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z- Test 1
MCB 4414 Dr. William T. Self Spring 2011
48
Microbiology
Undergraduate 4
02/05/2011

Additional Microbiology Flashcards

 


 

Cards

Term
Enzymes
Definition
protein catalysts
Term
Reaction coupling
Definition
ability to convert one form of energy into another, then use it to drive energetically unfavorable reactions
Term
Oxidation
Definition
all energy comes from oxidation of something, and electron transfer
Term
Membrane gradients
Definition
bacteria store energy as a potential using membrane gradients of ions
Term
regulation of catalysts
Definition
The regulation of these catalysts (allosteric regulation) is the most critical regulation to help a cell adjust to the environment IMMEDIATELY
Term
Substrate level phosphorylation
Definition
producing ATP by direct coupling to redox reaction
Term
Oxidative phosphorylation
Definition
– redox reactions in membranes leading to ion gradients (storing energy to be used to make ATP or drive uptake of nutrients, flagella motion)
Term
Growth metabolism
Definition
metabolic pathways that contribute to formation of a new cell
Term
Non-growth metabolism
Definition
all other pathways, such as maintaining intracellular pools of metabolites, repair of macromolecules, secretion, motility, and stress response
Term
Porins
Definition
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
Term
Periplasm
Definition
– 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
Term
Cell membrane (cytosol or outer membrane) what is their respective roles?
Definition
a. generation of H+ gradient
b. reoxidation of NAD+ & FAD+
c. nutrient transport
d. ion transport to maintain osmotic homeostasis
e. flagellum rotation
Term
unique aspects of archaeal membranes
Definition
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
Term
Flagella types / roles
Definition
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
Term
Pili types/roles
Definition
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
Term
Gyrase
Definition
i. Gyrase introduces supercoils
Term
Gyrase introduces supercoils
Definition
Topoisomerase relaxes supercoils
Term
Pangenome
Definition
If you have 40 strains the pangenome is all the genes of those 40 strains
Term
Open pangenome
Definition
If you get new genes every time you sequence the gene is open
Term
closed pangenome
Definition
Genes dont change (always conserved)
Term
closed pangenome
Definition
doesnt change
Term
phases of the batch growth curve
Definition
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.
Term
Rich (nutrient broth) medium
Definition
is easier to make, but tells us little about the requirements for growth
Term
the most common ways to measure growth
Definition
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
Term
What can trigger entry into stationary phase?
Definition
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
Term
equations
Definition
a. x = x0 2y
b. Y = t / g
Term
balanced growth
Definition
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
Term
growth rate affects physiology
Definition
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
Term
Maximum growth temperature
Definition
some vital component (probably a protein) becomes inactivated by heat (denaturation)
Term
Optimum growth temperature
Definition
usually reflects the environmental niche of the organism, where the dominant forces of evolution have pushed the efficiency of the organism
Term
Minimum growth temperature
Definition
chemical reactions slowed, assembly of large structures (polyribosomes) not efficient due to solvation of hydrophobic protein interactions
Term
mechanisms that we have observed that we think improve life at extremes
Definition
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)
Term
D (decimal reduction time)
Definition
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
Term
Barophiles
Definition
organisms that thrive (growth at a faster growth rate) when cultured under higher pressure
Term
halophilic
Definition
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
Term
Acidophiles
Definition
survive and thrive at pH environments as low as 0.0-1.0 (1 molar acid!)
Term
Alkaliphiles
Definition
can thrive at high basic conditions (pH 11.5)
Term
Substrate level phosphorylation
Definition
producing ATP by direct coupling to redox reaction
Term
Oxidative phosphorylation
Definition
redox reactions in membranes leading to ion gradients (storing energy to be used to make ATP or drive uptake of nutrients, flagella motion)
Term
Growth metabolism
Definition
metabolic pathways that contribute to formation of a new cell
Term
Non-growth metabolism
Definition
all other pathways, such as maintaining intracellular pools of metabolites, repair of macromolecules, secretion, motility, and stress response
Term
Cell composition
Definition
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%
Term
Heterotrophy
Definition
Organic nutrient (Carbon source = Organics)

Chemoheterotrphs
Photoheterotrophs
Term
Autotrophy
Definition
CO2 + inorganic energy source

Chemoautotrophs
Photoautotrophs
Term
Chemoheterotrophs
Definition
Source of Carbon
Organic Compound

Source of Energy
Organic Compound
Term
Photoheterotrophs
Definition
Source of Carbon
Organic Compound

Source of Energy
Light
Term
Chemoautotrophs
Definition
Source of Carbon
CO2

Source of Energy
Inorganic Compound
Term
Photoautotrophs
Definition
Source of Carbon
CO2

Source of Energy
Light
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