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Chapter 5—Microbial Metabolism.
I.
II.
Catabolic and Anabolic Reactions.
a. Metabolism is the sum of the chemical reactions in an organism.
i. Catabolism refers to the energy-releasing processes (degradative, hydrolysis reactions,
exergonic).
ii. Anabolism is the energy-using processes (biosynthetic, dehydration synthesis
reactions, endergonic).
iii. Catabolism provides the building blocks and energy for anabolism.
iv. ATP participates in coupling anabolic and catabolic reactions. Fig. 1.
v. A metabolic pathway is a sequence of enzymatically catalyzed chemical reactions in a
cell.
Enzymes.
a. Metabolic pathways are regulated and determined by enzymes.
b. Enzymes are encoded by genes.
c. The collision theory states that chemical reactions can occur when atoms, ions, and molecules
collide.
d. Activation energy is needed to disrupt electronic configurations.
i. Enzymes reduce the activation energy of a particular chemical reaction. Fig. 2.
e. Reaction rate is the frequency of collisions with enough energy to bring about a reaction.
i. Reaction rate can be increased by the presence and abundance of enzymes or by
increasing temperature or pressure.
f. Enzymes are biological catalysts.
i. Each enzyme is specific to a single chemical reaction; the enzyme is not used up or
altered in that reaction.
1. Specificity is due to the 3-D shape of the enzyme.
ii. An enzyme only acts on a specific substrate.
1. The enzyme-substrate complex forms when the substrates dock with the
enzyme. This orients the substrates into a position that increases the
probability of a reaction.
g. Enzyme turnover number is generally 1-10,000 molecules per second, but can be as high as
500,000 per second.
h. The names of enzymes normally end in –ase.
i. Enzyme Classification: Table 1.
i. Oxidoreductase = Oxidation-reduction reactions.
ii. Transferase = Transfer functional groups.
iii. Hydrolase = Hydrolysis.
iv. Lyase = Removal of atoms without hydrolysis.
v. Isomerase = Rearrangement of atoms in a compound.
vi. Ligase = Joining of molecules, uses ATP.
j. Enzyme Components. Fig. 3.
i. Apoenzyme: Protein portion.
ii. Cofactor: Non-protein component (ions of iron, zinc, magnesium, calcium, etc.) that
helps catalyze a reaction by forming a bridge between the enzyme and substrate.
iii. Coenzyme: Organic cofactor (often vitamin derivatives). Table 2.
iv. Holoenzyme: Apoenzyme + cofactor OR coenzyme.
k. Important Coenzymes:
i. NAD+ (nicotinamide adenine dinucleotide; derivative of niacin, a B vitamin).
ii. NADP+ (nicotinamide adenine dinucleotide phosphate; derivative of niacin, a B
vitamin).
III.
iii. FMN (flavin mononucleotide; derivative of riboflavin, a B vitamin). Component of
the electron transport chain (ETC).
iv. FAD (flavin adenine dinucleotide; derivative of riboflavin, a B vitamin).
v. Coenzyme A (contains a derivative of pantothenic acid, a B vitamin).
l. Mechanism of Enzymatic Action: Fig. 4.
i. The substrate(s) contact(s) a specific part of the enzyme called the active site.
ii. The enzyme-substrate complex forms.
iii. The substrate(s) is/are transformed by one of the following:
1. The rearrangement of existing atoms.
2. The breakdown of the substrate molecule (hydrolysis).
3. By combining with another substrate molecule (dehydration synthesis).
iv. The transformed substrate(s) is/are released from the enzyme because they no longer
fit the active site.
v. The enzyme is now free to catalyze the same reaction again.
m. Factors Influencing Enzyme Activity: Fig. 5.
i. Rate of enzyme synthesis.
ii. Temperature.
iii. pH.
iv. Substrate concentration.
v. Denatured enzymes. Can be accomplished by: Fig. 6.
1. Temperature.
2. pH.
3. Heavy-metal ions.
4. Alcohol.
5. UV radiation.
vi. Competitive inhibition. Fig. 7.
1. Competitive inhibitors fill the enzyme’s active site and compete with the
normal substrate for that active site.
2. The competitive inhibitor does not undergo a reaction.
3. Some competitive inhibitors bind reversibly while others bind irreversibly.
vii. Noncompetitive inhibition. Fig. 7.
1. Noncompetitive inhibitors do not go for the active site; rather, they bind with
another part of the enzyme called the allosteric site. This binding causes the
active site to change shape, making it non-functional. This is called allosteric
inhibition. This can be reversible or non-reversible.
viii. Enzyme poisons.
1. Cyanide and fluoride are examples of substances that permanently inactivate
enzymes.
ix. Feedback inhibition. Fig. 8.
1. In many metabolic pathways where multiple enzymes catalyze a series of
reactions in sequence, the end-product can allosterically inhibit the activity of
an enzyme earlier in the pathway. (This inhibition is reversible).
a. This stops the cell from wasting chemical resources by making more of
a substance than it needs.
b. As the end-product gets used up, the enzyme’s allosteric site will more
often remain unbound, and the pathway will resume activity.
n. Ribozymes.
i. RNA that cuts and splices RNA.
ii. Function like enzymes—have active sites that bind to substrates and are not used up in
a chemical reaction.
Energy Production.
a. Oxidation-Reduction Reactions. Fig. 9.
i. Oxidation is the removal of electrons.
1. Protons are typically also removed along with the electrons.
2. For this reason these reactions are also called dehydrogenation reactions.
ii. Reduction is the gain of electrons.
1. Protons are typically also gained along with the electrons.
iii. LEO the lion goes GER.
1. Lose electrons = oxidation. Gain electrons = reduction.
iv. A redox reaction is an oxidation reaction paired with a reduction reaction.
v. Fig. 10 shows a typical redox reaction.
b. The Generation of ATP.
i. The addition of PO4-3 (inorganic phosphate = Pi) to a compound is called a
phosphorylation.
ii. ATP is generated by the phosphorylation of ADP.
iii. Substrate-level phosphorylation:
1. This is the transfer of a high-energy Pi from a phosphorylated compound
directly to ADP. Compound-Pi + ADP  Compound + ATP
iv. Oxidative phosphorylation:
1. Energy released from the sequential transfer of electrons of one compound to
another is used to generate ATP by chemiosmosis via oxidative
phosphorylation in the electron transport chain. Molecular oxygen (O2) is the
final electron acceptor in aerobic oxidative phosphorylation (aerobic cellular
respiration).
v. Photophosphorylation:
1. Light causes chlorophyll to give up electrons. Energy released from the
transfer of electrons of chlorophyll through a system of carrier molecules via
an electron transport chain is used to generate ATP and NADPH.
2. ATP and NADPH are then used to synthesize organic molecules from CO2 and
H2O. (Carbon fixation).
c. Carbohydrate Catabolism.
i. This is the breakdown of carbohydrates to release energy.
1. Most organisms oxidize carbohydrates as their primary source of cellular
energy. Glucose is the most common energy source used for this, but lipids,
proteins, and nucleic acids can also be used.
ii. Cellular respiration and fermentation are the two general processes microorganisms
use to produce energy from glucose. Fig. 11.
1. Cellular respiration can be aerobic or anaerobic.
a. Cellular respiration involves:
i. Glycolysis.
ii. Krebs cycle.
iii. Electron transport chain.
2. Fermentation typically begins with glycolysis, but does not include the Krebs
cycle or ETC. Therefore the ATP yield is much lower.
a. Fermentation is considered a separate process from cellular respiration.
d. Glycolysis. Fig. 12.
i. The oxidation of glucose to pyruvic acid, producing ATP and NADH + H+.
Glycolysis does not require oxygen, and can occur whether it is present or not.
ii. Preparatory Stage:
1. 2 ATPs are used.
2. Glucose is split to form a pair of glyceraldehyde-3-phosphate molecules.
iii. Energy-Conserving Stage:
1. The pair of glyceraldehyde-3-phosphate molecules are oxidized to form a pair
of pyruvic acid molecules.
2. 4 ATP molecules are produced by substrate-level phosphorylation.
3. 2 NADH + 2 H+ are produced.
4. Glucose + 2 ATP + 4 ADP + 4 Pi + 2 NAD+ 
2 pyruvic acid + 4 ATP + 2 NADH + 2 H+ + 2 H2O
e. Alternatives to Glycolysis: [DO NOT COVER]
i. Pentose phosphate pathway: [DO NOT COVER]
1. Uses pentoses and NADPH.
2. Operates with glycolysis.
ii. Entner-Doudoroff pathway: [DO NOT COVER]
1. Produces NADPH and ATP.
2. Does not involve glycolysis.
f. Cellular Respiration:
i. Oxidation of molecules liberates electrons for an electron transport chain.
ii. ATP is generated by oxidative phosphorylation in the electron transport chain and by
substrate-level phosphorylation in the Krebs Cycle.
iii. Intermediate Step: Fig. 13.
1. Pyruvic acid (from glycolysis) which is a 3-carbon compound, is oxidized and
decarboxylated giving off a molecule of CO2 . This results in the formation of
a 2-carbon compound called an acetyl group. Also during this step, a molecule
of NAD+ is reduced to NADH + H+.
2. The acetyl group attaches to coenzyme A to form acetyl coenzyme A (acetyl
CoA).
3. Because glycolysis ended in the formation of two pyruvic acid molecules from
a single glucose molecule, the above series of events happens twice.
iv. Aerobic Cellular Respiration:
1. Krebs Cycle: Fig. 13.
a. Acetyl CoA enters the Krebs cycle, CoA detaches, and the acetyl group
combines with oxaloacetic acid (a 4-carbon molecule) to form citric
acid (a 6-carbon molecule).
b. Through a series of reactions, the Krebs cycle produces:
i. 3 NADH + 3H+
ii. 1 FADH2
iii. 1 ATP via substrate level phosphorylation
iv. 2 CO2
c. This process occurs twice, because 1 glucose  2 pyruvic acid  2
acetyl CoA molecules.
d. In the Krebs cycle, all remaining carbon atoms of the original glucose
molecule are individually cleaved, forming CO2.
e. The Krebs cycle ends with the formation of oxaloacetic acid, which is
then free to bind another acetyl group, and start the sequence over
again.
f. The 3 NADH + 3H+ and 1 FADH2 are destined for the electron
transport chain.
2. The Electron Transport Chain: Fig. 16.
a. The ETC shown in this figure is what exists on the inner mitochondrial
membrane of eukaryotes, which is best known.
b. The ETC is a series of carrier molecules that are, in turn, oxidized and
reduced as electrons are passed down the chain. There are 3 classes of
carrier molecules:
i. Flavoproteins—contain flavin, a coenzyme derived from
riboflavin (vitamin B2). Includes FMN (flavin
mononucleotide).
ii. Cytochromes—proteins with a heme group.
iii. Ubiquinones—aka coenzyme Q, which are small non-protein
carriers.
c. NADH is oxidized to NAD+ when it releases 2 electrons and a proton
to FMN, the first carrier in the ETC. Another proton follows from the
surrounding aqueous medium. [This step in Fig. 16 only shows a
single electron entering FMN, when there should be two].
d. The protons enter the space between the inner and outer mitochondrial
membranes (intermembranous space), while the electrons get passed
from one carrier molecule to the next in a series of redox reactions.
i. As the electrons are passed through the chain, there is a
stepwise release of energy, which is used to drive the
chemiosmotic generation of ATP.
e. The last cytochrome in the ETC, cyt a3, passes its electrons to
molecular oxygen (O2) which becomes negatively charged; it then
picks up protons (H+) from the surrounding medium to form H2O.
i. Molecular oxygen (O2) is the final electron acceptor in aerobic
cellular respiration.
f. As the electrons are moving down the ETC, some protons follow and
are released into the intermembranous space of the mitochondrion.
Other protons are pumped into this space from the mitochondrial
matrix.
g. This generates both a concentration gradient and an electrical gradient
across the inner mitochondrial membrane. This is called the proton
motive force.
h. The protons can diffuse from the intermembranous space across the
inner mitochondrial membrane and into the mitochondrial matrix
through special protein channels that contain ATP synthase.
i. This movement of protons is what drives the formation of ATP
from ADP and Pi.
i. A single molecule of NADH yields a production of 3 ATP during
oxidative phosphorylation due to chemiosmosis.
j. A single molecule of FADH2 yields a production of 2 ATP during
oxidative phosphorylation due to chemiosmosis.
i. This is because the electrons carried by FADH2 enter the ETC
at a lower point than the electrons delivered by NADH.
k. The ETC is found on the inner mitochondrial membrane of
mitochondria in eukaryotes and on the plasma membrane of
prokaryotes.
l. The ETC regenerates NAD+ and FAD, which can be used again in
glycolysis and the Krebs cycle.
v. Energy produced from the complete oxidation of 1 glucose molecule via aerobic
cellular respiration:
1. 36-38 ATPs are produced in eukaryotes.
2. 38 ATPs are produced in prokaryotes.
3. Table 3 provides a detailed summary of the ATP yield during prokaryotic
aerobic respiration of one glucose molecule.
4. C6H12O6 + 6O2 + 38 ADP + 38 Pi  6CO2 + 6 H2O + 38 ATP.
IV.
5. O2 serves as the final electron acceptor.
6. Fig. 17 shows a summary of aerobic cellular respiration in prokaryotes.
vi. Anaerobic cellular respiration: Final electron acceptor in the electron transport chain is
not O2. Instead, inorganic substances other than oxygen, such as nitrate ions (NO3-),
carbonate ions (CO3-), or sulfate ions (SO42-), serve as the final electron acceptor;
rarely, an organic molecule serves as the final electron acceptor.
1. Glycolysis occurs as above.
2. Anaerobic cellular respiration yields less energy than aerobic cellular
respiration because only part of the Krebs cycle operates under anaerobic
conditions, and not all the carriers in the ETC participate in anaerobic cellular
respiration.
a. ATP yield is less than 38 but more than 2.
3. Anaerobic cellular respiration by bacteria that use nitrate ions, carbonate ions,
or sulfate ions as their final electron acceptors are essential for the nitrogen,
carbon, and sulfur cycles to function.
g. Fermentation: Fig. 18.
i. Glycolysis proceeds as previously discussed, producing 2 pyruvic acid molecules, 2
net ATP, and 2 NADH + 2H+. The pyruvic acid is then converted to another organic
molecule, and NAD+ is regenerated so it can participate in another round of glycolysis.
ii. Alternatively, energy can be derived from other organic molecules such as amino
acids, organic acids, purines, and pyrimidines.
iii. Does not require oxygen.
iv. Krebs cycle and ETC do not occur.
v. Uses an organic molecule as the final electron acceptor.
vi. Produces only small amounts of ATP, which is only generated during glycolysis.
vii. Lactic acid fermentation. Fig. 19.
1. Glycolysis produces 2 ATP and 2 pyruvic acid molecules, which are reduced
by 2 NADH to produce 2 lactic acid molecules and 2 NAD+.
2. Lactic acid fermentation can spoil food, but it can also produce yogurt from
milk, sauerkraut from fresh cabbage, and pickles from cucumbers.
viii. Alcohol fermentation.
1. Glycolysis produces 2 ATP and 2 pyruvic acid molecules, which are converted
to 2 CO2 molecules and 2 acetaldehyde molecules.
2. The 2 acetaldehyde molecules are reduced by 2 NADH to produce 2 NAD+
and 2 ethanol molecules.
ix. Homolactic fermentation. [DO NOT DISCUSS]
1. Produces lactic acid only.
x. Heterolactic fermentation. [DO NOT DISCUSS]
1. Produces lactic acid and other compounds.
xi. Table 5.4 lists some of the various microbial fermentations used in industry.
xii. Table 5.5 gives a summary comparison of aerobic respiration, anaerobic respiration,
and fermentation.
Lipid and Protein Catabolism.
a. Organisms also use lipids and proteins as sources of energy
b. Lipid catabolism. Fig. 20.
i. Microbes produce lipases (extracellular enzymes) that break down tri-, di-, and monoglycerides into glycerol and fatty acids.
1. Glycerol enters the glycolysis pathway.
2. Fatty acids undergo beta oxidation, in which 2-carbon fragments are cleaved
from the fatty acids and bond with CoA to form acetyl-CoA, which then enters
the Krebs cycle.
V.
VI.
ii. Many bacteria that hydrolyze fatty acids can use the same enzymes to degrade
petroleum products.
c. Protein catabolism. Fig. 21.
i. Microbes produce proteases and peptidases (extracellular enzymes) that break proteins
down into amino acids, which can then enter the cell.
1. Before the amino acids can be catabolized, they must be broken into molecules
than can enter the Krebs cycle.
a. Deamination is the process where the amino group is removed from the
carbon backbone of the amino acid and is converted to NH4+ (an
ammonium ion) which can then be excreted as a waste product by the
cell.
b. The remaining organic acid can enter the Krebs cycle.
c. Other conversions involve decarboxylations (removal of –COO) and
dehydrogenations.
Biochemical Tests and Bacterial Identification. [DO NOT COVER]
Photosynthesis.
a. Conversion of light energy from the sun into chemical energy. The chemical energy is then
used to convert CO2 from the atmosphere into more reduced carbon compounds, primarily
sugars. This is also known as carbon fixation.
b. Photosynthesis is performed by cyanobacteria, algae, and green plants.
c. Oxygenic photosynthesis: 6 CO2 + 12 H2O + Light  C6H12O6 + 6 O2 + 6 H2O
i. Water is the electron donor.
d. Light-dependent (light) reactions: Photophosphorylation. Fig. 25.
i. Cyclic photophosphorylation. (Relatively uncommon photosynthesis pathway that
does NOT generate oxygen gas).
1. Light excites a pair of electrons from chlorophyll.
a. Chlorophyll is found in the membranous thylakoids of chloroplasts in
algae, green plants, and the photosynthetic structures of cyanobacteria.
Other bacteria use bacteriochlorophylls.
2. The excited electrons (existing in a higher energy state) enter an electron
transport chain.
3. As the electrons move down the chain, protons are pumped across the
membrane. (Proton motive force).
4. ADP and Pi are converted to ATP by chemiosmosis.
5. The electrons return to the chlorophyll molecule.
ii. Non-cyclic photophosphorylation. (More common photosynthesis pathway).
1. Light excites a pair of electrons from chlorophyll.
2. The excited electrons (existing in a higher energy state) enter an electron
transport chain (discussed below).
a. The electrons will not return to chlorophyll but will become
incorporated into NADPH.
b. The electrons lost from chlorophyll will be replaced by electrons from
some reducing substance (H2O in oxygenic photosynthesis), (H2, or
H2S in anoxygenic photosynthesis).
3. As the electrons move down the chain, protons are pumped across the
membrane. (Proton motive force).
4. ADP and Pi are converted to ATP by chemiosmosis.
5. The electrons are transferred to the electron carrier NADP+ (along with H+)
which is reduced to NADPH + H+.
e. Light-independent (dark) reactions: Calvin-Benson cycle. Fig. 26.
VII.
VIII.
i. The electrons bound up in NADPH and ATP are used to reduce CO2 to form sugar
molecules.
ii. To form one molecule of glucose, the cycle must turn six times, requiring a total
investment of 6 CO2, 18 ATP, and 12 NADPH.
iii. [Fig. 26 shows 3 turns of the cycle; this produces a single glyceraldehyde 3-phosphate.
A pair of glyceraldehyde 3-phosphate molecules are required to form a single
molecule of glucose].
Metabolic Diversity Among Organisms. Fig. 28.
a. Phototrophs:
i. Derive energy from light.
b. Chemotrophs:
i. Derive energy from organic or inorganic chemicals.
c. Autotrophs:
i. Use CO2 as their principal carbon source.
d. Heterotrophs:
i. Require an organic carbon source.
e. Photoautotrophs.
i. Oxygenic photoautotrophs include cyanobacteria, algae, and green plants.
1. Energy is used in the Calvin-Benson cycle to fix CO2. H2O is the electron
donor used to reduce CO2.
ii. Anoxygenic photoautotrophs include the green and purple bacteria (sulfur bacteria).
1. Anoxygenic photosynthesis: CO2 + 2 H2S + Light energy  [CH2O] + 2 S +
H2O. (Sulfur containing compounds are used to reduce CO2).
2. These organisms cannot carry on photosynthesis when oxygen is present and
cannot use H2O to reduce CO2.
f. Photoheterotrophs.
i. Anoxygenic. Include the green nonsulfur bacteria and the purple nonsulfur bacteria.
ii. Use light as the energy source and organics such as alcohols, fatty acids, other organic
acids, and carbohydrates as the carbon source.
g. Chemoautotrophs.
i. Many bacterial species.
ii. Use electrons in reduced inorganic compounds (such as H2S, S, NH3 [ammonia], NO2[nitrite ion], H2, Fe2+ [ferrous iron], CO) as the energy source and CO2 as the principal
carbon source.
h. Chemoheterotrophs.
i. Energy source and carbon source are usually the same organic compound, like
glucose.
1. Electrons from the hydrogen atoms of the organic compound are the specific
energy source.
ii. Many bacteria and fungi that can use a wide variety of organics as the carbon and
energy source fall into this group.
Metabolic Pathways of Energy Use.
a. Complete oxidation of glucose in the aerobic pathway is considered very efficient, but about
45% of the energy stored in the covalent bonds of glucose winds up being lost as heat during
the oxidation process (55% efficient!). The remaining energy winds up being trapped in the
bonds of ATP.
i. Gas engines ~ 25-30 % efficient; turbo diesels up to 50% efficient.
b. The energy stored in ATP is used for active transport, movement, and production of new
molecules (anabolism).
c. Polysaccharide Biosynthesis. Fig. 29.
d. Lipid Biosynthesis. Fig. 30.
IX.
e. Amino Acid and Protein Biosynthesis. Fig. 31.
f. Purine and Pyrimidine Biosynthesis. Fig. 32.
Integration of Metabolism. Fig. 33.
a. Anabolic and catabolic pathways are joined through a group of common intermediates.
b. Amphibolic pathways are metabolic pathways that function in both catabolic and anabolic
reactions; they bridge the pathways involved in carbohydrate, lipid, protein, and nucleic acid
metabolism.