Flashcards in Midterm 2 Deck (182)
Macro composition in percent dry weights of protein, lipids, RNA, DNA, and saccharides
Which elements are needed to synthesize oxygen molecules?
What are the 2 categories for carbon source organisms?
Get their carbon from CO2
Get their carbon from a source other than CO2
What are the 2 categories for energy source organisms?
Energy from light
Energy from oxidation of reduced compounds (organic or inorganic)
What are the 2 categories for electron source organisms?
Get electrons from reduced inorganic compounds (eg. plants)
Get electrons from reduced organic compounds
What is nitrogen needed for?
What is phosphorous needed for?
What is sulphur needed for?
Some amino acids
What is the reduced form of carbon?
CH4 (Methane)- Organic matter
What is the oxidized form of carbon?
CO2 and CO
What does CO2 fixation involve?
The conversion of CO2 into organic matter
What type of organism would perform CO2 fixation?
What carries out nitrogen fixation?
Not coupled to electron transport
Repressed by O2
Coupled to electron transport
Repressed by ammonia
What is the relationship between the carbon and nitrogen cycles?
They are coupled
Can make their own cofactors for enzymes
Solute is modified as it is transported
What molecule assists in iron uptake?
All components and amounts known
Simple uses only 1 carbon source
Specific amounts and composition not known
Usually contains digests of other organisms
Many are supportive media (allows growth of wide range of organisms)
Starts as complex, then other components added (ex: blood), for fastidious microbes
Allows growth of some
Allows for ID of bacteria based on colours, growth, or appearance of colonies
Ex of differential media
Eosin methylene blue agar
-Identified lactose fermentors
What types of media is blood agar?
EMB agar is...
Blood agar identified pathogens based on...
Blood agar- Alpha
Green zone around colonies that signify incomplete hemolysis
Blood agar- Beta
Clear zone of complete hemolysis within a yellow colony
Blood agar- Gamma
No hemolysis (Clear)
How do you typically isolate a pure culture?
From stock solution
Choose well-isolated colony
What are some features of ancient cells?
Some lack PTG wall
Must be osmotically protected
Do not divide by binary fission or use cytoskeletal proteins
What are all bacteria and archaea in regards to their genome?
What are some points of binary fission?
Can be symmetrical- not always
May involve formation of septum
What are the steps of binary fission?
What are the 2 main points in the bacterial cell cycle?
1. Replication and partitioning of DNA
What direction is DNA replication in bacteria?
5 steps of cytokinesis
1. Site selection
2. Assembly of FtsZ ring
3. Linkage of FtsZ ring to membrane
4. Assembly of synthesis apparatus
5. Constriction of cell, septum formation
What is FtsZ similar to in a eukaryotic cell?
Tubulin- Forms a ring that results in separation
What forms the divisome?
What forms the ring?
What is FtsA similar to?
Actin (hydrolyzes ATP)
What anchors the ring to the membrane?
What do the min proteins do? (MinB)
Align the FtsZ ring
What is MreB similar to? What does it do?
Actin- Forms the helical simple cytoskeleton in bacteria and archaea
What is the region of new growth of the PTG layer called?
What are 3 other forms of reproduction?
Baocyte formation (endospore)
Number of cells doubles in a constant time interval
Duration of exponential growth divided by the number of generations
Growth rate is another way to describe the division rate: Doubles per unit time
What are the 4 phases of the growth curve?
What phase would you normally perform experiments on these cells?
A closed system
Open system; replenish nutrients, remove waste, will eventually reach equilibrium
What does nutrient concentration affect in a culture?
Growth and yield
What are direct counts for measuring growth?
Use a counting chamber (hemocytometer)
Each chamber has a known volume- Count the cells and find the concentration (use a stain for viable cell counts)
What is flow cytometry?
Cells are fluorescently stained and then founded by their fluorescence- Can be used to sort too (FACS)
Based on electrical flow
What is a disadvantage of plate counting?
Time- have to culture
What is optical density?
The light is being bounced off particles and measured
What are some disadvantages of OD counting?
Differing cell sizes
Only accurate over a narrow range
What are advantages of dry weight and OD readings for cell counts?
Simple, cheap, and fast, but they are an estimate
What are the 3 types of cardinal temperatures?
Minimum, maximum, and optimum
What effects where the cardinal temperature ranges lay for an organism environmentally?
Media and nutrient content
What happens at minimum temperature?
Membrane is gelling
Transport is too slow to sustain life
What happens at maximum temperature?
Protein denaturation and collapse of membrane- Thermal lysis
What temp do enzyme catalytic rates double at?
10 degrees celsius
Prefer colder temperatures
Prefer moderate temperatures (human body temp)
High temperatures (above 45)
Prefer VERY high temperatures (above 80)
What class are hyperthermophile?
Can survive autoclaves
Can grow at low, but prefer higher
What is the lowest temperature microbes survive at?
What are some adaptations for cold temperatures?
Cold shock proteins and cryoprotectants
What are some adaptations for warm temps?
Heat stable proteins
Special solutes in cytosol
What is pH?
What are the 3 classes of external pH dwelling microbes?
(5.5-7.9), most bacteria and protists
(0-5.5), most fungi
(>8), most marine organisms
What is the internal pH range for all classes?
Cannot drop below 5, and is usually around 7
How do acidophiles stay neutral?
Transport cations into the cell, pump out H, highly permeable membranes
How do alkalophiles stay neutral?
Use Na instead of H to fuel transport
What is water activity (aw)?
Ratio of vapour pressure of air in eq with a solution to the vapour pressure of pure H2O
What is the aw of water?
>15%- Actually require this amount of salt
Live in high concentration of sugars
What are some adaptations for high solute concentration environments?
Compatible solutes (sugars, OHs, AAs)
Where do aerobes grow?
Where do anaerobes grow?
Away from the surface
Where do facultative anaerobes grow?
Throughout media, but prefer the surface
Where do microaerophiles grow?
Just below the surface
Where do aerotolerant anaerobes grow?
Throughout, without any preference
What is ROS?
Reactive Oxygen Species- damages cells
What is ROS a byproduct of?
How do cell combat ROS?
Have enzymes that break down ROS
Can survive at high pressure
Only survives at high pressure
How do microbes survive at high pressure?
Increased unsaturated fatty acids
What is a biofilm?
Non-motile extracellular polymeric substance, many species of bacteria and adherent to surfaces
What percentage of all bacteria live on biofilms?
What are some pros of living in a biofilm?
Recycling of nutrients
Protection from stress
Biodiversity facilitated gene pool
Large gene pool
What are the 4 stages of a biofilm formation?
4. Active dispersal
A chemical or physical agent that inactivates microbes- broad spectrum
All cells, spores, and acellular entities destroyed or removed
Killing or severely inhibiting growth of microbes that may cause disease (surfaces/inanimate objects)
Treatment of an object making it safe to handle
Related to disinfection- level of microbes deemed safe by public health standards
Chemical agent that kills or inhibits pathogenic microbes on tissues (generally not toxic)
Use of chemical agent to kill microbes within the host tissue
Decimal reduction time
Time required to kill 90% of microbes (one log cycle)
What is UV radiation good for?
Low amount of penetration- good for air and exposed surface and water
Where would we see UV radiation in use?
What is ionizing radiation good for?
Destroys spores- Not good at killing viruses, good for dry foods
Fibrous material in a think layer with small channels
2 types of depth filter
Chamberland (unglazed porcelain)
Made with a variety of material of different pore sizes
High efficiency particulate air filter- made of fibreglass, 0.3 um retention
Can filter out bacteria and viruses
Made from polycarbonate, uniform in pore size - used for prepping samples in SEM
How does triclosan work?
Inhibits production of fatty acids - toxic to aquatic animals, hormone issues in rats
What does alcohol work against?
Bacteriacide and fungicide, does not kill spores
What is the best % to use in alcohol?
75%- if higher it causes shrinkage of the membrane and makes it hard to kill.
95% is used for flame sterile
How do phenolics work?
Denatures proteins, disrupts membranes
Why are phenolics so useful?
Remain active on surfaces for long periods, can kill mycobacteria (tuberculosis)
What do halogens work as?
Disinfectants and antiseptics
What is iodophore?
Water soluble iodine with organic component - releases iodine slowly to reduce irritation - used in hospitals to prep skin
What is silver nitrate used for?
Drops in newborns' eyes to reduce chance of infection
What is copper sulfate used for?
Preventing algal growth
What are quaternary ammonium compounds?
Detergents - good for skin and utensils, work well with phenolics, but not good in presence of organics
What do aldehydes act as?
Sporicides - Highly toxic and reactive
Why would you use sterilizing gas?
Good for sterilizing materials that cannot be heated
What is the difference between bacteriostatic and bactericidal?
Bacteriostatic- Stops growth, but doesn't kill (if you remove the agent, they will continue to grow)
Bactericidal- Will kill off cells, but won't get rid of the debris
What is MIC? How is it determined?
Minimum inhibitory concentration
Inoculate solid media
Add disks soaked in different bactericide
See which ones inhibit growth
Phenol coefficient test
Similar to dilution test, but compare the results to the efficacy of phenols
Breaking down material
Building large macromolecules from small precursors
Synthesizing molecules (anabolism)
In/out of cell, or within- bacteria rely only on Brownian motion, whereas eukaryotes need energy input
Movement- Convert chemical energy to physical energy
What is free energy and what does it do?
It is the energy available to do work, and it drives all reactions in the cell
What are conditions for the standard free energy?
pH of 7, 25 degrees, 1 atm pressure, 1M conc. of products and reactants
What does a negative free energy mean?
Exergonic - occurs spontaneously
What does a positive free energy mean?
Endergonic - does not occur spontaneously
How do you calculate standard free energy?
What does G=0 mean?
The reaction is in equilibrium
What does the free energy under cellular conditions depend on?
Only on the G of reactants and products- provides no info on the rate of reaction
How do you calculate the free energy?
Standard free E + RTln (conc. products) / (conc. reactants)
How does ATP get used to drive reactions?
It conserves energy from exergonic reactions and this energy can then be used to drive endergonic reactions
What are metabolic pathways catalyzed by?
Enzymes and ribozymes
Why are redox reactions important?
They conserve energy
When you hydrolyze ATP what do you get?
ADP and orthophosphate (inorganic phosphate) + (-30.5 kJ/mol of energy)
What type of bond is very high energy?
What type of bond is very low energy?
How do enzymes increase reaction rate?
Stabilize transition state and lower activation energy
What do enzymes not change in terms of a reaction?
The free energy or the equilibrium constant
Who proposed the lock and key model?
Emil Fisher, 1890
Who proposed the induced fit model?
Daniel Koshland, 1958
What is methotrexate?
First chemo drug- a competitive inhibitor
How does penicillin work?
Suicide inhibitor for glycopeptide transpeptidase - does not allow cross linking of the PTG layer
What are the 3 methods of regulation of metabolism?
Metabolic channeling, amount of enzyme, enzyme effectors
What is metabolic channeling?
Compartmentalize substrates, or have them in a gradient
Why does feedback inhibition target the first step of a signal transduction or branch point?
Efficient, less wasteful (no intermediates), don't spend any more energy than needed
What is an allosteric enzyme?
The active site is separate from the regulatory site
What is allosteric regulation?
End product has different shape than starting product; can be used as a regulatory device for when the concentration of product becomes too high - the product can then bind to the regulatory site and inhibit the enzyme from reacting
Standard reduction potential (Eo)
The equilibrium constant that measures the tendency for the donor to lose electrons under standard conditions
How do we relate reduction potentials to standard free electrons?
Standard free E = -nF(standard reduction potential)
When looking at a redox tower, where are the oxidized and reduced forms?
Reduced on right, oxidized on left
If we have negative Eo, where does the equilibrium favour?