OK. So the thing that we're going to talk today about are
macromolecules. And often these are polymers.
Now, all macromolecules comprise of multiple carbons joined together in
some way. But the real definition of a polymer is that there is some
kind of monomer that is joined together in a repeated way to make
some kind of multimer that forms the polymer. OK.
Now, integral to understanding all of this is the notion of chemical
bonds. And you're going to, in this week's Section you're going
to be addressing, remembering, understanding what
chemical bonds are. And here are some concepts that are
essential that you understand for chemical bonds.
Let me list them on the board. And then we'll go through them in
some more detail. And then I'm going to move on.
And you are going to deal with this more in Section,
but this is really integral to understanding the rest of the course.
So one of the terms you need to know is electronegativity.
Anyone want to give me an electronegativity definition?
I may be able to find another chocolate fish for an
electronegativity definition. Where? A little hand.
Yeah? Say it again. OK. Good. Yeah. How strongly an atom
attracts electrons. This is good. You see,
you get to practice catching and I get to practice throwing.
So the relative affinity of a particular atom for electrons.
OK? So that's one think you need to know. Valance.
Super important. Valance. Yeah?
How many electron slots available for connections.
Try to rephrase. Yes, but rephrase it a bit.
We're talking about chemical bonds. So? OK, how many bonds. I did not
give that away. OK. How many bonds a molecule can,
an atom can make. OK? OK. And then we get into the
bonds per se. And I'm going to list them here. I'm going to list them
in order from strong to weak. Covalent bonds. Ionic. I'll go
through some slides in a moment.
Hydrogen and something I'll call hydrophobic. OK.
And covalent bonds are the strongest and these so-called
hydrophobic bonds are the weakest bonds. Ones that we are
particularly interested in, actually, we're interested in all of
them, but I would say covalent, hydrogen and hydrophobic bonds are
particularly important. And you will see when we talk about
DNA, hydrogen bonds are very important.
So let's go through some pictures. This is a table from your book, I'm
not going to dwell on too much, but you really need to be familiar
with this, you need to understand what is in this.
And it will indicate for you what the nature of the different
bonds are. OK. Covalent bonds,
really, the two atoms become very closely joined together.
And, again, you're going to deal with this. Let me just move onto,
in your recitation. Let me deal with two things that I want to dwell
on a little bit. The first is the notion of polar
and nonpolar molecules. OK? So polar molecules have got
differential charge distribution. All right? So we can add that
actually to our list. If you want to go back and add
something to your list, its part and parcel of the notion of
electronegativity, but let's also write polar versus
nonpolar molecules. In a polar molecule,
the charges in the molecule are asymmetrically distributed.
Whereas, in the nonpolar molecule the charges are uniformly
distributed and there is no net asymmetry of charge in that
particular molecule. And that will become important in a
little bit. Here is one that, again, you will dwell on in Section
but I will introduce now. Hydrogen bonds are between a
hydrogen and an oxygen, and the hydrogen or something else,
something that is more electronegative,
the hydrogen, it's the hydrogen, this is not a covalent bond.
And the hydrogen interaction is integral to the structure of DNA,
as we will discuss in this lecture and when we talk about molecular
biology. OK. So that is a very cursory introduction to something
that you will be dwelling on more in Section this week.
OK. So I want to talk now about polymers.
And I want to talk how they form biologically. And I'm going to tell
you about two types of reactions that you should understand.
Condensation reaction which forms a polymer and a hydrolysis reaction
which breaks a polymer.
So let's look at a diagram here that I've taken from your book.
Here are two monomers. And you can see there is a hydroxyl group and a
hydrogen group and a hydrogen. And those two things react with one
another and, with the use of energy, water is released, and the two
monomers are joined to one another. OK? Again, you're going to have
plenty of practice at this. Don't try to draw this diagram here.
OK? You can, we'll deal with it in a little bit.
Just look at it and understand what I'm saying at the time and it really
is sufficient. So, here, you've got the exclusion
of water, the use of energy to get two monomers joined up,
and then the process continues and you get a polymer being built up of
more and more monomers. Now, the converse of that is
hydrolysis where you add water and also use energy to break up a
polymer and release a monomer. So either hydrolysis reaction or a
condensation reaction are energy requiring reactions.
And this energy has to come from somewhere. And we will spend a
lecture talking about where the energy comes from.
So I want to draw the analogy, and it may seem hokey to you, but
it's actually quite useful, a useful way for me to think about
this, so I want to share it with you. I want to draw the analogy to the
cell as a factory. And I want to begin by talking
about the materials that the factory uses to synthesize whatever it is
it's going to synthesize. And then as we move through the
biochemistry section I'll talk about the machinery within the cell that
makes the synthesis take place. So we're going to talk about the
materials that are present in the cell. And particularly we're going
to talk about four groups of macromolecules,
the big four from which everything else is built and that really are
pivotal for life. These are proteins.
And, actually, let me not list them in that order.
Let me list them in the order in which I'm going to talk about them.
I'm going to talk about lipids, carbohydrates,
nucleic acids. And I'll talk about those three today.
And then next time I'll talk about proteins. So if you look at the dry
mass of a cell it's very interesting.
Lipids comprise about 5% of the dry mass, carbohydrates about 25%,
nucleic acids 10%, and proteins about 55%. OK.
So that's what we're going to be talking about,
these four groups of macromolecules that make up the components
of the cell. Now, two things that I want to point
out as we talk about these macromolecules is that very often in
biology the polymers have two properties that are very important.
One, they have polarity. That means one end is different from the
other end. OK? And the other thing that they very
often have, not always but some classes in particular,
is a linear order. OK? So that's, both of those properties,
if you give this a moment's thought, you will see are very similar to
sentences. There's a beginning and an end of a sentence,
and within a sentence the words come in a particular order.
And that gives you an information content. That gives you a way to
carry out or to store information. So I'll point this out.
This is particularly true for the proteins and the nucleic acids.
It's also somewhat true for carbohydrates and less so for lipids.
So these two properties of biological polymers are fascinating
and they are crucial for life to proceed. All right.
So let's move onto one of the big four. Lipids.
Lipids. So lipids are a somewhat large and almost amorphous group of
molecules in that I cannot give you a chemical formula,
really, to say this is definitely a lipid and this is not a lipid.
They have one property that is crucial for defining them as lipids,
and this is that they are hydrophobic --
-- or nonpolar.
And this property of being hydrophobic, so lipids in foods.
What are the lipids just, you know, in your food pyramid? It's just to
make sure we're all talking about the same stuff here.
Fats and oils, right. Yes. And you can come and get a
fish later. OK. So fats and oils.
They're used for a couple of things. One of the things about fats and
oils is that they store a lot of energy. So they serve as a
long-term energy source for the cell. And the other thing they do really
has to do with their insulation properties. And their insulation
properties fall into multiple categories. The most important one
we touched on last time when we talked about the components
of a cell. We talked about the fact that the
cell is a cell, and the organelles in the cell are
organelles because they are membrane bound. And I threw out at you the
term lipid bilayer, and I'll throw it out at you again
in a moment. This is something made of lipids that insulates the cell
from its environment or subcellular compartments from one another.
So part of the insulation property are membranes.
And, again, this term, I'll write on the board this time,
lipid bilayer. And the other aspect of insulation or the more classical
things you think about, you don't get cold because you've
got a layer of fat under your skin, and that stops yourself from losing
heat. So heat loss. And, for example,
birds use lipids to waterproof their feathers so that they can stand in
the rain and not get wet. OK. Another aspect that I'll throw
out at you also here is that lipids also make things called hormones,
which are substances that control various aspects of body function.
I'll have a little more to say about them in a couple of minutes,
and then will have quite a bit more to say about them when we talk about
reproduction. So let me see what is next here.
OK. So let's talk about some typical lipids and some examples of
lipids. This is a diagram from your book, so you can go and look at it
at your leisure, of a triglyceride.
Now, what I want you to take from this is that, so triglycerides,
tri meaning three. And the glyce- part is from glycerol,
which is this molecule up here, onto which three long carbon chains
are added. And these long carbon chains are called fatty acids.
And that's important to know. So a triglycerides is glycerol onto which
three fatty acid chains have been added.
And it's the fatty acid chains that are hydrophobic.
So triglycerides are a very common
type of lipid. Now, after I just told you,
ah, it's fixed. After I just told you that lipids were
all hydrophobic. I'm now going to tell you that some
lipids are amphipathic. And they're amphipathic,
so amphipathic means that they have both polar plus nonpolar components.
And one of the most important amphipathic molecules in the lipid
field is a phospholipid. So this is a molecule that's got
these fatty acid long carbon chains on one end and on the other end has
got a very polar phosphate group. OK? And here's phosphate with
something called choline added onto it. So this is phosphatidylcholine.
And phospholipids, and I spelt amphipathic incorrectly.
Phospholipids are essential for formation of the lipid bilayer
membranes. And the reason they are is because of this dual charged and
noncharged portion. So here is a diagram that I showed
you last time that was not as well labeled. This is a diagram of a
lipid bilayer, so one of the membranes that
surrounds your cells and your organelles.
Facing out onto the water of the cell are the hydrophilic heads of
this phospholipids, the charged heads. And then facing
one another are two rows, OK, of these hydrophobic fatty acid
tails. So the bilayer is because you have one layer of these
molecules with the hydrophilic heads facing the water,
the hydrophobic tails pointing in. And those interact with another
layer where the hydrophilic heads are pointing to the water and the
hydrophobic tails are pointing inwards. The hydrophobic tails
interact with one another and you get this very stable lipid bilayer.
OK. It's very cool. That's how things work, and they work very
easily. And you can get them to be synthesized in a test-tube very
easily. Here is another one. Saturated versus unsaturated fats.
Unsat, OK, as an unsaturated.
In saturated fats, the fatty acid side chain contains no double bounds.
OK? So it saturated four hydrogens. In unsaturated fats, there are some
double bonds that would allow one to add more hydrogens if they
were broken. OK? So saturated versus unsaturated fats.
So saturated fats are the things you find in butter and in hard fats.
And they're supposed to be bad for you. OK? So saturated fats have
been implicated in raising something called low density lipoproteins
which are involved in various aspects of cell function that are
believed to lead to heart disease. But it turns out that there's more
to it than that. So if you've ever been really bored
and you've read the ingredients on the box of cookies that you've eaten,
you may see something that says partially hydrogenated vegetable oil.
Yeah? OK. Now, your vegetable oil is rather
unsaturated. OK? It's got a lot of double bonds.
And one of the reasons that it is liquid is because these double bonds
are there and you don't get the chains of the lipid packing very
tightly and it's a liquid. But you can take your vegetable oil
with lots of unsaturated bonds and you can partially saturate it.
And you can get out of that two kinds of partially saturated fat,
partially hydrogenated fat. You can get this stuff called
transunsaturated fat. Now, if you look at this diagram,
you will see these fatty acid side chains are in nice order here.
OK? And they are because the hydrogens that are across from the
double bonds are intrans from one another. They're kind of diagonally
opposite from one another. And what that does is to allow
these side chains to pack very tightly, and you get a very
hard fat that way. Somehow this partially hydrogenated
stuff is very bad for you. It raises your LDL, it reduces this
stuff called high density lipoprotein, which is good for you,
and it increases your heart disease risk. Interestingly,
you do not find these types of molecules in nature.
You only find them when you hydrogenate your vegetable oil and
make your margarine or make the stuff that McDonald's cooks its
French fries in, OK, and its chicken nuggets.
So a couple of years ago there was so much issue about this that
McDonald's pledged to find a different vegetable oil in which to
fry its fries. And it's still searching,
apparently, because there's some issue with taste being compromised
as you go to healthier fats. OK. Now, in contrast to the
transunsaturated fats there's this sysunsaturated fat also.
And if you look here, you can see that these side chains
are kinked. And the reason they're kinked is that the hydrogens across
the double bond are on the same side of the molecule as one another.
That has the effect of not allowing the side chains to pack tightly.
So you get side chains floating all over the place,
and that changes the energy of the fat so that it is a liquid rather
than a solid. And these are much better for you,
these sysunsaturated fats. And you find them in lots of
vegetable oils and vegetable fats. OK. Here's another one.
Here's our joke for the day. OK. Steroids. Steroids are a
lipid. They are derived from, OK, so let me just say for this
unsaturated. I mentioned sys and transunsaturated fats.
I'm going to mention steroid hormones.
There are a few of them. Steroids are not all hormones,
although cholesterol, we don't think of cholesterol as a hormone,
although, actually, I think it really is. Vitamin D is a vitamin
that works together with other molecules. Cortisol and
testosterone are classically thought of as hormones.
Very small amounts of them will change body function in profound
ways. And we'll have more to say about testosterone later
on in the course. The androgens that lead to people
who have large green muscles are a class that are related to
testosterone, androsterone and so on, but they're all the structures with
these four rings in this characteristic way are all
characteristic of a steroid. All right. So that is all I have
to say about lipids. Let's move onto either number two
here, carbohydrates. So carbohydrates have as their --
OK. Carbohydrates.
Also classically known as sugars.
And because of that there are a couple of functions of carbohydrates.
They are the major source of short-term energy.
If you need short-term energy you use carbohydrates.
They're also a carbon source, so we'll talk extensively about
building up molecules. And you need carbons to do that.
Carbohydrates serve as a carbon source for building other molecules.
And, as I'll mention briefly, they also can convey information.
Carbohydrates have, as their chemical principle,
so we can find a chemical principle that unifies them,
they all contain carbons that are joined to a hydrogen and to a
hydroxyl, and obviously to other things as well.
So you can loosely give carbohydrates the formula of CH2O to
the N. Now, the monomer, now we can actually, with lipids
it's very hard to talk about a monomer and a polymer. In
carbohydrates one can. And one can talk about the monomer,
which is called a monosaccharide which polymerizes to form a
polysaccharide. And they do so.
One can also get, let me just write it here,
one can also get disaccharides where disaccharides are two and
polysaccharides are really more than two.
They're usually more than ten or so, but for our purposes more than two
is fine. OK. So in order to form a polymer of carbohydrates,
one forms a glycosidic linkage or glycosidic bond.
So it's a covalent bond where one has --
Two carbohydrates or two
monosaccharides interacting with one another through a condensation
reaction, classical condensation reaction with the elimination of
water to give you, excuse me, yeah, no.
I wrote this down incorrectly in my notes. Apologies.
OK. To give you a glycosidic linkage. OK? So this is a
classical condensation reaction. Now, polysaccharides or
carbohydrates are interesting. They can either be rings or they
can be linear. And they can also be modified.
So like the lipids where you could get phospholipids,
carbohydrates can have various extra things added onto them that changes
their properties. Let's take a look at a few of them.
Here are some monosaccharides. And the ones that are super important
for you to know are these two down here. OK? And you should know the
structures of these. This is ribose and deoxyribose.
And the reason for this will become clear when I move onto the next
class of macromolecules, DNA and RNA, because those sugars
are part of DNA and RNA. OK? So these ribose and deoxyribose
are five carbon rings. You can see they're not quite a
five, they're not a five carbon ring. They are five carbon sugars.
And this is an isomer of one of the forms that this five carbon sugar
can take. OK. So some of you may be lactose
intolerant and might not be able, in fact, to enjoy digging in and
enjoying a bowl of creamy delicious ice cream.
So, in fact, the reason, I didn't make that up, though the
reason you cannot is because you need a specific protein,
a specific enzyme that we'll talk about, not the specific enzyme,
but we'll talk about the notion of enzymes in a couple of lectures that
breaks a bond between the disaccharide that is lactose.
So lactose is a disaccharide that is a galactose joined together with a
glucose. OK. So these are six carbon sugars.
And there's a bond between the two of them that you have to break in
order to digest the lactose from milk. And if you cannot then this
lactose causes you digestive issues. Here on the top is sucrose which is
a dimer, a disaccharide, a glucose joined to a fructose.
OK. So here's an interesting question. I don't know when you
were little, but when I was little I used to try and eat grass.
And, clearly, that doesn't work very well. Humans cannot eat grass.
Whereas, cows and many animals can survive just very well on a diet of
just plants. And that is because we cannot deal with this carbohydrate
in plants called cellulose. Now, interestingly,
we can digest other plant carbohydrates,
particularly starch or amylose which is what most of the carbohydrates
that we eat come from. The reason for this is interesting,
and it has to do with these glycosidic linkages.
OK. So here we have a linkage between glucose,
two glucoses that give something called maltose.
And maltose is part of the starch carbohydrate, or the amylose
carbohydrates. And what you should know here about
these chains, these circles, and you should remember from old
chemistry as if there is a bold part in the front of this ring then it is
coming out of the board towards you. OK. So here you have these two
glucoses linked such that a bond joining them is coming out of the
board towards you. Now, conversely,
and this is called an alpha 1, 4 bond where the bonds coming out of
the board towards you in cellobiose, which is a precursor for cellulose,
the grass carbohydrate, the bond goes back, OK, back away
from the rings. And that's called a beta 1,
4 linkage. And we can break this alpha 1, 4 linkage but not this beta
1, 4 linkage. And I'll come back to this when we talk about enzymes.
We do not have the correct enzymes to do so. And finally with respect
to carbohydrates, I mentioned that they were sources
of information. One of the interesting sources of
information from carbohydrates is in your blood cells.
So your blood group is as a result of adding specific chains of
specific carbohydrates, specific monosaccharides,
and a whole bunch of them, onto particular red blood cell
surface proteins. So if you're an A blood group,
you have a series of specific carbohydrates added on in order to
one of these cell surface proteins. If you're a B blood group, you also
have this carbohydrate chain but the specific carbohydrates,
the specific monosaccharides are different. All right.
So let's move onto the reason that you're all really sitting here.
So, really, the reason that you're all sitting here is because of this
next group of macromolecules. And I don't mean that that's the
reason, you know, you're alive, that you exist in life.
I mean that's the reason you're talking 7.013.
Because nucleic acids are the thing that have, and the understanding of
nucleic acids is what has revolutionized biology so that --
So that everyone in every discipline
at MIT has some association, has some way of using the
information from nucleic acids to their advantage and in their careers.
OK. So nucleic acids, as I'll discuss, do serve as an
energy source or as a way of storing energy, but most important is their
function, and that's a super important function.
But the reason you're talking 7. 13 is not because of that.
The reason you are is because of the information content that nucleic
acids are able to carry and to perpetuate from one generation to
another. So, really, what they are involved in is
information storage and transfer. All right.
So, again, as for carbohydrates, we can talk about monomers and we
can talk about polymers. The monomers for nucleic acids is a
nucleotide. Oh, OK. Enough air play.
Watson and Crick get a lot of air play, so that's enough.
You can go and look at their picture at your leisure. OK.
So I've taken this from your book and I'm going to draw some stuff on
the board. I want to point out that in the new edition of your book,
you will find there is a mistake in the structure of your nucleotides.
That was true in the last edition. I wrote to the senior author. I
said there is a problem with the sugar structure in the nucleic acids.
Would you please change it for the next edition? And he said
absolutely we will. And the new edition came out and
there we are. OK? So we'll have to,
so we're going to deal with that, but I think we'll get you all free
copies, or your successors free copies of the next edition of the
book or something to make up for this. But, actually,
it's a good exercise for you because you can learn the proper structure
of the sugar. So what is a nucleotide? OK.
A nucleotide, as you gather, has a sugar associated with it.
It has, the sugar it has associated it with is either ribose
or deoxyribose. This sugar is joined to a phosphate
group. And the sugar is also joined to something called a base.
Now, the sugar is a five carbon ring. I'll come back to this slide
in a moment and we'll talk about the bottom part of it.
The sugar is a five carbon ring. OK? Here it is. It's actually a
four carbon ring with an oxygen and there's another carbon
sticking out. And what they've done in your book
is to forget about this carbon up here and turn this oxygen here into
a carbon. So it's kind of weird. Later in the book the structure is
correct, but you should bear this in mind. I've pointed this out in your
PowerPoint handouts. OK. So what's really important,
there are two things about nucleotides that are really
important. One is this phosphate and sugar because that is the way
nucleotides polymerize with one another.
And the other is the base which is the part of the molecule that gives
rise to the information. Actually, let me just stop this and
write the bases here. So let me tell you the names of the
bases. And you need to know these. There are four of them. Five
really. There is adenine,
guanine, cytosine and thymine. And then there's also something
that's an alternate to thymine called uracil.
And they are abbreviated by their first letters.
OK? So A, G, C and T and U. And you need to know these letters.
And you need to know what they stand for. All right.
So let me, in the last two minutes,
tell you about some properties. Actually, let me tell you about the
bond that forms the nucleic acid polymer. And then I'll finish this
off next lecture. The bond that forms the polymer is
called a phosphodiester bond.
And it forms by the reaction of the phosphate and the sugar with one
another, or groups on the phosphate and the sugar with one another.
The base has got nothing to do with this polymerization.
So we have here a phosphate with some oxygens that's joined onto the
sugar. So I'm abbreviating the phosphate P, I'm abbreviating the
sugar S, and I'm abbreviating the base B. OK? And the sugar is
attached to a base. And the sugar has, in one part of
it, a reactive hydroxyl group. And the phosphate has some reactive
oxygen groups. And let's not worry too much about
bonds and double bonds and things for now.
OK. And I'm not worrying about
charges on oxygens and things either. What happens,
basically, is that there is an interaction between this hydroxyl
group and the phosphate group, OK, or one of the oxygens on the
phosphate group. And you get out of this a linkage
that goes --
OK. Where you get between the sugar and the phosphate this
phosphodiester linkage. OK? An OPO linkage that joins the
two sugars to one another through a phosphate molecule.
This is your phosphodiester bond. And I want to point out that the
bases, which I will tell you next time, are the part of the molecule
that carries the information, have got nothing to do with the
polymerization of nucleic acids. So I'm going to continue with this
next time and briefly finish nucleic acids and then move
onto the proteins.