Unit 2 Test Lectures 8,9 & Cellular Respiration Flashcards
What are the 8 factors that affect growth of microbes the most?
Salt
Temperature
Energy/nutrient sources
Radiation
PH
Biological Interaction
Water
Gas
(STER-PH | BWG)
What is adaptation and why is it essential for growth and survival?
Changes in structure (anatomy) and function (physiology) that improves an organism’s survival in a given environment
What is nutrition?
A process by which organisms acquire nutrients from an environment and use them for metabolism and growth
What are the key elements in nutrition? How are each used by cells?
-Phosphorous – DNA/RNA, Lipids, ATP (adenosine triPHOSPHATE)
-Oxygen
-Nitrogen – DNA/RNA, Proteins
-Carbon – Backbone of all macromolecules (Protein, carbs, lipids, nucleic acid
-Hydrogen
-Sulfur – 2 amino acids
PONCHS
What are the nutritional categories (e.g. saprotroph) that we went over in class?
From where do organisms within these categories get their energy?
Photoautotroph - sunlight and inorganic carbon sources (CO2)
Chemoautotroph - Simple inorganic chemicals
Chemoheterotroph - metabolic conversion of nutrients from other organisms
Saprotroph (Saprobe) - Metabolizing organic matter of dead organisms
Parasite - Utilize tissues, fluids of live host
Photoheterotroph - Sunlight and carbon from what they consume
Compare and contrast chemically defined and complex growth media. When is each used?
Chemically defined (synthetic) media: The exact amount of every component is known
- For growing microbes with known nutritional needs
- Studying metabolic pathways and biochemical processes
Nonsynthetic (complex) media: One or more components are left undefine due to their complexity
- Cultivating fastidious organisms that require complex nutrients
- When specific nutrient requirements are unknown
Compare and contrast all-purpose and special purpose media.
What are the three general types (e.g. differential) of special purpose media and what is the purpose of each?
All-Purpose: Supports growth of wide variety of microorganisms
Special Purpose: Formed for specific types of microorganisms. for specific nutrients, inhibitors or indicators
Three types: Differential, selective and enriched
Purpose:
Differential: Contains indicators that change color when a particular biochemical reaction occurs (indicates, shows no preference)
ex: MacConkey agar differentiates between lactose fermenters (produce acid, change color) and non-fermenters
Selective: Inhibit growth of certain types of bacteria while allowing others to grow; isolates specific microorganisms from mixed culture
Enriched: Contains additional nutrients for fastidious (picky) organisms; such as blood, serum
Do microbes regulate their cellular temperatures as humans do (homeostasis)? What effect foes this have on where they can live?
Distinguish between: Minimum, Maximum, Optimum Temperatures for microbes.
- No, Microbial cells are the same temperature as the environment in which they are found.
- Their adaptations to temperature extremes define their habitats and roles in ecosystems.
Minimum: The lowest known temperature at which a microbe can live
Maximum: The highest known temperature at which a microbe can live
Optimum Temperature: The temperature at which microbes can produce the highest amount of generations per hour
What are the 4 categories that microbes fall into in terms of temperature requirements?
Psychrophile
Mesophile
Thermophile
Extreme-thermophile
What is the most important gas to consider when considering microbial metabolism?
What is the second?
Two most important gases: O2 (20%) and CO2 (0.04%
OXYGEN
Needed for oxygen | Break down by-products?
- Obligate Aerobe: yes yes
- All at top
- Obligate Anaerobe: no no
- All at bottom
- Facultative Anaerobe: no yes
- Evenly dispersed, slight buildup at top
- Microaerophile: in small amounts yes
- Mostly buildup at top
- Aerotolerant Anaerobes: no yes
- Complete even dispersal
What is a capnophile? Understand how gas requirements would affect growth of microbes on media.
Capnophile – CO2-loving species
How might world climate change effect the distribution of microbes?
It might lead to an increase of Capnophile (CO2 loving species)
- Potential decrease in obligate anaerobes
What are the three microbial categories for pH requirements?
As with temperature, pH is important because it affects microbial __________________ activity.
Neutrophiles – pH 6-8
Acidophiles – Prefer acidic environments
Alkinophiles – Prefer alkaline environments
What is osmosis? How does osmotic pressure affect microbes?
Define: hypotonic, isotonic, hypertonic solutions. How does each affect cells? What is a halophile?
Osmosis: diffusion of water
Affect on microbes:
- Osmotic pressure helps maintain turgor pressure = keeps cells rigid & prevents collapse
- Prevents cell lysis (bursting) or plasmolysis (shrinkage)
Hypotonic – Concentration is lower outside of the cell (dilute environment)
- Water moving into cell may cause cell to swell and burst (lysis)
Isotonic – Concentration is the same outside and inside the cell
- No net movement of water, cell maintains shape. Ideal shape for most cells
Hypertonic (osmophiles) - Concentration is higher outside of the cell
- Water moving out of cell make cause shrinkage (plasmolysis).
Halophile: prefer salty habitats (9%-25% NaCl)
How can humans use osmotic pressure changes to their advantages (think food preservation).
Humans can use osmotic pressure by salting/curing.
This creates a salty, hypertonic environment (high osmotic pressure), causing water to move out of microbial cells = death of bacteria and mold
Why are “wonder bugs” such as Staphylococcus aureus a threat to human health?
What precautions are necessary when dealing with these types of microbes that have such wide environmental ranges?
Staph:
Can survive at temps of 6-46 degrees Celsius
Is osmotolerant, tolerates salt concentrations from 0.1-20%
Some are antibiotic resistant
Precautions:
- General hygiene precautions
-
Cells found in hydrothermal systems are under extreme temperature and pressure. Can we collect samples and bring them up without harming cells? Why?
It is hard to collect and bring them up as they are used to withstanding high pressures, so they may burst in our relatively lower pressure environment
The word “growth” can refer to either of what two concepts?
1- Growth of a single cell: organelles increase, cell size increases
2- Growth of the population: the # of cells increases
What is the term used to describe growth (or cell division) in bacteria?
How does binary fission differ from mitosis in eukaryotic cells?
- Binary fission is simpler, DNA is replicated and cell divides into two identical cells
- ## Mitosis is more complex, requires multiple stages (PMAT), and requires mitotic spindle to separate chromosomes
What is a generation time?
What is the average doubling time for bacteria?
Are human pathogens going to have faster or slower growth rates?
Why?
Generation (doubling) time: Time lapse from when a bacterium is one parent cell until two new daughter cells are formed
Average time: 30-60 minutes
Human pathogens are going to have faster growth rates so that they can reproduce before human defenses kick in
Describe the steps of binary fission
DNA Replication: The bacterial chromosome (a single circular DNA molecule) begins to replicate. Two identical copies of the DNA are produced.
Cell Growth: The cell increases in size, and the two DNA copies move toward opposite ends of the cell.
Septum Formation: A septum (a dividing wall) starts to form in the middle of the cell. This involves the synthesis of new cell wall material.
Cell Division: The septum continues to grow inward, eventually pinching the cell in two.
Daughter Cells Separation: Once the septum is complete, the two daughter cells are separated. Each daughter cell contains one copy of the original DNA and is genetically identical to the parent cell.
What is a colony-forming unit (CFU)?
For what is it used?
How does CFU relate to cells that naturally form colonies?
1 CFU = 1 original bacterial cell
Can vary; if diplococcus, then CFU = 2 original cells
It is used: for each colony, you would know that it was started by an initial cell
What are the four phases of microbial growth?
What is controlling of limiting the rate of growth at each step?
- Lag – Population growth rate is very slow
Limiting factor: Cellular machinery, e.g. enzymes
Some enzymes may be turned off if substrate is absent in order to save energy - Exponential – Population growth rate is very rapid
Limiting factor: no real limiting factors - Stationary – Zero NET population growth (growth rate = death rate)
Limiting factor: 1) Lack of resources 2) Buildup of (toxic) waste products - Death – Population on decline; resources are exhausted and lots of waste products
K = carrying capacity = The maximum # of individuals from the same species that a given environment can support
How does the concentration of nutrients change in the culture over the course of the growth cycle?
Would we see this typical growth cycle in batch cultures or chemostat cultures?
Why?
The concentration of nutrients would decrease over time
Batch Culture – Closed systems, finite resources
Chemostat Culture – Open systems, maintains cells in exponential phase of growth
- Nutrient source is added, waste/cells is removed
This growth cycle would be seen in batch cultures because there is a definite amount of resources
What is a carrying capacity and how does it affect microbial growth?
Draw the shape of a typical growth curve and identify each of the four phases of growth.
K = carrying capacity = The maximum # of individuals from the same species that a given environment can support
We discussed a few different methods for analyzing microbial growth.
When would we use turbidity to measure growth?
Why?
When would we use more direct methods such as total cell count?
Turbidity:
- Provides quicker feedback
- For larger sample volumes
- General quality control
- Relative comparison
Total cell count
- Distinguish live vs dead cells
- Cultures w/ low microbial concentrations, as it’s more sensitive
- Where precise quantification is needed
Which method allows us to count and separate bacteria based on their size, whether they are alive or dead, etc.?
Turbidity – Cloudiness (not direct or quantitative, relative)
Total Cell Count is more direct and quantitative
Coulter Counter, Real-time PCR
Flow cytometer; Can tell size, living or dead
What is metabolism?
What are the two main types, and what generally occurs in each?
Metabolism - Includes all the chemical reaction that are occurring in an organism
Two types:
Catabolism – Large molecules are broken down into smaller molecules; energy out or released
Anabolism – Small molecules made into larger molecules; energy in, or stored
Has nature provided every organism with a complete set of enzymes or must organisms sometimes rely on other organisms (either directly or indirectly)?
Many organisms live in close association with other organisms that are capable of carrying out reactions they themselves cannot
What is the function of enzymes?
What type of biological molecule are they?
Enzymes – Speed up/catalyze a reaction
-Very specific for their substrate
-Folded in a very specific way, gives them their shape
-Will NOT work, if unfolded
-Act as a platform on which reactions take place
They are proteins
How do enzymes work, physically and energetically?
Physically: Provide a physical surface on which reactants (substrates) can be positioned for the various reactions that take place
Energetically: Speed up the rate of a reaction by lowering reaction’s activation energy ( = more stability)
What is enzyme specificity?
Folded in a specific way, if unfolded will NOT work
Specific for their subtrate
Define: active site, substrate, enzyme-substrate complex.
Active site: Specific region on an enzyme where substrate molecules bind
Substrate: reactants
Enzyme-substrate complex: Temporary formation that occurs when substrate binds to active site of enzyme
In terms of reaction energetics – if a reaction is considered spontaneous, does it necessarily mean that its occurrence will be instantaneous? Why?
No, it’s not. A reaction can occur spontaneously, or on its own, but take a very long time.
e.g. a burger may take a year to digest spontaneously–w/out enzymes
What is a co-factor? Why are they important?
Cofactors: any non-protein substance needed for enzyme activity (ex: help structure, function)
- Carriers for specific atoms, help transfer chemical groups form one subtrate molecule to another
Coenzymes: Organic cofactors that MAINLY help transfer chemical groups form one subtrate molecule to another
An inactive enzyme, termed apoenzyme, can be activated by what? What is the completed complex called?
Apoenzyme: an inactive enzyme, when added to a cofactor, becomes activated aka “holoenzyme”
- Can be activated by a cofactor
- The completed complex is a holoenzyme
What is the difference between an exoenzyme and an endoenzyme?
Endoenzymes: Metabolic processes within the cell
Exoenzymes: Metabolic processes outside the cell
-Single celled organism releases these enzymes into their environment
- Multicellular organisms release these outside of cells (think enzymes outside cell, but inside stomach/interstitial space)
What is the difference between constitutive and regulated enzymes?
Constitutive:
- Always present in the cell
- They’re used frequently
Regulated:
- Can be turned off, or production can be turned off
- Turned on only when needed
Enzymes can facilitate reactions that build larger molecules from smaller building blocks. These reactions are known as ________ reactions?
Synthesis reactions, as opposed to Hydrolysis reactions
What is the role of water in these synthesis reactions? Is energy stored or released?
Synthesis: Dehydration; water is removed as two smaller molecules are joined to form a larger molecule
- Energy is stored
Hydrolysis: water as an added reactant; used to break down complex molecules into simpler ones
- Energy is released
We discussed two mechanisms by which cells can “turn off” their cellular machinery. What were they (describe each) and how are they different?
Competitive Inhibition: Using a “mimic” substrate
Allosteric sites: Other locations to bind on enzyme, many times the products of the reaction that bind.
- Relies on negative feedback
- If there’s too much of the product, the product locks into allosteric site and tells enzyme to inactivate
Is catabolism an exergonic or endergonic reaction?
Catabolism = Exergonic
Anabolic = Endergonic
Where does respiration start in prokaryotes and eukaryotes?
They both begin within the cytosol, this is where the bonds are being broken
of ATP produced
Glycolysis
What Happens
Where
O2 needed
.# of ATP produced
.# of NADH produced
.#of FADH2
By-Product
How ATP is produced
of ATP produced
What Happens?
- Breakdown of glucose
- Glucose –> 2 Pyruvate;
C-C-C-C-C-C –> C-C-C + C-C-C
Where?
-Cytosol (for both prok and euk)
O2 needed?
- No
of ATP produced
- 4 produced - 2 used
- Net 2
of NADH produced
- 2 NADH
of FADH2
- 0 FADH2
By-Product
- Water
How ATP is produced
- Substrate Level Phosphorylation
Transition + Krebs Cycle
What Happens
Where
O2 needed
.# of ATP produced
.# of NADH produced
.# of FADH2 produced
By-Product
How ATP is produced
of NADH produced
What Happens
- All remainder Carbon (C-C) bonds broken
Where
- Euk: Mitochondrial Matrix
- Prok: Cytosol
O2 needed
- Yes
.# of ATP produced
- Net 2
.# of NADH produced
- 8
.# of FADH2
- 2
By-Product
-CO2
How ATP is produced
- Substrate Level Phosphorylation
Cellular Respiration: Where is CO2 produced?
- ## Krebs Cycle
Oxidative Phosphorylation
What Happens
Where
O2 needed
# of NADH produced
# of FADH2
By-Product
How ATP is produced
What Happens
- Energy from ETC is used pump H+ out=creates H+ gradient
- Gradient utilized by ATP Synthase to create ATP
Where
Euk: Inner mitochondrial membrane
Prok: Cell Membrane
O2 needed
- Yes
.# of NADH produced
- 0
.# of FADH2
-0
.# of ATP produced
- 26-28
By-Product
H2O
How ATP is produced
- By the ATP Synthase Oxidative Phosphorylation
What is the starting molecule and ending molecule at each of the three steps of cellular respiration?
Glycolysis
Start: Glucose
End: 2 Pyruvate, 2 NADH, 0 FADH2, 2 ATP
Krebs Cycle
Start: 2 Acetyl-CoA
End: 4 CO2, 6 NADH, 2 FADH2, 2 ATP
ETC and Oxidative Phosphorylation
Start: NADH, FADH2, O2
End: ATP, H2O
1)As electrons go down the energy gradient of the electron transport chain, what is being pumped out?
2)What is the final electron acceptor?
3)Where is there the most potential energy – at the beginning of the chain or the end?
1 - As electrons go down the gradient, H+ is being pumped out
2 - Oxygen is the final electron acceptor
3 - The most potential energy is at the beginning of the chain
What is the job of a cytochrome?
It is an electron transfer molecule
NADH and FADH2 do not make the same amount of ATP
Why?
How many does each make roughly?
NADH contributes to proton pumping through more complexes, but FADH2 starts later and thus, contributes less
NADH: 2.5 ATP ~
FADH2: 1.5 ATP ~
Describe the 2 parts of electron transport
1 - Chemiosmosis:
Uses energy produced from electrons going down energy gradient to pump H+ outside membrane
2 - ATP Synthesis
Utilizes H+ gradient to cause action in ATP Synthase to produce ATP
- What is the difference between substrate-level phosphorylation and oxidative phosphorylation?
- Which method of ATP production produces more ATP molecules during aerobic respiration?
- How many ATP in total (net) are produced during aerobic respiration?
- SLP - occurs when phosphate transfer from subtrate molecule to join with ADP = ATP
- Occurs in glycolysis and Krebs
- Doesn’t need oxygen or ETC
OP - ATP produced with energy from ETC and proton gradient
- Gradient powers ATP synthase to convert ADP = ATP
- Oxygen final electron acceptor - Oxidative Phosphorylation produces way more
3.Glycolysis - 2
Krebs - 2
Oxidative Phospho - 28-34
Total: 30-38
What is the difference between anaerobic and aerobic respiration?
Anaerobic:
-Final electron acceptor is an ocygen containing ion NO3-, NO2- instead of free oxygen (O2)
Other Metals, sulfate, carbonate
What is fermentation and how can we as humans use this process to our advantage?
Alcoholic fermentation:
pyruvic acid –> ethanol +CO2
Acidic fermentation:
pyruvic acid –> lactic acid
Uses: beer, wine, cheese, yogurt
