Chap 3 Metabolism and Growth
I. Metabolism
Definitions:

Metabolism includes two parts: anabolism and catabolism

Catabolism:


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Anabolism:



Aerobic metabolism: carried out with O2. The reactions are highly exothermic
catabolism
anabolism
catabolism
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anabolism

Anaerobic metabolism:
Ex: yeast can exist either aerobically or anaerobically (called facultative anaerobe), the
growth rate is lower under anaerobic conditions.
Energy Currency

ATP (adenosine triphosphate) that possesses high-energy phosphoanhydride bonds.

General representations:
Phosphoanhydride bond
adenine
adenosine
II. Catabolic Pathways
Purposes of breaking down a substrate:
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
Catabolism provides the following:
 building units for the synthesis of new cells
 energy, mainly in the form of ATP, to drive the synthesis of other intermediates and
products


A central pathway:
Glycolysis

Major form of degradation of glucose, also called EMP pathway.

10 steps are involved, and the overall reaction is
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Tricarboxylic acid cycle (citric acid cycle, Krebs Cycle)

The end product of the glycolysis, pyruvate, can be converted to acetyl coenzyme A
(acetyl-CoA). Acetyl-Co A can generate a large number of intermediates, but one of its
major roles is to go through TCA cycle under aerobic conditions.
pyruvate dehydrogenase
  acetyl-CoA +CO2 +NADH (see Fig. 19-1)
Pyruvate + CoA +NAD+ 

The main purposes of TCA cycle:
1.
Provides key intermediates for biosynthetic reactions (Fig. 2.5).
2.

The overall reaction is:
FAD: flavin adenine dinucleotide,
analogue of NAD+, an essential redox
cofactor
FADH: a half-reduced form
FADH2: fully reduced form, analogous to
NADH
GDP: guanosine diphosphate, an
analogue of ADP
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
The initial oxaloacetate needed as the priming reactant can be synthesized by:
pyruvatec carboxylase

 oxaloacetate +ADP +Pi
Pyruvate +CO2 +ATP 

If an organism grows on a C2 compound, or on a fatty acid, hydrocarbon or any substrate
that is degraded into C2 units, the TCA cycle is not sufficient, then alternative pathway
can be utilized, e.g. glyoxylate by-pass (Fig. 2-12, skip the details).

Many other carbon sources can be utilized by the specific enzyme systems in the microorganisms. Thus special microorganisms can be applied as “waste disposal units”,
forming the basis of environmental biotechnology.
Ex: microbial degradation of oils and fatty acids.

The oils, when consumed by the microorganism, are initially hydrolyzed by lipase,
into fatty acids and glycerol.
Glycerol glyceraldehyde 3-phosphate (Fig. 2-6).
 oxidation
 shorter acetyl-CoA units (Fig. 2-13)
Fatty acids fatty acly-CoA 
Energy production in aerobic organisms by electron transport chain




During electron transport, the flow of electrons creates a proton gradient (high [H+] on
the outside of the membrane), so H+ tends to flow back (proton motive force), which
together with ATP synthase on the membrane, drives the synthesis of ATP.
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Direction of etransport
(CoQ)
G=-69.5 kJ/mol
G=-36.7 kJ/mol
G=-112 kJ/mol
Voet, D., Voet, J., (2004) Biochemistry. 3rd Ed. (Vol.1) John Wiley & Sons. New York.
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For each co-factor, the overall reactions may be written as:

Overall ATP yields for glucose metabolism
Anaerobic Metabolism

Oxidative phosphorylation cannot occur  substrate-level phosphorylation (energy
provided by degrading the original substrate) is an alternative route, but the efficiency of
energy production is typically 8% of aerobic metabolism.

Anaerobic metabolism can occur in bacteria, yeast and even higher animals (e.g. lactate
accumulation in the muscles during hyper-activity of an athlete).

Several products of anaerobic metabolism stemming from glucose:



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III. Anabolic Pathways (Biosynthesis)

The provision of energy (ATP), reducing power (NADH and NADPH) and various
precursors from the breakdown of substrates provide the cell with the necessary means
of regenerating itself.

The cell undertakes the biosynthesis of the macromolecules (e.g. nucleic acids, proteins,
lipids (for membranes) and polysaccharides) from these simple building blocks.

Other pathways: pentose (C5) and tetrose (C4) phosphate pathways to provide C5 and C4
units, and NADPH for biosynthesis.

Two types of metabolisms: primary metabolism and secondary metabolism.
Primary metabolism

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
During this phase, the cells grow at an exponential rate and the cell components-DNA,
RNA, proteins, lipids, etc- are rapidly synthesized.

Eventually, the cells must run out of certain nutrient (even if this is only O2) growth
rate slows and eventually ceases.
Secondary metabolism

When active multiplication ceases, some primary metabolism continues to maintain vital
components: e.g. key proteins must be replaced (proteins under turnover)

But the cell mainly diverts its metabolism to the secondary metabolism to arise
sometimes as storage products (e.g. poly--hydroxybutyrate or triacylglycerol), or other
products not present during exponential phase (see Fig. 2-19).

Secondary metabolites are of considerable biotechnological importance (e.g. antibiotics).
References:
1.
2.
Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P. (2002) Molecular
Biology of the Cell, 4th Ed. Garland Science, New York.
Voet, D., Voet, J., (2004) Biochemistry. 3rd Ed. (Vol.1) John Wiley & Sons. New York.
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