Lecture 1 (Ch. 1):
1. Microorganisms are all around us. They are a major source of disease in the world but also
have many beneficial roles both in the environment and in/on our bodies.
2. We use microbes in the lab all the time. Pasteur’s Swan neck flask experiment used
microbes to prove that cells come from existing cells, and not spontaneous generation. He
also surmised that it was these microbes that were the cause of many illnesses. Koch
formulated his postulates to formalize how we determine if a specific microbe causes a
specific illness (also, there are limits to these postulates that you should now be able to
articulate).
3. We use microscopes to look at bacteria, viruses are too small. Microscopy can tell us a lot
about a bacteria (arrangement, shape, size, Gram designation).
Lecture 2 (Ch. 3)
1. There are many cellular structures we learned about. Some of the most important ones
come back again and again, usually because they have some role in disease, either by
helping bacteria to colonize, avoid the immune system, etc. or as targets for antimicrobials.
Think: capsule (and biofilms), cell wall, flagella, outer membrane (LPS/endotoxin), 30S
ribosome.
2. Transport in and out of the cell: it’s important to understand that it takes energy to move
something UP its concentration gradient but it does NOT to move something DOWN its
concentration gradient. Also, we talk about the electron transport chain/hydrogen pumps a
lot in Ch. 6.
3. Chemotaxis is a type of cellular movement that directs movement towards or away from a
stimulus. This should make sense, especially since we have spent some time talking about
how a cell senses the outside world and then responds to it (think lac operon). Chemotaxis is
simply a way bacteria (or other cells, like macrophages and neutrophils) sense the outside
world and then respond via movement.
Lecture 3 (Chs. 3 and 4)
1. Eukaryotic cells are characterized by the presence of a nucleus and compartments that have
specialized functions. Eukaryotic cells have different ways of taking in materials, and
phagocytosis is a specialized kind of endocytosis.
2. Mitochondria and chloroplasts are particularly interesting organelles because they have
many traits making them resemble bacteria (endosymbiotic theory).
3. Prokaryotes divide by binary fission and have varying generation times which reflect how
quickly they can grow (including during infections). Some grow in biofilms, which offers
protection from the immune system and the outside world.
4. It’s important to understand that bacteria have different nutritional and environmental
needs. Remember, some bacteria require NO growth factors (E. coli) and some require
many (N. gonorrhea). Bacteria have different oxygen requirements, as well (you should
know the terminology by now). You should be comfortable with terms describing where
bacteria get their carbon and energy, as well.
5. At this point you are all probably experts in the idea of selective and differential media.
Make sure you understand how these might be used to enrich for a particular bacteria.
Lecture 4 (Ch. 6)
1. All cells undergo glycolysis. Some then stop (fermentation), while others can undergo a
transition step to generate acetyl-coA from pyruvate. This enters the TCA cycle. The
reducing power (NADH, FADH2) can then be used to take excited electrons to the electron
transport chain. These electrons then gradually lose their energy as they are shuttled from
one membrane protein to the next and as they do this, this energy is used to pump
hydrogen ions UP their concentration gradient. As the hydrogen ions enter back into the cell
via ATPases, ATP is generated in large amounts. This process is cellular respiration (and
usually the terminal electron acceptor is oxygen). You should know what the major products
of each step are.
2. You should understand that these processes are often conducted by enzymes, which bind to
their substrates and allow some kind of chemical change to occur. Enzymes are regulated by
either competitive inhibition (competitor binds to the active site) or by non-competitive
inhibition (molecule binds to an allosteric site, a site other than the active site).
3. Photosynthesis uses photons to directly excite electrons found in the chloroplasts. These
electrons can either be recycled (no terminal electron acceptor, they return to Photosystem
I and are excited by photons again) or can instead be used to generate NADPH, which
provides reducing power that the cell needs during biosynthesis.
4. All this energy is used to either fix carbon (in the case of autotrophs) or fuel growth,
movement, reproduction, etc. The pathways that result in the generation of new cellular
structures is called anabolic and is essentially the opposite of catabolic pathways.
Lecture 5 (Ch. 5)
1. Different settings require different levels of microbial control. It is especially important in
the medical setting that pathogens be either reduced in number (like on the skin before
surgery) or completely absent (like on a scalpel). People in hospitals are especially
vulnerable to infection because of open wounds/incisions and potentially being
immunocompromised.
2. The bacteria that cause nosocomial infections are generally ubiquitous (found everywhere),
but they usually only cause problems in the special setting of a hospital. They can be
extremely drug resistant.
3. Sterilization will kill everything, including endospores (one of the hardiest forms of life on
the planet). Disinfection aims to reduce or eliminate the majority of bacteria and viruses,
but some small number may still remain. You should be familiar with the constraints of
different kinds of sterilization and disinfection methods (i.e. when would it be appropriate
to use an autoclave versus a filter?).
Lecture 6 (Ch. 7)
1. The central dogma of biology is that DNA is transcribed into RNA which is then translated
into proteins. DNA is made up of 4 nucleic acids: A, T, C, G which base pair (A-T, C-G). mRNA
is RNA that is transcribed from a gene in the DNA. Many copies of mRNA can be made for
the same gene and generally the amount of mRNA is related to the amount of protein to be
made. It is important that mRNA is unstable so that the cell can quickly stop making a
protein if necessary.
2. Three nucleotides of mRNA make up a codon. Each codon corresponds to one amino acid.
The mRNA is translated into amino acid chains (peptides, proteins) by ribosomes which are
composed of protein and rRNA. These are responsible for the catalysis of the addition of
new amino acids to the growing polypeptide chain. tRNA is responsible for “reading” the
codons and bringing the correct amino acid to the ribosome for incorporation into the new
protein.
3. The process of transcription is tightly regulated so that the cell only makes proteins
necessary for its environmental conditions. This is why sensor proteins help to communicate
what is going on and this signal then travels through the cell and to the DNA. Transcription
can be regulated by the presence of a repressor protein which must bind an inducer in order
to fall off the gene and allow the RNA polymerase to transcribe. Alternatively, often a corepressor will need to bind to the repressor in order to allow the repressor to bind to the
DNA. In some cases, an activator is required to turn a gene on and this activator must be
bound by an inducer. In all these cases, often the presence or absence of an inducer or corepressor is dictated by what the sensor protein is sensing. The Lac Operon was a complex
example of this.
Lecture 7 (Ch. 8)
1. Bacteria can evolve via spontaneous mutation or horizontal gene transfer. Spontaneous
mutation occurs rarely and can have different outcomes depending on the exact location of
the mutation (silent, missense or nonsense mutations). Deletions or insertions can be very
destructive since they cause frameshifts to occur.
2. Transposons are mobile genetic elements that can jump around the genome and plasmids
of a cell. Transposons can carry genes.
3. Mutation can be induced by introducing chemicals that can either modify or take the place
of the normal nucleic acids. Usually, this causes a mistake in base-pairing. Intercalating
agents can cause insertions or deletions.
4. DNA can be repaired by either light-dependent or light-independent methods. Usually, the
cell will excise a small piece of the problematic DNA (identified as the unmethylated new
strand) and then use the good DNA as a template for the repair. In the case of UV light,
thymine dimers form and some bacteria can use visible light to break these bonds. If not,
the cell will often start the SOS response (leading to the use of a polymerase that makes
many mistakes—this is how thymine dimers indirectly lead to mutation).
5. We can select for mutants that have gained an ability (like resistance to antibiotics) by
plating them on selective media. We can select for bacteria that have lost an ability (like
making the amino acid histidine) by replica plating on a minimal media and a rich media and
looking for colonies that can no longer grow on the minimal media.
6. You should understand conjugation, transduction, transformation in terms of how they
occur, what must happen to the DNA for it to become permanent and what kinds of genes
that we care about might be transferred in this way.
Chapter 12
1. How does “zombification” of ants help parasitic fungi to spread?
2. Why can eurkaryotic infections be harder to treat (why don’t we have any many drugs to
treat them)?
3. What diseases do protozoans cause?
Lecture 8 (Ch. 20)
1. Antimicrobial targets are generally something unique to bacteria. You should know the
general targets and be familiar with how different drugs target different parts of cell wall
synthesis. Also understand that pencillin (and all antimicrobials) must be able to access their
target or they cannot work.
2. While you don’t need to memorize all the different kinds of antibiotics again, you should be
familiar with the targets: 30S, 50S ribosome, nucleic acid synthesis, folate synthesis.
3. Be able to read a MIC test.
4. Understand the 5 general catagories of resistance (natural [having a Gram negative outer
cell membrane], drug-inactivating enzymes, alteration in the target molecule, decreased
uptake of drug, elimination of drug by efflux pumps). If I give you an example of one of
these, you should be able to explain why the cell is now resistant.
Lecture 9 (Ch. 13)
1. Viruses are very small and only have a few components, you should know what they are and
the general shapes of viruses.
2. Very key to understanding viruses is that they CANNOT replicate on their own and thus use
the host cell machinery. This is why it is hard to treat viruses, because if you inhibit these
processes you risk inhibiting the normal functions of your own cells as well.
3. Some viruses will be lytic (usually active infections) while some will be latent (prophages and
proviruses) while sometimes only low levels of virion are made (chronic). When virions are
being made, that is when illness occurs. Viruses can also bud out of a cell without killing it
out-right.
4. You should understand the general viral life cycle (lytic and provirus): adsorption, uncoating,
etc.
5. Viruses can use RNA or DNA as their genetic information, don’t worry about the +/- at this
point.
6. Prions are caused by misfolding of the PrP (prion protein). This causes a variety of diseases,
all of which are mediated by destruction of brain tissue. Some people are immune to Kuru,
in endemic areas.
Lecture 10 (Bacterial and Viral Pathogens)
1. Diarrheal diseases are spread via the fecal-oral route (water, food, your hands can be
contaminated). It makes sense that the bacteria would cause lots of diarrhea as the bacteria
is shed that way. For respiratory organisms, they cause coughs in order to be transmitted to
the lungs of the next host.
2. TB is a slow-growing bacteria that will slowly cause granuloma formation in the lungs.
3. Legionella is interesting because it infects free-living cells that resemble our macrophages.
4. Staphyloccocus aureus and Streptococcus pyogenes both cause a variety of infections
depending on where in the body the infection is located (the skin, the throat, in the blood,
under the skin in the fascia [necrotizing fasciitis]). Alternative treatments are important for
MRSA because we are running out of options.
5. HPV can cause cancer by pushing the cell cycle forwards for its own selfish benefit. E6, E7
and E2 are involved.
6. HIV causes illness by infecting and destroying T cells, effectively destroying the host’s
immune system. You should understand this process and why the loss of T cells has so much
impact on the host. HIV is very hard to treat because there are always mutants that can
escape the effects of HAART and the virus appears to hide in the body somewhere. There
are a number of barriers to an HIV vaccine, you should be able to identify them.
7. Influenza can be a very serious illness. The virus is made up of 8 pieces of RNA which means
this pieces can get swapped very easily, creating new strains of influenza. The avian
influenza H5N1 is very pathogenic but currently cannot go from person-to-person. However,
the quickness with which influenza can change is worrisome (including mutations that are
popping up in the wild that are involved in increased person-to-person transmission). The
H1N1 flu that killed millions of people in 1918 primarily targeted the young and healthy.