Lecture 12 - metabolism, energetics, catabolic pathways

Question 1

Catabolism

Answer 1

Breakdown of complex organic molecules

Question 2

Anabolism

Answer 2

Biosynthetic reactions to build cell mass

Question 3

How does catabolism support anabolism?

Answer 3

• supply energy to drive anabolic processes
• provide precursor molecules for biosynthesis

Question 4

Organotrophy

Answer 4

Organic compounds are electron donors

Question 5

Types of organtrophy

Answer 5

• fermentation
• organic respiration

Question 6

Lithotrophy

Answer 6

Inorganic compounds donate electrons

Question 7

Types of litotrophy

Answer 7

• lithotrophy/chemoautotrophy
• methanogenesis

Question 8

Is organotrophy aerobic or anaerobic?

Answer 8

• fermentation is anaerobic
• respiration can be aerobic or anaerobic

Question 9

Types of energy storage molecules

Answer 9

• ATP
• NAD+ (carries twice the energy of ATP)

Question 10

How are ATP and NAD used as energy sources?

Answer 10

• ATP –> ADP via removal of phosphate group releases energy
• NADH –> NAD+ (oxidation) releases lots of energy

Question 11

Fermentation

Answer 11

Partial breakdown of organic compounds without net e- transfer to an inorganic terminal electron acceptor

Question 12

Respiration

Answer 12

Complete breakdown of organic molecules with electron transfer to a terminal electron acceptor such as O2

Question 13

Examples of things that bacteria can break down that we can’t

Answer 13

Fats, cellulose, acidic sugars, lignin, man-made toxic chemicals

Question 14

Why does NAD+ need to be regenerated?

Answer 14

Used as an electron and proton acceptor for later transfer

Question 15

How is NAD+ regenerated?

Answer 15

Reduction of pyruvate or other compounds to form partially oxidized products

Question 16

How is ATP generated in most fermentation pathways?

Answer 16

Substrate-level phosphorylation; less efficient energy production

Question 17

What is the TCA cycle used for?

Answer 17

More efficient energy production
- carbon is sent through the cycle to produce NADH
- carbon is oxidized to CO2 and its electrons are transferred to NADH

Question 18

How is glucose catabolism connected to the TCA cycle

Answer 18

Decarboxylation of pyruvate to acetyl-CoA

Question 19

Where does the TCA cycle occur in prokaryotes

Answer 19

Cytoplasm

Question 20

What is the electron transport system (ETS)?

Answer 20

Series of membrane-localized electron carriers that transfer electrons from a reduced electron donor to an oxidized electron acceptor during aerobic respiration

Question 21

How does the electron transport system power the production of ATP?

Answer 21

Electron transport powers pumping of protons into the cytoplasm. These protons are later pumped back in through ATP synthase

Question 22

Examples of terminal electron acceptors

Answer 22

O2 and oxidized minerals (ex: Fe3+, NO3-)

Question 23

What values of gibbs free energy indicate a favorable, spontaneous reaction

Answer 23

Negative

Question 24

Reduction potential (E)

Answer 24

Measure of the tendency of a molecule to accept electrons
- negative values are poor electron acceptors (repel e-); good electron donors
- positive values are good electron acceptors (attract e-)

Question 25

General trend of electron transfer in terms of reduction potential

Answer 25

Electrons flow from more negative to more positive reduction potentials

Question 26

How to tell if a molecule is highly oxidized

Answer 26

Lots of oxygen atoms

Question 27

How to tell if a molecule is highly reduced

Answer 27

Lots of H+

Question 28

What is the quinone pool?

Answer 28

Bacterial ETS that shuttles electrons between membrane-bound complexes in aerobic NADH oxidation

Question 29

What kinds of organisms can use anaerobic respiration?

Answer 29

Unique to prokaryotes that can use alternative electron donors and acceptors

Question 30

Denitrification

Answer 30

Using nitrate (NO3-) as an electron acceptor
- nitrate is successively reduced to nitrogen gas by multiple bacterial species

Question 31

How can sulfate be used as an electron acceptor?

Answer 31

Sulfate (SO4 2-) is successively reduced to hydrogen sulfide (H2S)

Question 32

What happens in environments where O2 is depleted?

Answer 32

Alternate, less efficient, electron acceptors are used as the optimal materials are used up

Question 33

Is sulfate a good electron acceptor?

Answer 33

No, only used when there are no better options

Question 34

What kinds of electron donors and acceptors does respiration use?

Answer 34

• Organic electron donors
• Inorganic or organic electron acceptors

Question 35

What kinds of electron donors and acceptors does lithotrophy use?

Answer 35

• Inorganic electron donors
• Inorganic or organic acceptors

Question 36

Phototrophy

Answer 36

Involves light capture by chlorophyll, usually coupled to splitting of H2S or H2O or organic molecules

Question 37

Nitrification

Answer 37

• aka nitrogen oxidation
• takes ammonium and gradually oxidizes it to HNO3 to fix it into the soil

Question 38

Sulfur and metal oxidation example

Answer 38

H2S oxidized to H2SO4

Question 39

What are the components that drive proton motive force

Answer 39

• Electrical potential: from separation of charge between cytoplasm and extracellular solution
• pH difference: ratio of external to internal chemical concentration of H+

Question 40

Proton motive force

Answer 40

Electrochemical gradient of protons generated by transfer of H+ through a proton pump

Question 41

What is the proton motive force used for?

Answer 41

• ATP synthesis
• rotation of flagella
• uptake of nutrients and efflux of toxic compounds and antibiotics (secondary active transport)