Microbiology Lecture Notes

Introduction
WHAT is microbiology? The study of SMALL organisms- usually < 0.1 mm= 100 m in size, or
small that what is visible to the human eye.
NOTE- get VERY familiar with the smaller parts of the metric system- microns and nanometersFig 1.13
There are a variety of branches of microbiology, organized around organisms, and around the
roles of the organisms involved:
bacteriology- bacteria
mycology- fungi
virology- viruses
(parasitology)- parasites
Roles of microbes:
immunology- this arose out of microbiology, although it's more about us than the microbes.
Usually studied as part of microbiology, but now often considered a branch of cell biology.
Medical microbiology, soil microbiology, industrial microbiology, microbial ecology, etc. would
all be about the roles of microbes in health& disease, soils, industrial processes, and the
interactions of microbes with one another and with the environment and other organisms.
You can also have combinations- medical virology, etc.
WHY study microbes?
VERY VERRRRRY INTERESTING!!!
- Model systems: Sometimes its easier to study a process in a simple organism that it is to study
it in a more complicated organismmovement, responding to the environment, reproduction, respiration, etc. A MODEL system is a
simple organism that is studied to understand a complicated activity. E.G.- We used bacteria to
figure out how DNA is replicated, how genes are turned on and off, how cells respond to their
environmental changes. Other examples: mice, fruit flies, nematode worms.
- They do unusual things: fix N2, live off NH3, H2S, other bizarre things; unusual forms of
photosynthesis.

-agents of geochemical change- they are heavily involved in the globe- cycling carbon, nitrogen,
sulfur.
-they kill us/spoil our food, do commercially useful things, like cheese, beer, yogurt, and as
factories for recombinant DNA products.
Arrogant microbiology facts:
Microbiology is THE reason we enjoy the life expectancy that we do!
Treat our water and
Treat our sewage
Vaccinate against disease
Take antibiotics for infections.
Use sterile technique when doing surgery
I cannot think of five things that have done more to extend our life expectancy.
History of Microbiology- we talk about 4 people:
1674: Anton van Leeuwenhoek: invented first simple microscope, saw the microbial world in
things like pond water.
Over the next almost two hundred years, there was plenty of improvements in microscopes,
BUT- the next big event was disproving spontaneous generation: This was an important step- if
microbes just spontaneously appear, then studying them would be very tough, and even
THINKING about pure culture/ sterile technique would be impossible!
1861, Louis Pasteur: the swan-neck flask. This ruled out one of the major objections to the
results of canning (which had been going on for almost 50 years by the time P. did his
experiments). By allowing air, but not microbes, into his sterile flask, he showed that air only
provided contamination, not something essential for spontaneous gen. Fig. 1.2
Role of luck: his material that he boiled didn't have any endospores, one of the unique features
of the microbial world, so the exp. worked. Your book notes that Tyndall figured out why
Pasteurs work was sometimes repeatable, and sometimes not ( it had to do with endospores ).
He also figured out a kind of cheap way to sterilize things, if you didnt have an autoclave.
Role of philosophy: he was also a theist- God was the author of life; it didn't just show up. And
to say that it did removed God as the creator. So he had a personal stake in this, as a supporter of
God.

Pasteur also discovered another important aspect of microbiology: microbes CAUSE DISEASE;
AND he developed some of the first vaccines, including the first one for rabies and anthrax.
1870's ROBERT KOCH: A German, contemporary of Pasteur's. He developed much of the
sterile technique used today, including the use of pure culture techniques. Also developed
KOCH'S POSTULATES: To prove a microbe is the causative agent of a disease:
The microbe has to be associated with the diseased person.
The microbe must be isolated in pure culture.
When reintroduced into a susceptible host, it must cause the disease
The microbe, when reisolated, must be the same one that was introduced into the
susceptible host.
1875-1918 was the GOLDEN AGE OF MEDICAL MICROBIOLOGY! LOTS of microbes were
ID'd as the causative agent of diseases: tuberculosis, diphtheria, typhoid fever, plague, whooping
cough, etc.
One other person to mention: Joseph Lister: a surgeon, in the 1860's he applied the germ theory
of disease to medical practice. Doctors started washing their hands, doing antiseptic, then
aseptic, surgery.
Medical Microbiology: the future: the future looks bright for medical microbiology, which is a
bad thing for the rest of us. There was a time when infectious disease was thought to be on the
waneWe would eventually conquer it, leaving cancer and heart disease as the major health problems.
Ha
Unfortunately the microbes haven't cooperated. Antibiotic resistance in microbes is rampant, and
people today are dying because of this. Microbes that were once thought defeated are now on the
rise, such as tuberculosis. Partly because of microbial evolution and partly because of changes in
our lifestyles, new diseases have emerged- AIDS being the most spectacular example. Tracking
down and fighting off disease will be an ongoing challenge.
Fig 1.3
BASIC CELL TYPES
Prokaryote vs. Eukaryote: Table 1.2., Two basic types (P&E), but three really:

Bacteria about the

size of mitochondria

Prokaryotes: "prenucleus": no nuclear membrane, small size (1X3 m would be typical) ; few or
no organelles; single, usually circular chromosome; 70S ribosomes.
These include two basic Domains: Bacteria: most of the ones out there; and Archaea: These are
unusual bacteria; outwardly they look like Bacteria, but they are found in extreme environments,
and have a number of chemical differences that mark them as completely different from Bacteria
particularly the absence of a cell wall material called peptidoglycan.
Eukaryotes: true nucleus: nuclear membrane. Larger size; 10-20 m (over 1000X the volume!)
would be a typical size; can be larger or smaller, of course; Elodea leaf cells are usually about
40X100X 20 m in size.
Organelles: mitochondria, chloroplasts, lysosomes, vacuoles.

multiple chromosomes, almost always linear.

bacteria, archaea, and eukarya are considered domains: units larger than kingdoms. (Eukarya,
Bacteria, Archea). What this means is that, while Bacteria and Archea may look similar, they are
very different. At the cellular level, you and the fungus between your toes have more in common
with each other than Eubacteria and archaea!
Eukarya include four of the usual five typical kingdoms: fungi, protisa (including algae and
protozoa), plants, and animals. Fungi, algae, and protozoa are all included, usually, in the study
of the microbial world. We'll only include a little about fungi. Algae and protozoa are also
claimed by the botanists and zoologists, so they are studied there as well.
NONLIVING MEMBERS OF THE MICROBIAL WORLD
These are considered acellular infectious agents. Not really alive. We'll define life later.
Viruses: DNA or RNA as genetic material, but not both; protein coat, sometimes a lipid
envelope.
Many diseases of bacteria, plants, and animals.
Viroids: naked pieces of RNA. Plant diseases.
Prions: proteins that multiply themselves. Mad Cow disease, Kuru, Creuzfeld-Jakob disease.

Nomenclature: Bacterial groupings are not nearly as well-developed as those for plants and
animals, but bacteria and fungi still use the bionomial system for naming organisms. e.g.- genus
and species names. E.g., Escherichia coli, or E. coli; Saccharomyces cerevisiae- yeast. The other
categories family, order, class, phyla- are also used. In general there are MANY phyla of
bacteria & archea- many more so than phyla of animals, for instance.

Chapter 2- Molecules of life

Chapter 2: Outline for biomolecules: cover this chapter quickly; get help for those who need it. I
do not cover the first part- from chemistry/other courses, you should be familiar with atoms,
elements, molecules, covalent (polar and non-polar) and ionic and hydrogen bonds, etc.
Order in Nester, et al.: Proteins, Carbohydrates, Nucleic acids, and Lipids.
The first three are made of repeats of building blocks; lipids dont really follow that pattern.
Proteins: composed of amino acid building blocks, with peptide bond linkages produced by a
dehydration synthesis (aka condensation reaction) (2.16). This results in a free amino end, and
carboxyl end. 2.17. The AAs are typically L form (fig. 2.15)

20 different AAs, thus ENORMOUS variety in types, although the actual number of types of
proteins is probably a few billion.

They can be put into three groups: ionizable: with COOH or NH3 groups producing charges.

non-ionizable polar: usually have an OH group, or CONH2 groups.

Non-polar or hydrophobic: usually have a hydrocarbon group.

Two are sulfur-containing: Methionine and and Cysteine, and then theres proline, the imino
acid. Cys forms disulfide bonds, joining two proteins together, and proline is often at the site of a
bend in the tertiary structure.

1o,2 o,3 o,4 o structure: Fig. 2.16

What they do: They are enzymes- catalyze the thousands of reactions in a typical cell;
they do structural things, like compose the flagella, or pili.
The shape is related to what the protein does! Heres an example:

http://www.pdb.org/pdb/explore/explore.do;jsessionid=A29C00477930F778DE1527EA605CE9
57?structureId=1V7Y
http://www.pdb.org/pdb/explore/explore.do?structureId=3ONZ
Carbohydrates/polysaccharides: composed of monosaccharides linked by glycosidic bonds. Fig.
2.19-2.21
Monosaccharides : (CH2O)n
di- or tri-saccharides, polysaccharides- every time theyre linked, you lose a water- dehydration
or condensation reaction.
starch/glycogen: 1,4 linkages- NRG storage
cellulose: 1,4 linkage- cell walls of plants. Others make up the capsules of bacteria- Xanthan,
dextran
modified sugars make up the cell walls of bacteria.

Nucleic acids: Polymers of nucleotides; storage and transmission of genetic material.

Nucleotides: phosphate, + 5 carbon sugar (ribose or deoxyribose) + nitrogenous base.
RNA/DNA differences:
Ribose vs deoxyribose; uracil vs thymine.

Nucleoside

Nucleotide

Lipids: Much more diverse structurally; slight solubility in water, great solubility in organic
solvents like benzene.
Fats simple lipids, fig. 2.26: 3 fatty acids + glycerol, joined by ester linkage. Some FAs are
saturated, some are unsaturated.
Also sterols, such a cholesterol- membranes of eukaryotes, but in only one type of prokaryote,
the mycoplasma, and they probably get it from the eukaryotic cells that they parasitize.
Compound phospholipids: phospholipids, fig. 2.29. 2 FAs, glycerol, phosphate connected to a
polar group; cell membrane.
Lipoproteins, lipopolysaccharides.

Learning Objectives for Biomolecules:

Biomolecules
5. Be able to give the overall structure and function of the following types of chemicals:
Amino acid: be able to identify a given a.a. as ionizable polar, non-ionizable polar and
non-polar. Be able to identify a peptide bond.
Protein: know what is meant by primary, secondary (alpha helix and beta sheet), tertiary, and
quaternary structure of a protein.
sugars;
polysaccharides; be able to identify a glycosidic bond
fatty acids
lipids: be able to identify the hydrophobic and hydrophilic components of a complex lipid.
Be able to identify an ester bond.
purine and pyrimidine bases: be able to identify the five most common bases as one or the
other.
nucleoside
nucleotide
DNA and RNA: know the similarities and differences between these molecules, and which
bases are complementary to each other.

Chapter 3: Functional anatomy of Prokaryotes: Were going to cover the structure of P. in depth;
and in the process cover a few things related to structure, such as transport and motility.
NOTE: microscope information is covered in LAB!
1. Characteristics of Living things: Cells have to be able to do certain things; their structure
tends to be related to those things

a.It has to be separate from their environment- Surrounded by a membrane.

b. Obtain NRG from their environment- autotrophs or heterotrophs
c. Synthesis of all cell components from simpler precursors obtained from the
environment (they grow bigger). (cytoplasm with enzymatic components, information storage,
repair, and retrieval systems in the nucleoid and cytoplasm)
d. Reproduce themselvese. Respond to their environment ;
2. Components:
Overview: Fig. 3.2 3

a. Cell membrane: a typical unit membrane of phospholipid bilayer. Fluid Mosaic Model!
phospholipids
membrane proteins
Water flows in freely through osmosis; because the cell is full of other stuff, this flow would
normally burst the cell; its force is resisted by the cell wall.

Roles: Transport, and energy; - read 3.4-.3.5 in your text!

Differentially permeable: brings in some things, but not others.
It tends to be charged, because of the work of protein in the cell membrane, which are involved
in energy production. 3.26: proton motive force. This force is involved in some types of
transport.

transport: active vs passive; Table 3.4, p 60; simple diffusion, facilitated diffusion (both passive),

Active forms: Major facilitator superfamily: symport, antiport, uniport: 3.28

ATP-binding-cassette (ABC) transporters: directly spend ATP to bring things in: 3.29
Group translocation: 3.30

b. Cell Wall:
Function: protection from osmotic shock in a hypotonic environment; provides shape

Peptidoglycan- NAM, NAG, amino acid bridges; figs. 3.32, 3.33, 34

G+ve: thick Pg,

G-ve: Thin, outer membrane, with lipopolysaccharide directed to the outside, and porins that
allow some passage between outside and the periplasmic space.
The periplasm is a unique area; it often houses enzymes that work to break things down that are
large enough to pass into the space; the products are then brought more easily into the cell. The
periplasmic enzymes also can be concentrated and made w/o being lost to the environment.
Peptidoglycan is a GREAT target for killing bacteria! 1) unique to bacteria- cant hurt us; 2)
essential for life as a microbe- no cell wall= DEAD. Lysozyme and penicillin type antibiotics
attack the bacterial cell wall.

d. Capsule or glycocalyx: Bacteria often have a outer layer- collectively called the glycocalyx;
the capsule is a distinct layer, while slime layer is more diffuse and irregular. Composed usually
of polysaccharide (dextran and xanthan gums are derived from these), or sometimes simple
amino acid repeats, often with D-amino acids.
They are good for adhearance, often the first step in the formation of biofilms; Strep mutans,
plays a role in tooth decay, producing a capsule from the glucose part of sucrose that allows it to
stick to teeth, and making a place for other microbes to stick as well. In Strep pneumoniae, the
capsule is antiphagocytic- we defeat it by producing antibodies against the capsule before it
multiplies enough to kill us.
e. External structures: Pili: These are hairlike structures that are useful for attachment to specific
surfaces; Neisseria that stick to the epithelia of the urethra and pathogenic E. coli that cause
bladder infections have pili that help them attach. Others are used for sex- for transferring DNA
from a donor to a recipient.
f. Flagella
Very, very cool- one of the few examples of rotary motion in nature (along with ATP synthase)Fig. 3.39- NOT like our cilia at all.

Basal body consisting of a series of rings that act as a stator, an internal rod that acts as a rotor,
driven by the proton gradient, a hook, and the filament itself. Rotates typically @ 20,000 RPM,
but when detatched from the filament can go 100K RPM.
Notes on movement: While the ability to move is interesting in and of itself. It means something:
The microbe has somewhere to go! This means that it senses its environment. This sensing
utilzes receptors on the surface, and internal molecules that relay this information to the flagellar
motor. It also includes feedback mechanisms, so that the sensing is best able to pick up changes
in the concentration of a compound, not its absolute concentration. Sensing an increase results in
longer (but not necessarily run until the gradient decreases) runs. Sensing a decrease shortens
the runs. Net result is that the microbe makes its way to the attractant.

Heres a cartoon of the assembly of one:

http://www.youtube.com/watch?v=JXV7qVkCnAM

Heres a link to a youtube video of a neutrophil, following a chemoattractant.

http://www.youtube.com/watch?v=ZUUfdP87Ssg&feature=related

Larger organisms actually sense a gradient- theyre big enough to do that; the problem with
being only 3 m long is that it doesnt give you enough of a gradient to sense, so they sample
over time.
g. Internal structures: DNA, ribosomes, cytoplasm,
DNA: circular, single chromosome
Ribosomes; 30S and 50S (70S total)
Notes on storage granules:
C, NRG Storage: poly hydroxy-butyric acid, others, useful for making plastics; others store
glycogen. None store fats or regular starch.
phosphate: often limiting, volutin granules
some make sulfur granules
e. Spore formation: Endospores
Found in G+ rods, Bacillus (aerobe) and Clostridium (strict anaerobe). Some significant
pathogens are sporeformers: B. anthracis (anthrax), C. botulinum, tetani, and perfringens (food
poisoning)
Differ from fungal spores, in that they are a survival, NOT reproductive, structure; 1cell
produces
one spore, so there's no reproduction.
Can be considered a primitive developmental cycle.
VERY resistant to killing by heat, drying, etc. NOT easily stained
\

Process:Fig 3.48 Cell realizes life is bad; starts sporulation process. Triggered by nutrient
deprivation, usually.

a. asymmetric DNA/membrane division

b. engulfment of the spore by the membrane of the mother cell: forespore with two membranes.
c. CORTEX forms between the two membranes: uptake of Ca++, formation of dipicolinic acid,
dehydration; protein coat formed
d. lysis of mother cell, release of spore.

Germination is the reverse;

Spores may be able to survive millions of years!

Taxonomy- CHs 10& 11, along with these notes

Introduction: Now that weve learned a bit about the structure of microbes, I want us to learn
some about how we classify them, so Im jumping to chapters 10 and 11. In the process, well
be learning some terms, and discussing some technology, that we havent covered in detail. We
will address these terms and technologies as we encounter them; it will give you a first exposure
to some of these. If you find the terms or technologies confusing, just be patient- well cover
them in more depth later. However, I think its important that you have a better mental picture of
the microbial world, before we discuss it in much depth.
Some terms.
Taxonomy: Science that studies organisms to arrange them into groups- similar organisms in
similar groups. Often with the goal of identifying a particular organism. It can be divided into:
Identification: characterizing a microbe, so you know what it IS
Classification: putting it into a group of similar organisms, to help in ID and study.
Usually the groups represent presumed evolutionary relationships.
Nomenclature: giving it a name.
As an aside, its the one area of science where truth is most likely to change. The identification
of an organism usually doesnt change, but its classification often does, as new information
arises (with fungi, the name changes sometimes as well!)
This chapter divides things in to how we ID them, and how we classify them, using phenotypic
and genotypic characteristics.
With bacteria, ID is very practical- we want to know the microbe thats causing infection, or
spoiling our wine, or thats producing our wine, or cheese, etc. So well use whatever specific
characteristics (or set of characteristics) that a microbe may have to ID it.
With classification, we usually want to group things evolutionarily- determine the phylogeny of
our microbes. This is hard:
1) whats an advanced bacteria? 2) how old are bacteria? 3) they can exchange genes easily, so
some traits get passed along readily, messing up the whole system!
Heirarchies: species- genus family- order-class- phylum/division domain. I dont think
bacteria use kingdoms!

In addition, sometimes we group organisms according to similarities; this may or may not imply
genetic relatedness: lactic acid bacteria, anoxygenic phototrophic bacteria, sulfate-reducers,
endospore formers, etc.
The Bible of bacterial taxonomy: Bergeys manual- 25 phyla. This compares with 11 major
animal phyla, and 35 total.
Taxonomys gotten all messed up recently, thanks to what we know about DNA and RNA
sequences of organisms!- fig 10.1

Basic taxonomic groups: Table 10.3, 6th ed. Ive listed three of the major phyla:
Proteobacteria: These include most Gram- bacteria, in five classes. The five classes are pretty
much based on genotypic features.
Low G+C Gram+ bacteria: the phylum Firmicutes; most G+ bacteria, except for Mycobacteria
and Corynebacteria, are in this phylum.
High G+C Gram+ bacteria: Phylum Actinobacteria: Mycobacteria, Streptomyces,
Corynebacteria, etc.
There are a variety of other microbes, which are given their own phyla!
Back to ID of bacteria:
Identifying Bacteria Basically, we can ID and classify according to PHENOTYPIC differences,
or by GENOTYPIC differences.
ID via phenotypic differences: This is still commonly done- some factors:

Fig. 10.3: Phenotype: size, shape, staining, metabolism, serology, FA analysis.

Genotypes: Genetic makeup- PCR, DNA probes. As with classification, rRNA sequences have
been widely used for ID.
Strain differences: Phage sensitivity, antibiotic resistance, serology, biochemical differences. E.
coli O157:H7 is sorbitol-. MRSA strains, in addition to being methicillin resistant, often have
other features used to characterize them, such as specific toxin genes.

Classifying microbes

Phenotypes: Numerical taxonomy: Fig. 10.15. Organisms are grouped according to their
similarities.
Genotypes: 16S rRNA sequences; genomic sequences.
Species = very similar
strain: slight differences; lab strains may have a defined genetic difference
Read in the book about G+C content, and hybridization, and amino acid sequence similarities;
these are good, but somewhat outdated.
The typical method uses 16S rRNA sequences: part of the 30S subunit. EASY to sequence.
This has been used to provide assumed phyogenetic relationships among organisms
These two methods- using phenotypes and genotypes- are also the two ways you can classify
microbes according to their presumed evolutionary relatedness. At this point, rRNA is the tool of
choice for determining relatedness.
Whole genome sequencing is also a useful tool- there are over 200 microbes that have had their
entire genome sequenced.

Groups of Bacteria
This handout is an attempt to simplify a fairly confusing field- bacterial taxonomy.
The first thing you should realize is that there is a fair amount of disagreement among
taxonomists about evolutionary relationships among bacteria. The editors of Bergey's Manual
have made little attempt to determine phylogenetic relationships among organisms. They have
split bacteria in to 25 phyla; bacteria within a phylum are similar to one another, but no attempt
is made to link one section to another.
The proponents of molecular taxonomy have used 16S rRNA data to produce proposed
phylogenetic relationships. Their analyses have produced results that link some of the "sections"
in Bergey's manual to each other, often in unusual ways.
In terms of the relationships of bacteria with each other you should be aware of the
following:
a. Molecular taxonomists divide the living world into archea, bacteria, and eukaryotes;
bacteria and archea are considered no more related to each other than to the eukaryotes.
b. The bacteria now include the mitochondria, chloroplasts, and cyanobacteria.
Some important groups of bacteria
The sections in Bergey's Manual group organisms on the basis of phylogenetic
relationships, usually based on DNA sequence information. Sometimes this is useful for
microbiology students, and sometimes it is not. Ive lumped some groups together, that are
recognized as useful groupings. These groupings are based on either (1) a combination of
characteristics, such as shape, motility, use of oxygen, Gram reaction, and spore-forming ability,
or (2) the possession of some other unique characteristic. Below is a description of some of the
more common, or more interesting, of these groups. These are derived from Tables 11.1 and 11.2
in your text. In this section, well be first introduced to a number of metabolic concepts- well
expand on those later, but provide enough information for you to understand these differences.
1. Gram-negative, strictly aerobic rods and cocci- this includes the genus Pseudomonas
(opportunistic pathogens, biodegraders of complex organic compounds) and Neisseria
(gonorrhea, bacterial meningitis)
2. Gram-negative, facultative anaerobes- this includes many of the organisms in your intestines,
as well as some important pathogens. Most of the Gram - organisms in lab are in this group. Ex:
Escherichia, Salmonella, Proteus.

3. Gram-negative, obligate anaerobes- straight, curved, and helical. These include many colon
microbes (Ex: Fusobacteria, Bacteroides), some of which can become opportunistic pathogens.
4. Gram-positive cocci: several harmless and pathogenic species: Micrococcus,
Staphylococcus, Streptococcus
5. Gram positive, endospore-forming rods: these include the genera Bacillus (mostly aerobes)
and Clostridium (obligate anaerobes). Several pathogens.

6. Gram-positive, non-spore-forming rods: these include the genus Lactobacillus, used in milk
products such as yogurt.
7. Gram-positive, irregular rods: these include Corynebacterium diphtheriae (diphtheria) and a
number of non-pathogens that live on the skin and in the mouth.
The groups listed below possess some unique characteristic that defines the group.
8. Cyanobacteria: These are capable of oxygenic photosynthesis- similar to that of green plants.
9. Anoxygenic phototrophic bacteria: under anaerobic conditions, these use sunlight to generate
ATP. To provide "reducing power" (e.g., NADH), they either use H2S, or an organic substrate
such as acetate. Ex: Rhodopseudomonas, Chlorobium.

10. Chemolithotrophic bacteria (chemoautotrophs): These use inorganic compounds- Fe, S, Mg,
NH3, H2S, as a source of energy, and CO2 as a source of carbon. They are extremely important to
nutrient cycling of nitrogen and sulfur. Ex: Thiobacillus (S), Nitrosomonas (NH3).
11. Mycobacteria: these have a waxy cell wall, and unusual, branched cell division patterns.
Some species cause tuberculosis and leprosy.
12. Mycoplasma: These have no cell wall; they can cause an unusual form of pneumonia
13. Spirochaetes: These organisms are shaped like a corkscrew; some live in aquatic
environments. Two important pathogens: Treponema pallidum (syphilis) and Borellia burgdorfi
(Lyme disease).
14. Rickettsias and Chlamydias: These are obligate intracellular parasites. The chlamydia have
an extracellular form that can survive briefly outside a host cell. They cause typhus, Rocky
Mountain spotted fever (rickettsias), and one chlamydial species is a major source of third-world
blindness.
15. Budding, and/or appendaged bacteria: These either reproduce by budding, or they are able
to attach themselves by a stalk to a surface. They often live in very dilute aquatic environments.
Ex: Caulobacter.

16. Gliding, fruiting bacteria: These move very slowly by gliding across a solid surface.
Under conditions of nutrient deprivation, the cell aggregate to form a fruiting body that is
visible to the naked eye. Ex: Myxobacteria.

17. Archea: Taxonomically, these are a have been placed in a separate domain by the
molecular taxonomists. They are characterized by:
a. Similarity to each other in their rRNA sequences.
b. Cell walls that lack peptidoglycan. The cell walls that they do possess are variable; some
have pseudomurein, a peptidoglycan-like heteropolymer that lacks muramic acid and
diaminopimelic acid; others have a protein coat, still others a heteropolysaccharide coat.
c. Strange living conditions. They are found in extreme ecological niches: high salt
(Halobacterium), highly anaerobic (Methanobacterium) or high temperature/low pH
conditions (Thermoplasma)

36

Fungi:
Outline:
Definition: EUKARYOTES
non photosynthetic; usually chitin for cell walls
heterotrophic, mostly aerobic, some facultative anaerobes, such as yeast.
saprophytic- nutrients must be absorbed; doesn't engulf it's food.
Responsible for a great deal of decay, many plant diseases, and a few human diseases.
Some terms:
Yeast: single-celled fungi.
mold: filamentous, producing hyphae, a collection of which is mycelium. Most produce
asexual spores, that are vegetative in function
mushroom: fruiting body of a filamentous fungus.
Some are dimorphic- yeasts @ 37C, molds @ <30 C, including some major pathogens.
Reproduction: asexual: hyphal growth, budding/fission (yeasts) asexual spore formation.
Most are haploid.
Most are capable of producing two or more sexual types, which mate, temporarily
producing a diploid zygote that rapidly undergoes meiosis, producing haploid cells that
are vegetative.
Types of fungi: p. 308, Table 12.3 Classifcation is by type of sexual spore, in most cases.

37

Zygomycetes: aseptate, sporangiospores; zygospores for sexual reproduction; (gametes

are identical). Bread mold Rhizopus

Ascomycetes: septate hyphae with conidiophores bearing conidia; sexual reproduction by

ascospores in an ascus; bread yeast, neurospora, sacharomyces, morels, truffles, plant
pathogens.

Basidiomycetes: septate hyphae; sexual reproduction by basidiospores; mushrooms, some

plant pathogens. Characterized by a club-shaped spore-bearing structure (basidium), fig

38

12.17. Agraricus, Amanita, rusts, smuts.

Deuteromycetes: septate hyphae; no known sexual stage; many pathogens. Ex:

Microsporium, Trichophyton, most human and animal pathogens.
Water molds: no longer fungi; Oomycetes: non-septate hyphae; often have a flagellated
stage; cause some disease- potato blight that changed Irish history
Slime molds: Wonderful, strange creatures!
cellular slime molds: no sexual stage, and they remain cellular. Form false pseudoplasmodia that flow over wood, etc., eating things by dissolving them. When food runs
out, they form SLUGS. that will move around until they find a suitable place then
sporulate, producing a fruiting body. Loved by developmental biologists, evolutionary
biologists.
http://www.youtube.com/watch?v=leKI3Cv9YYw
http://www.youtube.com/watch?v=bkVhLJLG7ug

39

acellular: one large mass of protoplasm- plasmodial slime molds. These also reproduce
fruiting bodies, and the spores are haploid. They can have a flagellated stage, either the
flagellated or the amoeba stage fuse, producing a diploid cell that becomes a
plasmodium.

FUNGAL ACTIVITIES:
FOOD: mushrooms
Food production: beer, (Saccharomyces cerevisiae) bread
cheese: Penicillium
spoilage: Aspergillus flavusAntibiotics: Penicillium others
Allergies to spores.
Fungal diseases:
1. Allergic reactions: "farmer's lung" is often an allergic reaction
2. Mycoses: infections- see table 12.4- good reference to other chapters

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a. superficial: dermatophytes; athlete's foot, ringworm; trichophyton, microsporum

Candidiasis: normal candida albicans overgrows due to immunosuppression,
antibiotic treatment.
b. intermediate infections: usually lungs or skin. Many are dimorphic fungi.
1)Dimorphic fungi:
These are mostly lung infections that can go systemic, from heavily contaminated soils
Histoplasmosis- Histoplasma capsulatum: Ohio river valley fever
Coccidiodomycosis: Coccidioides immitis: San Joachin valley fever
Sporothrix- rose gardeners disease- fungal skin infection that can move up the arm!

c. Systemic- the worst kind: encapsulated yeast: Cryptococcus neoformans; bird

droppings; victims are often immunocompromised.

41

Antifungal agents: p. 527, Table 21.4 ; problem b/c they are eukaryotes. Many of these
agents need a long time to work.

Targets: Membrane permeability: amphotericin B; NASTY

Membrane synthesis: Azoles; fungi have ergosterol instead of cholesterol

42

Nucleic acid synthesis: 5-fluorocytosine

Keratin-lovers: griseofulvin- concentrates in the keratin, the fungi eat the keratin, and it
interferes with cell division. Take months of treatment.

End of notes for Exam I!!

43

Ignore all this- at least for now

Generation of Energy (NRG)

1. Basic principles: NRG needed to make more bacteria; also for movement; for active
transport;
and for maintaining the differences between inside and outside the cell; and for cell
maintenance.

NRG currency of the cell: ATP; also NADH/NADPH, used for "reducing power".

This is derived from "reduced carbon compounds" in most bacteria- chemoheterotrophs

from sunlight in some: phototrophs, both hetero and auto;
from reduced inorganic compounds in chemolithotrophs

2. Oxidation and Reduction:

Reduction: gaining e's or hydrogens; thus, and reduced compound has relatively more e's
or H's
that the oxidized form.

6CO2 + 6H2O <----> C6H12O6 + 6O2 ; CO2 gains H's; H2O loses H's.

44

NAD+ + 2H+ + 2e- ----> NADH + H+

With covalent molecules, there is increase share of the electrons upon reduction:
CO2 + 4 H2 ----> CH4 + 2 H2O; methane is more reduced than CO2; partly determined
by
counting H's, and the sharing of e's by methane vs CO2.

whenever there is an oxidation, there is also a reduction; the work in pairs.

Some redox rxns are endergonic; some are exergonic. These can be distinguished by use
of the
electron tower: a listing of oxidized/reduced compounds, along with the volts required to
put e's
on (reduce) the oxidized member of the pair. The source of e-'s isn't considered, so it's a
half
reaction.

2H+ + 2e-----> H2 : -0.43 volts.

O2+ 2e- + 2H+ -----> H2O, +0.82 volts.

45

Something with a negative half-rxn will tend to give up electrons to something with a +
half rxn,
releasing NRG.

H2 + O2 -------> H2O exergonic

H2O----> H2 + O2; endergonic.

You can look at the pairs on an e tower and tell if a rxn is ex or endergonic.

SUMMARY: The more negative (higher up the tower), the easier it gives up -donatese-'s; The
better reductant it is; the more positive (lower on the tower), the easier it accepts
electrons; the
better oxidant it is.

Moving down the tower is energetically favorable; moving up is unfavorable.

3. Enzymes help the favorable reactions to occur- the overall oxidation of reduced carbon
compounds.

46

They lower the activation energy; rxn goes at room temp.

The overall reactions, instead of going all at once, occur in several steps, releasing NRG
in small
steps, allowing it to be harvested at many locations, producing a lot of ATP/NADH.

4. Summary of metabolic processes: Chart.

5. Glycolysis: OH, MIM. Results: 2 ATP, NADH for other purposes.

6. Fermentation: Reoxidation of NADH, production of final fermentation end product.

7. Pentose Phosphate: p 123, 781. In case you haven't noticed, anaerobes have no source
of
NADH! The is rectified by the Pentose Phosphate pathway: it makes NADH; and it also
produces precursors for biosynthesis: Pentoses, and erythrose phosphates. The initial rxns
are
straighforward; after that, there are a series of condensation and hydrolysis rxns that end
up
regenerating glucose and producing 3,4, and 5 carbon phosphorylated intermediates.

47

8. Respiration: Glucose---> pyruvate----> acetyl-S-CoA; TCA cycle;

Products: CO2; NADH, FADH2; one GTP or ATP;

No O2 used yet.

9. Electron transport: use MIM e's go from high on the tower to lower on the tower, NRG
released us used to translocate protons from out to in; results in electrochemical gradient;
this can
do work, OR be conserved as ATP via ATP synthetase.

10. Anaerobic respiration: terminal e acceptor is NO3- + 2e- + H+ ------> NO2- + H2O;
SO4-----> H2S;

11. Inorganic chemicals: Chemoautotrophs:

a. use NH3, NO2-, H2S, S, Fe++; oxidize them via e transport.

O2 is almost always the terminal e acceptor---> obligate aerobes.

48

Don't make a lot of NRG this way; slow growing.

Important in a number of nutrient cycles.

Biosynthesis:

1. ALL biomolecules can be made from 12 precursors!

Organic e- donor
CO2<-------------Catabolism (degradation)
Intermediates:
Glu-1 PO4
Glu-6 PO4
Ribose-5-PO4
Erythrose-4-PO4
Phosphoenolpyruvate
Pyruvate
3-Phosphoglycerate
-ketoglutarate

49

succinyl-S-CoA
Oxalacetate
Dihydroxyacetone PO4 (=3PGA)
Acetyl-S-CoA
|
|
Anabolism (Biosynthesis)
|
|
Amino acid, nucleotides, vitamins, Carbohydrates, fatty acids, Etc.
Metabolism is regulated in a way that makes sense;

eg: They have ways of both making and degrading glucose, some of which use the same
enzymes;
they won't do both at the same time, however.

One method of control is end product inhibition; In a pathway, the end product inhibits
the first
enzyme that is unique to the pathway.

This occurs because the enzyme usually has a binding site for the end product that
influences the

50

active site.

Because the TCA cycle is a cycle, it is sometimes short-circuited to provide

intermediates. This is
called the glycolytic cycle.

Nitrogen enters by an amination rxn with -Ketoglutarate:

NH4+ + -Ketoglutarate -----> glutamic acid.

Summary of Metabolic Pathways

Metabolism: integrated network of chemical reactions that occur in the cell, through
which enery
and materials are changed from one form to another.
Catabolism: biochemical reactions involved in the step-wise breakdown of nutrients. In
general,
the nutrient is oxidized and and the energy released in these oxidations is trapped in a
form that

51

can be used by the cell.

Anabolism: biochemical reactions involved in the synthesis of cellular constituents from
simpler
molecules; anabolism usually requires energy.
Metabolic pathway: series of intermediate compounds formed in metabolism; the product
of one
reaction is the substrate of the next. Glycolysis is a catabolic metabolic pathway.

Fermentation
2 pyruvate ultimate
glucose glycolysis 2 NADH+ H+ ------------->fermentation
--------------> 2 ATP (SLP) end-product + NAD+

cellular work

Respiration

2 ATP(SLP)

52

glucose glycolysis 2 NADH+ H+

--------------> 2 Pyruvate)

pyruvate acetyl CoA + CO +NADH + H+

TCA cycle

2CO
1ATP
3 NADH + H+
1 FADH2

Electron Transport Chain

Chemiosmotic Energy reduced terminal

electron acceptor
e.g. 1/2O2 +

53

2e- + 2H+---->H2 O
Cellular work Electron transport ATPase
(motility, symport) phosphorylation -----------> ATP
ATP synthetase

Introduction

WHAT is microbiology?

1mM= ________m

1 m= ________nM

54

Types of microbiology:

By organism:

bacteriology- bacteria
mycology- fungi
virology- viruses
(parasitology)- parasites

By roles of microbes:

Immunology

Medical microbiology, soil microbiology, industrial microbiology, microbial ecology, etc.

WHY study microbes?

VERY VERRRRRY INTERESTING!!!

55

- Model systems: A "simple" organism that does complex things that are easier to study.
Examples:

- They do unusual things: fix N2, live off NH3, H2S, other bizarre things; unusual forms
of
photosynthesis.

-agents of geochemical change- they are heavily involved in the globe- cycling carbon,
nitrogen,
ssulfur.

-they kill us/spoil our food, do commercially useful things, like cheese, beer, yogurt, and
as
factories for recombinant DNA products.

56

History of Microbiology
1674: Anton van Leeuwenhoek:

1861, Louis Pasteur:

1874, Robert Koch

KOCH'S POSTULATES: To prove a microbe is the causative agent of a disease:

57

The microbe has to be associated with the diseased person.

The microbe must be isolated in pure culture.

When reintroduced into a susceptible host, it must cause the disease

The microbe, when reisolated, must be the same one that was introduced into the
susceptible host.

1875-1918 was the GOLDEN AGE OF MEDICAL MICROBIOLOGY! LOTS of

microbes
were ID'd as the causative agent of diseases: tuberculosis, diphtheria, typhoid fever,
plague,
whooping cough, etc.

1860's, Joseph Lister:

Future of medical microbiology:

58

BASIC CELL TYPES

Prokaryote vs. Eukaryote: Table 1.3., figs. 1.5, 1.6. Two basic types:

Prokaryotes:

Eubacteria and Archea:

Eukaryotes:

Eubacteria and Archea and Eukarya: domains

59

NONLIVING MEMBERS OF THE MICROBIAL WORLD

Acellular infectious agents

Viruses:

viroids:

Prions:

Bacterial nomenclature: the bionomial system

60