Ch. 11 - Catabolism

Question 1

Lithotrophs VS Organotrophs

Heterotrophs VS Autotrophs

Answer 1

lithotrophs - use reduced inorganic molecules for energy

organotrophs - obtain electrons from organic compounds

heterotrophs - use organic molecules for carbon source

autotrophs - use CO₂ has sole carbon source

Question 2

Answer 2

(understand picture)

• despite diversity of energy, electron, and carbon sources used by organisms, they all have the same basic needs:
  1. ATP as energy currency
  2. Reducing power to supply electrons for chemica reactions
  3. metabolites for biosynthesis

Question 3

Chemoorganoheterotrophy

Answer 3

-the complete or incomplete oxidation of an organic compound (ex. glucose) with release of energy *exergonic*

3 known chemohetertrophic processes in nature:

1. aerobic cellular respiration
2. anaerobic cellular respiration
3. fermentation

Question 4

Respiration

Answer 4

Aerobic cellular respiration = final electron acceptor is always oxygen

Anaerobic cellular respiration = final electron acceptor is never oxygen

-final electron acceptor is a different exogenous acceptor such as (NO₃^-, SO₄^2-, CO₂, or organic acceptors)

**In respiration, ATP is made primarily by oxidative phosphorylation**

Question 5

Fermentation

Answer 5

-Incomplete oxidation of an organic molecule where end products are organic acids/alcohols

Uses an endogenous electron acceptor:

• usually an intermediate of the metabolic pathway used to oxidize the organic energy source (ex. pyruvate)
• does not involve the use of electron transport chain, oxidative phosphorylation, or proton motive force
• ATP synthesized only by substrate-level phosphorylation (not much produced)
• oxygen not required
• used as an alternative to aerobic or anaerobic respiration (uses pyruvate from glycolysis to regenerate NAD⁺ for glycolysis and substrate level ATP production)
• fermentation end products are produced to regenerate NAD⁺ from NADH so glycolysis can continue (ATP production)

Question 6

Energy sources ofr metabolic pathway

Answer 6

• many different organic molecules can serve as energy sources and are funneled into common degradative pathways
• most pathways generate glucose or intermediates that can be used in metabolism

Question 7

Amphibolic pathways

Answer 7

• enzyme catalyzed reactions whereby the product of one reaction serves as the substrate for the next (both catabolic and anabolic functions)
• pathways release energy and also provide materials for biosynthesis of other materials

**ex. Krebs cycle (also know as: citric acid/tricarboxylic acid cycle) and glycolysis**

Question 8

Aerobic Cellular Respiration

Answer 8

process that can completely catabolize and oxidize an organic energy source into CO₂ using:

1. Glycolysis
2. Tricarboxylic Acid cycle (Krebs cycle)
3. electron transport chain with oxygen as final electron acceptor

**produces ATP and high energy electron carriers like NADH**

4 phases of aerobic cellular respiration:

1. Glycolysis
2. Formation of acetyl-CoA
3. Citric acid cycle (Krebs cycle)
4. Electron transport chain/oxidative phosphorylation

Question 9

Breakdown of Glucose to Pyruvate

Answer 9

3 common pathways in nature:

1. glycolysis
2. pentose phosphate pathway
3. entner-duodoroff pathway

Question 10

Glycolysis

Answer 10

• occurs in cytoplasmic matrix of most eukaryotic microorganisms, plants, and animals (occurs in inner cell membrane in prokaryotes)
• most common pathway for glucose degradation to pyruvate in aerobic respiration, anaerobic respiration and fermentation
• glycolysis functions with or without O₂ presence

Question 11

Answer 11

-addition of 2 phosphates is “activation energy” (two ATP required to start glycolysis give up a phosphate each)

**4 ATP made but NET production of glycolysis is only 2 ATP because 2 ATP are needed for activation energy**

oxidation steps:

1. generates NADH (Glyceraldehyde 3-phosphate oxidizes NAD⁺ by giving up an electron and a hydrogen atom)
2. generates ATP when bisphosphoglycerate gives up a phosphate to reduce ADP into ATP

EVENTUAL RESULT: the oxidative pathway of one glucose molecule results in two molecules of Pyruvate

Question 12

6-carbon phase

Answer 12

6 carbon phase:

1. Glucose 6-P = when glucose is phosphorylated (reduced) by ATP input and gains a phosphate group, it becomes glucose 6-P

(in between these two steps glucose 6-P is converted into fructose 6-P via the enzyme isomerase)

2. Fructose 1, 6-P (biphosphate) = when Fructose 6-phosphate is phosphorylated (reduced) by ATP input and gains a phosphate group, it becomes fructose 1, 6-biphosphate
3. Fructose 1, 6-biphosphate is split into two 3-carbon molecules via the enzyme aldolase, and both 3-carbon molecules become a molecule of glyceraldehyde 3-P

Question 13

3-carbon phase

Answer 13

1. Glyceraldehyde 3-phosphate is oxidized via the enzyme glyceraldehyde 3-P dehydrogenase that removes an electron and H⁺ molecule from glyceraldehyde 3-P to reduce NAD⁺ into a molecule of NADH.

**glyceraldehyde 3-P is simultaneously oxidized and phosphorylated to produce a molecule of 1, 3-biphosphoglycerate**

2. 1, 3-biphosphoglycerate is oxidized and gives away a phosphate group to reduce ADP into ATP (this is substrate-level phosphorylation)

Question 14

Production summary of Glycolysis

Answer 14

Glucose + 2ADP + 2P_i + 2NAD⁺

=

2 pyruvate + 2ATP + 2NADH + 2H

Question 15

Formation of Acetyl-CoA and the oxidation of pyruvate

Answer 15

so after glycolysis, the 3 carbon pyruvate is next converted to the 2 carbon acetyl group by the removal of a carbon dioxide (exergonic and spontaneous). the acetyl group then combines with coenzyme A to make acetyl-CoA (endergonic and non-spontaneous). Acetyl-CoA then enters the Tricarboxylic Acid Cycle

• 1 NADH is made per pyruvate

Question 16

Tricarboxylic Acid Cycle (Krebs Cycle)

Answer 16

1. Acetyl-CoA (2 carbon molecule) combines with oxaloacetate (4 carbon molecule) to produce the 6-carbon molecule citrate which is the beginning of the Krebs Cycle.
2. Citrate is then oxidized and loses an H⁺ ion and an e- to reduce NAD⁺ to NADH, and exergonically releases CO₂ to produce a 5-carbon molecule.
3. 5-carbon molecule is then oxidized and loses an H+ ion and an e- to reduce NAD+ to NADH, and exergonically releases CO2 to produce a 4-carbon molecule. Energy released from the exergonic release of Co-enzyme A reduces GDP and P_i to form a molecule of GTP.
4. 4-carbon molecule is oxidized to reduce FAD²⁺ to FADH₂ and reduce NAD⁺ to NADH, thus forming oxaloacetate, and starting the Tricarboxylic acid cycle all over again.

Question 17

Summary Production of Tricarboxylic acid cycle

Answer 17

for every acetyl-CoA molecule combined with oxaloacetate and oxidized:

• 2 molecules of CO₂ are produced
• 3 molecules of NADH are produced
• 1 FADH₂ molecule is produced
• 1 GTP molecule is produced

(alot of heat and NADH is produced, but very little ATP)

Question 18

Electron Transport Chain

Answer 18

• since only 4 ATP are synthesized from glucose oxidation, most ATP is made when NADH and FADH₂ are oxidized in electron transport chain. **from one glucose molecule, 10 NADH and 4 FADH₂ molecules are formed and go to electron transport chain**
• the difference in reduction potentials for electron carriers NADH and O₂ is large, resulting in release of a great deal of energy.
• electron flow from carriers with more negative reduction potentials (-E₀) to carriers with more positive reduction potentials (E₀)
• in eukaryotes, the ETC carriers are enzymes in the membrane, connected by coenzyme Q which helps channel more protons (H⁺ ions) across the membrane out of the mitochondria as electrons move across the inner membrane, thus eventually increasing the proton motive force.
• each carrier (membrane protein) is reduced by receiving electrons then oxidized by the electrons moving down the membrane to the next enzyme in the chain

**NADH oxidized, membrane enzymes reduced then oxidized as electrons move through inner membrane. H⁺ ions move across membrane as electrons move across inner membrane. O₂ is reduced via the Cytochrome C complex that is the last membrane carrier in the chain and donates two electrons to reduce O₂ along with binding to 2H⁺ ions inside the mitochondrion membrane, forming water.**

-concentration gradient and electrical potetnial of H⁺ ions outside of the membrane help drive the proton motive force

Question 19

ATP Yield Summary during Aerobic Respiration

Answer 19

• theoretical yield is in eukaryotes is around 38, and since substrate-level phosphorylation only produces about 4 ATP, the electron carriers NADH and FADH₂ account for most of the ATP production through their oxidation in the electron transport chain.
• ATP theoretical yield in prokaryotes is higher than eukaryotes but prokaryotes’ actual yield is much lower **NADH production to ATP prodution and FADH₂ production to ATP production ratios in prokaryotes’ is lower than that of eukaryotes**

Question 20

Factors Affecting ATP Yield (Aerobic respiration)

Answer 20

1. Bacterial electron transport chains are shorter and have lower P/O ratios (lower ratio of ATP produced to molecule of O₂ reduced)
2. ATP production for prokaryotes may vary with environmental conditions
3. Proton mtor forces in bacteria and archaea are more used for other purposes than ADP reduction to ATP (PMF used for flagellar rotation)

Question 21

Anaerobic Cellular Respiration General Principles

Answer 21

• involves the complete catabolism/oxidation of the starting organic molecule to carbon dioxide, via glycolysis, some other series of reactions, or the Tricarboxylic acid cycle to get CO₂.
• There is an electron transport system in anaerobic respiration, but the final electron acceptor is something other than oxygen
• Anaerobic yields less energy than aerobic respiration because the E₀ of the inorganic electron acceptor is less positive than E₀ of O₂, meaning the inorganic molecule is not as good of an electron acceptor as oxygen
• final electron acceptor is an oxidized form of an inorganic molecule (other than oxygen)

Question 22

Nitrate Reduction and Denitrification

Answer 22

ANAEROBIC RESPIRATION (complete oxidation of starting organic/inorganic molecule)

• oxidized inorganic nitrogen compounds are the most common electron acceptors in anaerobic respiration
• organic molecules are usually the energy and electron source
• nitrate is most oxidized form of nitrogen
• nitrate reduction produces less energy than aerobic respiration because nitrate has a less positive E₀ than oxygen, meaning it is not as good of an electron acceptor as oxygen)

**nitrate reduction is done by Enteric bacteria like E.coli**

-Denitrification is the main biological source of N₂ gas in our air (reduction of nitrate to nitrogen gas)

Picture: oxidation number represents how many electrons the elemental form of N has lost, or gained if number is negative

Question 23

Different metabolic pathways of E. coli

Answer 23

Question 24

Denitrification (picture)

Answer 24

Question 25

Sulfate Reduction

Answer 25

ANAEROBIC RESPIRATION (complete oxidation of starting organic/inorganic molecule)

• several oxidized inorganic sulfur compounds can be used as electron acceptors in anaerobic respiration
• the reduction of SO₄^2- to H₂S proceeds through several intermediates and requires activation of sulfate by ATP
• organic molecules (chemorganoheterotroph) or inorganic molecules (chemolithotroph).

**these prokaryotes live in the soil and in the water**

Question 26

Oxidation states and electron donors in sulfate reduction

Answer 26

Question 27

Electron transport of Sulfate Reduction

Answer 27

• H₂ gives gets oxidized and donates several electrons to the inner membrane along with the oxidation of NADH to donate electrons to the inner membrane.
• final electron acceptor is sulfate
• protons (H⁺ ions donated from H₂ and NADH) are brought back across the membrane via ATP synthase to produce ATP

Question 28

Methanogenesis

Answer 28

ANAEROBIC RESPIRATION (complete oxidation of starting organic/inorganic molecule)

• uses CO₂ as a final electron acceptor and reduces CO₂ to methane (CH₄)
• source of electrons is organic or inorganic molecule
• proton motive force generates ATP