1

Up to this point, weve looked at a bacterial cell. Looked at bacterial cytology. Seen what these cells are
made of. Whats inside the bacterial cells. Ribosomes, etc., appendages, the cell membrane, the cell
wall with capsule. Spent a lot of time going over then structure of the peptidoglycan especially, thats
important to know. Everything you can, Id tell you about it because its gonna come up over and over
again in this course. And today were going to take a look at what goes on inside a bacterial cell.

Metabolism. Now I know youre already well versed in this topic because you had the course in building
blocks just a little over a year ago. Youve gone through the glycolysis, the TCA cycle, electron transport,
etc, things like that. I just want to mention because they do indeed happen in bacteria as well, with a
couple of modifications, thats all. But just because Im gonna review it now, doesnt mean you dont
have to know it. Whatever I say-, Im trying point out some of the highlights of metabolism that youve
already gone through step by step. Im not going to ask you for every step in glycolysis or the TCA cycle,
electron transport. Basically, what are they used for, what are these systems used for when bacteria
and even our cells grow. How they get food, how do they break down food, how do they get energy to
do what they have to do? So thats metabolism. And I guess were already about an hour behind, but
Ill try to finish up if I can today. If not, I have one more lecture before the first exam. And Ill finish up
that time next week, if I dont do it today. So uhh

2
Metabolism. Metabolism are really all of the biochemical reactions that occur inside of cells. Bacteria
(prokaryotes) and also eukaryotes (us, animals, and plants). There are two parts of metabolism.
Anabolism, which refers to the actual synthesis of the macromolecules in our cells the proteins, the
lipids, the carbohydrates built up of building blocks like amino acids and simple sugars, etc.,
nucleotides. Thats anabolism. Making these large structures inside of our cell. Anabolic steroids. You
take them to build yourself up, you get muscular. So those are the steps involved in biosynthesis. And
these steps to make things in cells and bacteria and in us require energy. And catabolism are the part of
the metabolism that produces energy. For the cell to use for anabolism. To produce things, to
synthesize things.
So energy requirements in general. Well see those in the next slide. All cells need energy. And as you
know, in metabolism, you go back and look at glycolysis and other systems that occur in the cell. Series
of oxidation-reduction reactions. So one substrate is oxidized, another is reduced, over and over again.
A whole chain of reactions occur as youll see in glycolysis briefly, coming up. So oxidation-reduction
reactions occur in metabolism.

3
Why do you need energy? Why do bacteria need energy? For anabolic reactions, for transport, that is to
get things from outside the cell, foods from outside in the cellular environment to the interior of the cell,
in the cytoplasm, where they can use the food thats been transported for growth and energy. Motility
use flagella. That takes energy. Cell division itself, where one cell grows and divides into two, requires
energy in the form of ATP. And maintenance, just staying alive. Even when were asleep at night, were
in bed. To stay alive, we still are undergoing metabolism. We dont just give up. Were on a very low
rate of metabolism, but bacteria, too. To maintain, to stay alive, when were not growing that well.
Need energy just for that.

How do the cells derive energy? Oxidation-reduction reactions. One substrate is oxidized, another is
reduced. Oxidation of substrates (food, metabolites) is really hydrolysis of them. Its catabolism,
oxidation, breakdown of foods to produce energy. The energy is produced and trapped. And as you
know, the storage compound for cellular energy is ATP. So these things, like bacteria digest glucose and
other sugars. Theyre fiddled(?) energy. They have internal energy in them, but you have to break them
down. You have to hydrolyze or catabolize glucose and other sugars to produce energy. And as you
break them down step by step in glycolysis and the TCA cycle, electron transport, thats how you get
energy, ATP. Oxidation reactions, catabolic reactions.

4
This is just an overview of what were go through very briefly, once again. Just a review of the
importance of different steps involved in catabolism. We have the proteins, sugars, and lipids can be
broken down. Heres a bacterial cell growing in a very rich environment of large proteins and
polysaccharides and other things it cannot take inside. Theyre just too large. So first they have to
degrade them into amino acids, simple sugars, and then take them inside. Glycerol. Then many are
converted to glucose. And this pathway here, when cells break down glucose to produce pyruvate, is of
course glycolysis right here. Youre familiar with glycolysis. The breaking down of glucose. Thats the
typical example in all courses in biochemistry and building blocks. How cells begin to derive energy.
Were gonna look a little bit at that glycolysis. You can see the glucose, one molecule of glucose. How
many carbons are in glucose? 6. How many are in pyruvate? 3. Right. So youre breaking down
glucose to pyruvate in glycolysis. Another name for it is the Embden-Meyerhof pathway, remember
they use that. You get two molecules of pyruvate. two 3-carbon compounds, pyruvate. And this
reaction, glycolysis, can occur anaerobically. Youll learn more about what that means in about twenty
minutes or so. Anaerobic, it does not require oxygen. It does not require molecular oxygen. Right now,
we require, we need oxygen to grow. Right now, were breathing air. And theres about 20% free
oxygen, O
2
. We need that, we wouldnt survive without oxygen. But this reaction can go on inside a cell.
This pathway, glycolysis, doesnt need oxygen. Later on, well see oxygen is important, but glycolysis
itself, can occur under anaerobic conditions. It can occur in aerobic as well, but well talk about both of
those later on. But the key here is glycolysis can occur under anaerobic conditions. You dont need
oxygen.

And then the pyruvate, once you get to pyruvate in cells, there are many different, what they call fates,
for pyruvate. Pyruvate can go off in many different directions. Many, many things can be done by cells
(and bacteria cells in particular) to pyruvate. And one of the most important of course is using pyruvate
to go into the TCA cycle, the Krebs cycle. Combines with acetyl-CoA to go into another Krebs. And this
occurs only aerobically. Aerobically. So, well go back to point these things later on as well. So TCA
cycle cannot occur under anaerobic conditions. Only with air, oxygen, free molecule oxygen. And then
from there, the TCA cycle, the molecules are broken up further to get an electron transport chain to get
ATP. And thats where most of the energy-. ATP is derived in cells by electron transport. So thats the
overview, I think youre familiar with that. Glycolysis. Glucose to pyruvate. pyruvate, well see, can go
into the TCA/Krebs cycle, or it can do many other things. Ill point out some of them. And then from the
TCA cycle going around, around, and around, and then being changed, molecules being produced,
sending them into the electron transport chain, where you get energy production. So here is how you
get the ATP. And they say, it used to always be the number of ATPs that you can get under respiration
such as shown here, these pathways, Whats the total number? Anybody remember? 30-something? 38,
right. But now some people say 36 or 38 ATP. Thats a tremendous amount of energy. 38 ATPs (are
shown below right there) can be derived from the breakdown of glucose. Thats sugar. Glucose itself.
Reserve of energy. You break it down. You break it down, step by step. Energy is released. Finally the
energy is shuttled through the electron transport chain. ATPs are produced, 36 to 38 ATPs. These
catabolic pathways are breaking down stuff to produce energy for greater use in growing, the anabolic
steps.

[computer pop-up: batter power is low (7% left)]
Oh, thats not right. *closes pop-up*

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Glycolysis. Were going to look at ATP yield. Glycolysis well see the ATP is produced. But if you recall,
the ATP produced in glycolysis is very minimal. Not many at all. But when you produce ATP, during the
glycolysis pathway, its called substrate level phosphorylation. And well also look at the important of
molecule NAD. So were not gonna go through every step, but look at the whats happening with ATP
and NAD in this reaction, glycolysis.

6
So here you see glycolysis, two parts here. Glycolysis, so part one, part two, I guess. The 6-carbon
compound, glucose. A series of hydrolytic or catabolic reactions occur. One molecule is oxidized,
another reduced. Oxidation-reduction, redox reaction, over and over again. Then the 6-carbon
compound, fructose, as you recall, broken down into two 3-carbon compounds, and the pathway
continues to get pyruvic acid. So pyruvic acid is what is called the end point or the end product of
glycolysis.

Lets look at the ATP produced and used up in glycolysis. To begin glycolysis, remember one of the
reasons you were doing this, having this pathway is to produce ATP. But initially, to begin glycolysis, as
you recall, you need ATP. Kind of jumpstart the pathway. You use ATP here converted into ADP when
you use it. And heres another step here where you have to use ATP. So to begin glycolysis, you need
two molecules of ATP.

[computer runs out of batteries, screen goes black]
Is Dr. Li still here? I dont know. If its not plugged in or we didnt plug it in. Lets see. Or maybe we just
didnt plug it in.
[computer back on]
Okay, saved by Dr. Li, thank you.

So here we have glycolysis, and initially you use two ATP. Break it down. But look at that here. Once
its broken down into 3-carbon compounds. Remember it sort of splits these pathways going in twice
here. Once you get to fructose-6-phosphate, its broken down two 3-carbon compounds. You get ATP
produced here, and ATP produced here. Im not even gonna ask you where the steps are involved in
ATP production, but you get ATP produced. But since this is going on twice, you get two ATP on one side
and two ATP on the other. You produce four ATP in glycolysis. So overall in glycolysis, you use up two
ATP to start it. You produce four ATP. The net yield of ATP in glycolysis is only two. Not a lot of energy
in glycolysis. This has to take place, this reaction, but only two ATP of the 36 or 38 were gonna see can
be formed in these pathways.

One other thing to look at here is the use of this molecule in NAD. Here you can see in glycolysis, it is
reduced from NAD to the reduced form. NAD is used up. I mentioned that, thats critical to know, too.
Because NAD is critical for glycolysis. Its necessary. Its used up as is shown here. Its reduced, but it is,
well see, recycled. It is recycled. So itll kind of act like an enzyme, because its used over and over
again. So were gonna see later on where this NAD, this oxidized NAD, is reduced is regenerated, is
reproduced, so it can be used over and over again in glycolysis. So two ATP net yield. NAD reduced, but
has to be recycled, reused later on, reproduced as we will see. And further metabolism.

7
Heres the TCA cycle. Remember, its called an amphibolic cycle. Put that word down. This is critical.
Dentists always say when they think back upon their basic science, years in dental school. Oh boy, I
remember the TCA cycle, the Krebs cycle. I still use that every day of my life. That seems to be the big
whipping boy. I know, but its critically important. I mean, you dont have to know every step of it, but
this is what keeps us alive, the TCA cycle. Its involved in both catabolism and anabolism. Its involved in
further energy production in catabolic reactions, as well as producing these compounds that are used by
cells to make other things. So its involved in both types of central reactions that occur in metabolism.
Catabolism and anabolism. So thats basically what its used for. And here we see one fate of pyruvate
is to enter the TCA cycle. Forget about all of these, but you see two hydrogen atoms come off here,
here, here, and all these hydrogen atoms are gonna go into the electron transport chain. And thats
where most of the ATPs are gonna be formed. So over and over again, energy is going to be produced
because of these hydrogen atoms being produced here. And also you have all of these molecules being
formed, too. They are sometimes withdrawn from the cycle, right? And they are used for the building
blocks for our proteins and our nucleotides and our polysaccharides. So that would be energy
production. Also, finishing the building blocks of macromolecules as theyre withdrawn from the TCA
cycle. So what happens to these hydrogen atoms? As you know

8
Hydrogen atoms are composed of a proton, positive charge, and an electron, negative charge. And one
easy way to remember this, in case you cant remember it off of your head. A story about these two
hydrogen atoms that were walking along the street in the opposite direction in the sidewalk. And they
hadnt seen each other for quite a while. And they bump into each other on the street, these two
hydrogen atoms. And the first one says to the second one, How are you doing? The second one says,
Well, not too well. I think Ive lost my electron. And the first one says, Are you sure? The second
one says, Im positive. *chuckles+. Thats how I remember it. Electrons, protons. Hydrogen atoms.

So here we have these hydrogen atoms, and as they-. And then the electrons and protons are separated
from each other in this pathway here. Electron transport. The electron are transported. The hydrogens,
the protons, are sort of put outside of the bacterial cell. Just like in mitochondria, the protons are put
outside that inner membrane, and theyre kind of dying to get back in, trying to force themselves back in.
And the electrons are inside being transported along the electron transport chains by the cytochromes,
the dehydrogenases, and other components of electron transport. Theyre being transported while the
protons are kind of hanging around outside. The cell in the case of bacteria outside the cell membrane,
trying to get back in, neutralize that electron charge. So electrons are being transported down the
electron transport chain. And once again, [mumbles], but you can see, ATPs are being formed. Up to 36,
38 ATPs when all of this goes on inside a cell thats growing aerobically. So finally you get the third ATP,
in addition to the others in glycolysis and over and over again, up to 36 or 38. And finally, why do we
need oxygen to survive? I remember reading about bacteria when I took a micro course. I remember
reading about these bacteria called anaerobes that can grow without oxygen, and I thought, thats
impossible! How can you grow without oxygen, free molecular oxygen? I mean, all cells need oxygen
for their carbohydrates and theyre carboxyl groups, but as far as free molecular O
2
, we need it. And
why do we need it? Its because of this last step of electron transport. Thats why we simple need
oxygen among many other [things] to survive, really. Oxygen. And I wanna point this out in a better
slide that shows this terminal step of electron transport. So you go to glycolysis, you go to the TCA, the
electron transport, and finally after electron transport is over, what do you get? Water, H
2
O. Thats the
end product of all those metabolic pathways that occur in bacterial cells that are growing aerobically.
And oxygen well see play an important role. And finally saying this is enough. Were done with this
pathway now, these hosts of other sequences of different pathways are now over.

9
Okay, here it is, here again. And this is called respiration. Respiration, where phosphorylation occurs.
Where ATP is produced, thats called respiration. It can be aerobic or anaerobic, respiration, ATP
production. Aerobic respiration here. And heres that last step once again in electron transport.
Electron reactions. Finally, those electrons are being transported and those protons that were outside
the membrane just dying to get in, from the hydrogen atoms that began the whole process recombine.
Get together with oxygen, molecular oxygen to form water. So another way to refer to this process in
aerobic respiration where ATP is formed, the last step where water is formed, as you say, the oxygen is
the final electron acceptor. In aerobic respiration, where oxygen is used. Oxygen itself is the final
electron acceptor, by definition, aerobic respiration. And thats why it finally picks of the electrons. It
picks up the protons, too, but- you can say its the final proton acceptor, too, but by convention, we
say oxygen in aerobic respiration is the final electron acceptor. Form water, water is the end product.
And then youre done.

In anaerobic respiration, well see these are bacteria in the absence of oxygen. They lack the
cytochromes required to use oxygen as the final electron acceptor. So anaerobic bacteria, as the name
indicates, these cannot use oxygen. Another fact, to many anaerobes, oxygen is a poison. And well see
where that can occur, too. They cant deal with oxygen. So bacteria that grow anaerobically use
something-. They still have to go through glycolysis. They dont go through TCA cycle, but they go
through glycolysis, they go through electron transport. But at the end, instead of using oxygen, when
theyre anaerobic bacteria growing without air, they will use other electron acceptors, such as nitrate,
sulfate, or carbonate. So by definition aerobic respiration use oxygen as the final electron acceptor and
anaerobic respiration and a lot of bacteria were gonna talk about are strict anaerobes that can occur
severe oral infections like periodontal disease the final electron acceptor in their respiration is either
nitrate, sulfate, or carbonate. NOT oxygen. So another way to put it, the final electron acceptor in
anaerobic respiration is an inorganic compound other than oxygen. Because oxygen is an inorganic
compound, right? But these are inorganic compounds that acceptor electrons and they make
respiration. Thats why these bacteria can grow anaerobically, they dont need oxygen. Oxygen can
harm them. They use other things. They have to carry out glycolysis and electron transport. A different
electron transport chain in anaerobes, but they use it to derive energy in their electron transport chains
as well. In anaerobes.

10
So you can classify bacteria by the effect of oxygen on their growth. Obligate aerobes means some
bacteria will only grow in the presence of oxygen, in air, O
2
. Air and oxygen, we use them
interchangeably now. Obligate aerobes.
Obligate anaerobes, will not grow or will not grow well theres a whole gradient of different strict
aerobes to strict anaerobes of bacteria. But anaerobes mean they do not grow in the presence of
oxygen. As a matter of fact, oxygen is a poison to many strict anaerobes. Obligate or strict anaerobes.
Were gonna talk about the importance of these two enzymes, and which should determine whether or
not a bacterial cell is an aerobe or an anaerobe. These two enzymes well see in the next slide are
critically important in that role.
There are bacteria known as facultative anaerobes. They can grow in the present or absence of oxygen,
of air. Most bacteria are really facultative anaerobes. Can grow with or without air.
Microaerophilic bacteria are those that grow with a very small percentage of oxygen. Right now, what is
the percentage (I think I asked this before), the percentage of oxygen were breathing? Its about 20%,
right? Okay and in our mouth, its maybe 10%, 12%. And then farther back in the mouth and down
there in the gingiva, the gingival sulcus, between the teeth and the gums, there may not be any free
oxygen at all. Thats a good anaerobic environment. So some-. 20% is optimal for most bacteria if
theyre aerobes. These *Microaerophilic bacteria+ grow to about 5% oxygen best. They thrive, they
grow much better under 5%. We have special incubators well see that enable them to grow. You cant
grow them on a Petri plate and stick them in a regular incubator and have them grow well. You have to
reduce the oxygen content from about 20% to 5%. Microaerophilic.
And some bacteria, we characterize them as capnophilic. Whenever you see -philic of course that
always means love they love something. And these are bacteria that love capno- they love
carbon dioxide. This is another thing. Many bacteria are stimulated in their growth. They grow much
better when you enrich their environment with carbon dioxide. And we also have incubators that do
that as well. You put the plate in the incubator, you have this tank of carbon dioxide, a tube lead from
the tank of CO
2
into the incubator, and CO
2
builds up inside, interior of the incubator to about 5% as well.
5% CO
2
and they grow much better than they would in the absence of CO
2
, these capnophilic bacteria.

11
Here, an obligate aerobe would be Bacillus, that genus. Obligate anaerobe would be Clostridium.
Examples of facultative anaerobes are Streptococci that cause caries, E. coli, and most bacteria. So
microaerophiles well talk about when we get to infectious diseases, as well as capnophilic bacteria. But
majority of bacteria in the oral cavity are either obligate anaerobes, not Clostridium necessarily, but
those down in the gingival sulcus. And well talk about the cause of periodontal disease or facultative
anaerobes that can grow with or without air. Streptococci, youll learn an awful lot about that particular
group of bacteria. E. coli as well.

12
So what is it about oxygen that kills-, as I said oxygen can act as kind of a poison to anaerobes. Well
sometimes, well always, really, in metabolic reactions, imagine a bacterial cell growing and doubling
every 20 minutes. There must be a ferocious amount of activity going on inside that cytosol of the
bacterium. Within 20 minutes, they can lose all the cell wall, and the flagella, the DNA and RNA. Every
now and then, some things in metabolism that are harmful for cells unless theyre gotten rid of
instantaneously within nanoseconds. And some of these things that are dangerous that are toxic to
bacteria are reductions, molecular oxygen being reduced. Heres oxygen. Heres what we call the
superoxide radical. And here, the negative charge. Hydrogen peroxide. And even the hydroxyl anion.
One, two, three. These three things are very dangerous to bacteria. If they survive even a second or
longer, theyre gonna do some damage to the components of our cells, like our DNA, RNA, proteins, etc.
So you have to immediately get rid of these dangerous reduced compounds of oxygen. Superoxide
anion, hydrogen peroxide (which is used as you know a disinfectant and antiseptic), and hydroxyl ion.
So thats bad. Why do these things that are dangerous and they are produced in both aerobes and
anaerobes, so why is it that aerobes can exist when theyre produced, whereas anaerobes cannot exist
and survive when these compounds here are produced.

13
Well, heres what happens. Why are anaerobes killed by exposure to oxygen? Heres a superoxide
radical, and heres H
2
O
2
, and also OH, the hydroxyl on it are oxidizing agents. Oxidizing agents were
always told we have to take vitamins and things to get rid of our oxidizing agents so they dont harm
ourselves. The superoxide radical, hydrogen peroxide, and also the hydroxyl ions, should have that here,
are oxidizing agents. Generated during metabolism, split nanosecond, theyre gone.
Aerobes, but not anaerobes, contain these two enzymes that help aerobes survive. Superoxide
dismutase and catalase. Aerobes have these two enzymes, anaerobes do not, they lack them. Aerobes
can do, when they grow, is what they call the enzyme superoxide dismutase that mismutates, or
changes, the superoxide radical, shown here. This enzyme here, cause a disreaction when you get H
2
O
2

plus oxygen. Now this is also dangerous, so right away, aerobes breakdown H
2
O
2
using the enzyme
catalase to form water and oxygen. Danger of oxidizing agents to cells. So thats what happens.
Aerobes have these important enzymes that maintain their safety and a lot of them survive, whereas
anaerobes do not, and these hydroxyl ions and superoxide radicals build up and they destroy, danger,
destroying DNA, protein, other components of the cell. And the cells will die. So anaerobes will die very
quickly in the presence of these molecules shown here because they cant handle them, to let them
build up and these molecules shown here destroy components of the anaerobic cell.

14
Okay we talked about aerobic respiration and anaerobic respiration. And theres one other type of
pathway carried out by bacteria. And its very important to all of you, I think, and to all of us, really. In
addition to aerobic and anaerobic respiration, bacteria can also carry out fermentations. Fermentations.
And Im gonna mention a couple of them. One of them, well two of them shown here are lactic acid and
alcoholic fermentation. Im gonna show you the pathway of fermentation for the production of these
molecules, lactic acid and alcohol. Lactic acid is important because thats the one that causes the
demineralization of our enamel. When bacteria, such as Streptococci we will discuss and others,
produce lactic acid when theyre growing and the dental plaque, this biofilm on our teeth, lactic acid
begin the demineralization, begin to dissolve our enamel. Eventually lead to holes and cavities and
caries. So thats the result of bacterial fermentation. Lactic acid we will see. And alcoholic
fermentation is also reactions where ethyl alcohol is produced, which is very important to all of us,
particularly on the weekends when we have alcoholic beverages. But also many products that bacteria
produce in fermentation reactions are used to help identify them in the microbiology laboratory. Many,
many tests are available to identify bacteria based upon what kind of products they produce when they
ferment sugars. Fermentation, how is it defined? Its defined as a process in which the final electron
acceptor is an organic compound. So fermentation reactions are reactions and pathways in which the
final electron acceptor is some organic molecule. Not oxygen, not nitrate or sulfate or carbonate, but
organic, a carbon-containing compound acts as the final electron acceptor in fermentations. Lets take a
look at a couple here.

15
This is well, you can see how involved this must be. Heres what bacteria can do. Pyruvate. They get
pyruvate. Talked about all the end products of pyruvate, the end products. Some bacteria even carry
out this one, lactate. All these things can be formed. Alcohol. Others, butanediol, etc, etc. So these are
just a few of the many types of reactions can occur in bacteria. To help differentiate them from each
other. Not all carry out all these reactions, of course. But one or two, or few of them. But its by
determining what they produce when they change pyruvate to these different compounds. Identify
formate, identify acetate, identify butyrate. Then we can help identify bacteria. Series of reactions over
and over again, to see yes or no? Do they produce this fermentation end product or not? So
fermentation is often useful in helping identify bacteria by the end products that are formed during
bacterial fermentation.

16
Heres a very simple one thats important to you. Pyruvate. And here we have this is a fermentation.
This is a complete fermentation reaction. Glycolysis produce pyruvate. Here we see the pyruvate in one
simple step. Look what happens here. Its converted from pyruvate to lactate. Lactic acid or lactate.
Lactate always the salt. This is the culprit in caries. This is what demineralizes your teeth. This is what is
produced in the dumb plaque on the surface of your teeth. So heres pyruvate. Heres an enzyme,
lactate dehydrogenase (E for enzyme) that immediately converts pyruvate to form some bacteria like
the Streptococci to lactate. Thats a fermentation. Thats called lactic acid fermentation. And that
pathway is over. Lactic acid fermentation, just one simple step. Look at also here, we see that this
fermentation pathway, this fermentation reaction, NAD is reproduced. Remember I talked about its
important for glycolysis to have the NAD regenerated. NADH was reduced, for glycolysis has to be
regenerated, NAD. Now this can go back into glycolysis and be used over and over again. So
fermentation pathway, one simple step. Lactic acid form. Many Streptococci and other bacteria carry
out this fermentation and produce tons and tons lactate on our teeth. A lot. To demineralize them. So
thats a fermentation.
What is the final electron acceptor? Remember my definition of fermentation? In this pathway, which
compound shown here is the final electron acceptor? Gotta be one of these three, pyruvate, NADH, or
lactate. Actually it is Where is the final electron in this reaction? Its in here. We wanna oxidize it. So
the final electron acceptor, an organic compound, that picks up that final electron is pyruvate. So here,
in lactic acid fermentation, pyruvic acid is the final electron acceptor. It picks up the electron and is
converted to lactate.

17
How about this one. Heres another fermentation where ethyl alcohol is produced. And actually this
occurs more in yeast and fungi. A few bacteria can carry out this fermentation, but as far as in the world
of microbes, mainly its the yeast that ferment sugars, grapes, sugars, and other sugars to form alcohol.
Its a fermentation reaction. We need alcohol in our practices as well. We use alcohol for disinfection.
So its not just for drinking. Here pyruvate formed. The fate of pyruvate here, CO
2
lost, acetaldehyde.
Heres our friend, NADH, that was produced in glycolysis, has to be oxidized to NAD, and you form ethyl
alcohol, ethanol. Pyruvate decarboxylase is the enzyme involved here. What is the final electron
acceptor in alcoholic fermentation? What picks of the electron from NADH? Acetaldehyde, an organic
compound. So fermentation reactions in which the final electron acceptor is an organic compound.
Previously with pyruvate, with lactate fermentation. In alcohol fermentation, acetaldehyde picks it up.
Acetaldehyde is the final electron acceptor. Fermentation. Now, you get NAD regenerated in these
fermentation. Thats really great for the glycolysis to go on, its essential. But bacteria that carry out
fermentation dont really get much energy at all in the form of ATP. The only ATP they get is formed in
glycolysis. So remember glycolysis in bacteria that ferment, glucose, pyruvate is formed, and then they
convert it to ethanol, in this case for example. But no more ATP is formed. So they dont grow very well
at all in lab. They dont have robust growth because they dont produce much energy, but that net yield
from glycolysis helps them survive. And glycolysis can also occur anaerobically. It can occur under
anaerobic conditions, even though we see the final electron acceptor is an organic compound.

18
Here we have it again. Okay, I guess I was gonna ask you the same questions. Two enzymes involved.
This is a fermentation pathway. So we have aerobic respiration, anaerobic respiration, we have
fermentation. Those are the big three that occur in bacteria. And once again, many important
compounds are formed. We just mentioned a couple of them here. The lactate, the ethanol in
fermentations. And many, many other compounds are formed to help identify the bacteria.

19
Heres an example of that. Here pyruvic acid. You can see some bacteria and do an awful lot of things,
form an awful lot of different end products. Here its called mixed acid fermentation. So some bacteria,
pyruvate, they can do three or four or five different things with it. Form different acids, even. And so
its called mixed acid, many different acids may be the end products, such as acetic acid, succinic acid.
And some even produce gases such as hydrogen and CO
2
. So lets talk now how we can help
fermentations identify bacteria. Here we have a test tube. This tube here if you worked in lab, you
know what it is. Its a glass inverted, a little tube inside the broth in this test tube. And you put that
tube in and some of the media goes in there, some of the broth goes in there. And when you take this
tube and sterilize it and bring it back, this whole tube thats upside-down will open here at the bottom,
is completely filled with the broth and has this particular color. So this has a little gas already. Then,
here we have three different tubes. In this case here, I would say I dont know if they look like that

Initially, they all look the same. Initially, these three different tubes were purple. Take my word for it.
You inoculate some bacteria into this tube that do not carry out fermentation at all. The color of the
tube stayed the same, nothing happened. No acids produced, no gas. Whatever bacteria were
inoculated in that tube were not fermenters. In the middle one here, we see that indeed they did
ferment whatever sugar was in the test tube. The Durham fermentation test tube upside-down. And
when they did that, its acid, because the color of the media changed from purple to yellow as a result of
acid production, the pH went way down. You can see because of all the acid being formed. And also
some gas was produced. So H
2
and CO
2
were produced. Some bacteria can do this, others cannot. And
the other one on the left, only acid was produced, no gas. So just to point out the different usages of
fermentation test to, you know, say yes gas, yes no gas, yes gas and acid, or no fermentation at all. And
those are properties that help you pinpoint a microbial genus, species, and even well see later, even
more accurately stereotype that are-, as well.

20
And heres one I want to mention only because its commonly done in the lab, called butylene glycol
fermentation. I dont want to mention, once again, the whole pathway, but look at this compound here,
Acetoin. Youve probably never heard of this anywhere else, I dont know. Its a very rare compound,
but some bacteria when they breakdown pyruvic acid, they form butylene glycol, and in the process
they form the compound called acetoin. Forget about the structure of it, but the thing is, its a
compound thats produced in fermentation by some bacteria thats easily identifiable. A very simple
biochemical test. You have the bacteria growing in a broth test tube overnight. The next morning, you
say, I wonder if acetoin was produced overnight or not? You add a particular reagent, and if it did
produce acetoin, the color would change to red. Doesnt matter *the color+, but its a color test. And if
those bacteria didnt produce acetoin, did not carry out this fermentation pathway, the red color would
not appear. So once again, another fermentation case, not the end product, but the intermediate in the
pathway thats easily identifiable by Voges-Proskauer test. And we know for example, here are two
bacteria, Enterobacter and E. coli. These are very hard to distinguish between in the lab. They look alike,
they grow alike, so many different tests that are identical to these two Gram-negative bacteria. But this
is one here that helps differentiate these two Gram-negative bacteria. They look alike, stain alike,
everything. And thats because Enterobacter, that particular genus does produce acetoin. E. coli does
not. Very, very useful because E. coli, as we will see, can do a lot good, but also a lot of damage. It can
contaminate water, and thats indicative of sewages. Often running the test to see whether or not E.
coli is present in what we think is contaminated water, sewage in our drinking water. Look for E. coli, if
the Voges-Proskauer test is negative, it wasnt E. coli there, maybe the water is safe to drink. It could be
something else, but maybe its safe to drink, if E. coli is not there because acetoin was not found.

21
This is just another slide. You can look over it after. Ive mentioned some of these already, but just to
show you, so many different pathways of pyruvate in bacteria.

22
Another way to identify bacteria. Okay, now weve gone through two types of respiration and
fermentation. Some other ways to classify bacteria in addition to the effect of oxygen on their growth,
aerobes, anaerobes, facultative, microaerophiles, etc is the temperature of growth that they prefer.
Some bacteria, believe it or not, can grow very well in the cold. In the refrigerator, even. Theyre called
psychrophiles. They grow best at about, maybe, theres a curve... maybe from 2 degrees, 4 degrees, 8
degrees. They grow very well at 4 degrees. Psychrophiles, cold. And theres one or two bacteria were
gonna talk a lot later on in the other course that grow well in refrigerator and are pathogenic. And you
really have to be aware of them, because they grow better in the cold at 4 degrees centigrade, at
refrigerator temperature than they do at 37 degrees in a regular incubator. Thermophiles grow best at
above 50 centigrade. We found some even in hot springs. They can grow at incredibly temperatures.
And better than say, our body temperature. Mesophiles are the ones that grow in between these
extremes. Our body temperature is about 37 degrees centigrade. Most bacteria that inhabit us, such as
those that live inside of us, are mesophiles. They like to live at 37 degrees centigrade. Most pathogens
well talk about are mesophiles. Most of them, majority. They like body temperature because once they
get inside of us, its the temperature they like to grow in. They like to attack our tissues, they can
hydrolyze our tissues, break them apart to get food, so they can grow and the end result, they do a lot of
damage to our body and cause infections.

23
ATP requirements. I guess, I dont know. I started off doing research when I was in graduate school
with bacteria and trying to learn all about metabolism. But it always amazed me that heres an organism,
E. coli, shown here. E. coli can grow on this very, very simple medium we prepare in the lab that Dr.
Saxena will talk about probably on Friday, called minimal media. Media, plural. Its growth medium is
whatever we use to grow bacteria in the lab. Its called medium. All it takes for E. coli to grow is glucose
and 5 salts. Thats incredible! Glucose, the source of carbon. No other sugar has to be added to their
growth medium for them to grow. But you have to have salts to, you know, synthesize and produce
their phosphates, sodium, chloride ions, of course, for cells to grow. So 5 salts and only one carbon
source, and from this simple medium, E. coli can produce everything it needs to grow. Its flagella, its
capsule, its peptidoglycan, its cell membrane. Just from these simple salts and one carbon source,
glucose. This E. coli that grows on this simple medium is called a prototroph. And auxotroph is a term
Ill use later. So E. coli can grow on this simple medium, minimal medium. Its a prototroph. Sometimes
on these slides, we find bacteria like E. coli that need one additional supplement to grow, an additional
growth factor. And thats called an auxotroph. So an auxotroph is a bacterium that needs a growth
factor that its prototroph, or parent E. coli, did not need. So lets say E. coli grows on this medium, its a
prototroph. If you also have to add the amino acid histidine to grow, that would be an auxotroph. You
have to add histidine to grow. And any other amino acid that would help, that they need to grow. Or
any other product. Auxotroph, something that require that the parent E. coli did not need other than
the minimal medium.

24
Heres how the energy thats produced now in catabolism, so all that we just went through, especially
the electron transport. How is the ATP used. And from growing E. coli on that simple medium, and
following every step it uses in producing its polysaccharides and nucleic acids, every step. We know how
much energy is involved in the growth of E. coli, from a simple salt, one carbon medium, to large
population of cells. We know that the ATP that they produced, more than half is used for synthesis of
proteins. And this is true in our cells, too. We found this out initially in bacteria. How is energy used,
from catabolism, used for anabolic reactions in cells and in bacteria? And its the same in our cells,
roughly. 56% of ATPs produced are used for protein synthesis. Polysaccharides, 8%. Lipids, 0.3%. And
more energy is needed for RNA synthesis than for DNA synthesis. DNA synthesis does not require much
energy, not require much ATP at all. Other big uses are active transport, getting things from outside to
inside cells. And mRNA turnover 4%. So to me, thats really incredible. And why is it? A Darwinian
question, why is it that protein synthesis requires so much ATP? What is that step that thats involved in
protein synthesis where ATP is used? Remember? Think about protein synthesis now. Think about that
ribosome, and theres that string of mRNA on that ribosome. And all of a sudden, you have all the
amino acids there, lined up in a new-forming protein. And then you have tRNA coming down, right?
Transfer RNA with the new amino acid to add on to the ones that are already there to form this protein.
Every time the amino acid from the tRNA is transferred to the growing polypeptide chain, an ATP is used.
So protein synthesis is an incredibly energy demanding pathway. The production of proteins.

So I didnt finish. I still have a couple more slides to show when I see you next week. After Dr. Saxena
sees you on Friday.