Microbial Metabolism #3 Flashcards
- Describe the four basic resources needed by organisms to carry out biological processes.
Energy source
Reducing power
Carbon source
Minerals
- Provide a list of macro nutrients required by most microorganisms.
C HOPKNS CaFe Mg
Mg for mighty good
Provide a list of micro nutrients required by most microorganisms
Mn CuZn Mo ClB
Determine whether or not a compound could donate or accept an e- from another compound, when you are provided with redox potentials.
The more positive the redox potentials, the more favorable it is too be reduced, the less favorable it is too be oxidized
Provide and use the appropriate equation to calculate the amount of energy released from a reaction based on the change in redox potential and oxidation state.
∆G = -nFE n = # of e-'s transferred in the reaction
Provide the complete names and recognize the structures of two diffusible carriers of e- and two diffusible carriers of high-energy bonds. Identify the subunits that make up these molecules. Identify three vitamins that provide precursors necessary to construct these molecules.
NADH (Nicotinamide adenine dinucleotide)
FADH2 (Flavin Adenine Dinucleotide Reduced)
vitamin riboflavin (B2) --> FADH2 vitamin niacin (B3)--> NADH
ATP
Coenzyme A
vitamin Pantothenic acid –> long chain attached to adenine base in coenzyme A
Adenine (not a true vitamin)
Name and describe the process by which fatty acids are converted to acetyl CoA (at the level of detail presented in class—in this case, know the chemical structures of intermediates).
Beta oxidation
FADH2 and NADH will be produced for each rotation of the cycle
2 ATP must be used to activate a fatty acid for breakdown
C16 + beta oxidation =
7 NADH
7 FADH2
8 Acetyl CoA
Define what a high-energy phosphate bond is, and describe the molecular configuration that results in one. Explain what is meant by “substrate-level phosphorylation.”
An unstable arrangement which results from a resonant atom having two possible locations to which it could send it’s e-‘s, and not being able to send them to both locations. A form of resonant potential, with resonance incompatibility.
SLP = Formation of a high energy phosphate bond
- Describe the flow of C, energy and e- from glucose to CO2, ATP, GTP, NADH, and FADH2; including important intermediate compounds and sites of production of energy and reducing power (ie. describe glycolysis and the TCA cycle at the level of detail presented in class).
Glycolysis
TCA Oxaloacetate + acetyl CoA --> Citrate --> alpha-ketogluturate + CO2 + NADH --> succinyl CoA + CO2 + NADH --> Succinate + GTP --> oxaloacetate + NADH + FADH2
- Describe the three general functions of glycolysis, β-oxidation, and the TCA cycle (What cell resources do they produce? And how much do they produce?).
Make NADH, FADH2, ATP/GTP
Glycolysis 2 ATP 2 NADH Pre TCA 2 NADH TCA 2 GTP 6 NADH 2 FADH2
Electron transport chain
~34 ATP GENERATED BY ITSELF
SOME ATP LOST FROM LEAKY MEMBRANES,
SOME LOST FROM MOVING PYRUVATE AND ATP ACROSS THE MITOCHONDRIAL MATRIX
- Provide names of at least three membrane bound e- carriers, and explain how these function to create a proton gradient.
Flavoprotein Quinone cytochrome bc1 cytochrome c cytochrome a
Redox potentials rise as we go from carrier to carrier. Drop in redox is used to move H+ across the
membrane.
ATP synthase
- Explain why oxidation of FADH2 provides less energy than oxidation of NADH.
FADH2 comes into the chain later, and has a lower reduction power (flavoprotein FADH2 -.2, whereas NADH -.32)
- Describe in detail (at the level presented in class) two examples of glucose fermentation
Lactic acid Ferm.
pyruvate + NADH –> Lactic acid + NAD+
Ethanol Ferm.
Pyruvate –> acetaldehyde + CO2 (NADH enters) –> ethanol NAD+
identify the key characteristics of all fermentations.
No net oxidation or reduction
C skeleton is the e- acceptor and donor
little ATP generated
- Explain which of the following terminal e- acceptors would result in the most energy being released from a substrate such as glucose: NO3-, O2, CO2, SO4-2, H+. Explain which of the following e- donors would provide the most energy upon oxidation (per mole of e-): NO2-, CH4, H2O, H2S, H2, glucose (in other words, be able to rank these five couples according to their redox potential).
ability as terminal e- acceptor best O2 NO3- SO4-2 H+ CO2 worst
provide the most energy upon oxidation Best H2 CH4 H2S NO2 H20 worst
- Calculate the amount of energy released during chemolithotrophic growth or during anaerobic respiration based on changes in redox potential and oxidation state.
∆G = -nFE n = # of e-'s transferred in the reaction
Describe noticeable changes in the environment when anaerobic respiration occurs and either FeOOH, MnO2, or SO4-2 are used as terminal e- acceptors.
FeOOH (Fe3+) --> Fe2+ rusty red --> grey color MNO2 --> Mn makes a blue grey color SO4-2 --> H2S Which is a super smelly gas (sulfur smell)
Describe the environmental impacts that can occur when chemolithotrophs use H2S or FeS as a source of reducing power.
H2S –> H2SO4
FeS –> H2SO4
Acid will be formed, river acidification
Describe three mechanisms by which the specific activity of an enzyme molecule can be controlled.
Product Inhibition:
Allosteric Regulation:
Covalent Modification:
What is product inhibition?When would you expect it to be used?
Occurs when the ∆G is very close to zero. Producing too much product naturally shifts the reaction towards reactant
What is allosteric regulation? When would you expect it to be used?
A molecule called an effector binds to a site (the allosteric site), and causes a conformational change. This either inhibits (allosteric inhibition) or activates (allosteric activation) the enzyme.
This is used
1) when enzymes have a very negative ∆G value
2) It inhibits a one side of a branching point
Often the final product of a chain, inhibits the branching point which leads to it.
What is covalent modification? When would you expect it to be used?
Addition of Pi CH3 ADP AMP
Causes a more permeant change in the cell, as it has been truly modified.
Calculate the ΔG for a reaction when concentrations of products and reactants differ from standard conditions.
∆G = ∆G’ + RTln(Q)
Q = products/reactants ∆G' = Delta G under standard conditions
Give an example of an enzyme found in glycolysis that is controlled by allosteric regulation, and name the allosteric activator and inhibitor for this enzyme in bacteria.
Phosphofructo kinase
stimulate \+ AMP \+ ADP inhibit - Citrate - PEP (phosphoenolpyruvate) - ATP
Negative control of an operon
Without the presence of an protein (repressor), it would be able to transcribe DNA (the protein has a negative effect on transcription)
Possitive control of an operon
Only with the transcription factor present, can it transcribe DNA. (The protein has a positive effect on transcription)
Name two negative control mechanisms and when each would occur
Negative: transcription is active without interference
Repression: A molecule, called a corepressor, binds to a repressor, the repressor-corepressor complex now binds to the operator, repressing transcritption.
Repression == biosynthesis
(if there is not enough of the corepressor, transcription starts, likely the end result of this transcription is to make more of the corepressor)
Induction: A repressor is bond to the strand, stopping transcription. An inducer comes along, binds to repressor, and they leave the strand.
Induction == Catabolic
(Likely, the inducer, is going to be broken down by the gene that is getting transcribed)
Explain regulation of lactose
Positive control
The promoter is poor, CAP must bind to it to allow transcription
Negative control
A repressor is bound to the gene allolactose must bind to this in order to remove repressor (induction)
Positive control mechanism: if glucose is not present, the PEP system (which normally phosphorylates glucose) instead phosphorylates Adenylyl cyclase - cAMP rises in the cell - cAMP binds to CAP, bind together to CAP is a catabolite inducer
Negative control Mechanism:
A repressor is currently bound to the operator. allolactose must bind to this repressor to in order to allow transcription.
Provide a name for an organism that describes its sources of energy, reducing power, and C. When given a name (e.g. photoautotroph) be able to identify the source of energy, reducing power, or C used by the organism. Know which combinations are most likely to go together.
Source of energy
Phototroph: from the sun
Chemotroph: from chemicals
Source of reducing power (what molecules is donating e-‘s)
Lithotroph: inorganic e- donor
Organotroph: organic e- donor (often glucose)
Predominant source of C
Autotroph: makes C from CO2
Heterotroph: must take C from a living thing
