Molecular Biology Structure of Nucleic Acids

Welcome back to www.educator.com, today we are going to talk about the structure of nucleic acids.0000

As an overview of what we are going to talk about today, we are going to talk about nucleic acids.0008

We will talk about what they are actually composed of, the nitrogenous bases, the pentoses,0013

how they are made up of nucleotides.0019

We will talk individually about DNA and then RNA.0022

Nucleic acids are biopolymers, meaning they are on made up of monomers, multiple units making a polymer.0028

They are biological molecules.0037

These biopolymers are essential for all known forms of life.0039

DNA and RNA are composed of nucleotides.0044

Those are the monomer unit.0047

We have deoxyribonucleic acid and this would be DNA.0050

Then we have ribonucleic acid and that is RNA.0067

Nucleotides are composed of heterocyclic nitrogen bases.0077

As we are going to see later, those are A’s, T’s, G’s, C’s.0081

We are going to talk about RNA, they will also have a U.0089

Nucleotides also have pentoses, those are the ribose or deoxyribose.0096

As we can see the ribose would be for ribonucleic acid, RNA.0100

The deoxyribose is for deoxyribonucleic acid, DNA.0108

Finally, nucleotides have phosphate groups.0114

They have 1, 2, or 3 phosphate groups.0117

Remember, we have PO4 3-.0126

Nucleic acids are found inside cells.0133

If we see a eukaryotic cell right here, what we can zoom in on is the nucleus.0137

The nucleus is what houses our chromosomes.0147

Remember, our chromosomes are made up of DNA.0152

DNA is a nucleic acid.0158

Inside the nucleus, we can also find RNA.0161

As well as in the cytoplasm, we are going to find RNA as well.0165

The nitrogenous bases that we talked about, remember, I said A, G, T, and C.0172

Those can be split into two different categories.0177

We have our purines, those are our double ring, heterocyclic nitrogen structures.0181

We have adenine, adenine is our A.0189

We have guanine, our G.0199

Adenine and guanine are both going to be able to be found in DNA and they both be found in RNA.0204

They are only different, as we will see later is that, if they are in DNA, they will be attached to a deoxyribose.0221

If they are in RNA, they will be attached to a ribose.0229

Our pyrimidines are our single ring heterocyclic nitrogen structures.0236

Our heterocyclic nitrogen, that just means we have a ring structure,0241

a cyclic structure that has nitrogen to the ring, instead of all carbons.0248

That is why it is hetero, because we have nitrogen and carbon.0253

It is cyclic, we have the conjugated bonds around and it is the nitrogen we are talking about.0257

We have cytosine, it is one of our pyrimidines and that is going to be found in DNA.0264

We have thymine, another one of our pyrimidines, that is also going to be found in DNA.0273

We have uracil, it is not normally found in DNA.0281

Uracil is found in RNA.0286

Also found in RNA is cytosine.0292

What we actually have here is a switch of thymine for uracil, when we are going between DNA and RNA.0297

A good way to remember our pyrimidines, you can remember however it is useful for you.0309

What I always think of, when we have cytosine and thymine, they have a Y and so does pyrimidines.0315

If you want to think of all of them together, if you use the one letter abbreviation CU and T,0322

you could say CUT the PY, for pyrimidine.0329

CUT the PY, those are our 3 pyrimidines.0336

Then, if you know you are through pyrimidines, it is very easy to remember your two purines, your adenine and guanine.0340

As a review, what to remember, that our adenine and guanine,0348

both are going to be found in DNA and both are going to be found in RNA as well.0358

The nucleotides that we can find in DNA are A, G, T, and C.0370

The nucleotides that we will find in RNA are A, G, C, and U.0375

The other things that make up our nucleotides are our pentoses.0385

A pentose, all that is, that means 5 and the ose means a sugar.0391

It is a 5 carbon sugar.0399

Ribose occurs in RNA only, and this is ribose.0404

Deoxyribose occurs in DNA only, this is deoxyribose.0420

To be specific, it is a 2 prime deoxyribose.0429

How we can tell that this is the deoxyribose, without going into too much organic chemistry?0434

If we see right here, this is our anomeric carbon, it is the carbon bond in between two different oxygen.0445

Here is one oxygen, here is one oxygen, that is the carbon.0451

This is carbon 1, following all the way along to have the longest carbon chain, this would be carbon 2.0454

It is called the 2 prime carbon because when attached to a nitrogenous base, we count those carbons first.0468

Those would be the 1, 2, 3, 4, and so on.0477

Then, we count our sugar carbons with the prime notation.0480

This is the 2 prime carbon.0486

As we can see here, on the ribose off of the 2 prime carbon, we have an OH.0489

Off of the 2 prime carbon of the deoxyribose, all it is an H.0496

It is not shown here but I will write it in.0503

Let us write a little clearer, that is an H.0506

This is lacking in oxygen, therefore, deoxy.0513

It is a 2 prime deoxy and the whole molecule is called ribose, a 2 prime deoxyribose.0516

Important to know, is the proper terminology.0527

The difference between nucleoside and a nucleotide...0532

A nucleoside is a nitrogenous base and a pentose.0536

For example, we have ribose and guanine attached together, that is a nucleoside.0544

A nucleotide is when you have a nucleoside, therefore, a ribose and guanine, as well as a phosphate group.0556

When we say phosphate group, this is going to be either 1, 2, or 3 of them.0574

Let us say for example, one phosphate.0579

This right here will be called a nucleotide.0587

This would be called our monomeric unit that will be then added into, in this case, RNA.0590

We add the triphosphate form, if this were a 3.0602

We would add the triphosphate form into rRNA.0611

Inside the RNA, it would actually be in the monophosphate form.0614

We will talk a little more about that, as we get there.0620

For our first example, let us recognize these.0625

What bond here do we see?0630

We see adenine, right here.0633

What is adenine?0635

Adenine, if we remember back, is a nitrogenous base.0638

There is our natural base.0641

Adenosine, what do we see here.0649

Adenosine, we see that we have a sugar, a pentose, that pentose is a ribose.0654

Then, we see our adenine.0663

We have a pentose and a nitrogenous base.0669

This is considered a nucleoside.0674

Over here on the right, we have adenosine triphosphate.0687

What we can see is we have the pentose, once again, it is a ribose.0692

We then see we have the nitrogenous base, adenine.0700

Finally, we have 3 phosphate groups.0707

Therefore, this is considered a nucleotide, with a T.0712

This is how we point out the difference between a nucleoside and a nucleotide.0726

When we are going to talk about DNA and RNA, we talk about them normally in their full length chains.0740

Remember, the nucleotides make up the monomers that become the polymer of poly-ribonucleic acid ,or poly-deoxy-ribonucleic acid.0747

What these will look like, once again, we have our RNA being composed of cytosine, guanine, adenine, and uracil.0757

We have our DNA being composed of cytosine, guanine, adenine, and thymine.0771

What we see here is that most commonly, we find DNA in a double helical structure.0781

We find RNA in a single helical structure.0788

We still have the bonds between nucleotides which are phosphodiester bonds,0795

starting out between nucleotides of the same chain.0804

These are phosphodiester bonds, these are found in both DNA and RNA.0807

That is the linkage of the 5 prime phosphate.0813

The 3 prime hydroxyl will come into 5 prime phosphate.0819

In DNA, we can see that we have hydrogen bonding between base pairs.0825

Remember, the hydrogen bonding in the base stacking interactions which are a type of hydrophobic interaction,0832

are what stabilize DNA and keep it together as the double helical chain.0839

Remember, in RNA, we have ribose.0848

In DNA, we have 2prime deoxyribose.0856

Let us focus a little bit on DNA right now, and then, we will move on to a little bit of RNA specific.0871

When we talk about DNA, we have to talk about its grooves.0877

DNA has both a major groove and a minor groove.0881

The major groove is the wider of the two.0886

It is 22 angstroms wide, which is 2.2 nm.0890

In the major groove, all 4 chemical groups are visible.0895

In a minor groove which is much smaller, it is only about half the width and it is 12 angstroms or 1.2 nm wide.0901

We can only see 3 chemical groups in those grooves.0910

What does that mean, what do I mean by that?0916

To go into the next slide, I can tell you in this example.0919

In our grooves, let us say for example that this is a GC base pair, we have our 3 hydrogen bonds.0925

AT base pair on here, we have our 2 hydrogen bonds.0934

If we have our GC base pair, and we say that this is the major groove up here and the minor groove is down here.0938

I will do the minor groove in red.0950

I will do the same thing down here.0956

The minor groove is down here, the major is up here.0958

What do we mean by we can see 4 chemical groups in the major groove and only 3 in the minor.0970

Let us look at the major groove, first of all, we are looking at 4 different things.0975

First, we are looking for what are called acceptors and that is a hydrogen bond acceptor.0982

Then we have donors, and that is an H bond donor, hydrogen bond donor.1001

We then have methyl groups which is just simply a methyl group, that is a CH₃.1014

Finally, we have just hydrogen which is a non-polar hydrogen.1027

Where can we find these?1042

On a GC base pair in the major groove, we can find an acceptor which is this nitrogen.1044

This is a hydrogen bond acceptor.1056

We have another acceptor, this oxygen is making this hydrogen bond right here.1059

This hydrogen bond being made right here.1070

We have a hydrogen bond donor, which we have right there.1076

Finally, the 4th one that we can see, it is actually not written on here but I will write it for us,1084

is we have a hydrogen coming off of this carbon and that is the non-polar hydrogen.1089

We can see 4 different groups there.1110

In a minor groove, all we are able to see is 3.1112

And that is, right here, we have the acceptor, we have the hydrogen donor.1117

Then, we have the hydrogen acceptor which is this oxygen.1131

We can see that is that right there.1136

If we write this out, this is A, A, D, H and this is A, D, A.1143

In the major groove, we have a reading of acceptor, acceptor, donor, hydrogen.1171

In the minor groove, we have acceptor, donor, acceptor.1184

We can show the same thing in our AT bond.1189

Our adenine, we have an acceptor, we have a hydrogen donor coming right here.1194

We then have another hydrogen bond acceptor.1210

We can see it is already making that hydrogen bond.1217

And then, we have a methyl group.1221

Sorry, this should be an A.1236

In the minor groove, we can see the acceptor is the nitrogen.1247

We have the oxygen over here being another acceptor.1256

And then, we have the non-polar hydrogen that are not seen but it is coming off of this carbon.1262

In the major groove of an AT base pair, we can see A, D, A, N.1283

In the minor groove, we see A, H, A.1288

What is important, as I have said here, you can see in the major groove, we can see 4 different chemical groups.1293

In the minor groove, you will see 3.1301

What is important is that, in the major groove, let us draw this out.1303

In the major groove, we can see A, D, A, N, this one is in AT base pair.1309

We can see A, A, D, H, remember, acceptor, acceptor, donor, hydrogen, that is a GC base pair.1328

You are seeing both of this right here.1341

ADAN, AT, AADH, GC.1343

We can also see the reverse of that.1347

We can see a NADA, that is the reverse of this one.1349

That is going to be a TA base pair.1357

And then, we can see HDAA, the reverse of the GC base pair, therefore being a CG base pair.1360

In the minor groove, since we have less information, if we see as we have seen here, let us go this one.1373

In ADA, we know that ADA right here is a GC base pair.1384

We know that AHA down here is an AT base pair.1397

But if we look, since these are reciprocal, this ADA can also be a CG base pair.1410

This AT could be a TA base pair.1421

It is important for proteins recognizing what specific strand of DNA they want to be a part of.1427

In the minor groove, you cannot tell if it is a GC base pair or a CG base pair, or vice versa, an AT versus a TA.1434

It is important we get a lot more information from major groove and a little bit less from the minor groove,1442

that can affect the specificity of interaction between DNA binding proteins.1446

Let us move on to see more properties of DNA.1457

As this is a review from our first unit, we should know that DNA is in anti-parallel orientation,1460

meaning we have one strand going 5 prime to 3 prime, with the other strand going the opposite, 3 prime to 5 prime.1469

5 prime to 3 prime going down in this direction.1480

5 prime to 3 prime going up in the other direction.1483

It will base pair and have complimentarily.1486

There are phosphodiester linkages holding the nucleotides together on the same strand.1490

We have it right here, a phosphodiester linkages on both strands.1496

We see that the 5 prime end will have a phosphate group.1505

The 3 prime end will have a free hydroxyl group on the 3 prime, the 3rd carbon of the pentose.1516

We know very well by this point that purine base always pair with pyrimidines.1529

A’s pair with G’s, C’s pair with T’s.1536

If we are talking about RNA, we do not have a thymine.1542

In that case, adenine will pair with two hydrogen bonds to a uracil.1546

Generally, DNA is found in 3 different confirmations but the most common form is the B form.1557

The B form DNA is the one that we see in the middle.1564

B form DNA has about 10.4 base pairs per turn of the helix.1571

For simplicity sake, we often say 10 base pairs per turn.1577

As I stated in the previous couple of slides, there is a major and minor groove, as we can see.1581

As I mention one more time, hydrogen bonding between the bases ,1592

as well as base stacking interactions stabilize this interaction to keep the two strands together.1597

As we see here, we have the major groove and the minor groove.1606

We say here this would be the major groove and this would be the minor groove.1612

This is major.1627

If we are going to talk about DNA, we need to be able to talk about its topography.1638

When we talk about DNA topology, one thing that comes up is the linking number of DNA.1645

The linking number is the number of times one strand has to be passed through the other,1652

to completely separate the two strands.1660

It can be easier to find with the equation, linking number equals twist + writhe.1663

To understand that, we need to know what twist and writhe are.1672

Twist is the number of helical turns of one strand around another.1675

For example, in this up here, in this first thing on the left, the twist is 0 because1684

these two strands are not wound around each other at all.1694

If we look down here, the twist is 1 because now it is been wound around 1 time.1698

Strand A has been wound around strand B a single time.1704

Writhe is how we calculate or how we take into account super helical turns, what are called supercoils.1711

Writhe is the total number of nodes per molecule.1721

Writhe can be broken down into two separate parts.1727

We have plectonemic writhe and we have toroid writhe.1730

Plectonemic means it is just twisted around itself.1735

Toroid is when it is twisted cylindrically.1742

This is usually when the DNA is twisted around something like a protein.1745

Specifically, like something we will talk about in one of the next unit which is called a histone.1751

Let us look at this page.1759

I have already told you up here, the linking number we do not know yet.1761

But we do now right here in this first example, twist is a twist of 0 and a writhe of 0 right here, in both of these.1767

There is a linking number of however many bases it is.1785

Let us say for example, there are 360 bases in this.1788

360 base pairs in this piece of DNA.1795

For simplicity's sake, we will say that there are 10 base pairs per turn, from the previous slide.1799

Our linking number is going to be equal to 360/10 which is 36.1809

Remember, our linking number is equal to our twist + our writhe.1819

Linking number is 36, since twist and writhe do not come into play here.1826

At this point, we add 1 twist, and it is a negative twist.1834

In this case, our twist is equal to 1.1840

Our linking number, if it is equal to twist + writhe, our linking number has to decrease.1843

Our linking number is now going to be 35 because our twist is -1 and our writhe is 01853

In this case, what it would be, our linking number will be -1.1871

I will show you an example on the next slide, which will make this a lot easier.1876

As of right here, we have our single node.1880

This single node is our writhe, that is where a writhe comes into play.1889

In this case, it is a negative writhe.1895

The left side of the screen and the right side is just whether we are looking at positive twist and1897

writhe which is on the right side, or negative twist and writhe which is on the left side.1903

If we move on to the next slide, we can look at some of those extra writhe and twist.1911

Once again right here, twist is equal to 0, writhe is equal to 0.1916

If we twist this one time, we cross the strands over each other, we now have a twist.1925

Once again, right side is positive, left side is negative, in a way that this is shown.1933

Your red everything will be positive, your blue everything is going to be negative.1940

We see our super helical turn, which is once again just a supercoil.1944

This node that gives us a writhe, same thing would happen over here.1953

One more down, we can see we have a writhe of 2, 2 nodes.1961

1, 2, that is where we have a writhe.1969

Most organisms have negatively supercoil of DNA.1975

This is a way to store some energy, as well as relaxing the DNA.1980

Let us go over one example problem to try to clear this up.1985

It is a fairly simple concept but it is a little bit challenging to really understand it, at the same time.1989

If we have a linking number practice problem, let us say, if I tell you that the molecule has base pairs 360.1998

Then, if we assumed we have 10 base pair per turn then that makes our leaking number 36.2018

If this is an example of completely relaxed B form DNA, the linking number will be 36 and we would not have any writhe.2034

If linking number equals twist + writhe, we know our writhe is going to be equal to 0 and2043

our linking number is equal to 36, then our twist must be 36, since writhe is 0.2055

That is because we have turning of the strand around itself.2064

What this might look like is, I will just show you in two different colors.2069

The DNA molecules are turned around each other.2083

If I tell you that as long as we do not remove any DNA sequence, the linking number has to change.2087

If we are going to add supercoils or take out supercoils, whether it is positive or negative.2101

As long as we are not adjusting the number of base pairs, we are not taking out or adding in DNA,2105

if we add in or subtract writhe, then supercoils, we need to adjust the linking number.2111

For example, if our base pairs have not changed, they are 360.2123

Let us say in this molecule now, we have 1, 2, 3.2130

In this case, what do we see?2147

Once again, this would be a double strand of molecule.2150

We still have the proper twist.2158

If we have this molecule, what is our writhe?2166

Let us look at it, we see 1 node, 2 nodes, 3 nodes, and 4 nodes.2172

Let us write in our writhe.2183

Our writhe is going to be, in this case, we are going to call it a -4.2186

This is unwound, this is under wound.2192

If our writhe is -4 and our twist has not changed, that is still a 36, our linking number must change.2195

Remember, linking number equals twist + writhe.2207

If linking number is equal to 36 + -4, our linking number is equal to 32.2212

This is an example of how you might solve a linking number problem.2227

It is important to now, I know it is kind of hard to see on paper, but negative supercoiling,2231

negative writhe, refers to having to turn the helix to the right to remove nodes.2240

Negative supercoiling refers to having to turn the helix to the right to remove the nodes.2251

Therefore, positive supercoiling will mean you would need to turn it to the left.2286

In this case, we have a writhe of -4, meaning if you want to remove that writhe,2291

you need to turn the helix to the right 4 different times to remove those nodes.2298

As we can see, our DNA can supercoil.2308

What can be problematic with that is that DNA is not particularly flexible.2313

It can be flexible at points at times, but if you over coil things,2322

they will eventually have so much tensional stress that they break.2328

We need to have enzymes that can take care of this and relieve this tension.2334

We have what are called type 1 and type 2 topoisomerases.2340

Each one of these helps relieve torsional stress.2345

Type 1 topoisomerases, unwound DNA by making a nick in just a single strand.2350

This nick in just a single strand create a pivot point in that DNA backbone.2365

It helps swivel around, if we try to draw it out.2369

If the nick is right there, we can swivel this 360°.2383

That can help remove any torsional stress, we can go either way.2393

Action of topoisomerases 1 does not require ATP and it will change the linking number in steps of 1.2400

We have type 2 topoisomerases, they cut both strands at the same time which requires ATP energy2411

and will change the linking number in steps of 2.2421

How type 2 topoisomerases act, they separate two helixes by cutting both strand to the single helix,2426

passing it through the gap of another one while still holding onto the ends.2434

And then, re-ligating the strands together.2438

It is important because as we are going to talk about in DNA replication,2443

topoisomerases will move supercoils ahead of the replication fork.2447

Helicases which we will talk more about, generate positive supercoils ahead of the fork, the replication fork.2454

They generate negative supercoils behind the fork.2480

For every 10 base pairs that helicase unwinds, it will make 1 positive supercoil.2498

Helicase unwinds 10 base pairs, that is 1 positive supercoil.2505

We will talk more about helicase but this is important.2514

We are adding more and more supercoils.2518

Type 1 and type 2 topoisomerases are going to be able to act ahead of the fork to relieve this torsional stress.2520

If we think about it, if anyone of us ever had one of the corded phones growing up, they are normally always tangle up.2526

As they are extra tangle, those would be like writhe, the supercoils.2536

If you grab in the middle of it and pull it apart, you are basically making what we are talking about as a replication bubble.2540

If you see as you pull them apart to have a gap in the middle, you are going to increase the stress on either side of the bubble.2547

Because a phone cord is very elastic, you can do that, it is really not going to break.2557

But DNA is not as resilient, it is a little more fragile.2561

As we are opening up the DNA, we need to release torsion on either side of that bubble.2566

That is where our topoisomerases will come in to plot.2571

These are really important molecules.2574

That is the end of what we are talking about DNA for now.2579

To introduce you to RNA, I want to remind you of the central dogma of molecular biology.2584

Remember, DNA to DNA is replication, DNA to RNA is transcription, and RNA to protein is translation.2590

As we see here, this is actually transcription in action, where we have the mRNA being made from DNA.2606

As mRNA could then go to the cytoplasm and be made into a protein via translation at the ribosome.2614

RNA, remember that is ribonucleic acid.2626

It is most commonly found as a single stranded molecule, although it can be double stranded.2635

It is made up of a nucleotide, just as a DNA is, many nucleotides put together.2642

In this case, the nucleotides are attached or the nuclear bases are attached to a ribose2649

not a deoxyribose because deoxyribose is DNA.2656

Importantly, remember, uracil is found in RNA, thymine is not.2668

Whereas, uracil is not found in DNA and thymine is.2673

There are 3 major types of RNA.2678

The first is the most abundant, and that is rRNA and that is called ribosomal RNA, makes up about 75% of our total RNA.2682

Then, we have mRNA which is the smallest makeup of our RNA group and that is called messenger RNA, that makes up about 5% or less.2692

Then, we have tRNA or transfer RNA.2702

There are also things called non-coding RNA.2705

That is kind of ramped into the ribosomal RNA part.2709

We will go through in the next few slides and tell you what each one of these RNA has a function.2715

Our rRNA is the structural and catalytic constituents of the ribosome.2724

They will bind proteins and form a ribosome.2738

For eukaryotic rRNA, we have the 5S, the 5.8S, and the 28 S rRNA,2743

coming together with proteins to form this 60S subunit of the ribosome.2754

Then, we have the 18S rRNA coming together with proteins to form the 40S subunit.2761

Together, these make up the 80S eukaryotic ribosomal subunit or 80S eukaryotic full ribosome.2771

S stands for Svedberg, this is just a unit of density.2783

Yes, we do now 60 and 40 should equal 100 not 80.2796

Since this is a density unit, this is affected, 60 + 40 S does not make 100, it actually makes 80S ribosome.2803

For our prokaryotes, we have the 5S and 23S rRNA, along with proteins making it a 50S ribosomal subunit, the large subunit.2815

We have the 16S rRNA, along with proteins making up the 30 S subunit.2825

This makes a 70S prokaryotic ribosome.2832

Once again, 50 + 30 = 80, but we actually have a 70S ribosomal complex for prokaryotes.2839

Remember, Svedberg is a density unit not a weight unit.2848

This would be as an example of what an rRNA might look like.2853

The second type of RNA’s, we had mRNA or messenger RNA.2862

This is going to contain the codons for the sequence of amino acids of a polypeptide.2867

When DNA is transcribed to an mRNA, that mRNA becomes the messenger leaving the nucleus and going to the cytoplasm.2875

It will then associate with the ribosome.2887

Remember, the ribosomes are made up of rRNA and protein.2889

The mRNA will associate with ribosomes.2892

With our next RNA which is our tRNA, together that can all go through reactions to create new proteins.2896

One thing that is important to talk about is the fact that eukaryotic mRNA get post-transcriptional modified.2906

What happens is they get a 7G MTP cap - 7 methyl guanosine triphosphate cap added at the 5 prime end.2915

This is done for protection.2928

It has done that so that it cannot be eaten away from the outside by nucleuses.2932

Another way to protect it on the other side, we add a poly A tail.2938

This poly A tail is a bunch of adenosines, maybe about 200 or so.2942

Adenosine nucleotides added after all the coding sequent.2949

This would not be coded and turned into amino acids.2953

Remember, it will talk more and more about this but we have a stop codon.2957

We also have a start codon.2963

This initiation or start codon which is normally AUG which codes for methionine.2967

The start codon, in most cases, 99% or more, this is going to be an AUG codon coding for methionine.2976

Anything before the start codon, like our cap and like our 5 prime UTR2985

which means untranslated region, this does not get turned into a protein.2991

Only between the start codon and the stop codon, do we have our protein coming out, amino acids all the way through.2995

At the stop codon, that is going to be one of these 3 sequences, UAA, UAG, or UGA.3010

Anything past these stop codons, is not going to be translated as well.3023

We have a 3 prime untranslatable region, as well as our poly A tail.3028

None of these nucleotides will be turned into proteins either.3033

What is important about this stop codon is that it3038

does not actually code for any amino acid nor does any tRNA come in to bring anything to it.3040

As our last example, we will talk a little bit about the stop codon.3048

As a reminder, remember DNA is found in the nucleus.3056

Most frequently found in the nucleus.3064

Transcription occurs in the nucleus to make R, in this case we are showing mRNA.3066

MRNA can leave through a hole in the nucleus or holes in the nucleus called nuclear pores.3072

They can go to the cytoplasm where they can interact with ribosomes and tRNA’s, and3080

undergoing a process called translation to make new proteins.3086

We need that adapter molecule, we talked about rRNA which helps make up the ribosomes.3093

We talked about mRNA, the messenger.3099

What about the adapter molecule?3102

First, before we get to that adapter molecule, let us understand what is going on with RNA.3107

We have talked about the genetic code a couple times already.3112

We have our mRNA, it has a bunch of these bases.3116

It has what are called triplets or codons.3120

A codon is a 3 base pair sequence.3124

In this case, for example, if I had a UUU from 5 prime to 3 prime,3127

UUU is going to code for a phenylalanine amino acid to be added to the growing polypeptide chain.3136

If I had in AAC, that will add in a pair of gene amino acid to the growing polypeptide.3146

These amino acids have to be brought in by something and that something is going to be our tRNA.3155

The last thing before we jump in tRNA, we are going to give you this example on stop codons.3167

Our stop codons, once again, UAA, UGA, UAG, these do not code for an amino acid.3173

They do not have unassociated tRNA.3200

In fact, what they do is they signal a release factor, in eukaryote, it would be eukaryotic release factor neuron.3216

What that does is it comes in. Let us say, here is the ribosome, here is the mRNA coming through.3225

Here is the polypeptide coming out, all these amino acids.3238

tRNA’s would normally come in and add an amino acid, when it finds the proper codon.3249

Once we hit this, let us say for example, a UAA that will signal the eukaryotic release factor to come in.3255

What it does is, it acts like a pair of scissors, it will cut this chain off.3268

In which case, it is now free to float away and fold up into whatever protein it is supposed to be folded into.3280

Our tRNA, our last piece of RNA that we are going to talk about is an adapter.3294

It is the adapter between the codons in amino acids.3300

What it is, it is actually a 4 Svedberg RNA.3304

It has a form cloverleaf structure, we have hairpin loops stabilizing, intramolecular base pairs.3308

This is a single stranded RNA but it is making base pairs within itself.3315

For example, we have this is the 5 prime end and this is the 3 prime end.3336

It is a single strand but it is making intramolecular base pairs.3339

The tRNA will carry the amino acid and it will carry it at this point right here.3344

It will carry it into the ribosome during translation.3350

What is important to point out is that, there is only one tRNA for each of the 20 different amino acids inserted in the protein.3354

For example, if we go back to that UUU sequence.3364

If we had on the mRNA.3370

If this were a UUU, this is the codon on the mRNA.3380

The anticodon with tRNA would match base pairs.3395

This would be a AAA, this would only carry at this end.3400

For example, we have over here, we would have this part carrying a phenylalanine amino acid.3418

This tRNA would always have the same anticodon AAA, meaning it would only be able to carry that phenylalanine.3430

We have a phenylalanine tRNA, we have an asparagines tRNA, we have a glycine tRNA.3443

It will only match up properly its anticodon with the proper codon on mRNA and3448

only attach the single amino acid to the growing polypeptide chain.3455

One arm has that anticodon that I talked about.3464

Here would be our anticodon loop.3467

This would hydrogen bond to our codon on the mRNA.3470

Here is our mRNA, let us say again, it would hydrogen bond.3474

The CCA part on the 3 prime end carries a specific amino acid and that will be dictated by whatever this codon is.3483

For example, if this anticodon is AAA, it will match up with UUU on the mRNA.3494

Therefore, this will carry a phenylalanine amino acid.3507

That will be added to the growing polypeptide chain in the ribosome.3513

This shows it altogether, we see our messenger RNA here, our ribosome is here, our incoming tRNA are there.3521

For example, we are bringing in the phenylalanine, phenylalanine can be coded for multiple codons,3532

that is why we do not see just AAA.3537

For our purposes, we will change it and we will make it look like what we are used to.3540

We will just turn that into an A.3546

We will turn this into U, to say it is what we looked at the past few.3552

UUU matches out that codon with the AAA anticodon, and brings in phenylalanine.3560

That will make a peptide bond to the aspartate, in this case.3567

It is a growing polypeptide chain.3573

The only thing that would stop it would be our stop codons.3575

UAA, UGA, UAG, that would be our stop codons.3579

In which case no tRNA would come in but instead the eukaryotic release factor for talking about eukaryotes,3592

would come in and it would cut the chain releasing it from the loop.3600

Four our last slide, I just want to briefly talk about ribozymes.3610

I have mentioned before in proteins that a lot of them can be enzymes but not all enzymes are proteins.3615

This is where we have our exceptions.3624

Ribozymes are RNA molecules with enzymatic activity.3627

An example of those are the first one that was discovered is RNA’s P.3632

That is in the endonuclease meaning it cuts in the middle of a piece of DNA.3639

Let us say cut in here.3646

We have peptidyl transferase which is a ribozyme that is found as part of the ribosome.3649

I wrote on here telomerase but I did that to show you that, unfortunately, a lot of the times telomerase is taught as being as a ribozyme.3657

When in fact, it is not a ribozyme.3669

Telomerase is actually a ribonucleic protein.3672

That means it is a protein and ribonucleotide mixed.3689

The thing that is actually catalyzing the reaction is the protein component not the RNA component.3696

We will talk about telomerase a little more.3703

Telomerase, just in case we do not know what it is, it is the enzyme that will lengthen telomeres3706

which are the end of our DNA sequence.3713

That we do not keep shortening our sequence with every replication and how our cells die quickly.3715

That is the end of our lesson today, thank you for joining us at www.educator.com.3724

I hope to see you again.3729