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Lecture Comments (8)

1 answer

Last reply by: Bryan Cardella
Thu Jan 14, 2016 2:02 PM

Post by Jinhai Zhang on January 13 at 08:13:05 PM

Do have lectures explain the telomere of DNA replication?

3 answers

Last reply by: Bryan Cardella
Sat Oct 11, 2014 12:33 PM

Post by King Calculus on October 9, 2014

My question is this:
Is this going on in every cell in my body, even in brain cells?
Also, is the cell structure the same even in my brain? Such as mitochondria and all the DNA replications?

0 answers

Post by Lilian Comparini on March 14, 2014

You are not only brilliant and a great teacher, but hilarious as well.

0 answers

Post by Lilian Comparini on March 14, 2014

omg I fell out of my chair laughing at the library with that country song!!


Lecture Slides are screen-captured images of important points in the lecture. Students can download and print out these lecture slide images to do practice problems as well as take notes while watching the lecture.

  • Intro 0:00
  • DNA: Its Role and Characteristics 0:05
    • Deoxyribonucleic Acid
    • Double Helix
    • Nucleotides
    • Anti-parallel
    • Self-Replicating
    • Codons, Genes, Chromosomes
  • DNA: The Discovery 5:13
    • DNA First Mentioned
    • Bacterial Transformation with DNA
    • Base Pairing Rule
    • DNA is Hereditary Material
    • X-Ray Crystallography Images
    • DNA Structure
  • Nucleotides 12:54
  • The Double Helix 16:34
    • Hydrogen Bonding
    • Backbone of Phosphates and Sugars
    • Strands are Anti-Parallel
  • Nitrogenous Bases 20:52
    • Purines
    • Pyrimidines
  • DNA Replication Overview 24:33
    • DNA Must Duplicate Every Time a Cell is Going to Divide
    • Semiconservative Replication
    • How Does it Occur?
  • DNA Replication Steps 28:39
    • DNA Helicase Unzips Double Stranded DNA
    • RNA Primer is Laid Down
    • DNA Polymerase Attaches Complementary Bases in Continuous Manner
    • DNA Polymerase Attaches Complementary Bases in Fragments
    • DNA Polymerase Replaces RNA Primers
    • DNA Ligase Connects Fragments Together
  • DNA Replication Illustration 32:25
  • 'Junk' DNA 45:02
    • Only 2% of the Human Genome Codes for Protein
    • What Does Junk DNA Mean to Us?
    • DNA Technology Uses These Sequences

Transcription: DNA

Hi, welcome back to, this is the lesson on DNA, its role and characteristics.0000

What is this stuff, what does it do?0008

Most people know basically what DNA is, but we are going into a lot of detail about how it actually functions in cells.0011

DNA stands for deoxyribonucleic acid, there is the DNA.0018

Nucleic acids are general class of compounds, RNA is another kind that is in the next lesson on RNA.0026

DNA contains the instructions for life, it has the codes for how cells do everything.0034

How they maintain homeostasis, how they function, how they physically are?0040

They are able to retain their functionality and form because of DNA.0046

This is the substance that is copied and passed on to daughter cells when it divides, this is what keeps life going.0050

That might seem like common knowledge now, and it is in the scientific community.0058

But 60 years ago, that was not so common.0062

All proteins that cells make can be traced back to the code in the DNA.0066

DNA codes for a protein, proteins are so important cells.0072

It is very prolific in terms of what they do structurally and what they do chemically.0077

Proteins really are how DNA is expressed in cells.0083

Double helix, I put that in capital letters because this is very important.0088

Here is the double helix, this is that classic DNA shape.0092

Helical is spiral, double helix because it is pretty much two spirals attached to the center, this is the shape it is.0097

When we look at this particular structure when we discuss cell division, there is a lot of the double helix in here.0106

This is a heck of a lot bigger than this.0115

Here, we are looking at just several pairs of nucleotides attached together.0119

I will tell you more about nucleotides in a second.0124

In the 46th of these that you would see in a human cell that is about to divide,0126

There are 3 billion nucleotide pairs in all 46 combined.0132

There are hundreds and thousands of genes in these various chromosomes.0139

This structurally is a lot smaller than this.0146

Made of nucleotides, we look down this backbone of DNA on each side, it is nucleotide attached to a nucleotide.0151

Across the center, the nucleotides of these two strands are attached.0158

More details about that later on in the lesson.0163

These strands are antiparallel meaning they go on opposite directions.0166

I am making my arms parallel but it is really like this in DNA.0171

A better way to look at it is that two pens here, two identical looking pens, this would be parallel.0176

Also a mathematics term, I’m making them as parallel as I possibly can.0183

Here is what antiparallel means that this strand, as it curves around,0187

and this one curves connected to it, this is read in the opposite direction.0192

This strand is read in the opposite direction of the strings is attached to.0197

That is what antiparallel means.0202

Do not think it means perpendicular, no it just means these are parallel strands that are read in opposite directions.0204

There are terms about directionality, three prime to five prime coming up later in the lesson.0212

It is self-replicating, enzymes that are naturally found in cells, 0216

and DNA actually codes for those enzymes allow DNA to be copied.0220

As long as you have those little nucleotides available, 0225

they can be put next to the other strand and new strands can be made.0228

That has to happen before cell divides.0233

Codons, genes, and chromosomes, these terms have to do with what DNA is made up of.0237

I will give you an analogy, a codon is a set of three bases, three nucleotides side by side.0242

You will find these in DNA and RNA.0249

This is like a word in the genetic sentence, a bunch of codons together,0251

it could be a hundred codons or more, can code for a gene.0261

A gene is like a sentence, a bunch of codons together forms a gene.0266

A bunch of genes together, we are talking a lot of genes, would make a whole chapter of this book.0275

A chromosome is kind of like a chapter.0282

Actually this really good book about DNA that is in 23 chapters.0289

Surprise, because 23 is the haploid number for humans, 23 pairs equals our diploid number is 46 chromosomes.0293

Chromosome, a giant package of these genetic sentences,0302

they are made up of words that are known as codons.0307

More about that especially when you get to the RNA lesson.0310

DNA, the discovery, it took many years to get to the point where we really knew 0315

this is what DNA is, this is what it does, this is their functions.0319

We are still in the infancy though, if you ask me there is a lot more to be discovered about DNA.0324

There is this recently a new story that I read about that, there is a hidden code that is hidden up to this point,0330

that we did not even know what was going on until further research brought that out to us, that we can really see it.0337

There is a lot going on in the DNA that we still have to tap into, to fully understand it.0345

Miescher, this particular scientist back in the 19th century was able to say,0350

I got the substance inside the cell and I can detect it is not protein, but it is there.0360

He called it nucleon, like he knew it was in the center, in this region called the nucleus.0365

He knew it was not protein because it had these chemicals that are meant to break apart proteins in a cell.0373

The chemicals would not break this down, it would not get rid of it, like it is certainly not protein, it was DNA.0379

That is when it was first mentioned, back in 1869 by Miescher.0387

Griffith 1928, flash forward several decades,0392

this particular scientist proved that it is DNA that can actually transform a bacterium.0397

Generic transformation is when a bacterium sucks up DNA from outside itself and expresses it, changing how it is genetically.0406

He illustrated this with mice, he had a harmful strain of bacteria and a harmless strain of bacteria.0417

The harmful strain, when it was living, and he injected it into the mice, of course they died.0424

They kept dying, when he do that.0429

The harmless strain, when he injected that in to the average mouse, they were fine.0431

Their immune system dealt with it, they did not die.0436

He then took the harmful strain, killed it, and found that,0440

once you kill the harmful strain and inject it in, they cannot do what they do.0446

The bacteria can actually mess with the mouse.0453

This interesting thing happen, when he took the harmful bacteria, killed it, but they combine in a test tube with the harmless bacteria,0456

that harmless bacteria sucked up the DNA from those dead cells.0465

When he injected that mixture, the mice consistently died.0468

He proved that these harmless bacteria took up something from the harmful ones,0472

and they changed themselves, their characteristic is changed.0479

That was bacterial transformation proved in 1928.0482

Chargoff in 1950 figured out this based pairing rule.0486

His research suggested that, when you look at the bases of DNA,0489

the amount of adenines is approximately equal to amount of what is known as thymine the T.0494

A lot of cytosine is approximately equal to the amount of G or guanine.0501

The reason why I say approximately is, when you actually measure the amount of these bases 0506

and these are the only 4 bases of DNA in organisms.0511

When you measure the amount of these, let us say 60% of the genome is this and 40% is that.0514

This might not be exactly 30/30, this may not be exactly 20/20.0527

You will see the data that says this is 30.5 and this is 29.5, and a similar pattern with that.0533

As far as we know, it might be a shortcoming of the devices that are measuring those particular bases.0545

But, every time you see a C, cytosine in DNA it is attached to a G.0552

Every time you see adenine it is attached to a T, and vice versa.0557

That is why the amounts equal to each other.0561

Chargoff was not entirely certain at that time, that it meant that they were definitely attached to each other in the center.0563

His research was just showing a trend regarding these bases in many different species that he analyzed.0571

That helped Watson and Crick a few years later, to figure out their discovery.0578

But first, Hershey and Chase in 1952, helped demonstrate that DNA is the hereditary material.0583

They actually showed that, when a virus infects an organism, 0589

it is not the proteins of the virus that are being passed on to infect it because the proteins tend to not go in.0598

Some other time they do but in a lot of examples like with bacteria, the proteins do not go in.0605

The DNA is injected in, and they had one set of data where they tagged the proteins,0611

and showed the proteins and virus are not the ones that went in and harmed this bacteria.0618

But in the other set, the other set of data, they tagged the DNA in this.0624

It is the DNA that ends up inside of it, that is what is being passed on, that was making the change.0629

They helped to demonstrate that it is the DNA that is causing this expression to occur,0635

whether it is from a virus or we are talking about our DNA.0642

Roslyn Franklin, unfortunately she did not win the Nobel prize for the discovery of DNA0645

because she had passed away prior to being awarded.0651

She passed away because of a lot of radiation exposure, she took a lot of x-ray images,0656

crystallographic images of DNA samples.0661

That amount of radiation exposure give her cancer, she died very young.0665

The Nobel prize traditionally does not reward posthumous prices to people who are dead.0670

Roslyn Franklin gets a lot of credit now, we know that she did a lot of good.0676

This is a cake and then this is awesome, this is prior for a scientist birthday.0681

They have an image here of her famous image from her crystallography.0686

This particular pattern shows the helical shape of DNA.0694

If you think about how DNA is, there is little piece of it as it twists.0699

It is like this image is focused in right there, you can see the helix.0704

When Watson and Crick saw this, it helped support a theory of theirs about DNA and being a double helix.0710

That was thanks to the research of Ms. Franklin.0717

Watson and Crick, one of the most important discoveries in the 20th century.0720

In 1953 they had this publication of their research about DNA, in terms of the structure of DNA,0724

the bases being attached to the center, the shape of it.0734

They constructed a very accurate metallic model that took up like a whole room, almost from ceiling to floor of the DNA structure.0737

That was a major discovery and they had a good theory about how it is replicated, how the information is passed on.0748

Overtime, their theories that they were not entirely sure a lot of the time have been reinforced because of further research. 0756

It is all about standing on the shoulders of giants.0763

The people came before you, building up on what they discovered to figure out more and more about what this awesome molecule is.0766

Nucleotides, this is the building block or monomer for DNA.0775

DNA as a whole would be a polymer, nucleotides those are the building blocks.0780

When we look at what a nucleotide is made up of, it is a phosphate group.0785

We are just going to call it a phosphate, a pentose sugar which just means 5 sided sugar.0790

Specifically, the sugar is called deoxyribose, and then a nitrogenous base.0795

I highlighted phosphate sugar base, and I made this up.0803

Phosphate sugar base, your DNA determines your face.0809

It is a nice little jingle, it can help you remember.0814

Phosphate sugar base, the components of a nucleotide.0816

I even make a little country song out of it.0820

Phosphate sugar base, your DNA determines your face.0822

That is the components of a single nucleotide.0830

In DNA, this sugar would be deoxyribose.0835

It means it has one less oxygen atom than a ribose, deoxiribose.0847

In the corner, instead of having an OH hydroxide group, this particular one we just have an H, stands for the hydrogen.0851

Ribose, in RNA has one more oxygen but that is basically sugars to sugars.0861

Nitrogenous base, this could be any of these except for uracil.0866

I am going to cross this out because this particular base you can see is just in RNA.0872

It is part of nucleotides but not in DNA, you will hear more about that in the lesson on RNA.0879

This base here can be either C or T, you could see that this one has just one little hexagon, there and there.0885

Some of the bases though look like this, they actually are a much larger base.0893

These are called pure, this little hexagon shaped organic compound attached with another little buddy there, a pentagon,0900

and that makes up the whole base adenine or guanine.0907

More about those, a little bit later in the lesson.0911

You can see the difference here between deoxyribose and ribose.0913

As I mentioned, there is that H and OH difference, other than that, they look identical.0916

I just notice a typo, this just said in DNA, when they actually meant RNA.0924

There you go, that ribose in RNA, deoxyribose in DNA.0935

This is a really good illustration, in terms of how it is built.0941

A phosphate is a phosphorus with some oxygen around it.0944

This sugar, it is similar to other sugars you would see.0948

The glucose happens to have 6 carbons, this happens to have 5 that is the pentose.0951

The nitrogenous bases, you can see as you look down one side of the DNA molecule,0956

it is called a poly nucleotide because it is a bunch of nucleotides.0962

It goes phosphate sugar, phosphate sugar, phosphate sugar, phosphate sugar etc.0966

This would be more meaningful later on, but up here when you see this phosphate, this is called the 5 prime end.0972

And down here, whether is not an additional phosphate, they call it the 3 prime end.0979

That does not makes sense right now, but it will be very important when we talk about DNA replication and the formation of RNA,0983

that is part of that anti parallel thing I told you about earlier.0989

The double helix, looking more at the structure of this, 0996

it is two strings attached in the center via complimentary nitrogenous bases.1000

It is hydrogen bonds that are keeping those together.1005

When we look at this space filling molecule, they are making a sphere represent every single atom.1009

Here, where we see this yellow with reds, the yellow is the phosphorus and the reds are little oxygen.1016

Here is a phosphate, phosphate, phosphate, in between there are the sugars.1023

In the center where you see the blues, nitrogen is found in the center that is where you have those bases.1028

Just a different way of showing what DNA looks like.1036

Remember, for every adenine in the center, it is attached to a thymine.1039

For every cytosine, it is attached to guanine.1043

The amount of bonds between them is particular.1048

I have an equal sign here, I do not mean that as bonds.1052

I am going to raise the equal sign and show you something that represents hydrogen bonding.1055

These are the bonds between the bases on both sides of the double helix.1062

The amount of hydrogen bonds between A and T is 2.1068

I will make two dotted lines here.1073

1 and 2, it is not the most beautiful thing but you can see it.1080

1 and 2 hydrogen bonds between adenine and thymine.1085

Between cytosine and guanine, you have 3 hydrogen bonds.1088

Why? That is just how it is.1097

They way that these molecules is chemically attract to each other,1100

this one makes 2 H bonds and these two would like to make 3 H bonds.1104

This has something to do with the fact that G and T do not like to be next to each other.1121

They will be next to each other on one side, but here we are talking about attached at the center,1126

from the two different strands.1131

T and G could fit across with each other, but T wants to make 2 bonds, G wants to make 3.1135

The way that I remember how many each set make, 2 bonds, T has 2 lines.1141

To actually write out a T, two lines 1, 2.1148

To write out a G, I know people write G differently, but for me it is three strokes.1152

Three lines to make a G equals 3 bonds to make it with the C.1159

The backbone is made of phosphates and sugar.1164

I pointed that out on previous slide that it is just a sequence of phosphate sugars on the backbone.1166

The rungs of the ladder, the insides, are the bases connected.1172

The strands are anti-parallel and there are some designations for what that means.1177

There is a 3 prime to 5 prime running.1182

On the other side, it is also 3 prime to 5 prime but in opposite directions.1184

This will make more sense, when we talk about DNA replication, 3 prime to 5 prime that is how DNA is read.1190

By read, I mean enzymes are going along and saying here is where the code is.1203

When DNA is made, it is made in the opposite direction 5 prime to 3.1207

Same goes for RNA, when RNA is made in the next lesson, you are going to see it is made from a 5 prime to 3 prime direction.1212

DNA is made in this direction, it is read one way, it is made the other.1223

If you remember the pen example, just think of it this way.1229

Let us say my arm here up on the top, here is the 3 prime end, my elbow is the 5 prime end.1231

It was read from left to right to you, but it is made with the respect to the top strand in the opposite direction.1237

My elbow is the 5 prime end and here is the 3 prime.1245

It is just the opposite directions.1249

Nitrogenous bases, they are truly variable portion of DNA organisms.1253

The amazing thing is, whether you are looking at a fly's DNA, E-coli bacteria DNA, and aardvark’s DNA, 1257

a tree, a human, every single organism on this planet has phosphate sugar base making up their DNA.1267

The only thing that is different is the sequence of the bases.1276

Everything else structurally about DNA is the same.1280

It is just a matter of how many A, T, C, G they have and what order.1282

The sequence of bases in the DNA determines the genetic code.1287

The 4 bases of DNA, as you have already seen, are guanine and adenine.1291

Now, we are talking about what makes them purines, and cytosine and thymine what makes them pyrimidines.1294

The purine designation, I will do that in red, this is the big ones, adenine and guanine.1299

How do you remember that the purines are like that as opposed to this, and adenine are guanine are the purines?1308

I have a little hint for that, that will help.1314

This might seem very strange at first but it is helped a lot of my students in the pass.1317

Just follow along with me.1322

Would you agree that little babies are pure, they are pure, they are innocent.1325

Purism, purine, babies tend to be kind of chubby that you can squeeze their cheeks.1331

These are the chubbier of the bases, these are not purines down here but these are their larger bases.1340

Also babies saying gaga, GA.1346

Babies are pure, chubby, and say gaga, that way you can remember that G and A are the purines.1358

Cytosine and thymine, they are pyrimidines, I have a way to remember that.1365

A former student of mine came up with this one.1375

Pyrimid almost looks like the word pyramid, the word for pyramids of Egypt has an A in it, but it is close enough.1377

Pyrimidines, pyramids have coffins and tombs, cats and Tutenkhamun, 1388

whatever you want to remember, coffins and tombs, whatever it might be in pyramids.1400

If you look at just this part, what does it look like? A pyramid.1406

C and T, cytosine and thymine, those are the pyrimidines, coffins and tombs.1413

It will help you remember it.1420

Along with the DNA, you always have to have a purine attached to a pyrimidine, you always do, that what keeps it parallel.1422

Imagine, if you had two of these across one another, not only are they are binding,1428

because adenine and guanine want to make different amounts of hydrogen bonds, it would be too wide.1433

The DNA would be like too fat in that part, if you had two pyrimidines across one another, it will be too skinny.1438

To keep it parallel, you are always going to see a wider base with the shorter base, and vice versa.1448

You would not typically have guanine and thymine together because they like making different amounts of bonds.1454

That is why you are going to see guanine and cytosine, adenine and thymine across one another.1460

If you do not have that happening, there has been a mutation, there was a mistake somewhere along, replicating the DNA.1465

DNA replication overview, DNA must be copied or duplicated every time a cell is going to divide.1475

You want to pass on that genetic information to each daughter cell, so they can do the same thing that the parents have been doing.1481

It is known as semi conservative replication.1489

They were the scientist that initially revealed the semi conservative replication.1491

This is how it happens in every single organism that has ever been studied.1497

Bacteria do it this way, plans do it this way, fungi, perimysium, humans, everyone.1501

We all do the semi conservative replication.1508

Since that term semi conservative might be new, let me explain what that means.1510

Let us pretend that this DNA here is the original DNA, it has little bases connected.1516

That is a very simple depiction of DNA.1528

When this DNA gets split apart, and here is the little bases along your A, G, C, and T.1531

There is an enzyme that goes along and makes new DNA, strings together nucleotides.1544

There it is, the red is your new DNA.1551

Here is the red on this side.1554

What ends up going to the daughter cells is half old and half new.1557

You would need to reconnect the bases like that of their.1568

The point of making it is that, this is a semi conservative replication.1571

Other models were proposed, conservative replication not the semi.1576

Conservative replication would be, if the entire original DNA, both strands was conserved.1581

All of that black DNA went into one cell and all the red DNA went to the other,1589

that would be conservative replication, that is not how it happens.1594

This is how it happens where only some of the original DNA is conservative.1597

That is why it is semi conservative, only some of it goes, half of it goes to one cell and half of it goes to the other.1602

Each daughter cell has half newly formed DNA, as well.1608

There is another model called the dispersive model, that one was even more weird.1613

They thought that maybe they are all these little pieces that were passed on,1621

where you would look at one strand that ended up in the daughter cell.1628

It would be like old new, old new, kind of all glued together in different pieces, in sense.1631

That is not true either, semi conservative replication is how it happens.1638

How does replication go, how do you actually copy DNA and put the other new DNA? How does that happen?1643

Short answer is with lots of enzymes, that is really how it happens.1649

The many enzymes is this one right here known as helicase.1655

I will tell you more about that, later on the lesson.1659

DNA polymerase is another important one.1661

This, there are many different versions, many different types of DNA polymerase.1663

This one right here, its job is to link up or bond nucleotides to what is already been assembled on this new strand.1668

DNA polymerase here is doing the same exact thing, just in the opposite direction from the 3 prime 5 prime distinction.1678

In here, you can see what the different colors represent.1684

In real life, are the bases actually different colors?1687

Of course not, but this helps us visualize it so we can understand how these nucleotides are connected to one another.1690

Here, free nucleotides, this is what DNA polymerase is in a sense of grabbing, to put together and form the complement.1698

Here in green, if that is cytosine, DNA polymerase got the guanine there.1705

If that red one is adenine, DNA polymerase got to put thymine right there.1710

That is how it happens, let us get to the steps, the replication steps. 1715

On the next slide, I’m going to draw this out for you.1722

I just want to go through a summary of written steps.1725

DNA helicase unzips the double stranded DNA by breaking hydrogen bonds.1730

Remember, hydrogen bonds connect your A and T or C and G.1734

Helicase, specifically DNA helicase, goes in and breaks those bonds, unzips the DNA.1739

You will get something called a replication fork.1745

I will draw that for you on the next page.1747

After that unzipping happens and other enzymes got access to those exposed bases,1750

no longer connected to their complements, an RNA primer is laid down by something called RNA primase.1756

This is an enzyme that puts down a little bit of RNA.1761

That might seem weird because we are making a copy of DNA,1764

why do we got to down an RNA primer, we are not making RNA here.1768

It is because this enzyme, in the next step, DNA polymerase, what it knows how to do is attach nucleotides to nucleotides that are already there.1773

DNA polymerase is unable to just lay down nucleotides were there have not been any yet.1783

An RNA primer is put down so that DNA polymerase 3 has something to attach to.1789

And then later on, the RNA primer will be replaced with DNA by another enzyme.1796

That is why DNA polymerase cannot just lay them down on a bare space.1800

It got to have something to attach them to, that is the RNA primer there.1805

Step 3 is on the leading strand, I will tell you more about that in a second.1808

DNA polymerase 3 attaches complementary bases in a continuous manner to the primer.1812

Complementary bases to what was already there, you know that the original DNA,1819

if you see AAA and lay down TTT, if you see CCG it will lay down GGC, etc.1821

What is this leading strand thing?1829

The leading strand is the side of DNA where the DNA polymerase is going the same direction as helicase.1832

It is going right behind there in a continuous manner, you are going to see it, I will illustrate it on the next page.1840

You will see the lagging strand is on the other side.1846

Since, the strands are not that parallel, on the other side of DNA it is called the lagging strands, it is made in little pieces.1849

The DNA polymerase cannot continuously make it because it is going in the opposite direction.1858

Its helicase, I will illustrate it for you on the next page.1862

That lagging strand on the other side, DNA polymerase, same type of enzyme, can attach complementary bases and fragments known as okozaki fragment.1865

It is named after the Japanese scientists who have discovered that, in the opposite direction of helicase.1875

This will make more sense on the next age, I promise.1879

Number 5, once you have copied it all, you have made a continuous strand up there,1882

fragments on this side, the lagging side, DNA polymerase 1 replaces the RNA primers with DNA nucleotides.1888

Once DNA polymerase 3 has done its job, you can get rid of the RNA primer, put DNA there.1897

Finally, you got to connect the fragments together so that it is a continuous DNA polymer.1903

DNA ligase connects the fragments together on the lagging strand.1909

What it will also do is, in these different things called replication bubbles, 1912

you have thousands of these enzyme family, these enzyme units copying DNA.1918

Do not think that there is just one helicase unzipping all of your chromosomes, that would take forever.1925

Or there is just one DNA polymerase 3, there is a lot of them.1930

DNA ligase can also connect the very long leading strands to each other.1935

It is doing a lot more connecting on the lagging side.1940

Let us illustrate that on the next page.1943

Now that we have gone over the replication steps, the actual events of how DNA gets replicated,1946

I’m going to illustrate it for you.1951

This illustration is taking a very complicated process, I’m simplifying it for you.1954

As we go through, I will explain in detail what this all represents.1960

Here is a key up on top of what the different colors mean.1967

Just let you know what you are looking at here, this is just a part of DNA zoomed in 1970

on a specific replication fork, within a replication bubble.1982

What you are seeing here is, if we took the double helix and unwind it, so that it looks straight,1986

here it is like this, then there is these bubbles that exist.1995

These bubbles basically mean that there are multiple sites where replication is going to occur.2001

Like I suggested earlier, you do not want there to be one set of enzymes that replicate all of DNA to genome.2010

Because sitting there are three billion base pairs in the human genome,2017

having just one helicase and one DNA polymerase, it would take so long.2022

There is a lot of different sites where these enzymes are going to be working.2027

Here is one site, this DNA has not been separated yet, but this has.2032

There is one side, there is one side that has not been separated, here is one side of DNA, there is the other side, and so on.2038

These bubbles, these replication bubbles gradually get extended and they meet to the point where replication has occurred.2046

That has been double, the new DNA is in red.2057

As time goes on, you would see black and red, red and black, all connected.2061

This, what you are looking at here is zoomed in on this specific part or this part.2069

We are looking at an edge of the reparation bubble called the replication fork.2076

I’m going to make a sequence of DNA bases here that is random, I’m just going to pick A, G, C, and T.2081

It really does not matter, you just want to make sure that the amount you have here2094

equals the amount to the bottom, and that they are complementary,2098

because complementary bases will be put together for DNA to match.2101

Here we go.2106

You can follow long, and as I’m going through this, I will go slow.2149

As I go through, you will see TTA, GCG, see if you can name the complementary base that should go there, it is good practice.2152

There you go, if you go along, check to make sure that this original DNA has its proper complements.2193

It looks like it does, we are ready to go.2199

The first step to separate this would be helicase is going from left to right.2204

Your little black arrow is saying it is going that way.2216

These bases have yet to be unzipped, the hydrogen bonds that are connecting G and C, A and T, etc, is still intact.2218

You would see 3 between here, 2 between there, and so on.2226

Helicase is going this way, it unzips pretty fast but this is how far it is gotten so far.2231

Up on top, this is going to be the leading strand.2239

On bottom, this would be the lagging strand.2250

To actually get the leading strand to be synthesized in a continuous direction,2262

you first have to put an RNA primer down, and that RNA primase will be doing that.2268

Let us say that this primer was put down right here.2273

I’m going to have to draw a U there, this was not discussed extensively, not very much at all in this lesson.2278

Uracil takes the place of thymine, of the T in RNA.2286

Blue is our RNA primer, you will see more about that in the RNA lesson, about this uracil.2291

But, there you have your complements 2 DNA in RNA form.2297

This will replace with DNA bases, remember, DNA polymerase cannot just put down bases 2302

where there have not been any laid before hand.2308

DNA polymerase will add bases to this.2311

Let us say the DNA polymerase has gotten up to this point.2314

Here is DNA poly 3, it is going right my helicase.2318

Before we go any further, we got to mark the 3 prime 5 prime distinction.2325

On the leading strand, because the DNA polymerase is going from left to right, 2329

we know that this side has to be 3 prime and this has to be 5 prime.2333

Remember, DNA is always read by DNA polymerase in a 3 prime to 5 prime direction.2338

It is always made in a 5 prime to 3 prime direction.2344

On the edge of this, next to DNA polymerase, we are going to have a little red 3 prime.2349

Here is that new DNA being laid down by DNA polymerase.2356

You got a C, G, there you go.2362

It is going to continue to follow continuously right behind helicase.2377

Flash forward up, a fraction of a second later, helicase will be this much further.2380

DNA polymerase will continue its attachment of new nucleotides of DNA, to what is already been laid down.2387

On this side, the lagging strand, DNA polymerase is going the opposite direction as helicase.2397

Since, it has to go in this direction, it has to wait for helicase to get so far, before it can lay down another fragment.2403

Let us say that it already laid down a fragment right here.2410

Normally, the fragments would be longer but because this is a pre concise drawing, 2416

we will just say that this fragment is only 3 nucleotides long.2423

Here is what DNA polymerase has already laid down.2429

AT and T, these should match what is up here.2433

That is how you know that you are making an identical copy of your side of DNA.2439

Because we know DNA polymerase is going this direction on the lagging strand,2444

in the opposite of its helicase, here is the 5 prime, I compared it to the top, and here is the 3 prime.2448

DNA polymerase reads it from the 3 prime to the 5 prime direction always, that is why it has to go in this direction.2455

This is the previous Okazaki fragment, that term from before.2461

That is an okazaki fragment.2470

DNA polymerase is going to extend the DNA from another fragment.2472

Let us say that, we have a fragment right here that was put down.2478

Here is DNA polymerase going to the left.2489

Here is what we mean by making it in pieces, this is another okazaki fragment.2512

What DNA polymerase cannot do is, it cannot attach this fragment to that.2523

It will get all the way to this next nucleotide and then stop, dislodge and go over here,2528

and make another one as helicase move a little further.2533

It makes these little pieces.2536

Let us assume that this DNA polymerase did its job, it connected this all the way to here.2539

We should make that a T and this an A.2550

But, not connect, what first has to happen is DNA polymerase 1 will go and replace the RNA primer with new DNA.2555

This will be replaced, this will be replaced, and this will be replaced.2566

What a lovely DNA, there is that T again.2585

But, they will not be connected yet.2594

Let us assume that helicase is gone the whole route, but helicase is done with this whole replication bubble, 2603

before the replacement of the primers would actually occur.2609

There is the fragments, last step is DNA ligase, this purple thing here, this purple enzyme.2618

DNA ligase binds these two together.2627

Now, they are no longer fragments.2645

Now, it does the continuous like the top.2647

You just got to use your imagination, pretend that helicase got further, all way through here.2652

This leading strand got finished, by the end you will see that the whole top side would be black and red DNA,2658

the whole bottom side would be red and black.2665

In real life, in an actual living cell, when the new DNA is made, it is not actually colored in different colors.2668

The same molecule, this newly assembled vs. your previously assembled.2675

The way that scientist proved that semi conservative replication takes place like this is2680

they did for recently tagged nucleotides that were newly put together,2684

to show that this daughter cell got that part that is old and new.2690

This little daughter cell got the other half new and half old.2695

That is the illustration of DNA replication.2699

Finally, this lesson is a little bit about junk DNA.2704

Junk, makes it sound useless, it is not useless to us.2708

According to current DNA research, only 2%, let me emphasize this, only 2% of the human genome actually codes for protein.2712

That is crazy, look at this.2723

There are 3 billion base pairs, 6 billion nucleotides in the human genome.2726

2% ends up being something like 64 million, that is still a lot of bases that is coffer for protein.2730

What does the other 98% do, why is it there?2737

A lot of them tend to be in random sequences, that do not actually coffer protein, but can be useful to us.2740

They are the numerous regions, I wrote however because I do want you think that what is the point of it being there.2746

There are numerous regions that are promoters and operators, etc.2752

Meaning, regions that do not actually coffer protein sometimes promote the activity or enhance the activity,2755

or reduce the activity of transcription in various regions near there.2761

If you mess with them, you can actually throw off proper gene expression in a cell.2766

Some of it is that, but really, I think we just barely scrape or scratch the surface rather of what is going on with their DNA.2772

There is actually recent new story about a hidden code in DNA, that scientist did not know about until recently.2785

By recently, I mean 2013.2792

Even 50 years later, 60 years later, after DNA was kind of first discovered in terms of, here is this molecule,2795

here is what we know it does, we still are coming across some novel things, regarding this miraculous code.2803

What does this junk DNA mean to us, other than just being a bunch of random sequences, 2812

and promoters and operators, etc?2818

It is truly unique, meaning your junk DNA, my junk DNA, are completely different.2821

It is different from every other person that is ever lived, and ever will live, that exists now.2826

The reason it is very profound is because, think about trying to solve a crime.2831

If you got a piece of DNA from a crime scene, you know that whoever this DNA belongs to, they were here, they did is bad thing.2838

Would you want to compare the sequences for that DNA to the other sequences on people that code for hair, hair colored genes?2846

No, because there are millions or billions of people on earth with that same trait.2857

You do not want to compare those things.2863

You want compare the regions that are truly unique in that person's DNA.2864

Junk DNA has these random sequences and the reason why your sequence is a random, they came from your parents randomness.2868

The combination of your parent’s randomness equals your randomness.2877

No one else on earth has junk DNA sequences like yours.2881

You can use them to do what is called DNA fingerprinting.2885

When I write here that it can be used for forensic science, paternal test, etc., that is known as DNA fingerprinting.2889

It is like your DNA is a unique genetic fingerprint, it is a pretty good analogy because no one else on earth has your junk DNA.2900

But, plenty of people on earth have your DNA associated with metabolism or associated with how tall you are, or your eye color.2911

Those are the parts that you do not want to compare.2919

Forensic science like catching a criminal, comparing sequences in people around the world2921

to try to find interesting patterns of who came from who, and migration patterns,2928

very interesting in figuring out the history of our human genome.2934

Paternal tests, you do not want to compare the parts of your genome that have to do with hair, 2939

because that will not prove that someone is the father or mother, or not, because plenty of people have that same hair color.2946

But comparing the junk DNA is foolproof that someone is or is not the parent.2952

DNA technology uses these sequences, these junk DNA sequences.2959

Gel electrophoresis, I want to briefly explain.2963

There is a lot more on that in the genetics lesson, part 2, regarding genetic engineering.2966

But basically, what gel electrophoresis does, it takes these junk DNA segments, 2973

uses restriction enzymes which cut up DNA at very specific parts.2977

For instance, the restriction enzyme will target any spot where you see those 5 bases and their exact sequence.2984

It will cut the DNA right there.2991

In your junk DNA, the precise parts where you see that are very different2994

from the precise parts where you see those gene sequences in mine, or rather base sequences.2999

You will get DNA cut into different sizes, different lengths, based on the unique individual.3005

You can load those DNA sequences all cut up into these little wells.3011

This is what is called gel electrophoresis piece, this is a gel that you lay down with electrodes in a chamber.3017

This side is negative, this side is positively charged, you turn on the current.3023

Since DNA is negatively charged, the DNA migrates, you get different bonding patterns3027

based on how long or how small the DNA segments are.3033

I just drew 4 unique people, what I mean is, these sequences up here are very long, they actually drag in the gel as it got electricity pulls them, so it do not make it as far.3042

These sequences down here, very short DNA sequences that make this little pattern in the gel.3053

If two people are identical, if someone is identical to a sample, and they would actually have more patterns than this.3058

I will just give you a quick example.3071

But, you can see that 3 and well 4, it is the same individual.3073

It is like a 1 in 7 billion chance that this is going to be wrong because 3079

there is over 7 billion people on earth, 7 billion unique sets of junk DNA.3083

That is one application of using these, apparently, random sequences of DNA.3090

Apparently, use these genes for something that is very useful in our daily life.3095

Thank you for watching