Metabolism and energetics

Question 1

why is it important for microorganisms to use nutrients that are available in their environment?

Answer 1

to produce all the macromolecules and chemicals required for survival, growth and replication.

Question 2

What can food molecules lead to? (3 paths)

Answer 2

1. useful forms of energy (catabolic pathway) =>the many molecules that form the cell (anabolic pathway)
2. lost of heat (catabolic pathway)
3. the many building blocks for biosynthesis (catabolic pathway) => the many molecules that form the cell (anabolic pathway)

Question 3

define catabolism:

Answer 3

generation of energy (ATP) and reducing power (NADH) from nutrients.

Question 4

what is the purpose of the by products of catabolism?

Answer 4

By‐products of catabolism may be used as precursor molecules for anabolism.

Question 5

define anabolism:

Answer 5

production of macromolecules and chemicals from “building blocks” and energy (ATP). Reducing power is provided by NADH.

Question 6

do all building blocks of the cell have to be taken up from the environment?

Answer 6

Yes

Question 7

Nutrients used (3)

Answer 7

(N, S and P)

Question 8

Nutrient usage vs sources of carbon and energy usage

Answer 8

• Metabolism of most nutrients (N, S and P) is relatively simple; slight modifications are needed before incorporation into cellular material.
• In contrast, sources of carbon and energy usually undergo many transformations. 4

Question 9

define enzyme:

Answer 9

Enzymes are biological catalysts

Question 10

define free energy:

Answer 10

• ΔG*’: free energy

* The energy available to do work

Question 11

exergonic vs endergonic

Answer 11

– Negative: release of energy (exergonic)

– Positive: absorbs energy (endergonic)

Question 12

define activation energy:

Answer 12

energy needed to put all molecules in a reactive state.

Question 13

define catalyst:

give an example:

Answer 13

1. substance that lowers the activation energy. Does not affect the free energy, affects the rate.
2. enzymes such as lysozyme which cuts B(1-4) bond between NAG and NAP

Question 14

oxidation vs reduction

Answer 14

• Oxidation: removal of electron(s).
• Reduction: addition of electron(s).
• Can involve just an electron, or an electron and a proton (H+).

Question 15

why must redox reaction act in pairs

Answer 15

• Redox reactions occur in pairs because electrons cannot exist in solution. Oxidation of one substance is linked to the reduction of another substance.

Question 16

how are redox reactions written?

Answer 16

Redox couples always written so that Oxidized form on the left, reduced form is on the right

Question 17

define electron donor:

Answer 17

energy source: in an oxidation, the one giving away its electron is a donor

Question 18

What happens during a redox reaction?

Answer 18

• The chemical reaction, in which the electron donor and the electron acceptor participate, releases energy.

Question 19

How much energy is released during a redox reaction?

Which reaction is considered very energetic?

Answer 19

• How much energy is released depends on the difference in reduction potential between the donor and acceptor
oxidative respiration which involves hydrogen and, oxygen and water molecules

Question 20

define reduction potential:

Answer 20

– a measurement of the tendency to donate or accept electrons)

Question 21

define NADH (is it the oxidized or the reduced form)

Answer 21

• electron carrier providing reducing power
• Nicotinamide adenine dinucleotide (NAD)
• NADH: oxidation=> ready to give away its electrons
• NAD+: reduced => ready to receive electrons

Question 22

Name some energy rich compounds and explain why?

Answer 22

1. phosphoenolpyruvate: anhydride bond
2. acetyl-CoA: thioester bond between acetyl and coenzyme A
3. Acetyl phosphate: anhydride bond
4. glucose 6-phosphate: ester bond between phosphate head group and carbon chain
5. ATP Adenosine triphosphateL anhydride bonds btw phosphates+ester bonds btw phosphate and fructose
6. ADP

Question 23

Name the three basic metabolic pathways required to produce all the precursors needed for anabolism

Answer 23

– Glycolytic pathway (glycolysis, Embden‐Meyerhof pathway).
– Pentose phosphate pathway (hexose monophosphate pathway)
– Tricarboxylic acid pathway (TCA; citric acid cycle, Krebs cycle)

Question 24

What are the two methods that can produce ATP?

Answer 24

1. substrate level phosphorylation (ADP=>ATP)
   – Fermentation: organic compounds are electron donors and electron acceptors. ATP is produced by substrate‐ level phosphorylation.
2. oxidative phosphorylation (ADP+Pi=>ATP_from an energized compound to a less energized compound)
   - The process that uses the energy produced by respiration to synthesize ATP
   – Respiration: organic compounds are oxidized to CO2 with O2 (or substitute) as the electron acceptor.
   - Most of the ATP is produced by this path

Question 25

What does the glycolytic pathway yield?

Which of the two methods produces ATP?

Answer 25

• One molecule of glucose (6C) is oxidized to yield two molecules of pyruvate (3C).
• Net yield: 2 ATP, 2 NADH+H+.

ATP is produced by substrate‐level phosphorylation.

Question 26

What does the pyruvate pathway yield?

Answer 26

• Pyruvate is first oxidized to (2) acetyl‐CoA and (2) CO2 by the pyruvate dehydrogenase complex and (2) NADH.

During respiration, pyruvate can be fully oxidized to CO2 and H2O.

Question 27

what does the TCA cycle yield?
explain the 4 important points concerning the fate of:
- Acetyl-CoA
- GTP
- Succinate dehydrogenase
- Oxaloacetate

Answer 27

• The net effect of one turn of the TCA cycle is the complete oxidation of the acetyl group of acetyl‐CoA and the production of:
– 2CO2
– 1 GTP (ATP) 
– 3NADH
– 1 FADH2

• Acetyl‐CoA is then fed into the TCA cycle and fully oxidized to CO2.
• GTP can be used to phosphorylate ADP to
produce ATP and GDP. GTP can also be
used for some anabolic reactions. TCA
• Succinate dehydrogenase is a large protein complex located in the membrane.
• TCA cycle has both energetic and biosynthetic functions. Oxaloacetate must be regenerated (anapleurotic pathway), otherwise the TCA cycle will stop.

Question 28

Does NADH or FADH2 produce more energy?

Explain how they produce energy:

Answer 28

• More ATP can be produced from NADH and FADH2; their oxidation is coupled to the reduction of a terminal electron acceptor (O2 or other compounds) – a process called respiration – and the energy released is used to drive the synthesis of ATP.

Question 29

aerobic vs anaerobic respiration

Answer 29

• Aerobic respiration: O2 is the terminal electron acceptor.
• Anaerobic respiration: other compounds act as terminal electron acceptors, under anoxic
conditions.

Question 30

Define pmf:
Function:
Method involved:
Equation:

Answer 30

• Respiration results in the generation of a transmembrane proton gradient, a potential source of energy, called the proton motive force (pmf).
• The pmf is used to drive other energy requiring reactions: flagellum rotation (in bacteria), transport across the membrane and synthesis of ATP.
• The synthesis of ATP using pmf is called oxidative phosphorylation. 3 ‐ 4 protons are necessary to phosphorylate 1 ADP to ATP.
• Δp=ΔΨ+(−zΔpH)=ΔΨ−zΔpH
– Δp: pmf
– ΔΨ: membrane potential (mV)
– ΔpH: transmembrane pH gradient (pHOUT − pHIN)
– Z factor to convert pH into mV

Question 31

How do fermentable bacteria do to produce pmf?

Answer 31

• Some strictly fermentative bacteria (do not do oxidative phosphorylation) still have ATPases… because they are reversible! Can be used to generate a PMF.

Question 32

explain fermentation, and when it occurs

Answer 32

When no terminal electron acceptor is available, succinate cannot be oxidized by succinate dehydrogenase in the respiratory chain. Therefore, an organic compound serves as the electron donor during substrate level phosphorylation to produce an oxidized compound and an organic degradation product serves as the final acceptor of electrons.

The glycolytic pathway can still function, provided that the NADH+H+ can be oxidized back to NAD+.

NET YIELD = 2 ATP per glucose

lactate or apoxie pathway

Question 33

Does yeast grow better in the presence or absence O2? WHats the major by product?

Answer 33

In the absence of O2, the yeast population grows very slowly because fermentation yields only a fraction of ATP produced by respiration.

in yeast, production of ethanol and CO2 is inversely proportional to the concentration of O2.