Molecular structure of DNA

- [Voiceover] We already have an overview video of DNA

and I encourage you to watch that first.

What I want to do in this video is

dig a little bit deeper.

Actually get into the molecular structure of DNA.

This is a starting point.

Let's just remind ourselves what DNA stands for.

I'm gonna write the different parts of the word

in different colors.

It stands for deoxy.

Deoxyribonucleic.

Ribonucleic.

Ribonucleic acid.

Ribonucleic acid.

So I'm just gonna put this on the side

and now let's actually look at the molecular structure

and how it relates to this actual name,

deoxyribonucleic acid.

DNA is just a junction for nucleic acid

and it's the term nucleic that comes from the fact

that it's found in the nucleus.

It's found in the nucleus of eukaryotes.

That's where the nucleic comes from

and we'll talk about in a second

why it's called an acid but I'll wait on that.

Now each DNA molecule is made up of a chain

of what we call nucleotides.

What we call nucleotides.

It's made up of nucleo, nucleo,

nucleotides.

What does a nucleotide look like?

Well, what I have right over here

is I have two strands, I've zoomed two strands of DNA

or I've zoomed in two strands of DNA.

You could view this side right over here

as one of the, I guess you can say

the backbones of one side of the ladder.

This is the other side of the ladder

and then each of these bridges,

and I will talk about what molecules these are.

These are kind of the rungs of the ladder.

A nucleotide, let me separate off the nucleotide.

A nucleotide would...

What I am cordoning off,

what I am cordoning off right over here

could be considered,

could be considered a nucleotide.

That's one nucleotide

and then it's connected to another.

It's connected to another nucleotide.

Another nucleotide right over here.

On the right hand side we have a nucleotide,

we have a nucleotide right over there

and then, actually I want to do it,

let me do it slightly different.

We have a nucleotide right over here on the right side

and then right below that we have another.

We have another nucleotide.

We have another nucleotide.

Depicted here, we essentially have four nucleotides.

These two are on this left side of the ladder,

these two are on the right side of the ladder.

Now let's think about the

different pieces of that nucleotide.

The one thing that might jump out at you

is we have these phosphate groups.

This is a phosphate group right over here.

This is a phosphate group right over here.

Each of these nucleotides have a phosphate group.

This is a phosphate group over here

and this is a phosphate group over here.

Now the phosphate groups are actually what make DNA

or actually what make nucleic acid an acid.

You might say, wait, wait.

The way you've drawn it Sal,

you have a negative charge.

Something with a negative charge would attract protons,

it would sap up protons.

How can you call this an acid?

This actually looks more basic.

The reason why its DNA is typically drawn

with these negative charges here

is that it's so acidic and that if you put it in

into a neutral solution,

it's actually going to lose its hydrogens.

Actually the DNA if we actually want to be formal about it,

the DNA molecules would actually have

its phosphates protonated like this

but it so badly wants to lose these hydrogen protons

so it typically would be, let me draw it like this.

Let me get rid of the negative charge just on this one.

Whoops.

Just on this phosphate group over here.

If you get rid of the negative charge

and if this was bounded,

this is bonded to a hydrogen.

This so badly wants to grab these electrons.

These oxygen can grab these electrons

and then these hydrogen will just be grabbed

by another water molecule or something

so the proton will be let go.

That's why we call it an acid.

If it wasn't in a solution it would have the hydrogens

but it would be very acidic as soon as you put it into

a neutral solution it's going to lose those hydrogens.

The phosphate groups are what make it,

are what make it an acid

but it's confusing sometimes

because usually when you see it depicted,

you see it with these negative charges

and that's because it has already lost its hydrogen proton.

You're actually depicting the conjugate base here

but that's where it gets its acidic name from

because it starts protonated

or it gets in this acid form, it's protonated

but it readily loses it.

And so that's why it has its,

that's where it gets the name acid form from.

Each of these nucleotides they have a phosphate group.

Now the next thing you might notice,

the next thing you might notice is.

The next thing you might notice is

this group right over here.

It is a cycle, it is a ring

and it looks an awful lot like a sugar

and that's because it is a sugar.

This sugar is based on, it's a five-carbon sugar.

What I have depicted here, this sugar, this is ribose.

This sugar right over here is ribose.

This is when it's just as a straight chain

and like many sugars, it can take a cyclical form.

Actually it can take many different cyclical forms

but the one that's most typically described

is when you have that.

Let me number the carbons

because carbon numbering is important

when we talk about DNA.

But if we start carbonyl group right over here

we call that the one carbon or the one prime carbon.

One prime, two prime, three prime,

four prime and five prime.

That's the five prime carbon.

You form the cyclical form of ribose

as if you have the oxygen.

You have the oxygen right over here

on the four prime carbon.

It uses one of its lone pairs.

It uses one of its lone pairs

to form a bond.

To form a bond with the one prime.

With the one prime carbon

and I drew it that way

because it kind of does bend.

The whole molecule's going to have to bend that way

to form this structure.

And then when it forms that bond

the carbon can let go of one of these double bonds

and then that can, then the oxygen,

the oxygen can use that.

The oxygen can use those electrons

to go grab a hydrogen proton from some place.

To nab on to a hydrogen proton.

When it does that you're in this form

and this form, just to be clear of what we're talking about,

this is the one prime carbon.

One prime, two prime, three prime,

four prime and five prime carbon.

Where we see this bond,

this is the one prime carbon.

it was part of a carbonyl.

Now it lets go of one of those double bonds

so that this oxygen can form a bond

with a hydrogen proton.

It let go of a double bond there

so that this could form a bond with a hydrogen proton.

This hydrogen proton is

that hydrogen proton right over there

and this green bond that gets formed

between the four prime carbon and

or between the oxygen that's attached

to the four prime carbon and the one prime carbon,

that's this.

That's this bond right over here.

This oxygen is that oxygen right there.

Notice, this oxygen is bound to the four prime carbon

and now it's also bound to the one prime carbon.

It was also attached to a hydrogen.

It was also attached to a hydrogen

so that hydrogen is there

but then that can get nabbed up by another

passing water molecule to become hydronium

so it can get lost.

It grabs up a hydrogen proton right over here

and so it can lose a hydrogen proton right there.

It's not adding or losing in that net.

You form this cyclical form

and the cyclical form right over here

is very close to what we see in a DNA molecule.

It's actually what we would see in an RNA molecule,

in a ribonucleic acid.

And so what do we think we're talking about

when we say deoxyribonucleic acid.

Well, you can start with you have a ribose here

but if we got rid of one of the oxygen groups

and in particular one of...

Well, actually if we just got rid of one of the oxygens

we replace a hydroxyl with just a hydrogen,

well then you're gonna have deoxyribose

and you see that over here.

This five-member ring,

you have four carbons right over here.

it looks just like this.

The hydrogens are implicit to the carbons,

we've seen this multiple time.

The carbons are at where these lines intersect

or I guess at the edges or maybe

and also where these lines end right over there.

But you see this does not have an...

This molecule if we compare these two molecules,

if we compare these two molecules over here,

we see that this guy has an OH,

and this guy implicitly just has...

This has an OH and an H.

This guy implicitly has just two hydrogens over here.

He's missing an oxygen.

This is deoxyribose.

Deoxyribose.

Deoxyribose doesn't have this oxygen.

It does not have the oxygen

on the two prime carbon.

So this if you get rid of that, this is deoxyribose.

So let me circle that.

This thing right over here,

this thing right over here, that is deoxyribose.

Deoxy or it's based on deoxyribose

I guess before it bonded to these other constituents.

You could consider this deoxyribose.

That's where the deoxyribo comes from

and then the last piece of it,

the last piece of it is this chunk right over here.

These we call nitrogenous bases.

Nitrogenous.

Nitrogenous.

Nitrogenous bases.

You could see we have different types of nitrogenous bases.

This is a nitrogenous base.

This right over here is a different nitrogenous base.

This right over here is another different nitrogenous base.

Notice, this one only has one ring, this one has one ring,

this one has two rings.

This one over here has two rings

and we have different names

for these nitrogenous bases.

The ones with two rings, the general categorization

we call them purines.

Nitrogenous bases if you have two rings,

if you have two rings we call them purines.

That's a general classification term.

Let me make sure, purines.

If you have one ring.

Anyway, I'll just write this way.

One ring.

One ring, we call these pyrimidines.

Pyrimidine.

Pyrimidines.

We call these pyrimidines.

These particular, these two on the right,

these two purines,

this one up here this is adenine,

and we talk about how they pair

in the overview video on DNA.

This one right over here is adenine,

this nitrogenous base.

This one over here is guanine.

That is guanine.

And then over here, over here,

this single ring nitrogenous base

which makes it a pyrimidine, this is thymine.

This right over here is thymine.

This is thymine and then last but not least

if we're talking about DNA,

when we go into RNA, we're also gonna talk about uracil.

But when we talk about DNA

this one over here is cytosine.

Cytosine.

You could see the way it's structured.

The thymine is attracted to adenine.

It bonds with adenine

and cytosine bonds with guanine.

How are they bonding?

Well, the way that these nitrogenous bases

form the rungs of the ladder,

how they want they're drawn to each other,

this is our good old friend hydrogen bonds.

This all comes out of the fact,

that nitrogen is quite electronegative.

When nitrogen is bound to a hydrogen

you're going to have a partially

negative charge at the nitrogen.

Let me do this in green.

You're going to have a partial

negative charge at the nitrogen

and a partially positive charge at the hydrogen.

And then oxygen we've always talked about

as being electronegative

so it has a partial negative charge.

The partial negative charge of this oxygen

is going to be attracted to the partial

positive charge of this hydrogen,

and so you're going to have a hydrogen bond.

That's then going to happen between this hydrogen

which is going...

Its electrons are being hogged by this nitrogen

and this nitrogen with who,

which itself hogs electrons.

That forms a hydrogen bond.

And then down here you have a hydrogen

that has a partially positive charge

because its electrons are being hogged.

And then you have this oxygen

with a partially negative charge,

they're going to be attracted to each other.

That's a hydrogen bond.

Same thing between this nitrogen and that hydrogen,

and same thing between this oxygen and that hydrogen.

That's why cytosine and guanine pair up

and that's why thymine and adenine pair up,

and we talk about that as well

in the overview video of DNA.