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2/7/2017
1
Microbial metabolism
Chapter 5
BIO 220
Metabolism
• Sum of all the chemical reactions occurring in
an organism
• Metabolism = Catabolism + Anabolism
Fig. 5.1
Collision Theory
• In order for chemical reactions to take place,
atoms/ions/molecules must collide with each
other
• The energy transferred during these collisions
allows for the formation or the break down of
chemical bonds
Enzymes
• Enzymes increase reaction rate by increasing
the probability that the starting molecules will
interact in an orientation that promotes
product formation
• They lower the Energy of Activation of the
reaction (decrease the randomness of
substrate interactions)
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Activation energy
Fig. 5.2
Enzyme action
Fig. 5.3
Enzyme Characteristics
1. Biological catalysts
– Can process substrates very efficiently
– Turnover number
2. Induced fit vs. lock and key
3. Usually proteins
4. Substrate smaller than enzyme
5. Specificity (affinity)
6. Naming
– End in -ase
– Based on type of chemical reactions they catalyze
For oxidation-reduction rxns remember “OIL RIG”
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Enzyme components
• Some enzymes require additional factors in
order to function
• Holoenzymes are composed of an apoenzyme
(protein) and a cofactor (nonprotein)
Fig. 5.4
Enzyme components
Types of cofactors
• Metal ions
– Zn2+ , Fe2+ , Cu2+ , Mg2+ , Ca2+
• Coenzymes (organic)
– Often derived from vitamins
– Attachment to protein is non-covalent (not
permanent)
Examples of coenzymes
• Nicotinamide adenine dinucleotide (NAD+)
• Nicotinamide adenine dinucleotide
phosphate (NADP+)
• Flavin mononucleotide (FMN)
• Flavin adenine dinucleotide (FAD)
• Coenzyme A
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Factors that affect enzyme activity &
reaction rate
1. Temperature
2. pH
3. Substrate concentration
4. Inhibitors
Temperature
Figs. 5.5a and 5.6
pH
Figs. 5.5b and 5.6
Substrate concentration
Fig. 5.5c
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Inhibitors
• May be competitive or noncompetitive
Fig. 5.7
Competitive inhibition
Inhibitors
• May be competitive or noncompetitive
Fig. 5.7
Feedback inhibition
Fig. 5.8
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Energy production
• Oxidation – reduction
– Used to extract energy from nutrient molecules
– OIL RIG
• Mechanisms of ATP generation
Oxidation-reduction
• Oxidation and reduction reactions are coupled
(redox reactions)
• Most biological oxidation reactions involve the
loss of hydrogen ions (dehydrogenation rxns)
Figs. 5.9, 5.10
ATP generation
• Nutrient molecules are catabolized using a
series of oxidation-reduction reactions, then
the energy contained within the bonds of the
nutrients can be trapped within the bonds of
ATP, which can then serve as an energy source
for energy-requiring reactions
ATP generation
• Substrate – level phosphorylation
• Oxidative phosphorylation
• Photophosphorylation
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Carbohydrate catabolism
• Glucose is the most common carbohydrate
used as an energy source
• Microbes can use cellular respiration,
anaerobic metabolism, or fermentation to
produce energy from glucose
Fig. 5.11
(Cellular) Respiration
• An ATP-generating process in which molecules
are oxidized and the final electron acceptor
comes from outside the cell and is (almost
always) inorganic
• Aerobes use oxygen as the final electron
acceptor
• Anaerobes do not use oxygen, rather some
other inorganic molecule as the final acceptor
Cellular respiration
• Glycolysis
• Transition reaction
• Krebs cycle
• Electron transport chain (system)
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Glycolysis
Fig. 5.12
Alternatives to glycolysis
• Pentose phosphate pathway
– Used to catabolize pentose sugars
– 1 ATP and 2 NADPH are produced
– Bacillus subtilis, Escherichia coli, Enterococcus
faecalis
• Entner-Doudoroff pathway
– Produces 1 ATP and 2 NADPH
– Some gram negative bacteria (Pseudomonas,
Rhizobium) utilize
Transition reaction and Krebs cycle
Fig. 5.13
Electron transport chain (system)
Fig. 5.14
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Electron transport chain
Carrier molecules include
• Flavoproteins
– Contain coenzymes derived from riboflavin
– Flavin mononucleotide (FMN)
• Cytochromes
– Protein with iron-containing group
– Cytochrome b/c1, cytochrome c, cytochrome a/a3
• Ubiquinones (coenzyme Q)
Electron transport chain (system)
Fig. 5.16
Chemiosmosis
Fig. 5.15
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Fig. 5.17
Aerobic respiration (summary)
Anaerobic respiration
• The final electron acceptor is NOT oxygen
• Pseudomonas and Bacillus use nitrate ions
• Desulfovibrio uses sulfate
• Other organisms use carbonate
• Aerobic respiration is a much more efficient
ATP producer than anaerobic respiration!
Fig. 5.11
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Fermentation
• Releases energy from sugars or other organic
molecules
• Does not require oxygen
• Does not use the Krebs cycle or an electron
transport system
• Uses organic molecules as final electron
acceptors
• Does not produce buckets of ATP
Fig. 5.18
Types of
fermentation
Fig. 5.19
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Catabolism of nutrients
Fig. 5.21