have a molecule right here that has a negative charge and a positive charge.0533

Once again, this is when we are not talking about the R group at all, playing a part into it.0539

That is going to be completely separate.0545

This is what we call a zwitterion.0547

A zwitterion is a molecule that has both a positive and a negative charge on it.0550

This is going to exist until we have a pH above 9.1.0556

Right here, when the pH is greater than 9.1, we are going to move into the anionic state.0563

That is when our amino group loses this proton.0574

Right here, remember here is that proton, we no longer have it.0580

We no longer have it right here.0587

We have our negative charge, we do not have that positive charge anymore.0591

This is a negatively charged ion.0598

A negatively charge ion, we know is an anion.0602

Remember, we are not talking about the R group at this point.0604

We are just talking about the major backbone, this is important.0607

What is the physiological pH in a human cell in the human body?0613

It is about roughly 7.4, in physiological circumstances, we are always going to see our amino acids in the zwitterion form.0617

They both have the positive and the negative charge meaning it is a neutral charge.0632

The only thing that will affect whether it is a positively or negatively charged amino acid is the R group.0636

For our first example, if we can just do a little memory recall,0655

which amino acids would have a net charge at physiological pH, which as I said before is about 7.4?0660

What that is saying is, what amino acids have a negatively or positively charged side chains,0670

because that is the only thing that is going to be attributing to the charge because the zwitterionic form is a neutral charge.0677

Our acidic ones, otherwise known as negatively charged, which ones are those?0687

They are aspartate, by the way the single letter code is D.0706

And then, we have glutamate, its single letter code is E.0718

Aspartate and glutamate are also often refer to as aspartic acid and glutamic acid.0727

What about our basic amino acids, otherwise known as having a positive charge.0736

We have 3 of those, we have arginine, that was R.0753

We have histidine and we have thymine and glycine.0765

Those are the only 5 amino acids that will have a net charge at physiological pH.0782

When we talk about amino acids, we need to talk about what form they are normally found in.0794

Most of our amino acids occur as what are called L α amino acids.0800

This is a type of configuration.0805

Only L amino acids become incorporated into protein.0809

We will see that the difference between an L and a D, or an α and a β amino acid, actually look like.0815

What do they look like?0826

Here is going to be an example of an L or a D amino acid.0829

All it is, is what side the amino group is on.0834

This is an L and it also happens to be an α amino acid.0854

Let us draw a D.0872

What we are looking at is, there are plenty of other ways to see this but very simply, written out in planar form.0893

If the NH₂ is on the left, it is an L amino acid.0901

If it is on the right, it is a D amino acid.0908

What about the difference between α and β amino acids?0923

Let us do a general example, and then we will do a specific example.0929

For our α, what makes this α?0939

You are looking at where this NH₂ group is connected to.0985

This NH₂ group is connected to the carbon that is connected to the carboxylic acid group.0991

The way that we count, we would find our carboxylic group and they found the carbon that is attached to it,0998

they call that the α carbon.1006

Therefore, we have the NH₂ group attached to that carbon, being the α carbon.1011

If we go to the β, the β amino acid, if we look once again, we count a way from the carboxylic acid group.1018

This would be the α carbon, this would be the β carbon.1073

This is the carbon where we have the NH₂ group and the R group attached.1079

This makes it a β amino acid.1084

This is how we can tell between L and D, as well as between α and β amino acids.1088

It is important that we now the side chains of all of our amino acids because1102

they basically tell us what types of reactions these amino acids are going to take a part in.1108

The characteristics of our side chains, our R groups.1117

If they are non-polar, these groups are going to form or can form hydrophobic bonds.1120

These residues are often going to be buried in the interior of the proteins because they are hydrophobic.1129

In contrast, our polar groups, they can form hydrogen or ionic salt bridges, or ionic bonds which are called salt bridges.1137

They can form ionic or hydrogen bonds.1148

They often cluster on the surface of the protein because these are hydrophilic.1150

For example, we have a protein.1156

I will just make it easier, I will just make it look like this.1162

You might be more likely to see non-polar residues on the inside, and see polar residues on the outside.1171

If we get a little more specific, we can look at the hydroxyl groups are serine, threonine, and tyrosine amino acids.1192

They can be phosphorylated meaning they can get the phosphate group attached.1202

This makes them negatively charged and it can also alter their function, either on the positive or negative way.1214

The sulfhydryl group, cysteine is unique and that it can be oxidized to form a disulfide bond.1222

A disulfide bond is just a bond between two sulfur groups.1229

This is going to be important for our structure of our protein.1234

We can have covalent bonds to carbohydrate forming what are called glycoproteins.1241

They can be either O glycosylated or N glycosylated proteins.1250

All what that means is, the sugar making a bond to the amino acid via an oxygen or a nitrogen.1255

What we have here is that we can see these groups, this oxygen and hydrogen,1264

which we know as a hydroxyl group, from serine and thrinine, can participate in the O glycoscillation.1271

In the NH2 group, the amine group of a spare gene can also participate in glycoscillation.1280

In this case, it is an N glycoscillation.1287

Finally, we have proline having what it is called the pyrrolidine structure.1291

That is this big hunk of a secondary amine.1299

It has a not very nice structure.1305

In fact, it is not an open chain.1318

This is what we call helix breaker, prolines are not found in helixes because this is too bulky.1320

It is too big to be formed properly in a nice helix.1326

Often, they are found at turns because they help with the U turn type characteristic.1331

Our peptide bonds are also call amide bonds, as we stated earlier.1342

Remember, they come from a condensation reaction where water leaves.1347

The amino acid 2 makes a bond using its nitrogen, it is amine group, with the already existing amino acid ones , carboxylic acid group.1357

In this case, if we have this peptide bond forming or MI I bond between two different amino acids,1376

we would call this amino acid the N terminal amino acid.1386

We will call this amino acid the C terminal amino acid.1394

You would always add the next amino acid to the C terminal.1399

This one will always be the N terminal amino acid.1405

We will talk about other instances where we can lose those amino acids.1409

Now we have talked about the monomers of amino acids,1418

let us talk about how we can organize the actual protein molecules, the polymer of amino acids.1421

What are these levels of organization?1432

If we look in the graph over here, this is a good one to look at, follow along while I'm talking.1435

We have the primary structure, here is being the simplest sequent of the amino acids that are connected by peptide bond.1442

In this case, we have this pair of gene, glycine, phenelalanine, glutamate, adenine, so on and so forth,1450

that is very the simplest portion.1458

The next part is secondary structure.1462

This is just local 3D structure, imagine you have just a short sequence of the entire polypeptide1467

into something that we are likely going to see as in α helix or a β pleated sheet, or turns and loops.1475

This is important because it is stabilized by non covalent hydrogen bonding, not occurred between the peptide groups.1485

The next portion or the next higher order level of structure, we call tertiary structure.1498

Tertiary structure is the overall 3D structure of the protein.1507

If we look here, we are now looking at this part, just a 3D structure,1514

are not stabilized by side chain interactions between our secondary structures as well.1520

Quaternary structure can only occur when you have more than one polypeptide.1528

More than one polypeptide can come together for amino overall 3D structure that is called the quaternary structure.1541

A little more in-depth, our primary structure, that is our specific amino acid sequence.1557

We are looking back here again.1562

It is connected by a peptide bonds or amide bonds.1565

This is dictated by our mRNA codons.1569

If we remember back to the previous lesson, we know the molecular biology central dogma.1574

It is DNA to RNA, this is via transcription.1584

RNA can be made into protein via translation.1620

RNA gets turned into protein, therefore, the protein is dictated by the mRNA codons.1628

This is going to direct the subsequent organization.1635

The RNA is going to code a single codon for our cysteine amino acid, and then a serine, a leucine, a phenelalanine.1638

This is how it is dictating.1648

It is very important that even a slight change in the primary structure of a protein will affect its ability to function.1654

An example of this is found in sickle cell trait.1662

The substitution of one amino acid for another in hemoglobin causes sickle cell disease.1668

All this is, it is a single different in the 5th amino acid.1675

It is changed from a proline to a valine.1680

A normal hemoglobin which is found in red blood cells, carries oxygen very well.1684

It has no affect on the shape of our red blood cell.1693

Our red blood cells normally look like this. They look like a nice little donut shape.1702

When we have this proline to valine substitution, that causes the amino acids to chain together in an unnatural way.1706

It causes the proteins to stretch and alter the shape of the red blood cell molecules.1723

When they are looking the sickle shape, they can end up blocking blood vessels because1738

they do not flow through nice and easy like a rounded donut shaped one.1748

They can block small capillaries and veins, and it cause blockage which can cause pain or possibly even death.1752

This can come from just a single substitution in a single protein, a single amino acid substation.1762

Our levels of organization continue, the secondary structure.1773

By the way, a way to describe structure is by going like this.1777

This would be primary structure, secondary structure looks like this, tertiary, and quaternary.1783

It is just that little degree sign.1790

Our secondary structure, I will write it over here once again.1793

This one is actually secondary.1799

Our secondary structure is just our local 3D structure.1803

It includes things such as our α helix, our β pleated sheets, and even our turns and loops.1807

Our α helixes and β pleated sheets are held together specifically by hydrogen bonding.1813

If we look here, these yellow portions are hydrogen bonds.1818

These are all hydrogen bonds that are keeping this helix together .1832

What about proline in secondary structure?1839

Proline is going to look like this.1845

This is what proline is going to look like.1889

As you can see, it is very bulky secondary amine.1892

If we talk back here, this is our α carbon.1897

We have our amine group, it is all attached in one.1905

It is not free to be working around.1912

What we have is that, this is actually considered an amino acid not an actual amino.1917

What this does, this actually is not able to be fit in a nice α helix.1928

Because what do we do, if we incorporate a proline, it would break that helix.1938

What is often found in is our β pleated sheets.1943

Our β pleated sheets normally run like this, it has a nice little turn.1948

Maybe we go like this again, nice little turn.1955

Our prolines are often going to be found in the turns because they help with the U turn portion of this.1963

This is important to know, that proline is not going to be found in α helixes.1975

To continue on our levels of organization, our tertiary structure.1982

This is our overall 3D structure of a protein.1988

What is important is that 3D structure is related to function.1992

What that is saying is that, structure dictates function.2001

If it looks a certain way, it is probably going to perform a certain action.2023

We are going to talk more and more about structure dictating function, as we go throughout.2027

Our tertiary structure is stabilized by hydrogen bonds, ionic bonds, hydrophobic interactions, and our disulfide bonds.2033

If you remember correctly, our disulfide bonds are found in our cysteine residues.2045

Our quaternary structure only can occur when we have more than one polypeptide, more than one subunit.2054

We are looking at right here, the red is its own polypeptide.2064

This other multicolored one is its own polypeptide.2072

When they come together and form a complex, that now is a quaternary structure.2076

Hydrogen bonds, ionic bonds, and hydrophobic interactions, all stabilize quaternary structure.2083

What will ultimately determine a proteins native structure?2096

What do we think?2103

First of all, the proteins linear amino acid sequence is going to determine that.2105

What structure is that, what higher level order is that, primary, tertiary, quaternary, secondary?2123

Our linear amino acid sequence is primary structure.2132

What else will determine our native protein structure?2140

When we are talking about protein native structure, what we are even talking about, tertiary structure.2148

This question is asking what determines our tertiary structure.2156

What is our tertiary structure, that is the overall 3D, the total 3D depiction of it.2160

That is tertiary.2171

The answer to what ultimately determines a proteins native structure is its linear amino acid sequence, its primary structure.2174

Remember, structure dictates function.2184

Do no forget that one, we will come back to that multiple times.2221

Proteins, once they are made, once they have their tertiary structure, they can fold into a whole bunch of things.2228

They can be globular, they can look like a ball.2234

They can be fibrous, they can look like a filament or a string.2240

There is a whole bunch of ways and this is just a short small sampling of what they can look like.2245

Proteins can fold into many different shapes.2250

They are helped folding by what are called chaperones.2254

These are other types of proteins.2258

If a protein is poorly folded, sometimes you can unfold it which is called the denaturing,2261

and try to refold it again, that oftentimes does not help.2268

What you end up having to do is breakdown that protein, basically, throw it away.2273

You degrade it by sending it to either the lysosome or the peroxisome.2279

Those are basically like the cellular trash can.2294

When we have made our proteins, we can talk about what happens next.2303

We are not going to talk about the reactions right now.2310

We can alter what happens to a protein, after it leaves the ribosome.2314

That is when we are altering a protein, after its left being synthesized, after translational.2320

That is called post-translational modification.2327

These post-translational modifications can regulate a proteins activity.2332

It can regulate its localization, as well as how it interacts with other molecules.2338

It can alter its structure, it can alter its function.2344

Some common types of post-translational modifications are glycoscillation, that is the addition of sugar.2348

We can have phosphorylation which is the addition of a phosphate group.2358

We can have acetylrelation, that is the addition of acetyl group.2365

Methylation is the addition of a methyl group.2370

Lipidation that is the addition of a lipid, you know better as a type of fat.2374

Ubiquitination is the addition of a protein, a small protein called ubiquetin.2391

Proteolysis is cutting the protein.2402

Maybe the protein, you have a protein amino acids, you cutoff the first 5.2407

Proteins can be classified in many different ways.2424

One of the easiest ways to classify them is based on their function.2427

You do not necessarily want to classify them based on what they look like.2431

You want to classify them based on what they do.2433

As we can see here, a majority of our proteins are going to be ligand binding, DNA binding, enzymatic.2436

The rest of them can be broken down into many other things.2452

An enzyme is going to catalyze a reaction.2456

DNA and RNA binding, self explanatory, it is going to bind to nucleic acids.2459

Ligand binding in protein, protein interactions is going to bind to either a protein or maybe a compound in a cell.2464

We have plenty of others that serve structural purposes or make membrane proteins, things can go in and out.2472

We have transcription regulators, otherwise known as transcription factories.2480

They can either increase or decrease the speed of making in RNA, therefore, the making of a protein.2484

Some are involved in contraction, transport, some proteins are actually hormones like insulin is a peptide based hormone.2493

We have storage, some are used as protection.2505

There are many different types.2512

The majority are these 3 types.2514

Since we are talking about enzymes, we have talked about it before, in unit 1, enzymes are biological catalyst.2521

Most metabolic processes require a catalysts.2529

They need some form of catalysis.2533

Our enzymes, if you remember back from the first unit, accelerate reactions.2538

They do that by decreasing the activation energy.2546

That activation energy is the energy required to get over the energy barrier.2549

That is what allows you to get to the transition state.2554

What is very important is that, enzymes increase the velocity reaction2558

so highly that uncatalyzed reactions may never actually occur.2563

These can be increased on a hundred thousand fold to over trillion fold.2571

This actually allows you a reasonable amount of time for a reaction to occur, in the presence of the enzyme.2584

Most biological catalysts are enzymes, are proteins, but not all of them are proteins.2592

Not all of them are proteins, some enzymes can be called what are called by ribozymes,2598

that is where the active component is in RNA molecule.2607

It is important to know that enzymes have a specificity of reactant.2612

An enzyme is only going to allow a certain thing, a certain compound, combined in it.2620

For example, if my hand is an enzyme and the pen is the reactant.2627

It fits in there just fine, and now the enzyme is free to catalyze the reaction.2635

The product of the reaction is writing on this slide.2640

If my hand enzyme where to pick up my notebook, as the reactant, do I get the product of writing on the slide?2649

No, the enzyme is specific to the reactant.2662

It is only going to catalyze a reaction when it has the correct reactant in it.2665

And then finally, enzymes have an optimum pH in temperature, meaning they work in a certain environment.2671

The cells in our body at a pH around 7.4, had enzymes that are happy at about 7.4, in 98° F.2680

But if you were to throw those enzymes into our stomach acid which is around pH, anywhere from 1 to 4,2691

those enzymes would not work very well.2701

In fact, they will be denatured and then have to be degraded and thrown away.2702

This is important.2706

For our final slide, we are going to talk about just a quick example.2710

I want you to arrange the following three properties from least similar to most similar, between related proteins.2716

What I'm asking you is between two proteins that are related,2724

what is the most likely sequence that is going to be similar between any two proteins?2729

Let us say, remember we are looking at the 3D structure of a protein.2747

The structure dictates function, meaning multiple things that look alike can do the same thing.2755

We might see then that the protein structure is going to be the most similar.2774

If we remember back to the second unit, when we talked about the genetic code,2795

we have DNA being made into RNA, and RNA being made into a protein.2804

If you remember it correctly, to make a protein, we need our amino acids.2834

If we remember, multiple different codons on the RNA can be made into the same amino acid,2841

which we call the degeneracy of the genetic code.2857

Therefore, our amino acid sequent, we could get aspartate from multiple different pieces of RNA triplets.2861

123, 123, 123, 123, this is RNA codon.2878

Remember, our RNA is made from DNA.2885

This will have come from 123 of DNA, so on and so forth.2888

This should allow us to understand that, what is next most similar between related proteins would be the amino acid sequent.2899

Therefore, leaving us with the least similar being our nucleotide sequence.2919

From least similar, similarity increases as you go from left to right.2942

We could add in another one over here, that what could be either more similar, would be protein function.2958

We would go right here.2976

That ends our lesson for today, thank you for watching www.educator.com.2979

Please come back and see me again soon.2983