Transcribed by Kevin Lin Lecture Date: Tuesday, July 1, 2014

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[Microbiology] [2] [Bacteria Cytology The Cell Envelope] by [Dr. Boylan]

[11]- [Comparison of a prokaryote and a eukaryote]
[Dr. Boylan] Welcome back. We lost a few I think. Anyone gonna watch the game
this afternoon? (class: yeah!) That should be fun, exciting. Theyre really exciting
games this afternoon. Itll be great. So anyway, were talking about bacteria,
prokaryotes. Prokaryotes. Prokaryote. No nucleus. A nucleoid, a chromosome, but
no true nucleus. So.

[12] [Characteristics of eukaryotic and prokaryotic cells]
[Dr. Boylan] These, just point out some of the differences weve already discussed
between the two types of cells. And looking at the characteristics of the cell. A
eukaryote and a prokaryote. Only bacteria are prokaryotes, theyre the only ones.
Living cells with no nucleus. Maybe groups, algae, fungi, protozoa, plants, animals,
thats us of course. We are all eukaryotes. We have a true nucleus. Size of our cells
about 5 micrometers. Bacteria 0.5 to 3, but you know some are smaller, some are
larger than that. Nucleus: a classic membrane. No nuclear membrane.
Chromosomes: strands of DNA, eukaryote, but note here that our genome, our
chromosomes are diploid. That means diploid, of course means two. All our
chromosomes are paired. Pairs of chromosomes. That is not true in bacteria. They
only have one chromosome. Therefore its called a haploid genome. Another name
for the chromosome, nucleoid is also genome. The genome, the chromosome of
bacteria is haploid, only one. This is one of the reasons why theyre so much fun to
grow and work with in the lab to find out fundamental things about DNA and how
DNA replicates and really all things that go on in the cell. Work with these simple
cells. Heres a cell that only has one chromosome, so lets look at the genes and how
they function in these single chromosome cells. Get all the basic information down
about prokaryotes, about chromosomal replication and see if these apply to these
more difficult and more complex cells, such as eukaryotes. So a lot of fundamental
information, molecular biology. DNA replication was first found in bacteria and
these principles were applied to, related to eukaryotes later on. Mitochondria: we
have them, bacteria do not. Bacteria dont have Golgi bodies. Endoplasmic
reticulum. Course, we mentioned before, both types of cells have ribosomes. Now
to get back to the point here, but just remember this from the beginning. That
ribosomes of eukaryotes are larger, are 80S. The two subunits of the ribosome
being 60 and 40. In bacteria, you see the ribosomes are smaller, 70S, with the two
subunits being 50 and 30S. remember what S stands for in this regard? What does
70S mean and 50S? Remember Svedberg? He comes up somewhere always in
biochem. This Svedberg unit. Its Svedberg, but it helps relate this size of some
molecule. In Svedberg when he found out what the size of say a ribosome, or
ribosomal subunit, you get a big ultra-centrifuge, you get the centrifuge tubes and
you apply your ribosomes, in this case, on top of the stuff inside the centrifuge tube
and then you spin it down really, really, at high rates of speed forty, fifty thousand
revolutions per minute. And you stuff-, you apply the top of the centrifuge tube goes
down, down, down, down, down to the bottom. And then depending how far they
go, these samples you put on the top of the centrifuge tube, how far they get to the
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bottom, you give them a value of a Svedberg unit. The farther they go down, the
heavier they are, the larger they are. So, you can review that, but our ribosomes are
bigger and theres a major, major consequence, of the differences between these two
ribosomes. The cell membrane, or cytoplasmic membrane, of our cells has sterols.
Bacteria do not have sterols in their cell membrane. Important thing to remember,
no sterols. With one exception, and theres always an exception. Its hard to make
up a question these days Which one- There are no sterols in bacteria Well,
theres one exception. And well talk about what that one is too. So theres one
bacterium that does have sterols in its cell membrane. Only one. So you cant say
no bacteria have sterols! There is one and Ill point that out later. Cell wall, were
gonna talk about that in the next-. Uhh. Absent, we dont have any cell walls. We
have no cell walls in our body at all. Our cells are formed, they aggregate into
tissues and organs and thats how they help each other, protect each other. They
dont need a cell wall. Bacteria do have cell walls, with some exceptions. Cell wall. I
mean other eukaryotes do have cell walls. Plants, apples, pears, they have cell walls,
but we dont. we dont have cell walls at all. Bacteria do have cell walls. And cell
walls of bacteria are different from the cell walls of all other living-, eukaryotes that
have the cell wall. Reproduction: sexual and sexual. Bacteria only divide asexually,
binary fission. Binary fission, you know how binary means-. Basically one bacteria
cell grows, gets larger, and then at a certain point, it divides into two. Well see that,
cell enlarges as it grows, and then about right in the middle, it forms this sort of this
wall or septum between these two new cells, theyre gonna separate and its called
binary fission. One cell into two. So one cell divides into two. They separate. The
two cells begin to grow and divide. Then you have later on, you have 4 cells, then
you have 8 cells. Binary fission, one cell into two. Asexual reproduction.
Movement: complex flagellum, if present. Sperm cells in humans have flagellum.
Bacteria have a different type of flagellum. Not all bacteria have flagellum, but its
much different than the ones found in us, in eukaryotes. But not all have them.
Respiration: mitochondria. Respiration, remember, dont mix up respiration with
protein synthesis, whatever you do. It happens a lot. With protein synthesis carried
out by the side of the ribosome in bacteria and in all cells. Respiration, where we get
ATP production is different from protein synthesis of course. Where does that
occur? In our cells, in the mitochondria. Bacteria dont have mitochondria. They
need ATP. Where is it produced? Where are those enzymes in bacteria that are
found in the mitochondria of our cells? Well, they are found in the cell membrane.
So remember, just briefly back the electron transport and all those cytochromes, the
hydrogenations, the co-enzyme, quinol. Those things are found in the mitochondria
in our cells. Theyre found in the, lodged in the cell membrane of bacteria. Its
essential that the functions such as respiration be well monitored, well controlled.
You cant have enzymes in respiration thats floating around in the cytoplasm and
have a reaction occur and wait for some other enzyme to come along and continue
the reaction until you get more ATP. So, the enzymes are all lined up, 1, 2, 3, 4, 5, 6,
7, 8, 9, 10. So the electron transport chain in bacteria occurs via the components
and enzymes in their cell membrane because they have no mitochondria. As we
recall also, in prokaryote and eukaryotes, in the mitochondria, it is the inner
membrane of mitochondria. So remember mitochondria have two membranes,
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outer and inner. So the inner membrane of mitochondria, where this ATP
production occurs, is like the cell membranes of bacteria. So theres some you know,
theres probably some common derivation of these two things that have-,
mitochondria and bacteria, which we may get to later on when we talk about the
origin of these types of cells.

[13] [Cell Envelope]
[Dr. Boylan] The cell envelope of bacteria is composed of the cell membrane and
the cell wall. The cell membrane as you know is a phospholipid bilayer. Has
proteins in it. And the proteins are mainly enzymes, but there are a lot of functions
of proteins in the cell membranes of all bacteria, not just enzymatic, but other
functions as well, as you recall. Same thing in bacteria, cell membrane, phospholipid
bilayer and proteins. The cell wall in bacteria is to me probably the most interesting
feature of bacteria. The cell wall. Not that theyre the only, once again, cells in
nature that have cell walls. Plants cells have cell wall. But the composition of the
cell wall of bacteria is different than anything else that we know about in nature, in
the world, anywhere. And there are two basic types of cell wall in bacteria. One
type is found in what we call Gram-positive bacteria. Another type is Gram-negative
bacteria. Well have more about what that means, but essentially, there really onlt
are two types of bacteria. Gram-positive and Gram-negative. What does that mean?
Gram-positive bacteria or Gram-negative? These are bacteria that both have a cell
wall, but theres some fundamental differences in the composition of their cell wall.
Gram-positive bacteria have one type of cell wall. Gram-negative bacteria have a
different type of cell wall. Some of the components of each are the same, others are
different. Well talk about those. But there are some fundamental differences
between the cell walls of what we call Gram-positive and Gram-negative bacteria.
And well see later on the Gram is based on a stain that is used to distinguish
between Gram-positive and Gram-negative called the Gram stain, but thatll come
later on. The Gram stain. Depends upon the composition of the wall. Two
exceptions. Lets go to the-, well this one first. Mycobacterium tuberculosis. Thats
the TB bacterium that has a unique cell wall that has a lot of lipids and waxes in it.
Its just very unusual composition, the cell wall of bacterium that causes
tuberculosis. Mycobacterium tuberculosis, TB bacterium. Unless the ones were
gonna describe, it has waxes and lipids and all kinds of strange things. Not to go into
right now, except to remember that it is a different type of cell wall than other
bacteria. Its kind of complex and well talk in detail about that. Well discuss that in
infection. And then theres Mycoplasma. And sp. means species. Mycoplasma is
what we call the genus name of a bacterium. Lets look at, go back to Mycobacterium
tuberculosis. Thats the name of this bacterium that causes TB. Mycobacterium
tuberculosis. Mycobacterium is the genus name and tuberculosis is the species name.
So the genus is then Mycobacterium. Within that genus Mycobacterium, there may
be many different species, but the most dangerous one is tuberculosis. Mycoplasma
is another genus for another type of bacterium. Maybe different species in that.
Mycoplasma. The unusual feature of Mycoplasma, all species of Mycoplasma genus is
that it absolutely-, there is no cell wall at all. They are devoid of a cell wall. Its
important to remember that. No cell wall. And well see that the function of the cell
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wall, one of them is to keep the cell strong, keep it from getting so big itll burst,
therefore destroy itself. Well see one of the reasons Mycoplasma can survive
without a cell wall is because they have in their cell membrane they have sterols. So
thats the exception. Remember other bacteria do not have sterols in their cell
membrane. Mycoplasma bacteria do have sterols in their cell membrane, but they
have no cell wall. So that is some important differences, these two bacteria have
encounter as to others, the majority of bacteria.

[14] [Cell membrane]
[Dr. Boylan] Little bit of review of the cell membrane. One point of course being
that theyre-... I think youre familiar with most of this. We have-... its uhh. The
phospholipids here, bilayer. Heres one layer of phospholipid, heres another layer
of phospholipid. The hydrophobic core, water repellent. And then the hydrophilic,
the charged portions, the circles, shown on the inside and outside. They have
sugars, they have proteins, glycoprotein, glycolipids, peripheral proteins on the
surface, they have transmembrane proteins, integral proteins. There are
hydrophilic polar heads, charged portions. You can review that information. So
phospholipids and phospholipid bilayer. So bacteria have, once again, the same
major basic composition of the cell membrane. Phospholipid bilayer, lots of
proteins, lipoproteins, oligoproteins, glycoproteins, etc., is shown here. So its very
complex. And with bacteria, too, you remember the membranes are called fluid
mosaic structures, meaning lipids are kind of fluid in a way, and mosaic means
proteins can move around. All these proteins, oligosaccharides you see here
embedded in the phospholipid can move around a bit. Theyre not just stationary in
one fixed position. So they can move around, and its kind of like a mosaic piece of
art, where its all little different figures and pieces assembled to make one piece of
art that youve done way back when in arts and crafts shop. So if you took a picture
of a cell membrane and time zero, zero minute, and saw all the proteins there. You
go back and take another picture at 5 minutes, you can see theyre not in the same
spot. Theyre somewhere else and they move around a lot. So these proteins can
move around in the phospholipid bilayer of the cell membrane.

[15] [Functions of proteins in the bacterial cell membrane]
[Dr. Boylan] Functions of proteins in the cell membrane. Gatekeeper. The cell
membrane, as with our cells is the gatekeeper. It controls what gets inside of our
cells and what leaves our cells as well. What can get in, what can get out. Its not
just anything out there, not just any nutrient, not just any salt, ion, amino acid, sugar,
can pass through from the exterior of the cell to the interior. Only certain ones. And
the cell membrane itself that regulates what gets into a cell. What kind of nutrients
a bacterial cell may need for growth. What kind of ion or metals or vitamins or
whatever it may need to grow. It will allow for the passage of some and prevent of
others. So its the gatekeeper, which is really an essential, essential feature of
everything that is alive. I believe life didnt even exist before cell membranes
evolved because if things can back and forth between areas inside outside with
willy-nilly without any regulation at all, nothings gonna survive for very long. But
we can control what stays outside, whats poison or noxious or not need, and allow
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in things that are good for you. Thats when life really began, I think. Thats kind of
the gatekeeper. And also if things get made up inside of a cell and theyre also maybe
are not good for the life of the cell, are sort of poison, they can push them out as
well. Membranes, the proteins of membranes, regulate this gatekeeper, what gets
in, what gets out and allow for the life of the cell.
The generation of energy, we just mentioned the fact, like the inner
mitochondria membrane, ATP production, electron transport takes place in the cell
or cytoplasm membrane of bacteria. Oxidative phosphorylation occurs there, since
there are no mitochondria in bacteria. Respiration, oxidative phosphorylation. This
is one other reasons why there are so many more-, the composition of proteins in
the cell membranes of bacteria is so much higher than it is in our cells. All those
things that we dont need to have in our cell membranes, those enzymes and
components of electron transport, we have them in our mitochondria, we dont need
them in our cell membrane. So we dont need as many proteins in our cell
membrane as bacteria do to carry out these essential functions.
Synthesis of cell wall components, well talk about that next. The cell wall
well see is outside the membrane. The interior, it has the cytoplasm, in the cell
membrane. Cell wall outside, it has to be made, it has to be assembled, put together
and a lot of the enzymes that make the cell wall are embedded, are part of the cell
membrane.
Synthesis of the phospholipids in the membrane in the cells are carried out
by proteins that are located right there in the cell membrane.
Permease activity, well that kind of goes back to the function of the
membrane as the gatekeeper. There are proteins in the membrane that sort of stick
out and wait to identify the good food, the good stuff, the good nutrients, like amino
acids, salt, whatever, that the bacterial cell need and the permeases are enzymes
that kind of grab ahold of them and just rotate in the cell membrane, bringing it
from the outside to the inside. So permeases, enzymes, proteins in the cell
membrane that help bring stuff in that the bacterial cell may need to continue to
grow and divide.
Active transport of molecules into cell. Well see also that some molecules
have to get from the outside the exterior of the cell to the interior. But lets say-, but
sometimes, uhh. They wanna get inside, lets say a sugar like say, glucose is
prevalent in the area, in the environment of a growing bacterial cell, its out the cell.
Heres the bacterial cell. Inside the cell itself, it has glucose, it has what it really
needs to grow, enough sugar to grow. But heres more, heres more glucose outside.
It loves, the bacterial cells love the sugar glucose as well as other sugars. But
glucose. And theres much more of it outside- sorry, I should have just-. Theres
probably in the environment, just less glucose outside than inside. But it wants to
bring that glucose inside. Bring more glucose from outside to inside. So if its a
smaller concentration outside the bacterial cell and larger in, they get more inside.
More glucose taken in to pass through the cell membrane, it needs energy, and well
talk about active transport. So how bacterial cells, usually enzymes in their cell
membrane bring in food, good stuff, they want inside the cell, even though theyre
always kind of stuffed with these good things. To do that, to go from a low
concentration of some metabolite, like glucose, to a higher concentration, it takes
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energy. And bacteria are sometimes very greedy. Even though they have enough
already, they have enough food in them, they want more and more and more
because they dont know when the next meal may be coming.
Breakdown of large foods so. Enzymes in the membrane break down
polysaccharides, proteins, lipids, their component monomers, amino acids, single
sugars, carbohydrates, small lipids. So now, they can break them down, these foods
that they have in their environment. Break them down so they can be transported.
They go through the cell membrane. The enzymes are there to digest the food. So
we have enzymes, too, to digest our food, so they can pass into the cells. Large
polysaccharides, large proteins, couldnt get through the gatekeeper function have
to be hydrolyzed into smaller components first.
And another very important function, and there are others as well, but well
see later on when a bacterial cell grows and divides, of course we saw divides by
binary fission. One cell into two. It only has a single chromosome, right? The
bacterial cell, one chromosome, haploid. But it has to grow and has to divide into
two and form two daughter cells. Heres a mother cell, one cell, grows, divides, two
daughter cells. Each of these two daughter cells also have to have a chromosome, a
replicate, a genome. So, well see the bacterial cell, as it gets larger and grows, and
separates into two cells, the chromosome in the mother cell also has to replicate.
This haploid chromosome has to replicate itself to be sure that the two new cells
will each have a copy of it. So how do they ensure that this will occur? That each-
from one cell, the mother cell to two daughter cells. How can they be certain that
the two daughter cells are gonna have each one haploid chromosome? They dont
wanna have one of the two daughter cells having chromosomes and one having
none. Neither of those cells will probably survive for very long. What they do is
when these bacterial cells replicate their chromosome, this haploid chromosome is
replicated. Part of the chromosome is bound to a protein in the cell membrane. And
then as the chromosome replicates and bound to these proteins, and as the cell gets
larger and larger, this protein to which the chromosome was bound pulls them away
from each other as they are replicating, and then they separate after a while. And
then the cells can divide. To ensure equal distribution of chromosome from mother
cell to daughter cells, it didnt have a mitotic apparatus like we do. They have to
bind to this protein to ensure equal segregation into daughter cells.

[16] [Additional information on the bacterial cell membrane]
[Dr. Boylan] Additional information on the bacterial cell membrane. Sterols
absent, except Mycoplasma genus. Anybody ever hear of Mycoplasma? I bet
someone must have had infections caused by Mycoplasma. Does anybody what the
commonly cause is? Okay, some species cause STDs. If you have that, you have to
mention it out loud. Hahaha. No, but most of them are common ones, albeit at least.
Anybody ever have cough, coughing? Not pneumonia, but other type of mild
pneumonia? Walking pneumonia? Ya, thats a Mycoplasma, one of the things that
causes-, well talk about that later on also. And it has sterols to really-, because it
has no cell wall, sterols help to fortify its cell membrane. Make it a little bit stronger
and tougher, so it can survive.
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Mesosomes are invaginations of the cell membrane, as shown here. Heres a
cell membrane, heres a mesosome. And the purpose of having these is to increase
the surface area of the membrane. If you just have one round bacterial cell as a cell
membrane, its got a certain size to it, surface area. But if you can make it larger,
sort of push the membrane interiorly. Sort of like a blown up balloon and has a
surface area. But then if you push your fingers into it, you know, then you will
stretch it a big and it increases the surface area of the balloon. So theres more of
the balloon, in a way. Well, in this case, two mesosomes, theres more cell
membrane and that means often for bacteria that like growing very, very rapidly, its
good to have more cell membrane. They help them very fast.
Septum is formed at the site of cell division. So this is not a very good slide
here, but here when talking about a mother cell, chromosome. Here its beginning to
grow and divide and you can see the chromosome is being replicated and theyre
bound to that protein in the cell membrane. And finally, the cells grow to such an
extent where they feel that theyre about ready to separate from each other. Binary
fission occurs. So the cells then separate. So heres this mother cell, heres two
daughter cells. Heres the chromosomes, one in each. And this is the septum right
here, the septum formed at the site of the cell division. What happens first is that
the cell membrane goes in first because thats more inside, and then the cell walls
outside the membrane follows along. And then finally, you have two completely
new cells. And they can separate and go on their merry way and divide themselves,
over and over and over again, by binary fission.
Bactoprenol, and youll see why I mention this now. Its an unusual
compound, but its found in the cell membrane also. Other names for it are Lipid
carrier, Bactoprenol biphosphate, Undecaprenol biphosphate. I mention it now
because in a way, too, were building the basic information youll need later on when
we have a guest lecturer come in and talk about how antibiotics work. Penicillin,
anthramycin(?), other things, how antibiotics work to destroy cells. How to stop
bacterial cells from growing, and even destroying them. And another [target] of
some antibiotics is this compound thats found in the cell membrane, called the
bactoprenol. It plays an essential role in making the cell wall of bacteria. We can
jump ahead a bit to think the bacterial cell wall, youll see now when we discuss that
next, its found outside the bacterial cell, outside the membrane. But all components
that are part of the cell wall are manufactured inside the cell Then they have to
pass through the cell membrane and get outside where the cell wall is gonna be
assembled, as we will see, put down. Its like making the components of this room
or this building in New Jersey. You dont put the building together, a 12-story
building, in New Jersey say, and then transport it here and put it down inside of
course. You make all the building blocks somewhere else, the components like the
seats the rug, wood etc. And then you take them across East River, Hudson River
and take them here and assemble them. Well same thing with bacteria, they have to
assemble everything inside the cell, transport them out across through the cell
membrane. And then structure-, make that cell wall outside the cell. And the
bactoprenol helps the components of the cell wall move from inside the cell to the
outside. And that means if you can damage the bactoprenol, you can really upset the
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cell wall production in bacteria and kill the bacteria as you will see. So remember
that name, bactoprenol. Its gonna come up later.

[17] [Cell Wall]
[Dr. Boylan] Cell wall. Unique composition. Target of many antibiotics. Were not
just talking about these things because they just happen to be there. But they also
play an important role in infectious disease and also in control of infectious disease.
the cell wall, something unique to bacteria is the target of many antibiotics. In other
words, drugs that kill bacteria by attacking the cell wall. The cell wall is essential for
bacteria. Without the cell wall, the cell itself is gonna continue to grow and get
bigger and bigger and eventually its gonna burst. Its going to, another word we use
for bursting is lyse. It lyses, youll hear that word a lot, lyses. So the cell wall helps
to prevent that. Helps the bacteria keep certain size and shape. Not make it too big
that its gonna burst. So the cell wall is necessary for the viability of bacterial cells.
And if you can destroy that cell wall, the cell will get bigger and bigger and bigger
and lyse and youll treat the infection well, but its not good for the bacteria.
Contributes to pathogenicity, well see... [inaudible].
Rigid structural component protects the cell from bursting or lysis. Once
again, without the wall, the cell will take up so much water from outside that it
would get too large and burst. The shape of bacteria, whether theyre spherical, or
coccal-shaped, rod-shaped are also known as bacillus, or spiral-shaped. We saw
those three shapes that von Leeuwenhoek described over 300 year ago. The three
basic shapes of bacteria. Those are three ones that he described, the same three are
the only ones we know of today. And also it protects it from chemicals and any and
other noxious and disinfectants, other things perhaps. Theyre noxious agents that
might be, if they got inside the bacterial cell, kill the cell. So, many roles played by
the cell wall.

[18] [Peptidoglycan - composition]
[Dr. Boylan] Lets get into some of the biochemistry and I know youve already had
most of the fundamental stuff. Lets talk about the peptidoglycan. The composition
of it. Peptidoglycan, just look at that name. Peptidoglycan. You can tell right away
what its composed of. Peptides, amino acids, and glycans. Or sugars. So
peptidoglycan. Its a polymer. It surrounds the whole bacterial cell. Its assembled
outside the cell membrane. And remember the cell is growing and getting bigger. It
keeps making it larger and larger and larger. Cell wall, all those at the same time. So
it surrounds the whole bacterial cell. The monomer itself. Lets look at one-. Its a
large polymer, but made up of monomers. And bacteria like to keep things pretty
simple. In other words, why make up 50 different types of chemicals or more to do
a job when we can maybe just make one and just make it over and over again, like
an assembly line. And just make up these monomers. Well just attach one to
another over and over again to make a polymer. Why have 50 different types of
monomers to make up a large polymer? So bacteria think, lets make something
simple and then add these simple things to each other to make up a larger
component. So they make up monomers, well see this peptidoglycan to make up
the final polymer, the intact peptidoglycan.
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The peptide portion, the monomers, composed of amino acids. And here are
some unusual features of it. One of the unusual features here is the amino acids
well see. And there arent that many, 4 or 5 we should be concerned with in this
peptide portion. Both D- and L- amino acids and novel ones as well. For example, D-
alanine, well see more about where they are located soon. D-alanine. We dont have
D-alanine in our body. Thats an amino acid. We have L-alanine, we dont have D-.
So thats an unusual amino acid found only in bacteria and found in the
peptidoglycan. They have D-glutamic acid. We have that I guess. They have an
unusual amino acid called Diaminopimelic acid or DAP. Or lysine. Well, what I
mean is this the amino acid that can be found in the peptide portion in certain
location. It can be found either there or it can be replaced by a lysine. Well see
what this is made up of in the next slide. Its an amino acid, only found in bacteria,
DAP, Diaminopimelic acid. It looks a lot like lysine and one or the other are found in
the peptide monomer of peptidoglycan. And L-alanine is also present, we have that.
The glycan portion, the sugar portion of peptidoglycan. Two amino sugars
have amino groups. One, youre familiar with. This sugar, N-acetyl glucosamine,
which can be referred to as GluNAc, or just G in some of our structures and some of
our figures coming up. And another one called N-acetyl muramic acid, also known
as muramic acid, MurNAc, or M. These things in red that are shown here are unique
to bacteria. Thats what I want you to remember. Any novel component that we
dont have. No other cell, no other plant, animal, cell in nature have these particular
components. Theyre only found in bacteria, only found in the bacterial cell wall,
and actually only found in the peptidoglycan of the cell wall. So whats unique about
this particular thing? Well, thatll be coming up on a slide, too. So D-alanine, and L-
alanine are often in these peptide portions. DAP or lysine, and well see where they
are found. And this unusual sugar here. This is found all the time. This is another
one, this sugar N-acetyl muramic acid is very similar in composition to this one with
one major difference and thats what well point out. What is the difference? Whats
unique about this muramic acid?

[19] [Lysine vs DAP]
[Dr. Boylan] First, lets look at lysine, without putting all the oxygen groups and the
hydrogen. Lysine amino acid has two amino groups as you can see, and a carboxyl
groups. So thats the one youre familiar with, one of the 20 basic amino acids found
in proteins. Our proteins as well. And in bacteria, its also found. But unusual one
thats also found in bacteria that looks a lot like lysine is DAP. This unique amino
acid, Diaminopimelic acid. You can see how it looks like lysine, same number of
carbon backbone, etc. The one exception it has, an extra carboxyl group. Thats the
different between these two amino acids. So even though the name might throw
you. You think Diaminopimelic acid Oh, Di- meaning two amino groups. Maybe
thats the differences between it and lysine. NO. They both have two amino groups,
but this one has an extra carboxyl group to make it a unique amino acid found on
peptidoglycan.

[20] [Example of a monomer of peptidoglycan]
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[Dr. Boylan] Lets take a look at the sugar and see what the differences are here.
Heres one youre familiar with. So an example of a monomer of peptidoglycan, 2
amino sugars and a tetrapeptide. I dont know what that T is, forget that T. Heres
one you know: N-acetyl glucosamine. Theres that sugar. A glucose base. N-acetyl
group. N-acetyl glucosamine. Thats the one you learned about, the one found in
cells thats the sugar carrier, you know, it has all these functions inside of our cell.
Weve all have that, but thats also found in peptidoglycan, one of the two basic
sugars. The other one is muramic acid. And the difference. Everything here is the
same, but muramic acid differs right here. This part here. This is a lactic acid group.
A lactic acid moiety is shown. Lactic acid, right in here. This is not found in- This
makes it a unique sugar. One of the two sugars found in peptidoglycan backbone. A
unique sugar only in bacteria and well see it plays a major, major role in
susceptibility of bacteria to antibiotics and other antibacterial therapies that we use
today a lot. Unique sugar. Lactic acid moiety right here.
And so this represents the monomer peptidoglycan, one unit. Heres one
unit. Its attached to another unit, another, and so on. Here is an example of the
types of amino acids found in the peptide. Heres a tetrapeptide. L-alanine, heres
the glutamic acid is really what it is, lysine, and D-alanine. So here you have L-
alanine, which is commonly found everywhere. This really is glutamic acid, we
mentioned before, isoglutamamide. Lysine, and D-alanine. So D-alanine is unique.
And lysine is the one that can also be replaced by DAP. So different bacteria have
either lysine in position 3. Heres position 1, 2, 3, 4. Position is L-alanine, thats
always the case. 2, glutamic acid, always the case. 3, lysine or DAP depending upon
the bacterial species were gonna be looking at. And then we have this unusual
isomer D-alanine. So that is, look at that there, thats it, thats the basic monomer of
peptidoglycan that the bacteria synthesize. Says okay, were gonna perfect that.
Were gonna make this over and over and over again, and were gonna hook this
onto another one here, another one here, another one here, this shown here, bound.
Heres glucosamine, heres muramic acid. Glucasamine, muramic acid, etc., etc., etc.
Here is the tetrapeptide. Peptide. 4 amino acids shown here. So heres one of the
monomers. Heres just this small part of the polymer that surrounds the whole
bacterial cell.

[21] [Cross-linking in peptidoglycan]
[Dr. Boylan] Here it is again. So okay, what happens is bacteria form these
polymers of peptidoglycan and they begin to push them out. Make components
inside the cell, push it through the membrane, put it outside. And then the
peptidoglycan I mentioned is responsible for maintaining the structure of the
bacterial cell. The integrity of it. Makes it tough. Prevents it from bursting or lysing.
It wont do that unless all these different strands of peptidoglycan that are being
produced and put outside the cell start to interconnect. They have to bind to each
other. Another essential feature of peptidoglycan. And peptidoglycan synthesis,
these different strands that are formed over and over again have to bind to each
other. Its kind of like the cell is piece maybe half of a ladder. One side of the ladder
and then half a rung is no good, you cant climb that. But then when there comes
another half of a ladder and another half of a rung and they put them together, thats
Transcribed by Kevin Lin Lecture Date: Tuesday, July 1, 2014

11
solid. Now you can climb that ladder. In a way, thats what theyre doing here,
making these strands of peptidoglycan. By themselves, theyre not gonna support
the structure of the bacterial cell, but when theyre interconnected to each other,
then its tough. Its a tough layer, protects the cell. And the way it does it is by, you
see right here. It cross-links peptides, the amino acids, in adjacent strands. So here
we see three different strands of peptidoglycan. Heres muramic acid, glucosamine,
muramic acid, glucosamine. Muramic acid always has, and is the only one that has
the peptides attached to it. And you can see here that this strand is attached to this
strand by the amino acids here. Here, binding to this amino acid. This amino acid
binding to this amino acid. Im now-, I would think this is important to know this
because, once again, because the importance later on in therapy, bacterial infections,
and also in pathogenicity of bacteria. They gotta have this peptidoglycan. And its
essential that this peptide bond is formed. The amino acid between this here, here,
and this one here. Okay. Heres number 1, 2, 3, 4. What could that amino acid be,
the one thats dark? Lysine or DAP, right. Which one is this here. D-alanine. And
its always that way. This cross-linking, its a peptide bond being formed. A peptide
bond between the two amino acids. Lysine or DAP and a D-ala. Over and over and
over again. So how this complex is formed. This large structure around the
bacterial cell. And I wanna point this out because its not just this dense, solid
structure. In Gram-negative bacteria, there are many, many, many layers.
Multilayers of peptidoglycan, over and over and over and over again. But its not
like this floor here that things cannot pass through. Its still like a sieve. Things
even in peptidoglycan, there are pores here that metabolites, foods from outside can
pass through. Get to the cell membrane and then get inside. So, this fence here,
heres peptidoglycan, interconnecting strands of peptidoglycan. But still there are
openings in it, so stuff can pass through one layer, then the underlying layer, then
the underlying layer to get to the inside of the bacterial cell, where the food is
needed for the cell to grow.

[22] [Close-up of a type of bridge]
[Dr. Boylan] So thats another concept I wanna make there. Thats an important
bond, okay. Theres that bond again. The bond has to be synthesized, that peptide
bond. What kind of a bond is formed between the two sugars? Not a peptide bond,
but what kind of bond is formed between two sugars? Glycan bond. Okay... This
bond here. Heres an amino acid on one strand, here another amino acid on another
strand. Heres the linkage, amino, a peptide bond between them. Its essential that
that is produced. Theres an enzyme that produces that bond. Its a peptide bond,
there is an enzyme, and its called transpeptidase. trans- = across, -peptidase so
its a peptide bond the enzyme is called transpeptidase that carries out this
reaction. It hooks these two amino acids. This is the bond, this is the bond that is
unable to be formed in the presence of penicillin. Ill leave you with that thought
today. Penicillin is such an effective antibiotic. Why? Because it stops the
production of this peptide bond between adjacent strands of peptidoglycan. Whats
gonna happen once again? The cell will still grow and grow, but it wont form these
interconnecting bonds, linkage between them, and the cell will just burst and lyse.
So penicillin, what does penicillin do? It prevents that bond from being formed.
Transcribed by Kevin Lin Lecture Date: Tuesday, July 1, 2014

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How does penicillin do that? It actually binds to the enzyme that carries out this
reaction. So the transpeptidase enzyme carries out this essential reaction.
Essential. The cell wont live without it. Penicillin prevents that bond from being
formed. The cell continues to grow, but penicillin binds to the enzyme, enzymes
cant work, the cell gets larger and larger, and then it bursts and dies. So thats why
penicillin is such a great antibiotic. We dont have peptidoglycan. Penicillin works
on something in bacteria that is not found in us, thats why its such a fantastic drug.
The best drugs in the world are those that kill or inhibit something in bacteria, some
component of bacteria that are not found in us. Some do indeed, some drugs inhibit
protein synthesis in bacteria, but of course they also affect our protein synthesis. So
theyre good, and well see theyre very beneficial, but this is one that directs-,
penicillin directed against something only found in bacteria. And it will kill the
bacteria. And its that particular bond is what is [being affected].

So I guess well stop there and pick up on Thursday at about 1 oclock to finish the
discussion of bacteria.