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MICROBIAL METABOLISM Chapter 6, pp 129-166

I. Metabolism = sum of anabolic and catabolic pathways (Fig 6-1, p130)
A) anabolism = to build up, generally requires energy
B) catabolism = to break down, may release energy

Cells generally use energy from catabolic pathways to drive anabolic pathways, and the high energy intermediate here is usually ATP. Therefore, in catabolism we’ll discuss how ATP is produced.

C) enzymes - catalyze the steps in metabolism (review what was covered with Ch 2)
1) components
a) enzyme = protein in nature
b) cofactor = non protein component required for activity such as metal ions
(Zn, Fe, Mg, Ca, etc) or organic molecules (coenzymes). Many coenzymes are derived from vitamins (Table 6-5,p 139).
2) inhibitors = competitive vs. noncompetitive (Fig 6-14, p142 for competitive)

D) control of metabolism - metabolic pathways may be regulated by regulation of the
enzymes involved
1) control at gene level
2) control of enzyme activity
a) feedback inhibition = product inhibits earlier enzyme

b) allosteric enzymes = a subset of enzymes that can exist in more favorable (for catalysis) or less favorable confirmations depending on what effectors are present. Effectors bind to allosteric site and enhance or decrease enzyme activity depending on if they are activators or inhibitors (noncompetitive). Fig 6-13, p141


II. ENERGY METABOLISM
Two forms of energy are available to life:
1) chemicals = chemotrophs
2) light = phototrophs

A) Modes of ATP production (all involve oxidation-reduction reactions)
1) Substrate level phosphorylation
2) Electron transport phosphorylation (oxidative phosphorylation)
3) Photophosphorylation

B) Oxidation-reduction reactions Fig 6-8, p134
Oxidation involves loss or removal of electrons (e-) and is coupled to reduction where an electron acceptor takes up the electron. Also, as e- are transferred, many times protons are as well (1 e- plus 1 proton = H atom). Common electron carriers = Table 6-2, p135

1) redox reactions with organic molecules:

lactic acid ¤pyruvate

2) redox reactions with metal ions:

Fe+2 ---> Fe+3 + e- oxidation
Fe+3 + e- ---> Fe+2 reduction

Fe+3/Fe+2 together form a redox pair

Note: - energy is required to remove an e-
- energy is gained by adding an e-
* - the amount of energy in each case depends on the chemical nature of molecules involved

C) Chemiosmotic mechanism of ATP production involving redox reactions
Fig 6-19, p149; Accounts for how e- flow generates ATP


III. Energy producing pathways (generally catabolic) = generate ATP
(fermentation; respiration (includes aerobic and anaerobic); photosynthesis

A) Fermentation = an anaerobic process (oxygen not needed)
- incomplete oxidation where organic compounds serve both as e- donor and acceptor

Fermentation generally begins with glycolysis, the splitting of sugar. Glycolysis is generally divided into 2 parts: breakdown of glucose to pyruvate, then utilization of pyruvate

1) Glycolysis = glucose to pyruvate Fig 6-15, p143
1 glucose + 2Pi + 2ADP + 2NAD+ ---> 2 pyruvate + 2ATP + 2NADH + 2H+ + 2H2O


2) pyruvate utilization (a means by which NAD+ may be regenerated = NADH must be oxidized to produce NAD+; some bacteria accomplish this by reduction of pyruvate or reduction of the metabolic products of pyruvate)
a) lactic acid fermentation - Fig 6-22, p152 (Streptococcus, Lactobacillus)
pyruvate to lactic acid (if only lactate produced = homolactic)

pyruvate to lactic acid and other products = heterolactic

b) alcoholic fermentation
pyruvate to ethanol and carbon dioxide

c) other products from pyruvate Fig 6-23, p 152

B) Respiration = metabolic degradation of a substrate in which inorganic molecules function as terminal electron acceptors

1) aerobic = oxygen is terminal electron acceptor (reguires oxygen)

ATP produced here = substrate level phosphorylation and oxidative phosphorylation,
involves glycolysis and Krebs cycle (Fig 6-16 p145), generates NADH, FADH2
Electron transport chain takes e- from NADH and FADH2, passes the electron along different electron carriers to O2 producing water and ATP is produced via chemiosmotic mechanism

2) anaerobic = inorganic ions are terminal e- acceptors (NO3, SO4)
(ATP yield varies) Fig 6-20, p150

electron acceptors such as: NO3-1 SO4-2 CO3-2 (generating nitrite, hydrogen sulfide, methane respectively)

Pseudomonas and Bacillus reduce nitrate ion to nitrite ion to nitrous oxide or nitrogen gas
Desulfovibrio reduces sulfate to hydrogen sulfide
Methanogens generate methane

C) ATP yield from aerobic respiration Table 6-4, p137
per glucose oxidized = 38 ATP (36 in eucaryotes)

D) Photosynthesis (microbial) as done by photoautotrophs (Cyanobacteria, green and
purple sulfur bacteria)

1) Phase 1 = light phase = energy from light is captured
a) oxygenic = water is broken down into protons, electrons, and oxygen (water split as a source of electrons).
(Table 6-9, p157)
b) anoxygenic = water is not electron donor but rather sulfur, hydrogen or organic compounds = oxygen not generated

- produces NADPH2 and ATP Fig 6-27, p158

2) Phase 2 = dark phase = NADPH2 and ATP are used to reduce CO2 (fix) into
organic compounds (Calvin Cycle Fig 6-28, p160)

IV. Classification of organisms according to where they derive energy and carbon

A) energy source
1) sunlight = phototrophs
2) molecules = chemotrophs

B) carbon source
a) inorganic (CO2) = autotrophs (lithotrophs = “rock eating”)
b) organic = heterotrophs SEE TABLE 4-4, p91

photoautotrophs = “classical” photosynthesis (oxygenic) vs. anoxygenic
Cyanobacteria are oxygenic (=produce oxygen)
Green sulfur and purple sulfur bacteria are anoxygenic

photoheterotrophs = green nonsulfur and purple nonsulfur bacteria.

chemoautotrophs = inorganic compounds (e.g. hydrogen sulfide, sulfur, ammonia, nitrites, hydrogen gas, iron) serve as energy source, obtain energy by oxidation of inorganic substrates coupled to electron transport chains . Examples: (Table 6-8, p155)
a) sulfur oxidizing bacteria (Thiobacillus)
b) nitrifying bacteria oxidize ammonia to nitrate
NH3 to NO2 to NO3 (Nitrosomonas - Nitrobacter)


chemoheterotrophs = most bacteria et al
saprophytes = live on dead organic matter (decay)
parasites = obtain nutrients from a live host

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ATP generated is used to drive anabolic pathways, active transport, motility, etc.

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