Microbio Chapter 11: Catabolism

What do phototrophs use

light

What do chemotrophs use

oxidation of chemical compounds

What do organotrophs use

organic compounds

What do lithotrophs use

reduced inorganic substances

What do heterotrophs use

organic molecules

• can also be used for energy source

What do autotrophs use

a single carbon molecule

• usually carbon dioxide

What are the major classes microorganisms

• photolithoautotrophs / photoautotrophs

  • primary producer

• chemolithoautotrophs

  • primary producer

• chemoorganoheterotrophs / chemoheterotrophs / chemoorganotrophs

  • same organic nutrient can satisfy all three requirements

  • majority of pathogens

What are primary producers

organisms that produce things that other organisms are going to use

What are the basic needs that all organisms have

• ATP as an energy currency

• reducing power to supply electrons

  • NADH and FADH2

  • adds H atoms

• precursor metabolites to provide carbon skeletons

  • converted into monomers which are polymerized into macromolecules

What can chemoorganotrophs do

• fermentation

• aerobic respiration

• anaerobic respiration

What can chemolithotrophs do

• aerobic respiration

• anaerobic respiration

Where are electrons donated during respiration

ETC

Where are electrons donated during fermentation

an endogenous acceptor

What does respiration involve the use of

an ETC

Aerobic respiration

oxygen is the final electron acceptor

anaerobic respiration

exogenous acceptor is used

• NO₃^-, SO₄^2- , CO₂, Fe₃⁺, or SeO₄^2-

What is generated during respiration

pmf

What does pmf fuel

oxidative phosphorylation to generate ATP

What does fermentation use

an endogenous electron acceptor

• so it needs an organic compound

• ex. pyruvate

What does fermentation not involve

the use of an ETC or the generation of a PMF

• No OP

How is ATP synthesized

only by substrate-level phosphorylation (SLP)

• ADP + P —> ATP

What are the important carbon skeletons from EMP

• G6P

• F6P

• G3P

• 3PG

• PEP

• Pyruvate

What are the important carbon skeletons from PPP

• Erythrose-4-phosphate (E4P)

• Ribose-5-phosphate (R5P)

What are the important carbon skeletons from TCA

• Acetyl CoA

• Alpha-ketoglutarate

• Succinyl CoA

• Oxaloacetate

What is the overall goal of aerobic respiration

to completely catabolize an organic energy source to CO2

What are the 3 steps in aerobic respiration

1. Glycolysis: glucose —> pyruvate

   • EMP, ED, and PPP

2. TCA: pyruvate —> CO2

3. ETC: O2 is the final electron acceptor

   • generates pmf which fuels OP to produce ATP

Where are metabolic pathways located in prokaryotes

• glycolysis: cytoplasm

• TCA: cytoplasm

• ETC: inner/plasma membrane

Where are metabolic pathways located in eukaryotes

• glycolysis: cytoplasm

• TCA: mitochondrial matrix

• ETC: inner mitochondrial membrane

What do all the glycolytic pathways have in common

• provide precursor metabolites to all other pathways

• glucose → G3P

• G3P → pyruvate

  • oxidized in the same way in all pathways

What is the most common pathway for glycolysis

Embden-Meyerhof Pathway (EMP)

Embden-Meyerhof Pathway (EMP)

• functions in the presence or absence of O₂

• two phases

  • 6 Carbon phase (uses 2 ATP)

    • forms F1,6BP

  • 3 carbon phase (makes ATP)

    • F1,6BP → (2) G3P

• Net ATP gain/glucose: 2 ATP

What is the net ATP gain per glucose molecule in the EMP

2 ATP

Entner-Doudoroff Pathway (ED)

• used by Gram- soil bacteria

  • not by eukaryotes

  • many under aerobic conditions

  • E. coli and Enterococcus faecalis

• replaces first phase of the EMP

  • 2-keto-3-deoxy-6-phosphogluconate (KDPG) → pryuvate + G3P

  • Net yield / glucose: 1 ATP + 1 NADH + 1 NADPH

What is the net yield per glucose molecule in the ED pathway

1 ATP + 1 NADH + 1 NADPH

What is another name for the Pentose Phosphate Pathway (PPP)

hexose monophosphate pathway

What does the PPP do

oxidize G6P → → Ribulose-5-phosphate + CO2

The Pentose Phosphate Pathway (PPP)

• not oxygen dependent

  • works simultaneously with ED or EMP

  • anaerobic or aerobically

• not found in Archaea

  • found in both eukaryotes and bacteria

• needed for biosynthesis and catabolism

  • major source of NADPH (anabolism)

  • Produces E4P and R5P

  • intermediates used to generate ATP

    • can be degraded into pyruvate by EMP

    • can regenerate G6P by gluconeogenesis

Amphibolic Pathways

• functions in both anabolic and catabolic process

  • depends on levels of ATP, PEP, and F6P

• Includes

  • EMP/gluconeogenesis

  • TCA cycle

  • PPP

What is another name for the TCA Cycle

Citric Acid Cycle or Krebs Cycle

How many times does glucose have to go through the TCA

twice

Where does the TCA cycle occur

in the cytoplasm

What is the source of carbon skeletons for biosynthesis

TCA

What does the TCA cycle produce

2 CO2, 3 NADH, 1 FADH2, and 1 ATP per acetyl CoA

Where is most of ATP made

the ETC

What is the DE’₀ between NADH and O2

1.14 V

What is the ETC

a series of electron carriers

• from more negative reduction potentials to more positive

What happens as electrons move through the mitochondrial ETC

coupling sites move H+ across the inner mitochondrial membrane → pmf

• pmf powers OP to make ATP

What are the different complexes of the mitochondrial ETC

• Complex I - NADH-ubiquinone oxidoreductase (NADH dehydrogenase)

  • coupling site

  • CoQ connects complex I to III

• Complex II - succinate dehydrogenase

  • CoQ connects complex II to III

• Complex III - ubiquinol-cytochrome c oxidoreductase

  • coupling site

  • Cyt c connects complex III to IV

• Complex IV - cytochrome c oxidase

  • coupling site

  • transfers e- to O2

Prokaryotic vs Eukaryotic ETCs

• Location

  • prokaryotes: inner/plasma membrane

  • eukaryotes: IMM

• Different e- carriers

• may be branched

• may be shorter

• lower P/O ratio

  • how much NADPH produces ATP from oxygen available

    • number of ATP synthesized per oxygen atom reduced

Escherichia coli ETC

• facultative anaerobic bacterium

  • can do fermentation

• branched pathway dependent on oxygen levels

  • bd branch - stationary phase and low aeration

    • higher affinity for oxygen

    • moves fewer protons

  • bo branch - log phase and high aeration

    • lower affinity for oxygen

• H moves from cytoplasm to periplasmic space creating pmf

Paracoccus denitrificans ETC

• facultative anaerobic soil bacterium

  • non-fermenting

• can use aerobic respiration similar to mitochondrial ETC

  • similar electron carriers

  • protons transported to periplasmic space

• extremely versatile

  • both hetero and autotrophic

  • glucose: uses NADH to donate e- to NADH dehydrogenase

    • e- enter Complex I = pumps more protons out

  • 1-carbon molecule (methanol): no NADH involved, e- donated to cyt c via methanol dehydrogenase (MD)

    • e- enter Complex IV = pumps less protons out

How do protons move in the mitochondrial ETC

from the matrix to the intermembrane space

Where is the F1F0 ATP synthase found

mitochondria, bacteria, and chloroplast

F1F0 ATP synthase

• best studied ATP synthase

• can also catalyze ATP hydrolysis

• F0 is the proton conducting channel

  • goes through membranes

  • protons go across

  • rotates like a fan

• F1 is a complex that catalyzes ATP synthesis/hydrolysis

What is the theoretical maximum yield of ATP during aerobic respiration

• 32 ATP

  • maximum in eukaryotes is 30 ATP

  • less in prokaryotes due to shorter ETC and lower P/O

How to calculate maximum ATP yield

using P/O ratios of NADH (2.5) and FADH2 (1.5)

Anaerobic Respiration

• exogenous electron acceptor other than O2

  • yields less energy d/t lower reduction potential of acceptor

• done by all 3 domains

• most common electron aceptors: nitrate, sulfate, and carbon dioxide

Paracoccus denitrificans anaerobic respiration

• anoxic conditions: dissimilatory nitrate reduction/denitrification

  • NO3- → NO2- → NO → N2O → N2

  • enzymes are inhibited by O2

    • because aerobic respiration yields more energy than anaerobic

• nitrate as terminal electron acceptor → N is unavailable to cell for assimilation or uptake

  • causes loss of soil fertility

• also done by Pseudomonas and Bacillus (facultative anaerobes)

Fermentation

• energy source is only partially oxidized

  • less ATP per glucose

• oxidation of NADH produced by glycolysis

  • NADH is converted back to NAD+

  • pyruvate or derivative accepts electrons

• oxygen is not needed

• No ETC

  • OP does not occur

  • ATP is formed by SLP only

  • no pmf

Common Microbial Fermentation

• Fermentation pathways are named after what’s produced

  • Mixed acid fermenters (E. coli)

  • Butanediol fermenters (Enterobacter)

  • Alcoholic acid fermenters

Catabolism of Carbohydrates

• Carbohydrates can be supplied externally or internally

• disaccharides and polysaccharides are cleaved into monosaccharides

  • hydrolases (outside the cell)

    • uses water

  • phosphorylases (inside the cell)

    • adds a phosphate to one of the products to use less ATP

    • yields G1P to enter glycolysis after conversion to G6P

Lipid Catabolism

• used by chemoorganotrophs

• hydrolyzed by lipases to

  • glycerol degraded via glycolytic pathway as dihydroxyacetone phosphate (DHAP) → G3P

  • fatty acids oxidized via B-oxidation

    • shortened by two carbon units that are released as acetyl-CoA

      • which is then fed into the TCA cycle or for biosynthesis

Protein and Amino Acid Catabolism

• Proteases hydrolyzes protein to amino acids (proteolysis)

• Deamination followed by transamination

  • resulting in organic acids converted to pyruvate, acetyl-CoA, or TCA cycle intermediate

Chemolithotrophy

• e- released from inorganic molecule

  • common energy sources are: H2, reduced nitrogen, reduced sulfur, and Fe2+

  • directly donate electrons to ETC

• Terminal electron acceptor

  • oxygen, sulfate, and nitrate

• Must use CO2 as carbon source

  • CO2 fixation pathways

• ETC is used, ATP is synthesized by OP

  • they do NOT use fermentation

Three major groups of chemolithotrophs

• several bacteria and archaea oxidize hydrogen

  • reduces NAD+ or donate directly to the ETC

• Nitrifying bacteria carry out nitrification

  • oxidation of ammonia (NH3) to nitrate (NO3-)

    • Step 1: ammonia → nitrite

    • Step 2: nitrite → nitrate

• Sulfur-oxidizing microbes

  • oxidizes hydrogen sulfide (H2S), sulfur, and thiosulfate (S2O32-) to sulfuric acid (H2SO4)

Reverse Electron Flow

• used by chemolithotrophs which many of them are autotrophs

  • needs NAD(P)H and ATP to reduce CO2

  • but they cannot donate electrons directly to NAD(P)+ so they use reverse electron flow

• during reverse electron flow, electrons are moved up their ETCs to reduce NAD(P)+ to NAD(P)H

  • energy from H+ going from out to in (pmf) helps electrons move up the E0’ tower

Chemoorganotrophic fueling process

• energy source is oxidized

  • releases electrons that are accepted by NADH/FADH2

• releases energy (catabolism) and provides carbons and electrons needed for anabolism

Work without ETC

• • pmf is still needed for other functions

    • fermentation: end-products efflux

      • products go from high concentration to low concentration produced energy

    • facultative anaerobes: pmf redox-loop mechanism

    • strictly fermentative conditions: F1F0-ATP synthase operates reversibly

      • ATP → ADP

      • pumps protons out

Disaccharide cleavage