Download Summaries 1 to 4

In case the study guides are feeling a bit overwhelming, I thought I'd include these
summaries (note: they are not comprehensive, but highlight major concepts that are
important. For instance, I mention Koch in the summary for lecture 1 so it's probably
important that you be able to discuss his postulates in terms of why they are good and what
their limitations are [note: you should understand the postulates, but do NOT need to
memorize them, I would give you the text should I ask a detailed question]).
Here are some pared down summaries of the first 2 weeks of class.
As for what to focus on, there are definitely big ideas in each chapter. And I like the “why”
questions.
Chapter 1 (lecture 1)--This is mostly an introduction to microbiology. There are three major
domains: bacteria, archae and eukaryotes. Microbes cause disease but also have myriad
helpful roles, including being useful in the lab as well as in our bodies. They can live in
extreme environments (space?). Hooke, Van Leeuwenhoek, Pasteur (swan-neck flask,
spontaneous generation) and Koch (postulates) revolutionized microbiology. Pasteur and
Koch especially had important roles in disease theory (along with Lister).
Chapter 3 (lectures 2, 3)--These are basic cell structures that are important to know, and do
involve some memorization. We do revisit capsule and the cell wall when talking about
biofilms, avoiding the immune response (capsule) and antimicrobial targets.
Lippopolysaccharide (LPS), a component of Gram - outer membrane, is also important. This
is also called endotoxin. The selectively permeable membrane is a very important concept
because it allows for the cell to control what comes in and out of it. It also plays a vital role
in metabolism because the movement of H+ powers the cellular machinery which makes
ATP (which we talk about in Ch. 6).
Osmosis (movement of water) is also important. That’s why pickling works (high salt and
sugar concentrations cause water to move out of the bacterial cell (plasmolysis), eventually
causing the bacteria to die.
Diffusion does not use energy. Active transport uses energy. This can either be via the
break down of ATP to ADP or “piggy-backing” on the movement of protons down their
concentration gradient.
Bacteria move using one or more flagellum (flagella). Chemotaxis influences the “run” and
“tumble” and represents one way that we know that bacteria sense and respond to their
environment.
Most of the cellular structures and processes we discuss have evolved because they work.
At the risk of anthropomorphizing the bacteria, think about what the bacteria “wants” to do. It
wants to chemotax towards a nutrient, right? So, the bacteria first has to sense a nutrient. It
does that with receptors on the outside of its cell membrane. It then regulates the flagella
such that the “run” is longer in the direction of the nutrient, so that it moves towards the
nutrient. You can extend this line of reasoning to other structures. Why does the bacteria
“want” to make capsule [to help avoid dessication, to prevent detachment from a surface,
etc]? Or pili [sex, attachment]? Or an endospore? Etc.
Absence or presence of a nucleus is very important as that is what differentiates
prokaryotes and eukaryotes. Eukaryotic cells have complex internal structures and their
method of important nutrients and materials inside of the cell are different (like
phagocytosis) and material often moves around via vesicles in the cell (which fuse to
membrane-bound organelles).
They can also move, having flagella and cilia. We talk more about this when discussing
protists which can move using their flagella or cilia (and remember, mucus and lung cells
have beating cilia that move bacteria and other pathogens out of the lung). Besides being
interesting, the endosymbiotic theory (mitochondria and chloroplasts were once free-living
bacteria) is important because it may explain how eukaryotic cells rose into existence.
Ch. 4-- Some bacteria grow in biofilms. These are important because they can resist the
immune system and antibiotics and can form problematic physical structures. The important
idea about bacteria living in mixed communities is that bacteria can compete for limited
resources or can work together. This comes back over and over again whenever we talk
about our normal microbiota protecting us by keeping pathogenic bacteria from establishing
an infection.
Bacterial growth in the lab is important because it helps us grow bacteria to work with and
also helps us to understand the dynamics of bacterial growth. Also, bacteria have different
characteristics depending on what growth stage they are in, which influences what kinds of
proteins (metabolites) they make. Bacteria are more vulnerable to antibiotics during
exponential growth because they need their ribosomes, cell wall, etc. to function during
growth and this is what antibiotics target.
Bacteria have very different nutritional requirements, as different as humans and plants do
(or more different, in some cases!). In terms of bacterial nutrition, nitrogen is important
because some bacteria can fix nitrogen from the environment (they are about the only
things on earth that can do this). Without these bacteria, nitrogen would be lost forever to
the atmosphere (instead of being a cycle).
Bacteria need a carbon source and energy to suvive. Some bacteria can break down CO2
and use it for a carbon source instead of using “food” (organic carbon compounds), some
eat organic carbon molecules. This is analogous to plants vs animals. We eat organic
carbon compounds and produce CO2. Plants “eat” CO2 and produce carbon compounds.
Some bacteria get their energy source from the sun (just like plants) and some get it from
breaking down those organic carbon compounds (just like humans). So organic molecules
can either be broken down into energy OR used to make new cellular structures.
Different bacteria have different growth requirements. This is important because it means
that only certain bacteria can grow in certain places. We have talked about this in terms of
selective and differential medias. For instance, why do you think S. aureus and S.
epidermidis can grow on MSA plates and are not harmed by the presence of oxygen
(remember, MSA is also differential because mannitol fermenters turn it yellow)? Their
natural environment is aerobic and salty (our skin), so it makes sense they can grow on
salty media, incubated in the presence of oxygen. Catalase and superoxide dismutase are
closely linked to detoxifying toxic oxygen species, so it makes sense they are made by
bacteria that live in aerobic conditions (aerobes, fac. anaerobes, microaerophiles, and
aerotolerant [superoxide dismutase only]). What is the link between aerobic respiration and
reactive oxygen species by-products?
The point behind talking about the Mars rover is to get you to think about the tell-tale signs
of life and what life needs (at a bare minimum) to survive (like the chemolithoautotrophs).
Also, that life is hardy!
This leads in to Chapter 6 (metabolism), where we focus on oxygen-using (aerobic
respiration), organic carbon compound “eating” bacteria