Introduction to transformations

WEBVTT
Kind: captions
Language: en

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- [Voiceover] What I hope to
introduce you to in this video

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is the notion of a
transformation in mathematics,

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and you're probably used to
the word in everyday language.

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Transformation means
something is changing,

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it's transforming from
one thing to another.

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What would transformation mean
in a mathematical context?

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Well, it could mean that
you're taking something

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mathematical and you're changing it into

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something else mathematical,
that's exactly what it is.

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It's talking about taking

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a set of coordinates or a set of points,

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and then changing them
into a different set

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of coordinates or a
different set of points.

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For example, this right over here,

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this is a quadrilateral we've plotted

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it on the coordinate plane.

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This is a set of points,
not just the four points

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that represent the vertices
of the quadrilateral,

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but all the points along the sides too.

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There's a bunch of points along this.

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You could argue there's an infinite,

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or there are an infinite number

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of points along this quadrilateral.

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This right over here, the point X

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equals 0, y equals negative four,

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this is a point on the quadrilateral.

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Now, we can apply a
transformation to this,

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and the first one I'm going
to show you is a translation,

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which just means moving all the points

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in the same direction,

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and the same amount in
that same direction,

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and I'm using the Khan Academy
translation widget to do it.

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Let's translate, let's translate this,

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and I can do it by grabbing
onto one of the vertices,

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and notice I've now shifted
it to the right by two.

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Every point here, not
just the orange points

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has shifted to the right by two.

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This one has shifted to the right by two,

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this point right over here has
shifted to the right by two,

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every point has shifted
in the same direction

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by the same amount, that's
what a translation is.

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Now, I've shifted, let's see
if I put it here every point

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has shifted to the right one and up one,

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they've all shifted by the same amount

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in the same directions.

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That is a translation,
but you could imagine

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a translation is not the
only kind of transformation.

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In fact, there is an unlimited variation,

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there's an unlimited number
different transformations.

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So, for example, I could do a rotation.

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I have another set of points here

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that's represented by quadrilateral,

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I guess we could call it CD or
BCDE, and I could rotate it,

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and I rotate it I would
rotate it around the point.

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So for example, I could
rotate it around the point D,

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so this is what I started with,

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if I, let me see if I can do this,

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I could rotate it like,
actually let me see.

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So if I start like this I
could rotate it 90 degrees,

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I could rotate 90 degrees,
so I could rotate it,

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I could rotate it like, that looks

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pretty close to a 90-degree rotation.

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So, every point that was on the original

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or in the original set of
points I've now shifted it

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relative to that point
that I'm rotating around.

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I've now rotated it 90 degrees,

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so this point has now mapped
to this point over here.

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This point has now mapped
to this point over here,

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and I'm just picking the
vertices because those

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are a little bit easier to think about.

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This point has mapped to this point.

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The point of rotation, actually,

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since D is actually the point of rotation

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that one actually has not shifted,

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and just 'til you get some terminology,

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the set of points after you
apply the transformation

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this is called the image
of the transformation.

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So, I had quadrilateral BCDE,

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I applied a 90-degree counterclockwise

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rotation around the point D,

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and so this new set of
points this is the image

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of our original quadrilateral
after the transformation.

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I don't have to just, let me undo this,

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I don't have to rotate
around just one of the points

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that are on the original set
that are on our quadrilateral,

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I could rotate around, I could
rotate around the origin.

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I could do something like that.

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Notice it's a different rotation now.

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It's a different rotation.

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I could rotate around any point.

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Now let's look at another transformation,

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and that would be the
notion of a reflection,

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and you know what reflection
means in everyday life.

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You imagine the reflection of

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an image in a mirror or on the water,

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and that's exactly what
we're going to do over here.

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If we reflect, we reflect across
a line, so let me do that.

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This, what is this one,
two, three, four, five,

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this not-irregular
pentagon, let's reflect it.

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To reflect it, let me actually,

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let me actually make a line like this.

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I could reflect it across
a whole series of lines.

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Woops, let me see if I can, so
let's reflect it across this.

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Now, what does it mean to
reflect across something?

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One way I imagine is if this was,

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we're going to get its mirror image,

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and you imagine this
as the line of symmetry

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that the image and the
original shape they should

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be mirror images across
this line we could see that.

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Let's do the reflection.

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There you go, and you see
we have a mirror image.

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This is this far away from the line.

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This, its corresponding point in the image

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is on the other side of the
line but the same distance.

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This point over here is
this distance from the line,

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and this point over here
is the same distance

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but on the other side.

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Now, all of the transformations
that I've just showed you,

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the translation, the
reflection, the rotation,

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these are called rigid transformations.

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Once again you could just think about

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what does rigid mean in everyday life?

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It means something that's not flexible.

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It means something that you can't stretch

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or scale up or scale down it
kind of maintains its shape,

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and that's what rigid transformations

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are fundamentally about.

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If you want to think a little
bit more mathematically,

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a rigid transformation is one in which

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lengths and angles are preserved.

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You can see in this
transformation right over here

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the distance between this
point and this point,

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between points T and R,

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and the difference between
their corresponding

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image points, that distance is the same.

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The angle here, angle R, T, Y,

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the measure of this angle over here,

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if you look at the
corresponding angle in the image

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it's going to be the same angle.

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The same thing is true if
you're doing a translation.

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You could imagine these are
acting like rigid objects.

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You can't stretch them,
they're not flexible

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they're maintaining their shape.

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Now what would be examples
of transformations

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that are not rigid transformations?

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Well you could imagine
scaling things up and down.

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If I were to scale this out where it has

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maybe the angles are preserved,

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but the lengths aren't preserved

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that would not be a rigid transformation.

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If I were to just stretch one side of it,

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or if I were to just pull
this point while the other

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points stayed where they
are I'd be distorting it

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or stretching it that would
not be a rigid transformation.

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So hopefully this gets you,

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it's actually very, very interesting.

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When you use an art program,

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or actually you use a
lot of computer graphics,

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or you play a video game, most of what

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the video game is doing is
actually doing transformations.

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Sometimes in two dimensions,
sometimes in three dimensions,

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and once you get into more advanced math,

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especially things like linear
algebra, there's a whole field

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that's really focused
around transformations.

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In fact, some of the computers

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with really good graphics processors,

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a graphics processor is
just a piece of hardware

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that is really good at performing

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mathematical transformations,

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so that you can immerse yourself

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in a 3D reality or whatever else.

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This is really really interesting stuff.


Drawing line segments example

WEBVTT
Kind: captions
Language: en

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Any pair of points can be
connected by a line segment.

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That's right.

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Connect two pairs
of black points

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in a way that creates two
parallel line segments.

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So let's see if we can do that.

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So I could create
one segment that

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connects this
point to this point

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and then another
one that connects

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this point to this point.

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And they look pretty parallel.

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In fact, I think this
is the right answer.

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If we did it another way, if
we had connected that point

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to that point and this
point to this point,

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then it wouldn't
look so parallel.

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These clearly, if they
were to keep going,

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they would intersect
at some point.

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So let me set it back up the
way I did it the first time.

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Let me make these
two points parallel.

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And these are line
segments because they

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have two end points.

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They each have two end points.

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And they continue forever.

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Well they don't
continue forever.

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They continue forever in no
directions, in zero directions.

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If it was a ray, it
would continue forever

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in one direction.

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If it's a line, it
continues forever

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past both of these points.

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In fact, it wouldn't
have end points

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because it would
just continue forever

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in both of these directions.

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Let's do one more.

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Drag the ray so it
has an endpoint at A,

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so we want to make its endpoint
at A where the ray terminates

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and goes through one of
the other black points.

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The ray should also be
parallel to the pink line.

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So I have two options.

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I could make it go
through this black point,

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but it's clearly not parallel.

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In fact, it looks
perpendicular here.

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So let's try to make it
go through this point.

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Well, yes, when I do that, it
does indeed look like my ray

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is parallel to the pink line.

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And this is a ray because
it has one endpoint.

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This is where the
ray terminates.

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It's an endpoint.

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It literally ends there.

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And it continues forever
in one direction.

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In this case, the
direction is to the right.

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It continues forever
to the right.

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So it continues forever
in one-- continues forever

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in one direction.


Molecular structure of RNA

WEBVTT
Kind: captions
Language: en

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- [Voiceover] We've already payed a lot of attention

00:00:01.640 --> 00:00:03.448
to the molecular structure of DNA.

00:00:03.448 --> 00:00:06.435
In fact right depicted in front of us, we have two strands

00:00:06.435 --> 00:00:09.280
of DNA forming a double helix,

00:00:09.280 --> 00:00:12.733
and we can look at the telltale signs that this is DNA.

00:00:12.733 --> 00:00:15.619
In particular, we can look at the five-carbon sugar

00:00:15.619 --> 00:00:17.081
on it's backbone.

00:00:17.081 --> 00:00:19.174
We see, and let's actually number the carbons.

00:00:19.174 --> 00:00:24.102
This is 1', 2', 3', 4', 5'.

00:00:24.902 --> 00:00:27.057
We can see on the 2' carbon

00:00:27.057 --> 00:00:29.028
we don't have an oxygen attached to it.

00:00:29.028 --> 00:00:31.080
We don't have a hydroxyl group attached to it,

00:00:31.080 --> 00:00:33.761
and because of that, we know that this is not ribose.

00:00:33.761 --> 00:00:37.906
This is deoxyribose. This right over here is deoxyribose.

00:00:37.906 --> 00:00:40.141
And these two are also deoxyribose,

00:00:40.141 --> 00:00:42.294
so that tells us that we have two strands

00:00:42.294 --> 00:00:46.037
of DNA, deoxyribonucleic acid.

00:00:46.037 --> 00:00:47.577
So let me write this down.

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This part of the chain,

00:00:49.746 --> 00:00:53.245
this is derived from a deoxyribose being attached

00:00:53.245 --> 00:00:56.281
to phosphate groups and a nitrogenous base.

00:00:56.281 --> 00:01:01.011
So deoxyribose.

00:01:02.811 --> 00:01:04.722
So, what would we have to do if we wanted,

00:01:04.722 --> 00:01:06.225
instead of viewing this

00:01:06.225 --> 00:01:10.105
as two strands of DNA in a double helix formation,

00:01:10.105 --> 00:01:14.068
how would we have to edit the left hand strand,

00:01:14.068 --> 00:01:15.591
if instead we wanted to imagine

00:01:15.591 --> 00:01:18.029
that the left hand strand is a messenger RNA

00:01:18.029 --> 00:01:21.341
being generated during transcription

00:01:21.341 --> 00:01:24.429
with a single strand of DNA here on the right?

00:01:24.429 --> 00:01:28.758
Well, to turn this into RNA, or to make it look like RNA,

00:01:28.758 --> 00:01:32.637
on the 2' carbon, well, we want to turn the deoxyribose

00:01:32.637 --> 00:01:35.360
into just ribose, so we would want to add

00:01:37.280 --> 00:01:40.236
a hydroxyl group right over here.

00:01:40.236 --> 00:01:42.257
So I add a hydroxyl group over there,

00:01:42.257 --> 00:01:45.787
actually do the hydrogens in white.

00:01:45.787 --> 00:01:48.377
So add one hydroxyl group there,

00:01:48.377 --> 00:01:49.724
and I want to do on all the sugars

00:01:49.724 --> 00:01:51.660
on the left strand's backbone

00:01:51.660 --> 00:01:55.012
if I want this to be a single strand of RNA,

00:01:55.012 --> 00:01:57.270
and RNA tends to be single stranded.

00:01:57.270 --> 00:02:01.854
So oxygen, and then a hydrogen.

00:02:01.854 --> 00:02:05.639
So adding this hydroxyl group instead of

00:02:05.639 --> 00:02:09.473
just having another hydrogen,

00:02:09.473 --> 00:02:12.456
this tells us that this sugar is no long deoxyribose.

00:02:12.456 --> 00:02:13.766
This is ribose.

00:02:13.766 --> 00:02:18.906
So we now have ribose in our backbone,

00:02:19.216 --> 00:02:21.240
which is a telltale sign that

00:02:21.240 --> 00:02:25.122
at least now we have the backbone of RNA, ribonucleic acid,

00:02:25.122 --> 00:02:28.678
versus DNA, deoxyribonucleic acid.

00:02:28.678 --> 00:02:31.989
Now, you might think we're done, but we're not quite done,

00:02:31.989 --> 00:02:35.667
because the nitrogenous bases on RNA are slightly different

00:02:35.667 --> 00:02:38.755
than the nitrogenous bases on DNA.

00:02:38.755 --> 00:02:43.536
On DNA, your nitrogenous bases are

00:02:43.536 --> 00:02:48.316
Adenine, Guanine.

00:02:48.316 --> 00:02:52.800
Adenine and Guanine are the two ringed nitrogenous bases.

00:02:52.800 --> 00:02:54.664
Right over here, this is Adenine.

00:02:54.664 --> 00:02:56.288
This is Guanine.

00:02:56.288 --> 00:03:01.116
And you also have Cytosine

00:03:01.116 --> 00:03:06.056
I'm gonna do these all in different colors.

00:03:06.056 --> 00:03:11.066
Cytosine and Thymine.

00:03:11.066 --> 00:03:12.956
And this right over is Cytosine,

00:03:12.956 --> 00:03:14.596
and this is Thymine,

00:03:14.596 --> 00:03:18.251
Cytosine and Thymine are single ringed nitrogenous bases.

00:03:18.251 --> 00:03:19.649
We called them pyrimidines.

00:03:19.649 --> 00:03:21.584
Adenine and Guanine, we call them purines.

00:03:21.584 --> 00:03:24.044
This is a little bit of a review.

00:03:24.464 --> 00:03:29.248
In RNA, you still have Adenine.

00:03:29.258 --> 00:03:32.903
You still have Guanine.

00:03:32.903 --> 00:03:36.008
You still have Cytosine,

00:03:36.008 --> 00:03:40.885
but instead of Thymine, you have a very close relative,

00:03:40.885 --> 00:03:44.420
and that is Uracil.

00:03:44.420 --> 00:03:46.471
So the way that this is drawn right now,

00:03:46.471 --> 00:03:49.906
this nitrogenous base, remember when we started this video,

00:03:49.906 --> 00:03:52.658
it was double stranded DNA,

00:03:52.658 --> 00:03:55.519
this nitrogenous base right over here is Thymine,

00:03:55.519 --> 00:03:59.352
and it forms hydrogen bonds with Adenine right over here.

00:03:59.352 --> 00:04:01.242
If I want to turn it to Uracil,

00:04:01.242 --> 00:04:06.203
I just have to get rid of this methyl group right over here,

00:04:06.203 --> 00:04:11.149
so if I just do this and replace it with a Hydrogen,

00:04:11.149 --> 00:04:13.608
that is just implicitly bonded there,

00:04:13.608 --> 00:04:17.467
well, now I'm dealing with Uracil.

00:04:17.467 --> 00:04:21.999
So you see that Uracil and Thymine are very close molecules

00:04:21.999 --> 00:04:24.762
or very similar nitrogenous bases,

00:04:24.762 --> 00:04:27.688
and that's why they can play a very similar role.

00:04:27.688 --> 00:04:32.442
And it's still the case, what Uracil pairs with,

00:04:32.442 --> 00:04:35.590
it pairs with Adenine, the same thing Thymine pairs with.

00:04:35.590 --> 00:04:38.375
And everything else is, of course, still the same.

00:04:38.375 --> 00:04:43.657
An interesting question is why Uracil? Why not Thymine?

00:04:43.657 --> 00:04:46.258
Or you can say why Thymine? Why not Uracil?

00:04:46.258 --> 00:04:49.508
And based on what I've read, it actually turns out

00:04:49.508 --> 00:04:53.247
that Uracil is a little bit more error prone.

00:04:53.247 --> 00:04:55.543
It might be able to bond with other things.

00:04:55.543 --> 00:05:00.422
When you're coating, it's a little less stable than Thymine.

00:05:00.422 --> 00:05:06.801
So Uracil makes the RNA molecule,

00:05:06.801 --> 00:05:10.235
or actually makes the machinery of information transfer,

00:05:10.235 --> 00:05:12.307
it makes it less stable.

00:05:12.307 --> 00:05:16.878
It's a less stable way to transfer information.

00:05:16.878 --> 00:05:21.328
Based on what I've read, in evolutionary history,

00:05:21.328 --> 00:05:25.249
RNA molecules, most people believe, predate DNA molecules.

00:05:25.249 --> 00:05:28.703
So in the early stages, you had a lot of change,

00:05:28.703 --> 00:05:30.566
and so Uracil molecules were just fine,

00:05:30.566 --> 00:05:33.465
and there was a lot of errors and whatever else.

00:05:33.465 --> 00:05:36.464
But then information needed to be a little more persistent

00:05:36.464 --> 00:05:38.475
and a little less error prone, well then,

00:05:38.475 --> 00:05:42.681
Thymine helped stabilize things.

00:05:42.681 --> 00:05:45.769
There's also the view, "why has Uracil stuck around?"

00:05:45.769 --> 00:05:48.998
Well, RNA molecules, they have all of these roles in cells.

00:05:48.998 --> 00:05:51.682
Messenger RNA molecules are taking information

00:05:51.682 --> 00:05:54.018
from the DNA and getting it transcribed

00:05:54.018 --> 00:05:58.061
or getting it translated at the ribosome.

00:05:58.061 --> 00:05:59.685
But they shouldn't hang out forever.

00:05:59.685 --> 00:06:02.003
You actually want them to be somewhat unstable.

00:06:02.003 --> 00:06:04.055
So it's an interesting question to think about.

00:06:04.055 --> 00:06:06.391
Why do we have Uracil instead of Thymine,

00:06:06.391 --> 00:06:08.362
or why do we have Thymine instead of Uracil?

00:06:08.362 --> 00:06:10.739
But this is one of the telltale signs of,

00:06:10.739 --> 00:06:14.396
that we are now dealing with an RNA molecule.

00:06:14.396 --> 00:06:17.088
So now what we have on the left hand side,

00:06:17.088 --> 00:06:18.858
Now, all of this business,

00:06:18.858 --> 00:06:20.948
actually let me do this in a different color.

00:06:20.948 --> 00:06:25.193
all of this business, this strand right over here,

00:06:25.193 --> 00:06:27.605
we can now, the way it's drawn,

00:06:27.605 --> 00:06:29.511
we can now consider this an RNA molecule,

00:06:29.511 --> 00:06:33.088
and if we assume that this is happening during transcription

00:06:33.088 --> 00:06:35.751
where a single strand of DNA would want

00:06:35.751 --> 00:06:37.597
to replicate it's information,

00:06:37.597 --> 00:06:42.337
then this over here would be mRNA, messenger RNA,

00:06:42.337 --> 00:06:44.323
and so what's going on here?

00:06:44.323 --> 00:06:45.603
Well, let's think about it.

00:06:45.603 --> 00:06:50.787
The messenger RNA, the way it's oriented,

00:06:51.637 --> 00:06:54.358
if we go, we have phosphate group,

00:06:54.358 --> 00:06:57.716
then we go to 5' carbon, 4', 3', then phosphate group,

00:06:57.716 --> 00:07:00.373
then 5', 4', 3', then phosphate group,

00:07:00.373 --> 00:07:05.046
so this is oriented 5' on top, 3' on the bottom,

00:07:05.046 --> 00:07:07.742
while these DNA molecules are oriented the other way.

00:07:07.742 --> 00:07:10.227
This is a 5' carbon. This is a 3' carbon,

00:07:10.227 --> 00:07:12.929
so we have phosphate, 3', 5', phosphate,

00:07:12.929 --> 00:07:17.865
so we have 3' is on top, and 5' is on the bottom.

00:07:17.865 --> 00:07:21.097
So if we wanted to think about what's happening,

00:07:21.097 --> 00:07:23.555
maybe using the symbols for the nitrogenous bases,

00:07:23.555 --> 00:07:28.167
we could say, all right we have our mRNA molecule here,

00:07:28.167 --> 00:07:33.470
and this is it's 5' end, and this is it's 3' end,

00:07:33.470 --> 00:07:38.569
and then the top nitrogenous base over here, this is Uracil.

00:07:41.889 --> 00:07:47.123
And then the second one over here, this is Cytosine.

00:07:47.123 --> 00:07:50.475
This is Cytosine.

00:07:50.475 --> 00:07:56.449
This is Cytosine over here, and this is being transcribed

00:07:56.449 --> 00:08:00.471
from this DNA molecule on the right hand side,

00:08:00.471 --> 00:08:04.595
so this is DNA, and this DNA has an antiparallel orientation

00:08:04.595 --> 00:08:06.546
It's parallel, but it's kinda flipped over.

00:08:06.546 --> 00:08:10.914
The sugars are pointed in a different direction,

00:08:10.914 --> 00:08:13.879
so this is going from the 3' end.

00:08:13.879 --> 00:08:16.064
This is the 5' end.

00:08:16.064 --> 00:08:20.158
And we see that the Uracil is hydrogen bonded to Adenine.

00:08:20.158 --> 00:08:24.996
That is Adenine

00:08:26.106 --> 00:08:29.987
And I'll draw dotted lines to show the hydrogen bonds.

00:08:29.987 --> 00:08:34.578
And that the Cytosine is hydrogen bonded to Guanine.

00:08:34.578 --> 00:08:38.690
So this right over here, that is Guanine.

00:08:38.690 --> 00:08:42.310
Actually I'll do the hydrogen bonds in white.

00:08:42.310 --> 00:08:45.427
Actually there's multiple hydrogen bonds going on here,

00:08:45.427 --> 00:08:49.532
but just to be clear, this is mRNA,

00:08:49.532 --> 00:08:52.197
and on the right, we have DNA.

00:08:52.197 --> 00:08:56.615
This could be happening during transcription.

00:09:03.140 --> 00:09:05.387
Now, what are the types of RNAs out there?

00:09:05.387 --> 00:09:07.093
We've talked about this in other videos.

00:09:07.093 --> 00:09:09.983
Well, you have messenger RNA, which has an important role

00:09:09.983 --> 00:09:11.989
in taking information from DNA

00:09:11.989 --> 00:09:13.915
and getting it eventually translated

00:09:13.915 --> 00:09:16.460
with the help of tRNAs in ribosomes,

00:09:16.460 --> 00:09:19.385
and though I've just mentioned another type of RNA,

00:09:19.385 --> 00:09:24.757
and that's transfer RNA, so transfer RNA, tRNA.

00:09:28.407 --> 00:09:31.962
And in the overview video on transcription and translation,

00:09:31.962 --> 00:09:33.770
we talk about how tRNA does this,

00:09:33.770 --> 00:09:39.032
but it has amino acids attached on one end,

00:09:39.032 --> 00:09:41.916
and then it has anticodons on the other end

00:09:41.916 --> 00:09:48.748
that essentially pair with codons on the mRNA,

00:09:48.748 --> 00:09:51.202
and, then, thus allows it to construct proteins.

00:09:51.202 --> 00:09:56.056
And actually, this right over here is a visualization

00:09:56.056 --> 00:10:01.380
of a tRNA molecule.

00:10:01.380 --> 00:10:04.814
So a lot of times when we think about DNA,

00:10:04.814 --> 00:10:08.329
we think about, okay, mRNA or RNA is an intermediary

00:10:08.329 --> 00:10:10.991
to be able to eventually translate it into proteins,

00:10:10.991 --> 00:10:13.286
and that is often the case, but sometimes,

00:10:13.286 --> 00:10:15.643
you also just want the RNA itself.

00:10:15.643 --> 00:10:18.508
The RNA itself plays a role in the cell

00:10:18.508 --> 00:10:20.702
beyond just transmitting information,

00:10:20.702 --> 00:10:22.856
and that's an example here with tRNA.

00:10:22.856 --> 00:10:25.049
And you can see it's an interesting configuration,

00:10:25.049 --> 00:10:28.565
where the amino acid will attach roughly in that area,

00:10:28.565 --> 00:10:32.222
and then you see the anticodon

00:10:32.222 --> 00:10:34.618
right down here in the bottom right,

00:10:34.618 --> 00:10:37.240
and different tRNA molecules will attach

00:10:37.240 --> 00:10:38.990
to different amino acids,

00:10:38.990 --> 00:10:41.161
and they'll have different anticodons here.

00:10:41.161 --> 00:10:43.559
So this is another use for RNA,

00:10:43.559 --> 00:10:47.642
and then others include ribosomal RNA,

00:10:49.952 --> 00:10:53.128
and they actually play a structural role in ribosomes,

00:10:53.128 --> 00:10:56.033
which is where translation occurs.

00:10:56.033 --> 00:10:59.122
And you also have things called microRNA,

00:11:00.142 --> 00:11:03.390
which are short chains of RNA,

00:11:03.390 --> 00:11:06.923
which could be used to regulate the translation

00:11:06.923 --> 00:11:09.260
of other RNA molecules.

00:11:09.260 --> 00:11:11.776
So DNA gets a lot of the attention,

00:11:11.776 --> 00:11:14.115
but RNA is really, really, really important,

00:11:14.115 --> 00:11:16.147
and a lot of people believe that RNA came first,

00:11:16.147 --> 00:11:18.484
and there's potential that the first life

00:11:18.484 --> 00:11:22.242
or pseudo-life ever was just self-replicating RNA molecules,

00:11:22.242 --> 00:11:25.573
and that DNA eventually evolved from RNA,

00:11:25.573 --> 00:11:29.075
but RNA stuck around, because it's still very useful.


Antiparallel structure of DNA strands

WEBVTT
Kind: captions
Language: en

00:00:00.460 --> 00:00:03.570
- [Voiceover] In the video on the molecular structure of DNA

00:00:03.570 --> 00:00:08.229
we saw that DNA is typically made up of two strands

00:00:08.229 --> 00:00:11.030
where the backbone of each of the strands

00:00:11.030 --> 00:00:15.010
is made up of phosphate alternating between a--

00:00:15.010 --> 00:00:16.390
Do some different colors.

00:00:16.390 --> 00:00:21.110
A phosphate group and then you have a sugar.

00:00:21.110 --> 00:00:24.880
You have a phosphate group.

00:00:24.880 --> 00:00:27.660
And then you have a sugar.

00:00:29.960 --> 00:00:32.160
And then you have a phosphate group.

00:00:32.160 --> 00:00:34.470
And then you have a sugar.

00:00:34.470 --> 00:00:37.130
And so I could draw the strand something like this.

00:00:37.130 --> 00:00:41.320
So phosphate and then we have a sugar.

00:00:41.320 --> 00:00:43.850
Oops, let me just draw all the phosphates ahead of time.

00:00:43.850 --> 00:00:45.710
So you have the phosphates on that end

00:00:45.710 --> 00:00:48.950
and then you have the sugars.

00:00:48.950 --> 00:00:52.160
And you see the same thing on the other strand as well.

00:00:52.160 --> 00:00:53.660
Where we have

00:00:55.100 --> 00:00:57.129
phosphate with a sugar

00:00:57.129 --> 00:00:59.120
then another phosphate then a sugar

00:00:59.120 --> 00:01:00.850
then another phosphate.

00:01:00.850 --> 00:01:02.860
Let me circle the sugars as well.

00:01:02.860 --> 00:01:04.360
So we have a sugar there

00:01:04.360 --> 00:01:07.630
and then you have the sugar there as well.

00:01:07.630 --> 00:01:09.850
So on the other strand it's also going to look like this.

00:01:09.850 --> 00:01:11.420
So let me draw the phosphates.

00:01:11.420 --> 00:01:13.560
I'm just abstracting them now.

00:01:13.560 --> 00:01:16.750
So the phosphate and then you have the sugars

00:01:16.750 --> 00:01:18.660
in between the phosphates.

00:01:18.660 --> 00:01:20.320
And what links them, you can think of them

00:01:20.320 --> 00:01:22.000
as the rungs on the ladder.

00:01:22.000 --> 00:01:25.762
These are the complementary nitrogenous bases.

00:01:25.762 --> 00:01:27.730
And the reason why we call them nitrogenous bases,

00:01:27.730 --> 00:01:29.600
I actually forgot to talk about it in the last videos,

00:01:29.600 --> 00:01:32.000
is that these nitrogens are really electronegative

00:01:32.000 --> 00:01:34.990
and they can take up more hydrogen protons.

00:01:34.990 --> 00:01:37.100
They have an extra lone pair.

00:01:37.100 --> 00:01:39.200
The nitrogens have an extra lone pair

00:01:39.200 --> 00:01:41.830
that can be used up under the right conditions

00:01:41.830 --> 00:01:44.690
to potentially sop up more hydrogen protons.

00:01:44.690 --> 00:01:45.590
Now, a lot of people ask,

00:01:45.590 --> 00:01:48.060
"Well, if you have these nitrogenous bases here,

00:01:48.060 --> 00:01:50.500
"why is DNA called an acid?"

00:01:50.500 --> 00:01:52.120
Why is it called an acid?"

00:01:52.120 --> 00:01:54.620
Well the first thing is that the basic properties

00:01:54.620 --> 00:01:57.700
of the nitrogenous base are offset to a good degree

00:01:57.700 --> 00:01:59.010
based on the fact that they're able

00:01:59.010 --> 00:02:00.420
to hydrogen bond with each other.

00:02:00.420 --> 00:02:02.960
And that's what actually forms

00:02:02.960 --> 00:02:05.660
the rungs of the ladder

00:02:05.660 --> 00:02:08.590
when these complimentary nitrogenous bases

00:02:08.590 --> 00:02:10.671
form these hydrogen bonds with each other.

00:02:10.671 --> 00:02:12.980
But even more, the reason why we call it an acid

00:02:12.980 --> 00:02:16.220
is the phosphate groups, when they're protonated, are acids.

00:02:16.220 --> 00:02:18.750
Now the reason why we tend to draw them deprotonated

00:02:18.750 --> 00:02:22.660
is they're so acidic that if you put them in a

00:02:22.660 --> 00:02:25.160
neutral solution, they're going to be deprotonated.

00:02:25.160 --> 00:02:27.180
So this is the form that you're more likely

00:02:27.180 --> 00:02:29.520
to find it in the nucleus of an actual cell.

00:02:29.520 --> 00:02:33.557
Once it's actually already deprotonated.

00:02:33.557 --> 00:02:36.590
But in general, phosphate groups are considered acidic.

00:02:36.590 --> 00:02:39.100
And if I were to draw kind of a more pure phosphate group,

00:02:39.100 --> 00:02:41.250
and I talked about this already in the last video,

00:02:41.250 --> 00:02:43.763
I would have it protonated and so I wouldn't

00:02:43.763 --> 00:02:46.070
draw that negative charge like that.

00:02:46.070 --> 00:02:48.990
So that's just a review of last time.

00:02:48.990 --> 00:02:51.860
Since I already started abstracting it,

00:02:51.860 --> 00:02:53.420
let's abstract further.

00:02:53.420 --> 00:02:56.490
So let's draw the nitrogenous bases a little bit.

00:02:56.490 --> 00:03:00.600
So I have thymine here.

00:03:00.600 --> 00:03:03.760
And I will do thymine in this green color.

00:03:03.760 --> 00:03:06.260
So this right over there is thymine.

00:03:06.260 --> 00:03:09.500
So this is attached to thymine.

00:03:09.500 --> 00:03:14.060
And the complementary nitrogenous base

00:03:14.060 --> 00:03:16.680
to thymine is adenine.

00:03:18.060 --> 00:03:19.778
Which I will do--

00:03:19.778 --> 00:03:21.720
Let's see I'm running out of colors here.

00:03:21.720 --> 00:03:22.860
Let's see. Adenine.

00:03:22.860 --> 00:03:24.430
I'll do this in an orange color

00:03:24.430 --> 00:03:26.100
since it's got so many nitrogens on it.

00:03:29.500 --> 00:03:32.740
So actually should include that hydrogen right over there.

00:03:32.740 --> 00:03:35.380
So this right over here is adenine.

00:03:38.000 --> 00:03:39.390
Now they have these hydrogen bonds

00:03:39.390 --> 00:03:40.820
between them right over here.

00:03:40.820 --> 00:03:43.000
Because they have partially negative and positive charges

00:03:43.000 --> 00:03:45.070
on either end that are attracted to each other.

00:03:45.070 --> 00:03:48.130
And then we go to this rung, one rung below it.

00:03:48.130 --> 00:03:49.860
And what is going on?

00:03:49.860 --> 00:03:51.810
Well, let's see we have--

00:03:51.810 --> 00:03:53.770
Now I really am running out of colors here.

00:03:53.770 --> 00:03:58.313
We have this nitrogenous base is cytosine.

00:03:58.913 --> 00:04:02.510
This nitrogenous base right over here is cytosine.

00:04:03.160 --> 00:04:06.180
This nitrogenous base here is cytosine.

00:04:06.180 --> 00:04:09.230
And it is paired up with guanine.

00:04:09.230 --> 00:04:11.690
It is paired up with guanine.

00:04:11.690 --> 00:04:13.820
I'll do guanine in this color.

00:04:13.820 --> 00:04:17.490
So it is paired up

00:04:17.490 --> 00:04:20.620
with guanine right over there.

00:04:20.620 --> 00:04:25.190
And we even saw this in the introductory video to DNA.

00:04:25.190 --> 00:04:27.340
Now you might say, "Oh look, these two strands

00:04:27.340 --> 00:04:29.010
"seem parallel to each other."

00:04:29.010 --> 00:04:31.602
And in some ways that is true.

00:04:31.602 --> 00:04:33.500
But there might be another

00:04:33.500 --> 00:04:35.220
interesting thing that you might have noticed,

00:04:35.220 --> 00:04:39.990
is the direction in which they are oriented.

00:04:39.990 --> 00:04:42.020
I guess is the best way to phrase it.

00:04:42.020 --> 00:04:45.720
And you especially see that when you focus in on the sugars.

00:04:45.720 --> 00:04:49.760
Notice the sugars over here, the deoxyriboses

00:04:50.640 --> 00:04:54.160
or the parts of the nucleotide that come from deoxyribose.

00:04:54.160 --> 00:04:57.060
You see the oxygens on the top of the ribose,

00:04:57.060 --> 00:04:59.560
on the top of these five member rings.

00:04:59.560 --> 00:05:01.030
The oxygen is on top.

00:05:01.030 --> 00:05:05.020
Well on this side, the oxygen is on the bottom.

00:05:05.020 --> 00:05:07.060
And so they're actually in different orientations.

00:05:07.060 --> 00:05:08.560
Here the oxygen is pointing up,

00:05:08.560 --> 00:05:10.850
here the oxygen is pointing down.

00:05:10.850 --> 00:05:13.330
And to get a little bit more concrete about that.

00:05:13.330 --> 00:05:16.490
We can number the carbons on the ribose

00:05:16.490 --> 00:05:18.530
to think about the directions

00:05:18.530 --> 00:05:20.320
and use those numbers of the carbons

00:05:20.320 --> 00:05:23.930
to describe the different directions.

00:05:23.930 --> 00:05:25.980
So let's number our carbons.

00:05:25.980 --> 00:05:29.820
So these are both ribose,

00:05:29.820 --> 00:05:32.530
we saw that in the molecular structure of DNA videos.

00:05:32.530 --> 00:05:33.370
When we're talking about DNA

00:05:33.370 --> 00:05:35.300
we're talking about deoxyribose.

00:05:38.290 --> 00:05:40.530
Instead of having a hydroxyl group

00:05:40.530 --> 00:05:45.250
on the number two carbon, it just has a hydrogen.

00:05:45.250 --> 00:05:47.730
So instead of having a hydroxyl group

00:05:47.730 --> 00:05:51.430
on the number two carbon, it just has a hydrogen.

00:05:51.430 --> 00:05:52.990
But let's actually number them.

00:05:52.990 --> 00:05:55.750
So this is the one prime carbon

00:05:55.750 --> 00:05:57.250
starting at the carbonyl group.

00:05:57.250 --> 00:05:58.860
Let me do that in a different color.

00:05:58.860 --> 00:06:02.100
So this is the one prime carbon.

00:06:02.100 --> 00:06:03.850
And I'm just numbering them starting at the carbonyl group.

00:06:03.850 --> 00:06:06.220
One prime. Two prime.

00:06:06.220 --> 00:06:08.710
Three prime. Four prime.

00:06:08.710 --> 00:06:09.900
Five prime.

00:06:09.900 --> 00:06:11.590
And then when you look at it as a ring,

00:06:11.590 --> 00:06:13.200
this was the one prime.

00:06:13.200 --> 00:06:14.760
This is the two prime.

00:06:14.760 --> 00:06:16.390
This is the three prime.

00:06:16.390 --> 00:06:17.900
This is the four prime.

00:06:17.900 --> 00:06:19.590
This is the five prime.

00:06:19.590 --> 00:06:20.970
Or if you were to number them

00:06:20.970 --> 00:06:22.760
on this diagram right over here,

00:06:22.760 --> 00:06:24.480
actually in the DNA molecule,

00:06:24.480 --> 00:06:26.200
this is the one prime.

00:06:26.200 --> 00:06:28.060
This is the two prime carbon.

00:06:28.060 --> 00:06:30.060
This is the three prime carbon.

00:06:30.060 --> 00:06:32.960
This is the four prime carbon.

00:06:32.960 --> 00:06:35.690
And this is the five prime carbon.

00:06:35.690 --> 00:06:37.530
And so one way to think about it is

00:06:37.530 --> 00:06:41.010
we'll go phosphate group and it's connected with

00:06:41.010 --> 00:06:44.560
what we call phosphodiester linkages.

00:06:44.560 --> 00:06:47.260
Phosphodiester linkages, that's what's essentially

00:06:47.260 --> 00:06:49.340
allowing these backbones to link up.

00:06:49.340 --> 00:06:53.260
But we're going from phosphate to five prime carbon

00:06:53.260 --> 00:06:56.000
and then through the sugar we go to the three prime carbon.

00:06:56.000 --> 00:06:57.330
And then we go to another phosphate.

00:06:57.330 --> 00:06:59.960
Then we go to the five prime carbon.

00:06:59.960 --> 00:07:02.090
Let me label that, this is the five prime carbon.

00:07:02.090 --> 00:07:03.890
Then we go to the three prime carbon.

00:07:03.890 --> 00:07:05.790
And that just comes straight out of just numbering these

00:07:05.790 --> 00:07:08.600
starting with the carbon that was a number one carbon.

00:07:08.600 --> 00:07:10.030
When it's straight chain form,

00:07:10.030 --> 00:07:13.360
it's part of the carbonyl group.

00:07:13.360 --> 00:07:14.860
But you see we're going from five.

00:07:14.860 --> 00:07:16.320
We go phosphate, five prime, three prime,

00:07:16.320 --> 00:07:18.780
phosphate, five prime, three prime, phosphate.

00:07:18.780 --> 00:07:20.630
So one way to describe the orientation is saying,

00:07:20.630 --> 00:07:21.990
"Hey, we're going in the direction

00:07:21.990 --> 00:07:24.120
"from five prime to three prime."

00:07:24.120 --> 00:07:28.060
So we could say that we're going from

00:07:28.060 --> 00:07:32.530
five prime to three prime,

00:07:32.530 --> 00:07:34.650
that way on the left-hand chain.

00:07:34.650 --> 00:07:36.760
And what are we doing on the right hand chain?

00:07:36.760 --> 00:07:38.490
Well, let's number them again.

00:07:38.490 --> 00:07:41.400
So this is the one prime carbon.

00:07:41.400 --> 00:07:42.920
Now this thing relative to this

00:07:42.920 --> 00:07:44.660
is upside down, it's inverted.

00:07:44.660 --> 00:07:46.860
So one prime. Two prime.

00:07:46.860 --> 00:07:49.120
Three prime. Four prime.

00:07:49.120 --> 00:07:50.410
Five prime.

00:07:50.410 --> 00:07:51.360
I could do it up here.

00:07:51.360 --> 00:07:53.300
One prime carbon. Two prime carbon.

00:07:53.300 --> 00:07:55.260
Three prime carbon.

00:07:55.260 --> 00:07:57.520
Four prime carbon. Five prime carbon.

00:07:57.520 --> 00:07:59.360
Here you're going from phosphate,

00:07:59.360 --> 00:08:02.120
three prime, five prime, phosphate,

00:08:02.120 --> 00:08:05.060
three prime, five prime, phosphate.

00:08:05.060 --> 00:08:06.930
So the way that the sugars are oriented

00:08:06.930 --> 00:08:08.060
if you're going from top to bottom

00:08:08.060 --> 00:08:08.830
the way we're looking here,

00:08:08.830 --> 00:08:10.970
you're going from three prime to five prime.

00:08:10.970 --> 00:08:12.460
So on the right hand side,

00:08:13.330 --> 00:08:16.050
it's three prime, five prime.

00:08:16.050 --> 00:08:17.170
And so if you wanted to draw an arrow

00:08:17.170 --> 00:08:18.300
from five prime to three prime,

00:08:18.300 --> 00:08:20.271
you could look at it like that.

00:08:20.271 --> 00:08:21.920
And so you could say these are parallel

00:08:21.920 --> 00:08:23.150
but since they are essentially

00:08:23.150 --> 00:08:25.790
pointing in different directions

00:08:25.790 --> 00:08:27.390
even though they are actually parallel,

00:08:27.390 --> 00:08:31.400
we would call this structure of DNA antiparallel.

00:08:31.400 --> 00:08:34.200
So this would be an anti...

00:08:36.330 --> 00:08:39.400
antiparallel structure of DNA.

00:08:39.400 --> 00:08:41.120
So these two strands, they're complementary.

00:08:41.120 --> 00:08:42.590
They're defined by each other.

00:08:42.590 --> 00:08:44.590
The thymine bonds with the adenine,

00:08:44.590 --> 00:08:46.990
the cytosine bonds with guanine.

00:08:46.990 --> 00:08:49.520
They are attracted to each other

00:08:49.520 --> 00:08:51.060
through these hydrogen bonds.

00:08:51.060 --> 00:08:52.670
But the two backbones,

00:08:52.670 --> 00:08:55.050
they're pointed in different directions.

00:08:55.050 --> 00:08:56.990
And now another interesting thing to think about,

00:08:56.990 --> 00:08:59.190
since we're talking about the molecular structure of DNA,

00:08:59.190 --> 00:09:00.130
is how do these things form?

00:09:00.130 --> 00:09:03.664
How did these things know to orient in this way?

00:09:03.664 --> 00:09:06.220
What plays part of that role

00:09:06.220 --> 00:09:08.420
is the fact that these phosphate groups are negative.

00:09:08.420 --> 00:09:09.490
So you think these things that have

00:09:09.490 --> 00:09:10.810
outright negative charge,

00:09:10.810 --> 00:09:12.230
they're gonna try to get as far away

00:09:12.230 --> 00:09:13.930
from each other as possible.

00:09:13.930 --> 00:09:16.230
And then when they just keep kind of orienting

00:09:16.230 --> 00:09:17.690
and getting far away from each other.

00:09:17.690 --> 00:09:18.620
And these are long.

00:09:18.620 --> 00:09:21.120
These are very, very, very, very long molecules.

00:09:21.120 --> 00:09:22.673
In the introductory video to DNA

00:09:22.673 --> 00:09:25.494
we talk about how long these chromosomes are,

00:09:25.494 --> 00:09:27.200
how many base pairs we actually have.

00:09:27.200 --> 00:09:28.200
And these are long molecules.

00:09:28.200 --> 00:09:29.760
So all of these phosphate groups on either strand,

00:09:29.760 --> 00:09:31.660
they want to get away from each other.

00:09:31.660 --> 00:09:34.950
And then these things want to get close to each other

00:09:34.950 --> 00:09:36.150
because of the hydrogen bonds.

00:09:36.150 --> 00:09:40.179
And so that's what helps form this actual ladder structure.

00:09:40.179 --> 00:09:42.520
So DNA, fascinating molecule,

00:09:42.520 --> 00:09:43.929
we could speak for days about it.

00:09:43.929 --> 00:09:45.370
It's actually mind blowing when you

00:09:45.370 --> 00:09:47.960
think about its implications for who we are.

00:09:47.960 --> 00:09:50.160
But hopefully this gives you a better sense

00:09:50.160 --> 00:09:53.390
of what it is molecularl-aly. molecularl-aly.

00:09:53.390 --> 00:09:55.819
I cannot say it. Molecularly.


Parabola intuition example 1

WEBVTT
Kind: captions
Language: en

00:00:00.615 --> 00:00:02.449
- [Voiceover] Adjust
the leading coefficient

00:00:02.449 --> 00:00:03.970
and vertex coordinates to make

00:00:03.970 --> 00:00:06.442
the blue parabola match
the orange parabola.

00:00:06.442 --> 00:00:08.655
Now we've already seen how we can go

00:00:08.655 --> 00:00:11.535
about shifting these parabolas.

00:00:11.535 --> 00:00:14.096
If we subtract something from y,

00:00:14.096 --> 00:00:17.176
it actually shifts the
parabola up by that amount

00:00:17.176 --> 00:00:18.756
and we've already talked about that

00:00:18.756 --> 00:00:21.956
in the video on shifting
and scaling parabolas.

00:00:21.956 --> 00:00:23.336
But let's actually see it in practice

00:00:23.336 --> 00:00:25.836
cause this is actually going
to allow us to experiment.

00:00:25.836 --> 00:00:28.077
We'll see if we increase this,

00:00:28.077 --> 00:00:30.757
that's actually shifting it down.

00:00:30.757 --> 00:00:32.511
While if we decrease it, it shifts it up.

00:00:32.511 --> 00:00:33.900
But we actually do have to shift it down

00:00:33.900 --> 00:00:35.258
for this example.

00:00:35.258 --> 00:00:37.369
Now at least the y-value of our vertexes,

00:00:37.369 --> 00:00:39.419
vertices look the same.

00:00:39.419 --> 00:00:43.996
Similarly, when we shift the,

00:00:43.996 --> 00:00:47.037
whatever we are squaring,
whenever we, if we shift,

00:00:47.037 --> 00:00:50.570
if we subtract a value here,
it shifts it to the right,

00:00:50.570 --> 00:00:53.091
while if we add a value here
it shifts it to the left.

00:00:53.091 --> 00:00:54.031
Let's verify that.

00:00:54.031 --> 00:00:55.871
If we subtract a value here,

00:00:55.871 --> 00:00:57.911
it shifts it to the right

00:00:57.911 --> 00:01:01.058
and if we add values here
it shifts it to the left.

00:01:01.142 --> 00:01:02.358
Just like that,

00:01:02.358 --> 00:01:05.579
it looks like I've been able
get our vertices to coincide.

00:01:05.579 --> 00:01:07.339
This vertex right over here is

00:01:07.339 --> 00:01:12.295
at the point x=-4, y=-3.

00:01:12.295 --> 00:01:13.765
It's no coincidence.

00:01:14.810 --> 00:01:17.267
x=-4 makes this zero

00:01:17.267 --> 00:01:20.344
and y=-3 makes this zero.

00:01:20.344 --> 00:01:22.565
But these parabolas still don't match up.

00:01:22.565 --> 00:01:26.217
This yellow parabola
seems to increase faster.

00:01:26.217 --> 00:01:28.987
The scaling factor right over here seems

00:01:28.987 --> 00:01:30.788
too low for our blue one.

00:01:30.788 --> 00:01:32.257
Let's increase it.

00:01:32.257 --> 00:01:33.078
There we go.

00:01:33.078 --> 00:01:36.598
If we put a two there,
it's growing fast enough.

00:01:36.598 --> 00:01:39.039
If we put three there
it's growing too fast.

00:01:39.039 --> 00:01:41.166
If we put a zero there,

00:01:41.166 --> 00:01:43.319
it's a flat line and
then it becomes negative.

00:01:43.319 --> 00:01:44.860
Let's bring that back

00:01:44.860 --> 00:01:47.146
to just +2.

00:01:47.146 --> 00:01:49.301
And we are done.


Molecular structure of DNA

WEBVTT
Kind: captions
Language: en

00:00:00.390 --> 00:00:03.020
- [Voiceover] We already have an overview video of DNA

00:00:03.020 --> 00:00:04.910
and I encourage you to watch that first.

00:00:04.910 --> 00:00:06.220
What I want to do in this video is

00:00:06.220 --> 00:00:07.220
dig a little bit deeper.

00:00:07.220 --> 00:00:10.650
Actually get into the molecular structure of DNA.

00:00:10.650 --> 00:00:11.690
This is a starting point.

00:00:11.690 --> 00:00:14.250
Let's just remind ourselves what DNA stands for.

00:00:14.250 --> 00:00:15.890
I'm gonna write the different parts of the word

00:00:15.890 --> 00:00:17.320
in different colors.

00:00:17.320 --> 00:00:21.030
It stands for deoxy.

00:00:21.030 --> 00:00:24.459
Deoxyribonucleic.

00:00:24.459 --> 00:00:27.859
Ribonucleic.

00:00:27.859 --> 00:00:32.109
Ribonucleic acid.

00:00:32.109 --> 00:00:34.189
Ribonucleic acid.

00:00:34.189 --> 00:00:36.619
So I'm just gonna put this on the side

00:00:36.619 --> 00:00:38.219
and now let's actually look at the molecular structure

00:00:38.219 --> 00:00:40.219
and how it relates to this actual name,

00:00:40.219 --> 00:00:43.079
deoxyribonucleic acid.

00:00:43.079 --> 00:00:46.119
DNA is just a junction for nucleic acid

00:00:46.119 --> 00:00:48.659
and it's the term nucleic that comes from the fact

00:00:48.659 --> 00:00:50.859
that it's found in the nucleus.

00:00:50.859 --> 00:00:53.789
It's found in the nucleus of eukaryotes.

00:00:53.789 --> 00:00:56.189
That's where the nucleic comes from

00:00:56.189 --> 00:00:57.489
and we'll talk about in a second

00:00:57.489 --> 00:01:00.389
why it's called an acid but I'll wait on that.

00:01:00.389 --> 00:01:04.519
Now each DNA molecule is made up of a chain

00:01:04.519 --> 00:01:07.109
of what we call nucleotides.

00:01:07.939 --> 00:01:09.419
What we call nucleotides.

00:01:09.419 --> 00:01:13.459
It's made up of nucleo, nucleo,

00:01:13.459 --> 00:01:15.019
nucleotides.

00:01:15.019 --> 00:01:17.089
What does a nucleotide look like?

00:01:17.089 --> 00:01:18.389
Well, what I have right over here

00:01:18.389 --> 00:01:21.519
is I have two strands, I've zoomed two strands of DNA

00:01:21.519 --> 00:01:24.429
or I've zoomed in two strands of DNA.

00:01:24.429 --> 00:01:26.889
You could view this side right over here

00:01:26.889 --> 00:01:29.789
as one of the, I guess you can say

00:01:29.789 --> 00:01:32.519
the backbones of one side of the ladder.

00:01:32.519 --> 00:01:34.259
This is the other side of the ladder

00:01:34.259 --> 00:01:36.189
and then each of these bridges,

00:01:36.189 --> 00:01:38.659
and I will talk about what molecules these are.

00:01:38.659 --> 00:01:41.219
These are kind of the rungs of the ladder.

00:01:41.219 --> 00:01:45.419
A nucleotide, let me separate off the nucleotide.

00:01:45.419 --> 00:01:48.119
A nucleotide would...

00:01:48.119 --> 00:01:51.419
What I am cordoning off,

00:01:51.419 --> 00:01:53.909
what I am cordoning off right over here

00:01:53.909 --> 00:01:55.589
could be considered,

00:01:55.589 --> 00:01:57.819
could be considered a nucleotide.

00:01:57.819 --> 00:01:59.189
That's one nucleotide

00:01:59.189 --> 00:02:01.189
and then it's connected to another.

00:02:02.579 --> 00:02:06.632
It's connected to another nucleotide.

00:02:06.989 --> 00:02:09.709
Another nucleotide right over here.

00:02:09.709 --> 00:02:14.419
On the right hand side we have a nucleotide,

00:02:14.419 --> 00:02:17.459
we have a nucleotide right over there

00:02:17.459 --> 00:02:18.919
and then, actually I want to do it,

00:02:18.919 --> 00:02:20.659
let me do it slightly different.

00:02:22.479 --> 00:02:27.459
We have a nucleotide right over here on the right side

00:02:27.459 --> 00:02:30.019
and then right below that we have another.

00:02:30.019 --> 00:02:32.719
We have another nucleotide.

00:02:32.719 --> 00:02:34.659
We have another nucleotide.

00:02:34.659 --> 00:02:36.559
Depicted here, we essentially have four nucleotides.

00:02:36.559 --> 00:02:39.489
These two are on this left side of the ladder,

00:02:39.489 --> 00:02:41.759
these two are on the right side of the ladder.

00:02:41.759 --> 00:02:42.919
Now let's think about the

00:02:42.919 --> 00:02:45.559
different pieces of that nucleotide.

00:02:45.559 --> 00:02:47.289
The one thing that might jump out at you

00:02:47.289 --> 00:02:50.189
is we have these phosphate groups.

00:02:50.189 --> 00:02:52.789
This is a phosphate group right over here.

00:02:52.789 --> 00:02:54.919
This is a phosphate group right over here.

00:02:54.919 --> 00:02:57.789
Each of these nucleotides have a phosphate group.

00:02:57.789 --> 00:02:59.659
This is a phosphate group over here

00:02:59.659 --> 00:03:02.619
and this is a phosphate group over here.

00:03:02.619 --> 00:03:05.919
Now the phosphate groups are actually what make DNA

00:03:05.919 --> 00:03:08.689
or actually what make nucleic acid an acid.

00:03:08.689 --> 00:03:09.549
You might say, wait, wait.

00:03:09.549 --> 00:03:10.779
The way you've drawn it Sal,

00:03:10.779 --> 00:03:12.159
you have a negative charge.

00:03:12.159 --> 00:03:15.019
Something with a negative charge would attract protons,

00:03:15.019 --> 00:03:16.519
it would sap up protons.

00:03:16.519 --> 00:03:17.759
How can you call this an acid?

00:03:17.759 --> 00:03:19.319
This actually looks more basic.

00:03:19.319 --> 00:03:22.519
The reason why its DNA is typically drawn

00:03:22.519 --> 00:03:23.959
with these negative charges here

00:03:23.959 --> 00:03:26.139
is that it's so acidic and that if you put it in

00:03:26.139 --> 00:03:28.689
into a neutral solution,

00:03:28.689 --> 00:03:30.889
it's actually going to lose its hydrogens.

00:03:30.889 --> 00:03:33.619
Actually the DNA if we actually want to be formal about it,

00:03:33.619 --> 00:03:35.119
the DNA molecules would actually have

00:03:35.119 --> 00:03:37.849
its phosphates protonated like this

00:03:37.849 --> 00:03:42.679
but it so badly wants to lose these hydrogen protons

00:03:42.679 --> 00:03:45.579
so it typically would be, let me draw it like this.

00:03:45.579 --> 00:03:48.379
Let me get rid of the negative charge just on this one.

00:03:48.379 --> 00:03:49.189
Whoops.

00:03:49.189 --> 00:03:53.189
Just on this phosphate group over here.

00:03:53.189 --> 00:03:54.519
If you get rid of the negative charge

00:03:54.519 --> 00:03:56.259
and if this was bounded,

00:03:56.259 --> 00:03:58.859
this is bonded to a hydrogen.

00:03:58.859 --> 00:04:01.359
This so badly wants to grab these electrons.

00:04:01.359 --> 00:04:03.209
These oxygen can grab these electrons

00:04:03.209 --> 00:04:04.719
and then these hydrogen will just be grabbed

00:04:04.719 --> 00:04:06.709
by another water molecule or something

00:04:06.709 --> 00:04:08.719
so the proton will be let go.

00:04:08.719 --> 00:04:10.869
That's why we call it an acid.

00:04:10.869 --> 00:04:14.159
If it wasn't in a solution it would have the hydrogens

00:04:14.159 --> 00:04:16.199
but it would be very acidic as soon as you put it into

00:04:16.199 --> 00:04:19.589
a neutral solution it's going to lose those hydrogens.

00:04:19.589 --> 00:04:21.719
The phosphate groups are what make it,

00:04:21.719 --> 00:04:23.049
are what make it an acid

00:04:23.049 --> 00:04:24.319
but it's confusing sometimes

00:04:24.319 --> 00:04:25.889
because usually when you see it depicted,

00:04:25.889 --> 00:04:27.419
you see it with these negative charges

00:04:27.419 --> 00:04:31.719
and that's because it has already lost its hydrogen proton.

00:04:31.719 --> 00:04:34.819
You're actually depicting the conjugate base here

00:04:34.819 --> 00:04:37.019
but that's where it gets its acidic name from

00:04:37.019 --> 00:04:38.319
because it starts protonated

00:04:38.319 --> 00:04:40.219
or it gets in this acid form, it's protonated

00:04:40.219 --> 00:04:41.979
but it readily loses it.

00:04:41.979 --> 00:04:43.419
And so that's why it has its,

00:04:43.419 --> 00:04:46.259
that's where it gets the name acid form from.

00:04:46.259 --> 00:04:50.249
Each of these nucleotides they have a phosphate group.

00:04:50.249 --> 00:04:52.689
Now the next thing you might notice,

00:04:52.689 --> 00:04:55.319
the next thing you might notice is.

00:04:55.319 --> 00:04:56.859
The next thing you might notice is

00:04:56.859 --> 00:04:58.419
this group right over here.

00:04:58.419 --> 00:05:01.089
It is a cycle, it is a ring

00:05:01.089 --> 00:05:02.889
and it looks an awful lot like a sugar

00:05:02.889 --> 00:05:05.459
and that's because it is a sugar.

00:05:05.459 --> 00:05:09.119
This sugar is based on, it's a five-carbon sugar.

00:05:09.119 --> 00:05:12.779
What I have depicted here, this sugar, this is ribose.

00:05:12.779 --> 00:05:16.459
This sugar right over here is ribose.

00:05:16.459 --> 00:05:19.489
This is when it's just as a straight chain

00:05:19.489 --> 00:05:22.159
and like many sugars, it can take a cyclical form.

00:05:22.159 --> 00:05:24.079
Actually it can take many different cyclical forms

00:05:24.079 --> 00:05:26.159
but the one that's most typically described

00:05:26.159 --> 00:05:27.319
is when you have that.

00:05:27.319 --> 00:05:28.579
Let me number the carbons

00:05:28.579 --> 00:05:30.089
because carbon numbering is important

00:05:30.089 --> 00:05:31.379
when we talk about DNA.

00:05:31.379 --> 00:05:33.679
But if we start carbonyl group right over here

00:05:33.679 --> 00:05:36.659
we call that the one carbon or the one prime carbon.

00:05:36.659 --> 00:05:40.489
One prime, two prime, three prime,

00:05:40.489 --> 00:05:43.589
four prime and five prime.

00:05:43.589 --> 00:05:45.219
That's the five prime carbon.

00:05:46.889 --> 00:05:49.279
You form the cyclical form of ribose

00:05:49.279 --> 00:05:52.009
as if you have the oxygen.

00:05:52.009 --> 00:05:54.319
You have the oxygen right over here

00:05:54.319 --> 00:05:56.019
on the four prime carbon.

00:05:56.019 --> 00:05:58.219
It uses one of its lone pairs.

00:05:58.219 --> 00:06:00.189
It uses one of its lone pairs

00:06:00.189 --> 00:06:02.319
to form a bond.

00:06:02.319 --> 00:06:07.319
To form a bond with the one prime.

00:06:07.319 --> 00:06:08.519
With the one prime carbon

00:06:08.519 --> 00:06:09.219
and I drew it that way

00:06:09.219 --> 00:06:10.619
because it kind of does bend.

00:06:10.619 --> 00:06:12.519
The whole molecule's going to have to bend that way

00:06:12.519 --> 00:06:13.859
to form this structure.

00:06:13.859 --> 00:06:15.359
And then when it forms that bond

00:06:15.359 --> 00:06:17.989
the carbon can let go of one of these double bonds

00:06:17.989 --> 00:06:20.319
and then that can, then the oxygen,

00:06:20.319 --> 00:06:22.459
the oxygen can use that.

00:06:22.459 --> 00:06:24.859
The oxygen can use those electrons

00:06:24.859 --> 00:06:28.279
to go grab a hydrogen proton from some place.

00:06:28.279 --> 00:06:31.049
To nab on to a hydrogen proton.

00:06:31.049 --> 00:06:32.919
When it does that you're in this form

00:06:32.919 --> 00:06:35.589
and this form, just to be clear of what we're talking about,

00:06:35.589 --> 00:06:38.019
this is the one prime carbon.

00:06:38.019 --> 00:06:42.519
One prime, two prime, three prime,

00:06:42.519 --> 00:06:47.869
four prime and five prime carbon.

00:06:47.869 --> 00:06:49.319
Where we see this bond,

00:06:49.319 --> 00:06:50.489
this is the one prime carbon.

00:06:50.489 --> 00:06:51.959
it was part of a carbonyl.

00:06:51.959 --> 00:06:55.019
Now it lets go of one of those double bonds

00:06:55.019 --> 00:06:56.419
so that this oxygen can form a bond

00:06:56.419 --> 00:06:57.889
with a hydrogen proton.

00:06:57.889 --> 00:07:00.189
It let go of a double bond there

00:07:00.189 --> 00:07:04.889
so that this could form a bond with a hydrogen proton.

00:07:04.889 --> 00:07:06.989
This hydrogen proton is

00:07:06.989 --> 00:07:08.889
that hydrogen proton right over there

00:07:08.889 --> 00:07:12.189
and this green bond that gets formed

00:07:12.189 --> 00:07:14.149
between the four prime carbon and

00:07:14.149 --> 00:07:15.989
or between the oxygen that's attached

00:07:15.989 --> 00:07:19.579
to the four prime carbon and the one prime carbon,

00:07:19.579 --> 00:07:20.759
that's this.

00:07:20.759 --> 00:07:22.389
That's this bond right over here.

00:07:22.389 --> 00:07:25.289
This oxygen is that oxygen right there.

00:07:25.289 --> 00:07:27.859
Notice, this oxygen is bound to the four prime carbon

00:07:27.859 --> 00:07:30.419
and now it's also bound to the one prime carbon.

00:07:30.419 --> 00:07:32.759
It was also attached to a hydrogen.

00:07:32.759 --> 00:07:34.109
It was also attached to a hydrogen

00:07:34.109 --> 00:07:35.289
so that hydrogen is there

00:07:35.289 --> 00:07:37.159
but then that can get nabbed up by another

00:07:37.159 --> 00:07:39.159
passing water molecule to become hydronium

00:07:39.159 --> 00:07:40.959
so it can get lost.

00:07:41.879 --> 00:07:44.789
It grabs up a hydrogen proton right over here

00:07:44.789 --> 00:07:46.919
and so it can lose a hydrogen proton right there.

00:07:46.919 --> 00:07:50.119
It's not adding or losing in that net.

00:07:50.119 --> 00:07:52.349
You form this cyclical form

00:07:52.349 --> 00:07:53.689
and the cyclical form right over here

00:07:53.689 --> 00:07:56.419
is very close to what we see in a DNA molecule.

00:07:56.419 --> 00:07:59.389
It's actually what we would see in an RNA molecule,

00:07:59.389 --> 00:08:01.119
in a ribonucleic acid.

00:08:01.119 --> 00:08:02.249
And so what do we think we're talking about

00:08:02.249 --> 00:08:05.659
when we say deoxyribonucleic acid.

00:08:05.659 --> 00:08:07.919
Well, you can start with you have a ribose here

00:08:07.919 --> 00:08:10.259
but if we got rid of one of the oxygen groups

00:08:10.259 --> 00:08:11.589
and in particular one of...

00:08:11.589 --> 00:08:13.509
Well, actually if we just got rid of one of the oxygens

00:08:13.509 --> 00:08:16.749
we replace a hydroxyl with just a hydrogen,

00:08:16.749 --> 00:08:18.819
well then you're gonna have deoxyribose

00:08:18.819 --> 00:08:20.226
and you see that over here.

00:08:20.226 --> 00:08:22.189
This five-member ring,

00:08:22.189 --> 00:08:23.919
you have four carbons right over here.

00:08:23.919 --> 00:08:25.719
it looks just like this.

00:08:25.719 --> 00:08:28.489
The hydrogens are implicit to the carbons,

00:08:28.489 --> 00:08:29.589
we've seen this multiple time.

00:08:29.589 --> 00:08:33.459
The carbons are at where these lines intersect

00:08:33.459 --> 00:08:35.319
or I guess at the edges or maybe

00:08:35.319 --> 00:08:39.649
and also where these lines end right over there.

00:08:39.649 --> 00:08:41.619
But you see this does not have an...

00:08:41.619 --> 00:08:44.889
This molecule if we compare these two molecules,

00:08:44.889 --> 00:08:47.389
if we compare these two molecules over here,

00:08:47.389 --> 00:08:50.319
we see that this guy has an OH,

00:08:50.319 --> 00:08:53.119
and this guy implicitly just has...

00:08:53.119 --> 00:08:54.749
This has an OH and an H.

00:08:54.749 --> 00:08:58.189
This guy implicitly has just two hydrogens over here.

00:08:58.189 --> 00:08:59.819
He's missing an oxygen.

00:08:59.819 --> 00:09:02.249
This is deoxyribose.

00:09:02.249 --> 00:09:04.359
Deoxyribose.

00:09:04.359 --> 00:09:06.889
Deoxyribose doesn't have this oxygen.

00:09:06.889 --> 00:09:08.859
It does not have the oxygen

00:09:08.859 --> 00:09:10.679
on the two prime carbon.

00:09:10.679 --> 00:09:14.119
So this if you get rid of that, this is deoxyribose.

00:09:14.119 --> 00:09:16.049
So let me circle that.

00:09:17.589 --> 00:09:19.389
This thing right over here,

00:09:19.389 --> 00:09:22.600
this thing right over here, that is deoxyribose.

00:09:23.519 --> 00:09:26.289
Deoxy or it's based on deoxyribose

00:09:26.289 --> 00:09:28.819
I guess before it bonded to these other constituents.

00:09:28.819 --> 00:09:32.289
You could consider this deoxyribose.

00:09:32.289 --> 00:09:35.519
That's where the deoxyribo comes from

00:09:35.519 --> 00:09:37.189
and then the last piece of it,

00:09:37.189 --> 00:09:42.459
the last piece of it is this chunk right over here.

00:09:42.459 --> 00:09:45.589
These we call nitrogenous bases.

00:09:45.589 --> 00:09:47.559
Nitrogenous.

00:09:47.559 --> 00:09:49.789
Nitrogenous.

00:09:49.789 --> 00:09:51.889
Nitrogenous bases.

00:09:51.889 --> 00:09:53.859
You could see we have different types of nitrogenous bases.

00:09:53.859 --> 00:09:55.419
This is a nitrogenous base.

00:09:55.949 --> 00:09:59.359
This right over here is a different nitrogenous base.

00:09:59.359 --> 00:10:02.089
This right over here is another different nitrogenous base.

00:10:02.089 --> 00:10:04.549
Notice, this one only has one ring, this one has one ring,

00:10:04.549 --> 00:10:05.859
this one has two rings.

00:10:05.859 --> 00:10:09.489
This one over here has two rings

00:10:09.489 --> 00:10:10.619
and we have different names

00:10:10.619 --> 00:10:11.859
for these nitrogenous bases.

00:10:11.859 --> 00:10:14.789
The ones with two rings, the general categorization

00:10:14.789 --> 00:10:17.189
we call them purines.

00:10:17.189 --> 00:10:20.319
Nitrogenous bases if you have two rings,

00:10:20.319 --> 00:10:23.540
if you have two rings we call them purines.

00:10:24.359 --> 00:10:26.189
That's a general classification term.

00:10:26.189 --> 00:10:28.059
Let me make sure, purines.

00:10:28.059 --> 00:10:29.519
If you have one ring.

00:10:29.519 --> 00:10:30.389
Anyway, I'll just write this way.

00:10:30.389 --> 00:10:31.889
One ring.

00:10:31.889 --> 00:10:34.189
One ring, we call these pyrimidines.

00:10:34.189 --> 00:10:35.840
Pyrimidine.

00:10:36.519 --> 00:10:38.119
Pyrimidines.

00:10:38.119 --> 00:10:39.589
We call these pyrimidines.

00:10:39.589 --> 00:10:41.459
These particular, these two on the right,

00:10:41.459 --> 00:10:42.759
these two purines,

00:10:42.759 --> 00:10:44.689
this one up here this is adenine,

00:10:44.689 --> 00:10:46.089
and we talk about how they pair

00:10:46.089 --> 00:10:47.919
in the overview video on DNA.

00:10:47.919 --> 00:10:50.559
This one right over here is adenine,

00:10:50.559 --> 00:10:52.019
this nitrogenous base.

00:10:52.019 --> 00:10:54.989
This one over here is guanine.

00:10:54.989 --> 00:10:57.289
That is guanine.

00:10:57.289 --> 00:11:01.789
And then over here, over here,

00:11:01.789 --> 00:11:05.619
this single ring nitrogenous base

00:11:05.619 --> 00:11:08.919
which makes it a pyrimidine, this is thymine.

00:11:08.919 --> 00:11:12.119
This right over here is thymine.

00:11:12.119 --> 00:11:14.659
This is thymine and then last but not least

00:11:14.659 --> 00:11:15.619
if we're talking about DNA,

00:11:15.619 --> 00:11:18.119
when we go into RNA, we're also gonna talk about uracil.

00:11:18.119 --> 00:11:19.319
But when we talk about DNA

00:11:19.319 --> 00:11:21.689
this one over here is cytosine.

00:11:21.689 --> 00:11:24.059
Cytosine.

00:11:24.059 --> 00:11:25.519
You could see the way it's structured.

00:11:25.519 --> 00:11:28.259
The thymine is attracted to adenine.

00:11:28.259 --> 00:11:29.789
It bonds with adenine

00:11:29.789 --> 00:11:32.689
and cytosine bonds with guanine.

00:11:32.689 --> 00:11:34.119
How are they bonding?

00:11:34.119 --> 00:11:37.319
Well, the way that these nitrogenous bases

00:11:37.319 --> 00:11:38.709
form the rungs of the ladder,

00:11:39.669 --> 00:11:41.659
how they want they're drawn to each other,

00:11:41.659 --> 00:11:44.589
this is our good old friend hydrogen bonds.

00:11:44.589 --> 00:11:45.959
This all comes out of the fact,

00:11:45.959 --> 00:11:48.079
that nitrogen is quite electronegative.

00:11:48.079 --> 00:11:50.689
When nitrogen is bound to a hydrogen

00:11:50.689 --> 00:11:52.159
you're going to have a partially

00:11:52.159 --> 00:11:54.819
negative charge at the nitrogen.

00:11:54.819 --> 00:11:56.919
Let me do this in green.

00:11:56.919 --> 00:11:57.919
You're going to have a partial

00:11:57.919 --> 00:11:59.459
negative charge at the nitrogen

00:11:59.459 --> 00:12:02.559
and a partially positive charge at the hydrogen.

00:12:02.559 --> 00:12:04.189
And then oxygen we've always talked about

00:12:04.189 --> 00:12:05.259
as being electronegative

00:12:05.259 --> 00:12:07.689
so it has a partial negative charge.

00:12:07.689 --> 00:12:09.619
The partial negative charge of this oxygen

00:12:09.619 --> 00:12:11.289
is going to be attracted to the partial

00:12:11.289 --> 00:12:13.619
positive charge of this hydrogen,

00:12:13.619 --> 00:12:17.589
and so you're going to have a hydrogen bond.

00:12:17.589 --> 00:12:19.519
That's then going to happen between this hydrogen

00:12:19.519 --> 00:12:20.559
which is going...

00:12:20.559 --> 00:12:23.419
Its electrons are being hogged by this nitrogen

00:12:23.419 --> 00:12:26.499
and this nitrogen with who,

00:12:26.499 --> 00:12:28.389
which itself hogs electrons.

00:12:28.389 --> 00:12:31.789
That forms a hydrogen bond.

00:12:31.789 --> 00:12:34.089
And then down here you have a hydrogen

00:12:34.089 --> 00:12:35.819
that has a partially positive charge

00:12:35.819 --> 00:12:37.979
because its electrons are being hogged.

00:12:37.979 --> 00:12:39.419
And then you have this oxygen

00:12:39.419 --> 00:12:40.919
with a partially negative charge,

00:12:40.919 --> 00:12:42.409
they're going to be attracted to each other.

00:12:42.409 --> 00:12:43.859
That's a hydrogen bond.

00:12:43.859 --> 00:12:46.219
Same thing between this nitrogen and that hydrogen,

00:12:46.219 --> 00:12:48.849
and same thing between this oxygen and that hydrogen.

00:12:48.849 --> 00:12:51.719
That's why cytosine and guanine pair up

00:12:51.719 --> 00:12:54.159
and that's why thymine and adenine pair up,

00:12:54.159 --> 00:12:55.789
and we talk about that as well

00:12:55.789 --> 00:12:59.069
in the overview video of DNA.


Lipid overview

WEBVTT
Kind: captions
Language: en

00:00:00.619 --> 00:00:02.906
- [Voiceover] Let's talk about lipids.

00:00:02.906 --> 00:00:05.309
Now for those of you who are familiar with the term

00:00:05.309 --> 00:00:08.884
you might associate it with things like fat molecules,

00:00:08.884 --> 00:00:10.382
and that would not be incorrect.

00:00:10.382 --> 00:00:12.959
Fat molecules are a very common form of lipid,

00:00:12.959 --> 00:00:15.862
in fact this is an example of a fat molecule,

00:00:15.862 --> 00:00:19.089
or a triglyceride right over here.

00:00:19.089 --> 00:00:22.583
Fat or triglyceride,

00:00:22.583 --> 00:00:24.383
tryglyceride molecule right over here.

00:00:24.383 --> 00:00:27.923
This one in particular is a polyunsaturated tryglyceride

00:00:27.923 --> 00:00:30.827
and we have, we have a, go into in depth,

00:00:30.827 --> 00:00:32.567
we go into a lot of depth on this

00:00:32.567 --> 00:00:33.960
on the video on the molecular structure

00:00:33.960 --> 00:00:36.224
of fats slash triglycerides

00:00:36.224 --> 00:00:38.998
or on saturated and unsaturated fats.

00:00:38.998 --> 00:00:40.182
But you see the tell-tale signs,

00:00:40.182 --> 00:00:42.760
you see a glycerol backbone right over here

00:00:42.760 --> 00:00:46.499
and three fatty acids, or what were three fatty acids

00:00:46.499 --> 00:00:49.645
attached to what was a glycerol molecule.

00:00:49.645 --> 00:00:51.224
We go into a lot of depth on that.

00:00:51.224 --> 00:00:54.543
But fats are not the only type of lipids.

00:00:54.543 --> 00:00:56.924
And so what makes all of these other things

00:00:56.924 --> 00:00:58.595
that I'm about to show you also lipids?

00:00:58.595 --> 00:01:00.975
What commonality do they have with fats?

00:01:00.975 --> 00:01:03.436
Well lipids are just the general term,

00:01:03.436 --> 00:01:06.118
the general term for a whole class of molecules

00:01:06.118 --> 00:01:08.158
that tend to not be so soluble in water,

00:01:08.158 --> 00:01:10.224
that tend to kind of clump up or ball up

00:01:10.224 --> 00:01:11.605
when placed in water.

00:01:11.605 --> 00:01:15.786
So not, not so soluble,

00:01:15.786 --> 00:01:19.083
not so soluble in water.

00:01:19.083 --> 00:01:21.030
And I'm being a little bit careful with my words,

00:01:21.030 --> 00:01:23.049
I didn't say outright hydrophobic.

00:01:23.049 --> 00:01:26.543
There are definitely lipids that are outright hydrophobic,

00:01:26.543 --> 00:01:27.762
but there are also some lipids

00:01:27.762 --> 00:01:30.526
that have some end of their molecule that's hydrophobic,

00:01:30.526 --> 00:01:31.838
but then other parts of the molecule

00:01:31.838 --> 00:01:33.788
actually might be hydrophilic.

00:01:33.788 --> 00:01:35.321
And there's actually words for that.

00:01:35.321 --> 00:01:36.482
So you have some lipids

00:01:36.482 --> 00:01:39.139
that are just straight out hydrophobic,

00:01:39.139 --> 00:01:40.661
hydrophobic.

00:01:40.661 --> 00:01:43.122
They literally try to avoid the water,

00:01:43.122 --> 00:01:46.557
they're non-polar molecules, so they just clump together.

00:01:46.557 --> 00:01:49.518
But then there's some that have hydrophobic parts

00:01:49.518 --> 00:01:51.619
and hydrophilic parts.

00:01:51.619 --> 00:01:52.943
And these are called,

00:01:52.943 --> 00:01:55.056
and I always have trouble saying this word,

00:01:55.056 --> 00:01:56.519
amphi,

00:01:56.519 --> 00:01:59.177
amphipathic,

00:01:59.177 --> 00:02:02.161
amphipathic molecules.

00:02:02.161 --> 00:02:03.778
Where some part is hydrophilic

00:02:03.778 --> 00:02:05.078
and some part is hydrophobic.

00:02:05.078 --> 00:02:07.040
And we're gonna see that in a few seconds

00:02:07.040 --> 00:02:08.781
when we look at phospholipids,

00:02:08.781 --> 00:02:13.018
which are crucial for the structure of cell membranes.

00:02:13.018 --> 00:02:14.620
And you're gonna see that a lot when you,

00:02:14.620 --> 00:02:16.153
when you go into biology.

00:02:16.153 --> 00:02:17.801
So what are all these other molecules?

00:02:17.801 --> 00:02:19.414
And let's think about what parts of them

00:02:19.414 --> 00:02:23.338
might be hydrophobic and what parts might be hydrophilic.

00:02:23.338 --> 00:02:26.333
When you look at fats you have this long hydrocarbon chain,

00:02:26.333 --> 00:02:29.515
there are any obvious, and there aren't any obvious,

00:02:29.515 --> 00:02:32.476
there aren't any obvious charges over here.

00:02:32.476 --> 00:02:36.295
In fact, there's aren't any, oxygen is more electronegative,

00:02:36.295 --> 00:02:38.918
so you might have a little bit of a partial negative

00:02:38.918 --> 00:02:40.925
or partial positive charge.

00:02:40.925 --> 00:02:42.413
A partial negative at the oxygen

00:02:42.413 --> 00:02:44.791
or maybe a partial positive end at the carbon,

00:02:44.791 --> 00:02:47.113
but carbon isn't, is still more electronegative

00:02:47.113 --> 00:02:48.171
than say hydrogen,

00:02:48.171 --> 00:02:49.575
so you're not going to be able to form

00:02:49.575 --> 00:02:51.793
the type of polar bonds that,

00:02:51.793 --> 00:02:53.755
the type of, I should say, hydrogen bonds

00:02:53.755 --> 00:02:56.493
you would if you had hydroxyl groups here,

00:02:56.493 --> 00:02:58.130
if this was an alcohol.

00:02:58.130 --> 00:03:00.453
And these hydrocarbon chains over here,

00:03:00.453 --> 00:03:03.586
these are very hydrophobic,

00:03:03.586 --> 00:03:06.791
so that's what makes fat not be so soluble in water

00:03:06.791 --> 00:03:09.287
and clump up with you put it into water.

00:03:09.287 --> 00:03:11.029
This molecule right over here,

00:03:11.029 --> 00:03:13.536
which we would classify as an ester,

00:03:13.536 --> 00:03:15.927
and that's because we have an ester group,

00:03:15.927 --> 00:03:18.226
we have an ester functional group right over here

00:03:18.226 --> 00:03:20.850
where you have a carbon double-bonded to an oxygen,

00:03:20.850 --> 00:03:22.568
and then single-bonded to another oxygen,

00:03:22.568 --> 00:03:25.713
and then that oxygen's bonded to a long hydrocarbon chain,

00:03:25.713 --> 00:03:26.747
and that carbon is bonded

00:03:26.747 --> 00:03:29.986
to a long hydrocarbon chain right over there.

00:03:29.986 --> 00:03:32.993
This is clearly going to be hydrophobic.

00:03:32.993 --> 00:03:34.855
And this particular molecule

00:03:34.855 --> 00:03:35.923
that we're looking at right over here,

00:03:35.923 --> 00:03:39.996
this is a major constituent of beeswax.

00:03:39.996 --> 00:03:43.391
Of bees, of beeswax.

00:03:43.391 --> 00:03:45.190
And if you've even dealt with beeswax,

00:03:45.190 --> 00:03:46.514
or really any type of wax,

00:03:46.514 --> 00:03:49.533
and waxes in general are considered to be lipids.

00:03:49.533 --> 00:03:52.470
You can see they don't, they're not soluble in water,

00:03:52.470 --> 00:03:55.093
in fact they're often used to repel water,

00:03:55.093 --> 00:03:58.390
to keep water from penetrating into something.

00:03:58.390 --> 00:04:00.468
So wax, and in particular beeswax,

00:04:00.468 --> 00:04:02.371
and beeswax isn't made up of only this molecule,

00:04:02.371 --> 00:04:03.672
this is one of the main constituents,

00:04:03.672 --> 00:04:07.086
it has other molecules mixed in there,

00:04:07.086 --> 00:04:09.860
but this is also a lipid.

00:04:09.860 --> 00:04:11.393
Now what's this thing over here?

00:04:11.393 --> 00:04:14.992
This thing I have one six carbon ring,

00:04:14.992 --> 00:04:18.044
another six carbon, whoops, I have another six carbon ring,

00:04:18.044 --> 00:04:20.691
another six carbon ring, and then I have a five carbon ring.

00:04:20.691 --> 00:04:22.583
This is the tell-tale sign,

00:04:22.583 --> 00:04:26.193
and let me circle these four rings right over here,

00:04:26.193 --> 00:04:29.026
these rings are the tell-tale signs

00:04:29.026 --> 00:04:31.429
that we are looking at a steroid,

00:04:31.429 --> 00:04:32.185
at a steroid.

00:04:32.185 --> 00:04:34.529
And in popular culture steroids have,

00:04:34.529 --> 00:04:36.491
you know, you think of steroids as something

00:04:36.491 --> 00:04:40.450
that bodybuilders might inject illegally

00:04:40.450 --> 00:04:42.505
to pump up their muscles,

00:04:42.505 --> 00:04:44.004
but steroids are actually,

00:04:44.004 --> 00:04:45.362
when you think about it in chemical terms,

00:04:45.362 --> 00:04:46.582
they're actually referring to things

00:04:46.582 --> 00:04:48.322
that have this general, these molecules

00:04:48.322 --> 00:04:49.658
that have this general structure

00:04:49.658 --> 00:04:51.899
where they have this six carbon ring,

00:04:51.899 --> 00:04:53.662
this six carbon ring, and another six carbon ring

00:04:53.662 --> 00:04:56.647
in this orientation, and then another five carbon ring.

00:04:56.647 --> 00:04:58.818
And this steroid that we're looking at,

00:04:58.818 --> 00:05:00.500
this has an O-H group attached to it,

00:05:00.500 --> 00:05:02.567
so it's actually going to be an alcohol,

00:05:02.567 --> 00:05:03.785
so a steroid that's an alcohol

00:05:03.785 --> 00:05:05.679
you would call a sterol,

00:05:05.679 --> 00:05:07.036
sterol.

00:05:07.036 --> 00:05:10.485
And this particular sterol is one that you've actually

00:05:10.485 --> 00:05:12.562
dealt with a lot, or at least you've heard about,

00:05:12.562 --> 00:05:14.525
this is cholesterol.

00:05:14.525 --> 00:05:19.260
So this one in particular is cholesterol.

00:05:19.260 --> 00:05:21.861
And cholesterol is often viewed as a negative thing,

00:05:21.861 --> 00:05:24.937
people don't, people wanna lower their cholesterol,

00:05:24.937 --> 00:05:26.842
but it's essential for life.

00:05:26.842 --> 00:05:29.465
It's essential to the functioning of your cells,

00:05:29.465 --> 00:05:33.134
and it is a precursor molecule for your steroid hormones,

00:05:33.134 --> 00:05:35.096
which make you you.

00:05:35.096 --> 00:05:37.418
And this right over here is a steroid hormone,

00:05:37.418 --> 00:05:39.158
it's a very well known one.

00:05:39.158 --> 00:05:41.062
This is testosterone.

00:05:41.062 --> 00:05:45.196
Testos, testosterone,

00:05:45.196 --> 00:05:48.423
testosterone, testosterone.

00:05:48.423 --> 00:05:49.920
And you see the tell-tale,

00:05:49.920 --> 00:05:52.858
you have a six carbon ring right over here,

00:05:52.858 --> 00:05:55.933
another six carbon ring right over here,

00:05:55.933 --> 00:05:57.419
the double-bond is in a different place

00:05:57.419 --> 00:05:58.313
than cholesterol here,

00:05:58.313 --> 00:06:00.415
you have a double-bond right over there.

00:06:00.415 --> 00:06:02.935
Then you have another six carbon ring,

00:06:02.935 --> 00:06:05.315
and then you have the five carbon ring.

00:06:05.315 --> 00:06:06.695
And instead of an O-H group here

00:06:06.695 --> 00:06:08.995
you have a double-bond, you have a carbonyl group,

00:06:08.995 --> 00:06:11.119
you have a carbon double-bonded to an oxygen,

00:06:11.119 --> 00:06:14.172
but it actually does still have an O-H group up here.

00:06:14.172 --> 00:06:16.633
But this is a derivative of cholesterol,

00:06:16.633 --> 00:06:20.000
this is a testosterone, it is a steroid hormone.

00:06:20.000 --> 00:06:21.695
This is another steroid hormone.

00:06:21.695 --> 00:06:24.852
This is cortisol, cortisol.

00:06:24.852 --> 00:06:27.778
Also can be derived from cholesterol.

00:06:27.778 --> 00:06:29.194
And you see the tell-tale signs.

00:06:29.194 --> 00:06:31.110
You see the six carbon ring,

00:06:31.110 --> 00:06:33.351
this has a double-bond right over there.

00:06:33.351 --> 00:06:37.831
You see another, you see another six carbon ring,

00:06:37.831 --> 00:06:39.712
six carbon ring like this.

00:06:39.712 --> 00:06:41.093
It's actually hard to see the double-bond,

00:06:41.093 --> 00:06:42.638
so I won't even refer to them,

00:06:42.638 --> 00:06:44.890
I'll just refer to the general shape.

00:06:44.890 --> 00:06:47.409
So you have a six carbon ring there,

00:06:47.409 --> 00:06:51.587
six carbon ring there, six carbon ring there,

00:06:51.587 --> 00:06:54.094
and then five carbon, whoops,

00:06:54.094 --> 00:06:56.811
and then a five carbon ring just like that.

00:06:56.811 --> 00:07:00.745
So once again, they all have this steroid base structure,

00:07:00.745 --> 00:07:02.917
but then they all, they also have other parts

00:07:02.917 --> 00:07:03.974
that make them different.

00:07:03.974 --> 00:07:06.435
For example, that is different than that

00:07:06.435 --> 00:07:08.372
is different than that.

00:07:08.372 --> 00:07:09.580
And just so you can visualize

00:07:09.580 --> 00:07:11.171
these things in three dimensions,

00:07:11.171 --> 00:07:12.899
in an actual molecule their not going to look

00:07:12.899 --> 00:07:15.059
exactly like this and even talk about what something

00:07:15.059 --> 00:07:17.207
in an atomic scale looks like is kind of strange

00:07:17.207 --> 00:07:19.540
because light behaves in weird ways,

00:07:19.540 --> 00:07:21.664
but you can imagine the molecule would look like this

00:07:21.664 --> 00:07:25.867
if you actually, this is kind of a ball and stick model,

00:07:25.867 --> 00:07:27.306
well here you're thinking about

00:07:27.306 --> 00:07:29.385
what it actually might look like in space

00:07:29.385 --> 00:07:31.382
where the white balls are hydrogen,

00:07:31.382 --> 00:07:34.401
the grey ones are carbon, and the red ones are oxygen.

00:07:34.401 --> 00:07:36.966
So this is also, this right over here,

00:07:36.966 --> 00:07:39.763
is what a cortisol molecule would look like

00:07:39.763 --> 00:07:43.140
if you think in a space filling visualization.

00:07:43.140 --> 00:07:46.786
Now I talked about amphipathic molecules

00:07:46.786 --> 00:07:48.528
and phospholipids are probably

00:07:48.528 --> 00:07:50.792
the most well-known example of it.

00:07:50.792 --> 00:07:53.369
And phospholipids, they have a lot in common

00:07:53.369 --> 00:07:55.423
with triglycerides in that you have

00:07:55.423 --> 00:07:58.790
this three carbon backbone right over here.

00:07:58.790 --> 00:08:01.448
Three carbon, three carbon backbone,

00:08:01.448 --> 00:08:03.247
let me do that in a different color.

00:08:03.247 --> 00:08:06.406
So you have a three carbon backbone right over here,

00:08:06.406 --> 00:08:10.350
so this is a carbon, that's a carbon,

00:08:10.350 --> 00:08:11.462
that's a carbon there.

00:08:11.462 --> 00:08:13.522
Each of them are attached to an oxygen,

00:08:13.522 --> 00:08:14.869
so you can imagine that this

00:08:14.869 --> 00:08:17.353
could have been derived from glycerol.

00:08:17.353 --> 00:08:18.886
And then two of the carbons,

00:08:18.886 --> 00:08:23.554
like in a triglyceride, are bound to a fatty acid like this,

00:08:23.554 --> 00:08:26.153
but then one of the carbons, the third carbon,

00:08:26.153 --> 00:08:28.267
instead of being bond to a fatty acid

00:08:28.267 --> 00:08:30.165
like you have in a triglyceride,

00:08:30.165 --> 00:08:32.823
it is bounded to a phosphate group.

00:08:32.823 --> 00:08:34.750
So this right over here,

00:08:34.750 --> 00:08:36.968
this right over here is a phosphate group.

00:08:36.968 --> 00:08:39.603
And this R could just be another chain,

00:08:39.603 --> 00:08:43.886
another chain of, another organic chain, so to speak.

00:08:43.886 --> 00:08:46.881
But when we talked about amphipathic molecules,

00:08:46.881 --> 00:08:48.043
I always have to say it slowly,

00:08:48.043 --> 00:08:50.712
so it's a bit of a tongue twister for me.

00:08:50.712 --> 00:08:52.768
We're talking about having a hydrophobic end

00:08:52.768 --> 00:08:54.103
and a hydrophilic end.

00:08:54.103 --> 00:08:56.203
Well what's the hydrophobic end here?

00:08:56.203 --> 00:08:59.653
Well this, these, this chains from the fatty acids,

00:08:59.653 --> 00:09:01.607
especially the hydrocarbon chains right over here,

00:09:01.607 --> 00:09:03.615
these are gonna be hydrophobic.

00:09:03.615 --> 00:09:07.468
Hydro, hydrophobic.

00:09:07.468 --> 00:09:10.734
While the phosphate end right over here it has charge,

00:09:10.734 --> 00:09:13.674
charged molecules dissolve in water very, very well.

00:09:13.674 --> 00:09:17.076
And so this one over here is going to be hydrophilic.

00:09:17.076 --> 00:09:19.234
It's going to be, it's going to be, I guess you could say

00:09:19.234 --> 00:09:20.929
it's going to be attracted to water.

00:09:20.929 --> 00:09:22.253
And that's why phospholipids,

00:09:22.253 --> 00:09:24.087
and this is just one type of phospholipids,

00:09:24.087 --> 00:09:25.770
these chains could be different.

00:09:25.770 --> 00:09:28.486
We have a, we have a unsaturated chain here,

00:09:28.486 --> 00:09:29.926
and then, a fatty acid chain,

00:09:29.926 --> 00:09:32.365
and then we have a saturated fatty acid chain on the left,

00:09:32.365 --> 00:09:35.465
and this just actually just made up in this molecule,

00:09:35.465 --> 00:09:36.406
but, and they could be different

00:09:36.406 --> 00:09:38.588
depending on the phospholipid you're talking about.

00:09:38.588 --> 00:09:42.187
But this general property of having a hydrophilic head

00:09:42.187 --> 00:09:44.451
and hydrophobic tails make them very well suited

00:09:44.451 --> 00:09:45.959
for cellular membranes.

00:09:45.959 --> 00:09:47.504
Because you could imagine,

00:09:47.504 --> 00:09:52.089
so hydro, that end is hydro,

00:09:52.089 --> 00:09:53.204
hydrophilic,

00:09:53.204 --> 00:09:56.246
and then you have these hydrophobic,

00:09:56.246 --> 00:09:57.883
hydrophobic tails.

00:09:57.883 --> 00:09:58.926
Actually, let me see if I can copy

00:09:58.926 --> 00:10:00.228
and paste this really fast.

00:10:00.228 --> 00:10:02.026
I actually can just draw it really fast.

00:10:02.026 --> 00:10:04.153
So let me just draw a bunch of them.

00:10:04.153 --> 00:10:06.820
Whoops, nope, I'm having trouble.

00:10:06.820 --> 00:10:08.561
Alright, let me just switch back

00:10:08.561 --> 00:10:09.977
to my drawing tool.

00:10:09.977 --> 00:10:14.842
So let me just draw a bunch of the hydrophilic heads

00:10:14.842 --> 00:10:17.535
and then a bunch of the hydrophobic,

00:10:17.535 --> 00:10:19.172
whoops, actually I'll draw a few more

00:10:19.172 --> 00:10:21.794
hydrophilic heads out here,

00:10:21.794 --> 00:10:24.175
and then I'll draw the hydrophobic tails.

00:10:24.175 --> 00:10:28.134
Hydrophobic, hydrophobic tails, let me draw them,

00:10:28.134 --> 00:10:29.851
draw them really fast.

00:10:29.851 --> 00:10:34.495
I'm almost done right over here.

00:10:34.495 --> 00:10:36.883
Hydrophobic tails right over here.

00:10:36.883 --> 00:10:39.343
And this configuration that I've just drawn

00:10:39.343 --> 00:10:41.840
where you have a bilayer of phospholipid,

00:10:41.840 --> 00:10:45.322
of phospholipids, a phospholipid bilayer,

00:10:45.322 --> 00:10:48.167
this is how cellular membranes are constructed.

00:10:48.167 --> 00:10:51.777
Because this you have water,

00:10:51.777 --> 00:10:53.483
or things that are very water based

00:10:53.483 --> 00:10:55.873
inside the cell, this could be inside,

00:10:55.873 --> 00:10:59.450
inside the cell, and this could be outside,

00:10:59.450 --> 00:11:01.052
this is outside the cell.

00:11:01.052 --> 00:11:03.571
And so the phosphate ends is attracted to the water

00:11:03.571 --> 00:11:05.486
and then, but the hydrophobic,

00:11:05.486 --> 00:11:09.352
the hydrocarbon tails, those are going to,

00:11:09.352 --> 00:11:11.326
they're going to orient themselves in this way

00:11:11.326 --> 00:11:13.404
to get away, to get away from the water.

00:11:13.404 --> 00:11:15.167
Really they'll just let the phosphate,

00:11:15.167 --> 00:11:18.209
the phosphate ends interact with the water.

00:11:18.209 --> 00:11:21.008
And so this forms a nice boundary for the cell.

00:11:21.008 --> 00:11:23.143
And we're gonna study that thoroughly

00:11:23.143 --> 00:11:25.431
as we go more into biology.

00:11:25.431 --> 00:11:26.870
So hopefully this gives you more appreciation

00:11:26.870 --> 00:11:30.092
of what a lipid is and the different types of lipids.