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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

disrupts electrons and 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)

– Many of the coenzymes we will discuss act as

electron carriers

Examples of coenzymes

• Nicotinamide adenine dinucleotide (NAD+)

• Nicotinamide adenine dinucleotide

phosphate (NADP+) (anabolic reactions)

• 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

Fig. 5.7

Competitive inhibition

Inhibitors

• May be 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 (decarboxylation)

• Krebs cycle

• Electron transport chain (system)

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Glycolysis

Fig. 5.12

Alternatives to glycolysis

• Pentose phosphate pathway

– Used to produce pentose sugars

– 1 ATP and 2 NADPH are produced

– Bacillus subtilis, Escherichia coli, Enterococcus

faecalis

• Entner-Doudoroff pathway

– Produces 1 ATP, 1 NADPH, and 1 NADH

– Some gram negative bacteria (Pseudomonas,

Rhizobium) utilize

Decarboxylation 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

– Proteins with iron-containing groups

– Cytochrome b/c1, cytochrome c, cytochrome a/a3

• Ubiquinones (coenzyme Q)

Electron transport chain (system)

Fig. 5.16

Chemiosmosis

Fig. 5.15

Proton motive force

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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

Fig. 5.33

Metabolic diversity

Fig. 5.28