z- Test 1

Enzymes
protein catalysts
Reaction coupling
ability to convert one form of energy into another, then use it to drive energetically unfavorable reactions
Oxidation
all energy comes from oxidation of something, and electron transfer
Membrane gradients
bacteria store energy as a potential using membrane gradients of ions
regulation of catalysts
The regulation of these catalysts (allosteric regulation) is the most critical regulation to help a cell adjust to the environment IMMEDIATELY
Substrate level phosphorylation
producing ATP by direct coupling to redox reaction
Oxidative phosphorylation
– redox reactions in membranes leading to ion gradients (storing energy to be used to make ATP or drive uptake of nutrients, flagella motion)
Growth metabolism
metabolic pathways that contribute to formation of a new cell
Non-growth metabolism
all other pathways, such as maintaining intracellular pools of metabolites, repair of macromolecules, secretion, motility, and stress response
Porins
a. Porins serve to allow small nutrients (less than 700 daltons) to pass through the outer membrane and into the periplasm
b. Porins also help to regulate osmolarity – when changes in salt concentrations occur
Periplasm
– space between outer membrane and cytosolic membrane where enzymes involved in defense are located, along with proteins used for breaking down nutrients and taking up small molecules with high affinity
Cell membrane (cytosol or outer membrane) what is their respective roles?
a. generation of H+ gradient
b. reoxidation of NAD+ & FAD+
c. nutrient transport
d. ion transport to maintain osmotic homeostasis
e. flagellum rotation
unique aspects of archaeal membranes
a. Membranes are built using isoprenoid subunits
b. Ether linkage rather than ester linkage
c. Some are monolayers of 40 carbon linked lipids (B)
d. More stable for high temperature ??? Maybe not
Flagella types / roles
a. Types
i. Polar
ii. Multiple Polar
iii. Peritrichous
b. Flagella serve to move the cell towards nutrients and away from danger and toxic chemicals
c. Proton motive force drives the turning of the ‘motor’ – energy intensive (test tube mutant story)
d. Flagella require a great deal of energy – in the form of proton motive force
e. Recent studies have focused on potential to use this as a biological scaffold to build nanomolecular motors
Pili types/roles
a. Roles
i. Binding to host cell – adhesins at the tip
ii. Conjugation of DNA from similar cell types
iii. Recent evidence suggest electron transfer to inorganic materials
iv. pili can be used to transfer electrons to inorganic metal oxides
1. Lovley’s group has been studying iron and metal reduction for several years
2. This study was significant due to direct evidence for electron transfer in pili
b. Fimbriae
i. Fimbriae are adhesive pili
ii. enable host/tissue specificity & biofilm formation
iii. often bind to oligosac on other cell surface receptors e.g. Type I
c. Sex Pili (G-)
i. adhesive pili for DNA transferadhesions attach to mannose glycoside residue of host
Gyrase
i. Gyrase introduces supercoils
Gyrase introduces supercoils
Topoisomerase relaxes supercoils
Pangenome
If you have 40 strains the pangenome is all the genes of those 40 strains
Open pangenome
If you get new genes every time you sequence the gene is open
closed pangenome
Genes dont change (always conserved)
closed pangenome
doesnt change
phases of the batch growth curve
a. Lag
i. adapt from stationary, cell size increases
b. Exponential
i. steady state, largest cells
c. Stationary
i. substrate limited, product accumulation, cell size decreases
d. Death
i. energy (ATP & Dp) depleted, autolysis, sporulation, cysts, etc.
Rich (nutrient broth) medium
is easier to make, but tells us little about the requirements for growth
the most common ways to measure growth
a. Most common method – turbidity
i. Limitations:
1. Can not differentiate between live/dead cells
2. Assumes cells of equal size
3. Does not always directly correlate to mass
b. Live/dead cell count – counting chamber
i. Limitations:
1. time consuming – labor intensive
c. Direct plating (plate count)
i. Limitations:
1. cells tend to clump
2. some genus/species don’t ‘plate well’
3. time (24 or more hours to get data)
d. Electronic counting
i. Limitations:
1. specialized equipment
2. live/dead is not determined
What can trigger entry into stationary phase?
a. Lack of carbon, nitrogen, phosphorus or trace mineral
b. Toxic buildup of metabolic end product
c. * Always realize – pure cultures are almost never found in nature – and thus what we are studying are well defined ‘artifacts’ of the laboratory
equations
a. x = x0 2y
b. Y = t / g
balanced growth
a. Defined as growth in which the number of molecules of DNA, protein, ribosomes in a daughter cell is matched to the parent cell
b. If achieved, experiments can be more reproducible – organisms are in the same physiological state
c. Cells are the same size – same growth rate
d. Batch growth is changing nearly all the time, thus is not as reproducible
e. Usually achieved using a continuous culture device, or chemostat
f. Medium can be automatically added, either in steps or continuously
g. Since cells and medium removed, a balanced steady state can be reached
h. Once established, perturbations such a nutrient limitation can be carried out to determine how the cell responds to the ‘stress’
i. Growth rate and density determined by medium composition and flow
growth rate affects physiology
i. Protein synthesis is ‘one speed’ – to make more cells faster you have to make more protein synthesis machines (ribosomal RNA and protein)
ii. Protein synthesis is limited by mRNA – to make more protein you must increase the level of mRNA
Maximum growth temperature
some vital component (probably a protein) becomes inactivated by heat (denaturation)
Optimum growth temperature
usually reflects the environmental niche of the organism, where the dominant forces of evolution have pushed the efficiency of the organism
Minimum growth temperature
chemical reactions slowed, assembly of large structures (polyribosomes) not efficient due to solvation of hydrophobic protein interactions
mechanisms that we have observed that we think improve life at extremes
a. High levels of chaperones (up to 80% dry weight)
b. Thermoprotective DNA binding proteins
c. Reverse gyrase (positive supercoiling)
d. Higher magnesium concentrations (DNA stability)
D (decimal reduction time)
a. D value is the time it takes to kill 90% of the organisms in a given experiment (or one log reduction in viability
b. This can vary since the size (and volume and environment) of the population can vary for each experiment
c. This is not specific to killing by heat, but this is the best studied parameter for sterilization
Barophiles
organisms that thrive (growth at a faster growth rate) when cultured under higher pressure
halophilic
can withstand salt concentrations over 5 Molar – close to saturation point (Halobacterium) – this is actually an archaebacteria*

i. With less water, these organisms synthesize or transport compatible solutes such as proline, glycine, betaine, glycine betaine
ii. These compounds are also used in biotechnology to allow for more efficient folding of expressed proteins

Acidophiles
survive and thrive at pH environments as low as 0.0-1.0 (1 molar acid!)
Alkaliphiles
can thrive at high basic conditions (pH 11.5)
Substrate level phosphorylation
producing ATP by direct coupling to redox reaction
Oxidative phosphorylation
redox reactions in membranes leading to ion gradients (storing energy to be used to make ATP or drive uptake of nutrients, flagella motion)
Growth metabolism
metabolic pathways that contribute to formation of a new cell
Non-growth metabolism
all other pathways, such as maintaining intracellular pools of metabolites, repair of macromolecules, secretion, motility, and stress response
Cell composition
Protien 55%
tRNA 21%
23S RNA 11%
16S RNA 5.5%
5S RNA .4%
transfer RNA 2.9%
Phospholipids 9%
DNA 3.1%
Murin 2.5%
Glycogen 2.5%
Metabolites 3%
Ions 1%
Heterotrophy
Organic nutrient (Carbon source = Organics)

Chemoheterotrphs
Photoheterotrophs

Autotrophy
CO2 + inorganic energy source

Chemoautotrophs
Photoautotrophs

Chemoheterotrophs
Source of Carbon
Organic Compound

Source of Energy
Organic Compound

Photoheterotrophs
Source of Carbon
Organic Compound

Source of Energy
Light

Chemoautotrophs
Source of Carbon
CO2

Source of Energy
Inorganic Compound

Photoautotrophs
Source of Carbon
CO2

Source of Energy
Light

Categories: Microbiology