Macromolecule Lecture: Carbohydrates, Lipids, Proteins, and DNA

Name: Biology 1A Lecture 2
Uploaded: 2015-05-07T15:06:31+00:00
Duration: 53 min 2 s
Channel: Saylor University
Description: Summary and key takeaways on Biology 1A Lecture 2: Summary & Key Takeaways, covering The lecture begins with a brief review of the previous class on thyroid

Saylor University

May 07, 2015

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53 min video

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2 min read

YouTube video ID: zTO9ETVIsxA

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The lecture begins with a brief review of the previous class on thyroid versus thymus anatomy, then shifts to an overview of the four major classes of biological macromolecules that compose all living cells.

Carbohydrates

Monosaccharides such as glucose (C₆H₁₂O₆) represent the simplest sugars and follow the general formula CH₂O. Classification depends on the position of the carbonyl group (aldose or ketose) and the length of the carbon chain. Disaccharides arise through dehydration reactions that create glycosidic bonds, while polysaccharides are formed by further polymerization. Energy‑storage polysaccharides include starch in plants and glycogen in animals; structural polysaccharides include cellulose in plant cell walls and chitin in insect exoskeletons.

Lipids

Lipids are defined by their hydrophobic character and predominance of non‑polar bonds. Fats consist of a glycerol backbone esterified to fatty acid chains; saturated fats lack double bonds and are solid at room temperature, whereas cis‑unsaturated fats contain double bonds and remain liquid. Trans fats are artificially produced, often solid, and are metabolically challenging. Phospholipids incorporate a polar phosphate head, enabling bilayer formation in cell membranes. Steroids, exemplified by cholesterol, possess a four‑ring core and function in signaling and membrane stability.

Proteins

Proteins are polymers of 20 common amino acids linked by peptide bonds. Each amino acid contains an amino group, a carboxyl group, and a variable R group that determines its chemical behavior (non‑polar, polar, acidic, or basic). Protein structure is hierarchical:
- Primary – linear amino‑acid sequence.
- Secondary – local hydrogen‑bonded motifs such as α‑helices and β‑pleated sheets.
- Tertiary – three‑dimensional folding of a single polypeptide chain.
- Quaternary – assembly of multiple polypeptide subunits, as seen in hemoglobin.
X‑ray crystallography remains the principal technique for resolving three‑dimensional protein structures.

Nucleic Acids

DNA and RNA are polymers of nucleotides, each comprising a nitrogenous base, a pentose sugar, and a phosphate group. DNA contains deoxyribose, while RNA contains ribose distinguished by a 2′‑hydroxyl group. DNA is typically double‑stranded and antiparallel; RNA is usually single‑stranded. Base pairing follows the rules A↔T (or U in RNA) and C↔G, enabling faithful replication and transcription.

Mechanisms & Explanations

Dehydration reactions join monomers by releasing water, forming covalent bonds such as glycosidic bonds in sugars or peptide bonds in proteins. Hydrolysis reverses this process, adding water to break those bonds. In X‑ray crystallography, purified proteins are crystallized; X‑ray diffraction patterns are transformed into electron density maps that model atomic positions. Genetic information flows from DNA in the nucleus to messenger RNA, which travels to ribosomes for translation into protein.

Hard Facts & Numbers

Water is the most abundant molecule in cells.
Glucose formula: C₆H₁₂O₆.
There are 20 standard amino acids.
Proteins constitute more than half of the dry mass of most cells.
DNA bases are adenine, thymine, cytosine, and guanine.

Takeaways

Carbohydrates range from simple monosaccharides like glucose to complex polysaccharides that store energy or provide structural support.
Lipids are hydrophobic molecules whose saturated, unsaturated, and trans forms differ in bond structure and physical state.
Proteins are built from 20 amino acids, with hierarchical structures from primary sequence to quaternary assemblies such as hemoglobin.
DNA and RNA are polynucleotides that store and transmit genetic information through base pairing and transcription‑translation pathways.
Dehydration creates covalent bonds in macromolecules, while X‑ray crystallography reveals protein three‑dimensional structures.

Frequently Asked Questions

What is a glycosidic bond and how is it formed?

A glycosidic bond links two monosaccharides through a dehydration reaction that removes a water molecule, creating a covalent connection between the sugar units. This bond defines disaccharides and polysaccharides and determines their structural and functional properties.

How does X‑ray crystallography determine protein structure?

X‑ray crystallography first crystallizes a purified protein, then directs X‑ray beams at the crystal lattice. The resulting diffraction pattern is mathematically converted into an electron density map, which researchers interpret to model the protein’s three‑dimensional atomic arrangement.

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Helpful resources related to this video

If you want to practice or explore the concepts discussed in the video, these commonly used tools may help.

Molecular Biology Model Kit For Students Recommended

Provides a hands-on way to visualize complex molecular structures like amino acids, nucleotides, and polysaccharides, helping students understand 3D spatial arrangements.

Amazon →

Campbell Biology Textbook

This is the standard comprehensive reference for university-level biology, covering all four classes of macromolecules and their functions in detail.

Amazon →

Dna Double Helix Model Kit

Allows for the physical assembly of nucleotides to demonstrate base pairing and the antiparallel structure of DNA discussed in the lecture.

Amazon →

Protein Structure And Function Reference Book

Provides in-depth diagrams and explanations of primary through quaternary protein structures, which are central to understanding biological function.

Amazon →

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Summarize another video

Full Transcript YouTube

Good morning everyone. Happy Friday.
How are you guys doing?
Good.
So, uh, today we're going to talk about
biological polymers. And, um, if you
took a look at the syllabus and the
textbook, you'll see that we're already
on chapter five. Okay? So, but don't let
less that scare you. If you look at the
first four chapters of the book, as we
talked about last time, they're really
mostly review. And so um be do be sure
to have a look at that and and if that
material is review for you great. If
it's not be sure that you uh feel that
you really understand it. So you know
you need to know sort of some of the
basics of of chemistry and and beginning
organic chemistry to understand some of
the stuff that we're going to be talking
about today and then of course um for
the rest of the course as well. So uh
when I want to do one quick thing first
before we move on to today's lecture and
that is just to correct something I said
last time. So we were talking about um
deficiencies in uh various elements and
we talked about the disease goer which
is shown on the right panel there and
and that's actually in the thyroid gland
right in the neck in the thyroid gland.
So I think I said thymus I meant to say
thyroid gland some of you caught it. So
that's that.
So I want to move on today to uh talking
about um biological macroolelecules. And
when we talk about macroolelecules,
we're really talking about uh molecules
that are big, right? Macro, big. And um
and so we're going to really focus today
on four types of molecules in
particular, sugars and carbohydrates,
fats and lipids, amino acids and
proteins, and nucleotides and nucleic
acids. And so what you might notice is
that on in each case on the left is the
building block of uh the macroolelecule.
Okay. So um first of all all living
things are basically made up of four
these four classes of large molecules.
And these are the carbohydrates, lipids,
proteins and nucleic acids. And so um
this doesn't mean that there aren't
other molecules in cells. Of course
there are. You all know that the most
common abundant molecule in the cell is
what?
Water, right, from last time. Yeah. So,
that's for sure the most abundant
molecule. Um, and there's also lots and
lots of small molecules, right? Things
that are not polymers or or have a large
very high molecular weight, but are
small molecules. But um but the
components that are required to actually
build a cell make the structures that
are required and have the functions that
carry out the uh life uh processes
replication and division that occur in
the cell all uh come together with these
four types of macroolelecules.
Okay. And so as I said so the uh the
building blocks in each case uh sugars
make up polysaccharides,
fatty acids make up lipids and and cell
membranes. Amino acids make up proteins
and nucleotides
make up uh nucleic acids DNA and and
RNA.
Okay. So let's first talk about
carbohydrates. Um these are uh sugars
and the polymers that are formed from
sugars. The very simplest carbohydrates
are are called monossaccharides.
Monossaccharides. These are single
sugars. Okay. things like glucose and um
what carbohydrates are the
macroolelecules are polysaccharides. So
these are the polymers that are co
composed of many uh sugar building
blocks. And your book has a very nice um
more detailed discussion of of all of
this than than we're going to go into
today. But please do read that part of
of chapter 5 to get a a good handle on
the chemical structures of
monossaccharides and how they come
together uh to form polysaccharides. But
we're going to I'm going to call your
attention to a few things in particular.
Okay. So, first of all, uh
monossaccharides have a chemical formula
that allows us to very quickly tell that
this is likely to be a sugar. Okay. So,
um these are molecules that typically
have a chemical formula that is a
multiple of C H2O. Okay. So for example,
glucose, the chemical formula is C6 H12
06 and it's the most common
monossaccharide. But if I gave you a
chemical formula that uh was something
like C20 H4020,
even without knowing what exactly what
that uh structure is of that molecule or
drawing it out, you would know that
that's very likely to be some kind of a
saccharide, right? Some kind of a sugar.
Um, okay. And so monossaccharides are
classified by the location of the
carbonial group as an aldos or a ketos.
We're going to look at this on the next
uh slide, so hold on. And also by the
number of carbons in the carbon skeleton
of the molecule. And very importantly,
monossaccharides are the major fuel for
cells. And they're also the raw material
for building uh molecules that are used
both for fuel storage in the cell and
also as we're going to see very
importantly for building various kinds
of cellular structures especially in
plants and insects. Okay.
So um to make a carbohydrate polymer
what happens is that monossaccharide
individual monossaccharide building
blocks come together and react to form a
disaccharide or they can and then of
course those can react to form much
longer polymers as well. So this is just
showing you an example of two
monossaccharides coming together to form
a disaccharide.
And um just again a couple things in
passing. So be sure that you are
familiar with the different ways of
drawing sugar molecules and you may
remember this from chemistry class but
if you don't again there's a nice
discussion in your book. So you know you
might know that or you might remember
that sugar molecules we can draw them as
linear molecules but the re in in
reality in solution in aquous solution
where these are found in biology these
molecules are almost always circularized
and in the form that we're showing here.
Okay, so this is the typical way that
we'll draw these uh molecules. And what
this slide is showing you is a
dehydration reaction between a glucose
monomer on the left hand side. So this
uh monomer right here with a fructose
monossaccharide over here. And the
chemistry that's going on is really um
exactly like this word implies,
dehydration. we're losing a water
molecule when these two monossaccharides
come together and form a covealent bond
that links them together to form a
disaccharide that in this case is
sucrossse. So this is table sugar,
right? And so you may know that glucose
is the the simple sugar that is mostly
used by our brains for example for fuel
metabolized uh burned in our uh in our
cells for to provide energy. Fructose is
a fruit sugar right? So this is the the
sugar that's very commonly found in
fruit plants. But if we combine them
together to make this disaccharide, we
have a much sweeter molecule. Tastes
much sweeter to us um called sucrossse.
And that's the the structure right
there. Okay. So this is an example of
what's called a condensation reaction
where we losing dehydration. We're
losing water. And once uh two
monossaccharides are hooked together
like this, this bond that forms is
called a glyositic bond. Okay? It's
glyosidic bond. And um you might also
notice that there's a directionality to
this bond, right? So the the uh
in this case the bond is pointing down
with respect to the plane of each of
these sugar molecules. And this is
actually turns out to matter a lot. So
depending on the the orientation of
those of the of the uh bonds that come
together to make these uh sugar
linkages, we can have molecules that are
uh that are e either easily metabolized
by uh our cells for example or are not
very easily metabolized by our cells.
Okay? And we'll say a little bit more
about that later. And if you take uh if
you take um MCB 110 or 102 later, you'll
learn a lot more about this and how it's
important biologically.
Okay. And then I just also want to point
out that of course if we have molecules
that can come together in this kind of
condensation reaction, they can also be
hydraized, right? So they can also be
broken apart. And hydraysis just means
we're doing the reverse kind of
chemistry. So instead of losing a water
molecule in this condensation, we would
be adding water and that would break
apart these two sugars. And that's
actually what happens when sugars get uh
when when polysaccharides get
metabolized, right? They get broken down
in a hydraytic reaction that's typically
catalyzed by enzymes in the cell.
Okay? And so these are just a couple of
examples of different kinds of
polysaccharides. Um, and I want you to
notice that that these can be very large
molecules, right? So each of those
little green hexagons there is an
individual sugar molecule. In this case,
a a glucose molecule. And you can see
that these can come together to form
very very very long uh polymers. Now the
example on the left hand side. So both
both of these examples are that are
shown here are examples of storage forms
of sugars that are used for uh for
storing energy in cells. And so on the
left hand side this is showing you an
example of the structure of starch um
which is uh stored in the form of either
amalos or amilopectin.
And um this is a a way that plant cells
are able to store sugar molecules for
use later. Right? So it's a it's a a way
of um of keeping energy available for um
for use in the future. And it also turns
out that starch can be digested by
animals like us. So when you eat a
potato or something, a root vegetable
like that, typically there's a very high
concentration of these molecules and we
have enzymes that can break them down
into the individual monossaccharides
that are then used as fuel in our
bodies.
Okay. And then just you might just also
notice that amalos is a linear molecule
whereas amilopectin if you look closely
is actually a branched molecule. Okay.
So that's a much uh it's a it's a it's a
different kind of chemical structure
than the one that you're seeing on the
left hand side. Okay. And then on the
right is a storage form of sugar that's
found in animal cells like in our cells.
Um if we eat a a meal that is very
calorie dense and we don't need all
those calories right now. Our our cells
will typically uh form uh glycogen
produce glycogen in which all of these
monossaccharides are hooked together
into these long chains. And again, you
might notice that glycogen is also a
branched molecule, right? It's not just
linear. And um and this is a way that
animals are able to store sugars for
later use. So it's interesting that
plants and animals both do this, but
they make slightly different kinds of
polysaccharides to store their energy.
And this has consequences for the way
that those uh sugars are or
polysaccharides are later metabolized.
And then I want to just point out to you
that um there are other forms of
polysaccharides that play roles
structurally in cells. And I'm going to
have more to say about this next week. I
want to tell you a really interesting
story on Monday that has to do with the
structure of cellulose and the interest
in using it as a uh bofuel and some of
the challenges enzyatically that have
come up in with people trying to do
that. But before we discuss that, we
have to know a little bit about the
chemistry of this. And so um if you look
in your book uh your book talks very
nicely about the differences between the
structures of the cellulose uh
polysaccharide compared to these uh
glycogen and amilopectin forms and
cellulose you might know is used in
plants to form uh plant u uh um
structures such as tree bark and things
like that right so plants typically are
very rich in cellulose um and then kiten
is yet another form of a polysaccharide
that's used typically to form structures
like the the outer shells that we find
on insects. Okay.
Okay. So, um so that's what I want to
say for now about carbohydrates and and
I want to move on now to talking about
lipids. So, this is the second type of
macroolelecule that we find in cells
biology. And it's a um it's interesting
that this is the one class of
macroolelecules that typically don't uh
include true polymers. Okay, as you'll
see. Okay, not not in the way that we
see for carbohydrates and proteins and
nucleic acids. Okay. And the common
theme with olive lipids is that these
are very hydrophobic molecules.
Hydrophobic means they don't like water.
They fear water, right? They get away
want to get away from it. Um and so
these are uh molecules that are um
primarily composed of what are called
nonpolar
uh uh uh bonds, right? So remember last
time we talked about the structure of a
water molecule and the fact that the
structure means that water is a polar
molecule, right? It's polar. So it's
what that means is that if you remember
the water molecule had sort of an L
shape to it, right? kind of a um an
acute shape to it and the with the
oxygen at that apex. And so that creates
a partial positive charge on one side of
the water molecule, whereas the there's
a partial negative charge where the
hydrogen atoms are. So that creates a
polarity to that molecule. Well, in
lipids, what we find is that typically
the bonds and lipids are are uh
non-polar. That means there isn't a
charge or a partial charge that gets
localized to one atom or the other.
they're shared equally. Okay, that means
that they're not uh going to be
molecules that typically are going to be
available to form hydrogen bonds very
easily. And that's why they don't tend
to interact with water very well.
Okay. And there's three types that I
really want to focus on. One of of
lipids that we'll just mention today,
fats, phospholipids, and steroids. Okay?
And I we'll say a little bit about what
each of those uh types of molecules do.
Okay? So fats are constructed from two
building blocks. A glycerol molecule
which is a type of sugar and a fatty
acid. Okay, or multiple fatty acids.
Okay. And so glycerol is a is a sugar
that has three carbons in it. Um it's a
three-carbon alcohol and it has uh
there's a hydroxal group on each of the
carbons and we'll look at this in just a
moment. And when this is converted into
a fatty acid, each of those hydroxal
groups on the three carbons of glycerol
is coupled to a longer chain uh carbon
uh skeleton basically. And it's a it's a
it's again it's a pretty hydrophobic
molecule. So the overall um property of
a fat is that it's hydrophobic.
Okay. So let's look at a couple of
examples of this. Um, and again, this is
a this is a a figure that you'll find in
the textbook, and they have more a more
detailed discussion of this, but there's
a couple of points here that I want to
that I think are really interesting I
want to point out to you. So, um, first
of all, on the top, you'll see that um,
Whoops, where did my
Okay, sorry about that.
We go. Um
so on the on the top uh what you can see
is that uh here's the glycerol backbone
of the fat. Okay? So there's the three
carbons. Here are the three uh oxygens.
So if this were just a glycerol
molecule, these would just be hydroxal
groups, right? They would be O groups.
But in this case, this is a fat. So each
of these oxygens is coupled to a
longchain
uh lipid that you can see right here
through this carbonial group. And um
this is actually a fat that's called
steeric acid that is called it's what's
known as a saturated fatty acid. And the
what makes this a saturated molecule is
that you might notice that so each of
these points on this chain is a carbon,
right? And we don't see any double bonds
there. So that means that this uh fatty
acid has as many oxygens on that uh on
that long lipid molecule as it can
possibly have because there are no
double bonds there, no conjugated uh
systems. So uh what that means is that
this is a molecule whose chains uh tend
to be fairly flexible. Okay, it's fairly
um uh flexible. And so this is a
molecule that can actually even at room
temperature pack together pretty well
and form a solid. So if you see
something that is a fat like butter or
margarine, something like that that is a
solid at room temperature, you know that
that is t probably a substance that has
a lot of saturated fat in it. If it's
made of of fat, okay, saturated fat.
Okay? And then here's an example of
unsaturated fat. This is a this is now a
little jug of olive oil. And so very
typically so these kinds of saturated
fats are very commonly found in animals,
right? We have we and other kinds of
animals have a lot of uh saturated fat
in our cells. Whereas plants uh
typically have and fish as well
typically have unsaturated fat. So
what's the difference there? What are we
talking about? So here you might see
another here's another um you know that
this is a fatty acid because of the
chemical structure. There's the glycerol
backbone. And in this case, we've got
three um lipids that are coupled to this
glycerol backbone. But you notice that
one of them contains a double bond in
the middle. And um and importantly, this
double bond has directionality to it in
the sense that the carbons that are
coming off of either side of the double
bond, you can see in this case, are both
pointing in the same direction. So who
remembers from organic chemistry, what's
that called?
cis. Right. Exactly. So, it's a cis
double bond. And if it were it could be
a different kind of double bond, what
would that be called?
Trans. Okay, good. Everybody knows that.
Great. And so, um, this is a this is a a
fat called oleic acid. And because it
has this unsaturated site in it, it
means that the chains tend to be, uh,
less able to pack together efficiently,
right? they're uh this you can just sort
of get a sense of this by even looking
at this cartoon and what that means is
that at the same temperature as uh
what's shown up here. So the these are
both sitting at room temperature this uh
m this uh substance butter will tend to
be a solid whereas uh something like
olive oil which has a lot of unsaturated
fat in it will tend to be a liquid.
Okay? And that's why and um I I don't
have it in here but I think it's
something really interesting. You know,
you've heard a lot in the news about
trans fats and how bad they are for you
and and things like this. And that's
because um you know, when I was growing
up, we were told it's bad to eat butter
because there's a lot of saturated fat
in butter. It's much better to eat um uh
vegetable fat, but it's not very handy
if you need to have something that you
want to spread on your toast in the
morning. And so um
uh you know food companies figured out
ways to chemically treat
um plant oils like olive oil and other
kinds of plant oils so that they they
artificially created molecules that were
unsaturated. But when they do that they
create not these kinds of cis double
bonds but typically trans double bonds.
Okay? And that's why they're called
trans fats. And those um molecules have
you know the structure tends to be more
straight. So it tends to mimic what you
see up here. We tend to get h end up
with uh fats that are solid at room
temperature. So they're you know people
like to use them. But later it was found
out that those are really artificial in
the sense that our bodies don't really
recognize them the way we do uh fats
that are found in nature. And so they're
very hard to metabolize and they tend to
build up over time in our cardiovascular
system. and cause uh various kinds of
health problems. So now the thinking is
that it's actually better if you want to
have something to spread on your toast
in the morning, just use the natural
fat. Use butter.
Oops. Let's see.
I seem to be frozen.
Um, okay. Let me just
I don't think you in the booth have the
power to advance the slide, do you? No.
Okay. I'm I am uh in a frozen state
here.
Okay, I may have to just restart this.
I'm really sorry. Okay, two minute
two-minut uh break here.
I can restart the computer and try to
pull it up if you want to just keep
you can keep that would be good. Okay.
So, uh let's keep going. So, if you look
at your at your handout, the next page
in the handout talks about
phospholipids. All right. And uh the
slide will come up here again in a in a
couple minutes. But for now, you can
just use your handout. And what I want
to point out here is that phospholipids
are essentially a variation on the um
the um fatty acid that we were just
talking about in the sense that the
structure again has a um glycerol
backbone. But in this case, we have two
lipid molecules coupled to those
hydroxils on the glycerol backbone. And
at the third site we have a uh phosphate
group. Okay. And um this is very
important because it changes
fundamentally the chemistry and the
behavior of this molecule. And the
reason is that when you have a fatty
acid where you've got three hydrophobic
chains coupled to glycerol that's a very
hydrophobic molecule as we were talking
about. But if we have we replace one of
those long chains with a phosphate
group. Now we have uh one position on
the lipid on one end of that uh that
fatty acid that's now polar, right? So a
phosphate group is a polar molecule.
It's a molecule that can hydrogen bond
with water. And so that creates a
molecule that has the kind of structure
that's shown in that little cartoon down
on the bottom right where we've got on
one end. Thanks. On one end we have the
charged phosphate group and on the other
end dangling down are those two um
hydrophobic chains.
And this is critical because cells make
uh great use of this type of molecule of
phospholipid to build membranes.
And your book again has a nice uh
cartoon of this and a discussion of
this, but and we're going to talk about
it a lot more when we talk about the
structure of uh cells, but um
essentially uh cell membranes wouldn't
exist if we didn't have uh phospholipid
or something similar to it because we
really need to have the ability to um
create structures that can on the
outside interact with water molecules,
aquous solution in the cell, but on the
inside are protected from water and can
basically seal off the cell or
compartments within the cell from the
rest of the environment. And that's this
that's the function of phospholipids.
That's what they that's their job. Okay.
And then the third, if you go on to the
next slide, the third uh type of lipid
that I want to mention is uh uh a
compound called a steroid. And so we've
probably all heard about steroids in the
news and athletes using them when they
shouldn't and things like that. But the
bottom line is that steroids are also um
a type of lipid. These are tend tend to
be hydrophobic molecules and they're
incredibly useful in biology because
they're often used for various kinds of
signaling. Okay, it looks like we're
back up here. Thank you, Mike.
Is that showing? Okay, good. So um
so these molecules are um that are
should be showing that is okay good. So
if you look at the structure of a
steroid it's a bit different in fact
quite a bit different than what we were
talking about with uh fatty acids and
phospholipids right because these are uh
molecules that typically have this four
ring type structure and then um various
substituents coming off of sites on
these rings. Um, and so if you see this
uh four ring structure, even if you
don't know anything else about that
molecule, you know that this is probably
some kind of a steroid, right? And we
find these in in plants and we find
these in animals, but they have
different uh detailed details in terms
of the chemistry of the substituents
that are coming off of these rings that
change their properties. So um this
particular example is the is uh
cholesterol. So this is, you know, this
is a very important um molecule in human
health and one of the reasons it's so
critical, it's actually essential uh for
us in our bodies because it's a it's an
essential component of cell membranes
and we'll talk a little bit later about
what it does uh in those membranes. Um
so it sits with within the the interior
of a membrane that's made up of of
phospholipids.
Um but like many things, if we have too
much of it, it can also be bad. Okay?
they can also build up in our blood
vessels and create health problems.
Okay, so uh I now want to move on to
talking about the third kind of uh large
macroolelecule in cells and we're going
to actually spend quite a bit of time on
this in later lectures because proteins
play such a fundamental role in all of
biology. Um so these account for more
than half of the dry mass of most cells
for example. So that's that's a lot. And
uh proteins function in all sorts of
things, right? They function often in
catalyzing biochemical reactions. Um
they are important structurally for for
um building up the the kinds of uh
structures that we see inside of cells.
They are involved in storing and
transporting different kinds of
molecules. They help cells communicate
with each other and with the
environment. They help cells to move and
they also um provide defense against
foreign u invaders of cells. Okay. So
all sorts of things. Now there's a
couple of different uh terms that your
book will use and and you should just be
familiar with these. A polyeptide is a
word that we use to mean a polymer
that's built from the set of 20 amino
acids that are found in basically all of
biology. So there's 20 common amino
acids and we're going to talk about the
structures of those in a moment here um
that are used as building blocks for
polyeptides. And when when we use the
word polyeptide, we're typically talking
about a polymer of amino acids. Okay?
And it might or might not have a
particular structure to it, but it just
means a polymer of of amino acids. Um,
and then the other word that we use is
protein. And when we talk about a
protein, we're typically referring to um
a a molecule that might be comprised of
one or maybe more than one poly
individual polyeptide chains. Okay?
Okay. So, it could just be one a protein
could be a polyeptide, but it also could
be more than one polyeptide. And we'll
look at examples of this. And um and a
protein as as we're going to see is
associated has a particular structure to
it, a three-dimensional structure that
is critical for the function that it
carries out. And there's many many many
different kinds of proteins. They have
different uh uh amino acids in them and
they also fold up to form different
kinds of structures. And it's those
different structures that allow them to
carry out this huge variety of
functions.
And this is just again a table uh from
the textbook that goes through different
kinds of proteins and the functions that
they carry out and then some examples of
those proteins. And we're we're going to
be um as we go through the rest of the
my section of the course, we'll be
talking about some specific examples of
these.
Okay. David, I want to I want to uh draw
your attention to the fundamental
building block of polyeptides which are
um uh amino acids which is shown up
there on the left hand side of the
slide. And so these are uh fairly small
organic molecules as you can see that
have a uh caroxile group on one side and
an amino group on the other side. Okay,
so amino acid just describes the fact
that they have an amino group and an
acidic group in the same molecule. And
what makes these so interesting and and
so useful in biology is that they have
another important property was which is
that you can see that there's a carbon
that's in the center that's colored uh
red or pink or something which right
here and um this is called the
alphaarbon. Okay, this is the alphaarbon
and the alphaarbon links together the
amino group on one side, the caroxile
group on the other side. It's got a
hydrogen attached to it and then it's
also got an R groupoup and the R
groupoup is what makes amino acids
different from each other. Each of the
20 amino acids that are common in
biology have a different R groupoup at
that position. And those R groupoups can
have a wide variety of different
chemical properties. And so on the right
hand side um you'll see that this is a
chart showing you the different chemical
groups that make up the 20 common amino
acids. So, we've got a set up here on
the top that are all non-polar. So,
these are side chains that are um do
they like water or they don't like
water?
They don't, right? Yeah, they're
non-polar. That means they tend to
they're not polar and so they tend to
not be so good at interacting with a
polar molecule like water and forming
amino uh forming hydrogen bonding
interactions. And then we've got a set
of side chains that are very polar.
Okay, so those are the ones shown down
here. And you can see a lot of these
have either a hydroxal group or some in
some cases a theol group um associated
with that uh that side chain. And then
we've got uh some uh side chains that
are charged. So they're either acidic,
these ones over here, or they're basic
over here. Okay. Now, I don't want you
to have to I don't think you should have
to memorize the chemistry of each of
these side chains, but I do want you to
know the different kinds of chemical
properties that they can have. Okay? And
if I ask you a question about the
behavior of a protein, you would know
that if it's got if it's packed into a
into a membrane, it's probably got to
have um
particular properties that would allow
it to interact with those lipid uh side
chains on on a phospholipid, right? It
would have to have probably non-polar
amino acids on the outside that would
interact with those and things like
that. Okay? So I want you to understand
that there are these different chemical
properties of the side chains, but you
do not I'm not going to ask you to draw
out a chemical structure of a spartic
acid or something like that. Okay?
All right. And so um just like we saw
with sugars, it turns out that these
amino acids can come together in a
similar in sort of a chemically similar
kind of way in a condensation reaction
in which water is lost in the process of
hooking together two amino acids to form
a uh a peptide. And so this is the this
is a what the resulting uh bond that
forms is called a peptide bond. There it
is right there. So you definitely want
to know what a peptide bond is. Okay.
What it looks like, where it occurs, how
it forms. And there's something very
important that I want you to see in this
the way that this uh drawing is
represented, which is that when we have
a polyeptide, we end up with a chain
running through this polymer that's
highlighted in the purple boxes that um
is the same across this polyeptide.
Right? So, this is called the backbone,
the polyeptide backbone. And it's not
chemically unique in each case, right?
Each of each unit of the backbone looks
the same. Essentially, what's different
is that depending on the amino acid
that's added to this chain, we have a
different side chain at each position.
And it's the chemistry and behavior of
those different side chains that creates
the ability of a polyeptide to fold up
into a three-dimensional structure that
has unique properties. Okay? Okay. And
so you can imagine or you probably some
of you know this has been a huge field
of research in molecular biology over
the last few decades and is ongoing now
is to try to understand all sorts of
things about uh polyeptides. how they
how they fold, how they form stable
structures, um how they form active
sites for catalyzing chemical reactions
in specific ways and very importantly
how their three-dimensional structures
allow them to interact with other kinds
of molecules. So when we talked last
time about systems biology,
uh really we have to be thinking at some
level at least about the structures of
these kinds of molecules like proteins
because it's really their structures
that allow them to interact in large
systems in the cell.
All right. And so this is an example of
uh protein structure. So as I mentioned
a functional protein might be one
polyeptide but it might be multiple
polyeptides that come together and fold
up to form a unique structure. This is
showing an example of um a protein
called lysosyme shown over here. And
these are just a couple of different
ways that uh scientists use to represent
the three-dimensional structure of a
molecule like this. You have to remember
that, you know, we might have, you know,
a typical protein has, you know, maybe a
couple hundred um amino acids or more in
the polyeptide chain if it's a single
chain polyept protein. And so we
probably don't or we could draw out
every atom in that structure, but it
would be pretty overwhelming. So we come
up with ways that we can draw these
structures that give our eye the ability
to pick up the overall features of the
structure without getting distracted by
the details of where every hydrogen atom
is sitting unless we want to know that.
And so what this shows you on the left
is what's called a ribbon model of
lysosyme where we have a you can see
there's kind of a groove here. And so if
you were looking at this and you knew
this was an enzyme, you might make a
guess that that might be where chemistry
goes on or where lians, you know, small
molecules or substrates for this thing
can bind. And that turns out to often be
true. Um, and you can actually see that
better uh in this space filling model of
the same uh protein that's shown over
here where you see this cleft that
occurs on the surface of the protein
where it turns out that substrate
molecules can interact.
All right. And so um we'll come back in
a moment to how we can figure out the
molecular structure of proteins. This is
in been in itself a whole a huge field
that's uh of course ongoing. Um but we
know that we can basically divide
protein structure into four different
levels. Okay. And I want you to know
what these levels are. So um the first
level is called the primary structure of
the protein. And what that means is the
actual amino acid sequence of the
polyeptide chain. So if we talk about
primary structure, we're just talking
about the order in which amino acids are
hooked together to form a particular uh
polyeptide or protein that folds up into
a protein. Um and then the second level
of structure in proteins is called
secondary structure. And so it turns out
that in secondary structure what happens
is that we have um hydrogen bonding
interactions typically that occur very
locally between adjacent amino acids
that are close together in uh the
polyeptide chain. And so what that does
is to create um local regions of
structure that are later going to be
used to build up a a higher order
three-dimensional structure. And these
are in in proteins are typically uh
helyses such as an alpha helix which is
shown right here. And uh sheets beta
pleated sheets are very uh common also
in proteins and they're shown uh an
example of this is shown right here. So
hel these alpha helyses and beta pleated
sheets are examples of secondary
structure in proteins. Okay. And then um
those secondary structural units which
kind of occur usually fairly locally
within the polyeptide chain can then
fold up three-dimensionally to interact
and form a um a higher order structure
such as this example here like the
lysosyme that we looked at. Okay. Okay.
And so there you can see that now we
have we might have multiple uh helical
units like here's one right here. And
then we might have multiple beta pleated
sheets that are all coming together and
interacting to form in some cases a
globular structure something that's kind
of essentially round or has some sort of
you know 3D globular-like shape to it.
Or in some cases we have proteins that
form more fibrous kind of structures.
They form elongated uh structures. And
these you can imagine would have uh
different kinds of functions depending
on what they can interact with. Um and
then finally the fourth level of protein
structure is called quadinary structure.
And in proteins that so so not all uh
proteins have a quadinary structure. If
we have a protein like lysosyme which is
a single polyeptide that folds up that
doesn't really have a quadinary
structure to it. Right? It has a
tertiary structure. But once we form
that folded uh structure of the single
polyeptide, we're done. We have lysosyme
and it works as an enzyme. Um but in
some cases we have more complicated
proteins such as something like
hemoglobin let's say that are formed
from multiple polyeptides and in that
case those proteins are said to have
quadinary structure. Okay. So they have
multiple polyeptides that fold up in
their individual tertiary structures and
then those tertiary structures in turn
come together to form even an even
bigger assembly. And there's lots of
interest right now in molecular biology
in understanding uh the quadinary
structures of various kinds of uh
proteins in the cell because we know
that many proteins actually do form
quadinary structures that are critical
for their function in cells. And the
challenge for scientists, people like me
that do uh use methods to try to
understand the structures of these kinds
of molecules is to figure out how to
purify them and how to study them in a
way that we don't where we don't disrupt
that critical quadinary structure in the
process.
Okay. So here's just a couple of
examples um of important proteins in
biology and and the different kinds of
structures that they have. So on the
left hand side it is an example of a
protein that is made up of three
separate polyeptide chains that come
together to interact and form a long
sort of a superhelical kind of structure
coiled structure. And so this is a
molecule called collagen. Does anybody
know? So where's collagen found in the
body?
Connective tissue. Yeah. Right. hair is
keratin, which is a protein that would
also have an elongated kind of
structure. Collagen would be found in a
lot of our connective tissue and our
joints, things like that. Um, and so
it's obviously a very important uh
molecule biologically. And then on the
right hand side is a uh the structure of
hemoglobin. So this is again a protein
that is um uh very uh important in
biology not only in in us in our blood
but also in other kinds of systems as
well for carrying oxygen and um
hemoglobin is formed of four different
polyeptide chains that come together. So
this is a protein that does have a
quadinary structure and furthermore it
doesn't form a fibrous kind of shape to
it but it actually has a more globular
fold and um this allows iron to bind
within a a special uh type of smaller
molecule called pferin pferin ring that
has iron chelated here and allows that
iron to interact with oxygen and so this
is critical and again if you take mcb
110 or 102 you'll learn a lot more in a
lot more detail about how this molecule
actually uh functions, but we'll say a
little bit more about it later in this
class as well. Okay. And then I want to
just um mention so you might be
wondering, well, how do we know uh what
proteins look like? Can we see them? You
know, this is something my mom asks me
every now and then. You know, she says,
well, can you how do you study the
molecules that you're studying? Are you
looking at them under a microscope?
Well, you know, we wish we had a
microscope that was that powerful, but
the answer is we don't, right? And so
scientists have had to come up with
other ways of getting at the structures
of these molecules which although
they're big in the cell, they're
actually still very very small, right?
Too small for us to see directly. And so
um typically the way that this is done
in uh or I would say the most common
method for determining protein
structures right now is to use a method
called X-ray crystalallography. And so
the idea here is that uh if you can
purify the protein sample that you're
interested in, you can in some cases
coax it to crystallize. And we can do
this um in a way that's very kind of
analogous to what you might have done in
organic chemistry lab when you're trying
to crystallize a small molecule, right?
You find ways of creating a super
saturated solution and growing crystals
of that molecule. And uh we can turns
out very amazingly one can do the same
thing in some cases with macroolelecules
find ways of coaxing those molecules to
crystallize. And when we get a crystal
we have an array of molecules that where
uh every single molecule in that
three-dimensional array has exactly the
same structure and it packs together
those molecules pack together such that
they create a diffraction grading. So
just like in you know probably a physics
class that you might have taken in high
school or or here um we can then use
that defraction grading to defract
X-rays and um and that's shown in this
little cartoon here. So the crystal will
be mounted such that we can uh shoot an
X-ray uh beam at the crystal. Those
X-rays interact with the molecules in
the lattice of the crystal and they
bounce off. And then we have a detector
placed on the other side where we can
actually measure those uh defracted
X-rays to get uh a specific pattern that
will uh correspond to the lattice that
the the X-rays were defracting with
which is made up of our molecules that
we want to find the structure of.
And it turns out that then with uh with
some uh cle a couple of clever tricks,
we can actually use that defraction
information to ultimately calculate an
electron density map for that
corresponds to the molecules in the
crystal. And once we have an electron
density map, we can build a model of the
macroolelecule such as a protein into
that electron density. And then we kind
of know what the protein looks like.
Very cool. It's really fun.
Okay. So, um, now in the last few
minutes of class, I want to move on to
talking a little bit about nucleic
acids. Um, and so, um, this hopefully is
territory that's that's familiar to to
many of you. You know that there are two
fundamental types of nucleic acids, DNA
and RNA. And they're not that different
from each other. On the one hand,
they're chemically they're fairly
similar. And yet, biologically, it turns
out they they they have very distinct
kinds of functions. there's some overlap
in their function, but they also can do
really different things as well. And
we'll talk a little bit about why that
is today, but probably more later on as
well. Um,
and um, and so nucleic acids are
important because they are the uh,
inheritance unit of cells, right?
They're the way that cells are able to
pass along information from one
generation to the next. And the amino
acid sequences in proteins for example
are determined by the nucleot the
sequence of individual building blocks
that we find DNA. Okay. And so genes are
made up of DNA.
And then there's just a I have just a
very simple uh depiction here of the way
that genetic information is actually
handled. So this would be a cartoon that
would uh represent a typical ukareotic
cell where the cell has a nucleus that's
shown in that purple sphere and inside
of the nucleus is the cell's DNA, the
cell's genetic material. And um to pass
along that the information and use that
information that's in the DNA and the
genes in the DNA, first thing that has
to happen is that a copy of the DNA
sequence is made in the nucleus as RNA.
Okay? And RNA is typically a single uh
strand as shown here. Whereas DNA forms
this doublestranded double helical kind
of structure. All right? And once the uh
messenger RNA, that's what that M stands
for, this messenger RNA is made, um it
gets uh sent out of the nucleus and
eventually in the cytoplasm interacts
with very large uh structures called
ribosomes that are able to bind to the
messenger RNAs and travel down their
sequence and read the genetic code and
translate it into protein. It's an
amazing process. And so from this piece
of nucleic acid, this RNA that was
transcribed from the DNA, we end up with
a specific polyeptide that can then fold
up into a protein and carry out
functions that are needed by the cell.
And there's all sorts of interesting
regulation that goes on in cells to
control when and how and where this kind
of process goes on, where genetic
information is translated in protein.
Okay. Okay. And so I want to just say a
little bit again about the structure of
nucleic acids. So nucleic acids are are
again they're polymers and we call these
polyucleotides. So it's sort of
analogous to polyeptide, right?
Polyucleotide. And that's because each
um nucleic acid molecule is made up of
individual building blocks that are
called nucleotides.
Okay? And so each nucleotide has three
components to it. It has a base that has
nitrogen in it. So we can call it a
nitrogenous base.
It has a sugar. It's a pentos sugar.
That means it has five members in the
ring of the sugar and it has a phosphate
group. Okay, so those three components
and um there's another related word to
nucleotide called nucleioide and that
refers to a um an individual unit that
doesn't have the phosphate. Right? So if
we just have a sugar and a base and no
phosphate then we call it a nucleotide.
Okay. And so what do these actually look
like? And here is a cartoon that shows
the the the structure of a typical um uh
nucleotide or nucleotide if it has the
phosphate there. Here's the base.
Here's the sugar.
And then here's the phosphate.
All right. And very importantly, um, the
sugar has we you should really need to,
this is sort of not so great because it
doesn't show you the hydroxal groups on
these carbons because they're very
important for a couple of reasons. Um,
first of all, I want you to notice that
there's a difference in the sugars that
make up DNA versus RNA. And you have to
look a little bit closely to notice it,
but it's this site right here. Right? So
in DNA, this carbon has two hydrogens on
it. In RNA, this carbon has a hydrogen
and a hydroxal group on it. Okay, that's
called the two prime carbon. That's the
two prime carbon. And in RNA, this has a
hydroxal group on it. Seems like a small
difference chemically, but it turns out
to have very interesting and fairly
dramatic consequences for the
polyucleotide that forms from these
building blocks. All right. So that's
the difference between DNA and RNA is
the is the presence or absence of this
group. And the other reason these are
really important is that these uh this
uh group right here on the threep prime
carbon this hydroxil is what is used to
build a growing polyeptide chain. So the
way that these uh individual units are
hooked together is through um this
carbon
here which is actually the called the
fivep prime carbon on the sugar and the
threep prime carbon which is here. So um
and that's sort of shown in this
cartoon. So we build up a polyeptide
chain where we have sugars hooked
together by these fivep prime to threep
prime linkages and the consequence of
that is that the polymer that builds up
has a directionality to it and um
actually reminds me I didn't point that
out for polyeptides but they also have
directionality to them. Okay, we'll we
can go back to that later. Um they have
a they end up with an n terminal end and
a c- terminal end in polyeptides amino
group on one end caroxal group on the
other end. Here in DNA or RNA, we end up
with polymers that have a fivep prime
hydroxil or phosphate on one end and a
threep prime hydroxil or phosphate on
the other end. Okay? And um this results
in a molecule that can form a double
helical structure in DNA where the
strands wind around uh each other. And
very importantly um these strands are
running in opposite directions, right?
They're antiparallel. One strand is
running five prime to threep prime. The
other strand is running three prime to
five prime. So they're antiparallel.
And the bases pair up with each other in
a very specific way. There are four
flavors of the bases in DNA, adenosine,
thyodine, cytoodine,
and um guanosine. So A, C, G, and T. A
always pairs with T and C always pairs
with G. And because of that, it's a very
uh elegant way that cells can pass along
their genetic information by peeling
apart the two strands of the DNA
molecule and allowing enzymes to come in
and copy the template strand. In this
case, the blue strand by by making a
next a new polyeptide chain, a
polyucleotide chain in orange that has
bases arranged so that they match by
base pairing the sequence on the
template strand.
Okay. And this because of this mechanism
of replicating DNA, it means that when
we look at DNA sequences from ourselves,
other kinds of organisms or even from um
material that we might isolate from uh
that that's preserved from ancient
organisms. We find that DNA sequences
across evolution are related among
organisms that are related to each
other. And we can tell by comparing DNA
sequences which organisms are more
closely related than others. Okay. And
the last couple slides here are just
some summaries that I put together of
what we talked about. And importantly,
the last two slides are a summary of
what I think you should now be able to
do based on what we talked about in the
first two lectures. So you can use that
as you study this material to make sure
that you're getting the key points. Have
a great weekend.

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Acid Base Introduction

Saylor University

Jun 13, 2026

Carbohydrates

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