Microbial Metabolism #3

Question 1

1. Describe the four basic resources needed by organisms to carry out biological processes.

Answer 1

Energy source
Reducing power
Carbon source
Minerals

Question 2

2. Provide a list of macro nutrients required by most microorganisms.

Answer 2

C HOPKNS CaFe Mg

Mg for mighty good

Question 3

Provide a list of micro nutrients required by most microorganisms

Answer 3

Mn CuZn Mo ClB

Question 4

Determine whether or not a compound could donate or accept an e- from another compound, when you are provided with redox potentials.

Answer 4

The more positive the redox potentials, the more favorable it is too be reduced, the less favorable it is too be oxidized

Question 5

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.

Answer 5

∆G = -nFE
n = # of e-'s transferred in the reaction

Question 6

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.

Answer 6

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)

Question 7

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).

Answer 7

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

Question 8

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.”

Answer 8

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

Question 9

10. 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).

Answer 9

Glycolysis

TCA
Oxaloacetate + acetyl CoA
-->
Citrate
-->
alpha-ketogluturate + CO2 + NADH
-->
succinyl CoA + CO2 + NADH
-->
Succinate + GTP
-->
oxaloacetate + NADH + FADH2

Question 10

11. 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?).

Answer 10

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

Question 11

12. Provide names of at least three membrane bound e- carriers, and explain how these function to create a proton gradient.

Answer 11

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

Question 12

14. Explain why oxidation of FADH2 provides less energy than oxidation of NADH.

Answer 12

FADH2 comes into the chain later, and has a lower reduction power (flavoprotein FADH2 -.2, whereas NADH -.32)

Question 13

15. Describe in detail (at the level presented in class) two examples of glucose fermentation

Answer 13

Lactic acid Ferm.
pyruvate + NADH –> Lactic acid + NAD+

Ethanol Ferm.
Pyruvate –> acetaldehyde + CO2 (NADH enters) –> ethanol NAD+

Question 14

identify the key characteristics of all fermentations.

Answer 14

No net oxidation or reduction
C skeleton is the e- acceptor and donor
little ATP generated

Question 15

17. 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).

Answer 15

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

Question 16

18. Calculate the amount of energy released during chemolithotrophic growth or during anaerobic respiration based on changes in redox potential and oxidation state.

Answer 16

∆G = -nFE
n = # of e-'s transferred in the reaction

Question 17

Describe noticeable changes in the environment when anaerobic respiration occurs and either FeOOH, MnO2, or SO4-2 are used as terminal e- acceptors.

Answer 17

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)

Question 18

Describe the environmental impacts that can occur when chemolithotrophs use H2S or FeS as a source of reducing power.

Answer 18

H2S –> H2SO4
FeS –> H2SO4

Acid will be formed, river acidification

Question 19

Describe three mechanisms by which the specific activity of an enzyme molecule can be controlled.

Answer 19

Product Inhibition:
Allosteric Regulation:
Covalent Modification:

Question 20

What is product inhibition?When would you expect it to be used?

Answer 20

Occurs when the ∆G is very close to zero. Producing too much product naturally shifts the reaction towards reactant

Question 21

What is allosteric regulation? When would you expect it to be used?

Answer 21

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.

Question 22

What is covalent modification? When would you expect it to be used?

Answer 22

Addition of 
Pi
CH3
ADP
AMP

Causes a more permeant change in the cell, as it has been truly modified.

Question 23

Calculate the ΔG for a reaction when concentrations of products and reactants differ from standard conditions.

Answer 23

∆G = ∆G’ + RTln(Q)

Q = products/reactants
∆G' = Delta G under standard conditions

Question 24

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.

Answer 24

Phosphofructo kinase

stimulate
\+ AMP
\+ ADP
inhibit
- Citrate
- PEP (phosphoenolpyruvate)
- ATP

Question 25

Negative control of an operon

Answer 25

Without the presence of an protein (repressor), it would be able to transcribe DNA (the protein has a negative effect on transcription)

Question 26

Possitive control of an operon

Answer 26

Only with the transcription factor present, can it transcribe DNA. (The protein has a positive effect on transcription)

Question 27

Name two negative control mechanisms and when each would occur

Answer 27

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)

Question 28

Explain regulation of lactose

Answer 28

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.

Question 29

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.

Answer 29

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