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Chapter 8 – Microbial Metabolism
Catabolic and Anabolic Reactions – Fig 8.1
1. Metabolism – sum of all chemical reactions within a living organism
2. Catabolism
a. Breaks down large molecules
b. Breaks chemical bonds
c. Releases stored energy which is then used to make ATP
d. Examples: cell respiration -- sugars get broken down into CO2 + water, digestion,
hydrolysis reactions ( break polymers back down into monomers)
3. Anabolism
a. Builds large organic molecules
b. Polymers are built from monomers by condensation or dehydration synthesis
reactions
c. Biosynthesis
d. Requires energy ( use ATP)
e. Examples; amino acids linked together to build proteins; simple sugars are combined to
build carbohydrates
4. ATP couples anabolic and catabolic reactions
ATP  ADP + Pi + energy ( used to run anabolic reactions)
ADP + P + energy ( from catabolic reactions)  ATP
5. metabolic pathways
a. sequence of events
b. each step controlled by a specific enzyme
Enzymes
1.
2.
3.
4.
Activation energy – the amount of energy required to trigger a reaction
Enzymes are Biological catalysts – speed up chemical reactions without raising temperatures
Lower the activation energy needed for the reaction to proceed
Most are proteins ( exception: ribozymes are enzymes composed of RNA)
5. Enzyme Components
a. Simple enzymes – consist of proteins alone
b. Some enzymes consist of a protein component and a non-protein cofactor Fig 8.2
 Coenzymes – organic helper molecules
1. Accept or donate atoms or electrons
2. Act as energy carriers
3. Many are derived from vitamins
4. NAD, NADP – from Vit B – niacin
5. flavins - FMN, FAD – riboflavin
6. coenzyme A - CoA
 Cofactors – inorganic helper molecules
1. Minerals – Fe, Cu, Mg, Zn, Ca, Co
6. Mechanism of Enzyme Action – Fig 8.4
a. Enzyme surface has an active site – specific shape binds to only one substrate
b. Substrate – specifically fits into the active site of the enzyme
c. Enzyme-substrate complex forms
d. Reaction occurs; the substrate transforms and is released from the active site
e. Enzyme is released unchanged – free to react with other molecules of the same
substrate
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7. Naming enzymes- Insight 8.3
a. Most are named with “ASE” suffix – e.g., maltase is the enzyme that breaks down
maltose –
b. Classified according to function
8. Classified by location of Action
a. Exoenzymes-function when released outside of the cell – Fig 8.5
b. Endoenzymes – remain in the cell and function there – Fig 8.5
9. Types of Reactions
a. Dehydration (Synthesis) Reactions – Fig 8.7
b. Hydrolysis Reactions – Fig 8.7
c. Transfer Reactions
 Oxidation/reduction reactions
 Transfer of functional groups
10. Role of Microbial Enzymes in Disease
a. Virulence factors, toxins, etc.; clot serum, break down connective tissue, break down
blood clots, digest cell membranes, etc.
11. Factors that Influence Enzyme Activity
a. Temperature – each enzyme has its own optimal temperature
 Generally – increased temperature = increased reaction rate
 High temperatures – denature proteins
 Acids, bases, alcohol, heavy metals, UV light can also denature proteins
b. PH – different enzymes have different optimal pH ranges
c.
Substrate concentration
 High concentrations of substrate can result in a condition where all the available
enzyme is filled ( saturated ) with substrate; reaction reaches a maximum rate
d. Inhibitors – control enzyme action – Fig 8-9
 Competitive Inhibitors – compete with the normal substrate to occupy the
active site of the enzyme
e.g., PABA is converted to folic acid by a specific enzyme
sulfa drugs will also bind to the active site of the enzyme, but can’t be
converted to folic acid; folic acid synthesis is inhibited; organism may die
 Non-competitive inhibitors – bind to the allosteric site – a site on the enzyme
that is remote from the active site.
This binding alters the active site so that it will no longer accept the
normal substrate
12. Feedback Inhibition
a. Method to control metabolic pathways
b. Usually non-competitive inhibition
c. When the end product of the pathway builds up, it acts as a non-competitive inhibitor of
one of the early enzymes of the pathway; by inactivating the enzyme, it temporarily
shuts down the pathway and allows the end product to be used up.
d. When end product is all used up, the inhibitor falls off the enzyme and the pathway
starts back up again.
13. Ribozymes
a. RNA enzymes that catalyze reactions involving other RNA molecules
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Energy Production
ATP – the “energy storage” molecule – Fig 8.13
1. nucleotide
2. contains 2 high energy, unstable bonds
ATP  ADP + Pi + energy ( used to run anabolic reactions)
ADP + P i + energy ( from catabolic reactions)  ATP
Oxidation – Reduction Reactions ( REDOX reactions) – Fig 8.12
1. Oxidation – removes electrons; produces energy
2. Reduction – the gain of electrons
3. Dehydrogenation – removes H+ (proton) and an electron
4. Biological Oxidations –
a. The organic molecule ( e.g. glucose) is oxidized
b. 2 electrons and 2 H+ protons are transferred to a coenzyme, NAD+
c. The NAD accepts the one H atom ( electron and H+) and one electron
d. The NAD+ is reduced to NADH
e. The other H+ proton is released to the surrounding medium
5. The Generation of ATP
a. Energy release by redox reactions is used to generate ATP
b. Phosphorylation -- adds a phophate to a compound
ADP + P + energy ( from catabolic reactions)  ATP
Substrate level phosphorylation – the energy from a catabolic reaction is directly used to
add phosphate to an ADP molecule  ATP
d. Oxidative phosphorylation – NADH transfers electrons to a chain of proteins that act as
energy carriers , and eventually to oxygen. This releases energy to add phophate to an
ADP  ATP
e. Chemiosmosis – the method of using a proton gradient across a cytoplasmic membrane
to generate ATP ( the method used to make ATP on the electron transport chain)
f. Photophosphorylation – occurs in photosynthetic cells – Light energy is used to generate
ATP
c.
Carbohydrate Catabolism
1. Carbohydrates are the main source of cellular energy for most organisms. ( Glucose is the most
common)
2. There are 3 main pathways that produce energy from glucose: aerobic respiration, anaerobic
respiration and fermentation. Fig 8-15
3. Overall, there is a flow of electrons from glucose to produce CO 2 , H2O, and ATP
Cell Respiration
1. organic molecules ( usu. glucose) are oxidized
2. electrons are passed to electron carrier molecules
3. electrons pass down an electron transport chain
4. final electron acceptor is an inorganic ion
 aerobic respiration – final electron acceptor is oxygen
 anaerobic respiration – final electron acceptor is an inorganic ion other than oxygen
5. Occurs in Three Stages
 Glycolysis
 The Krebs Cycle ( also called the Citric Acid Cycle, or TCA cycle)
 Chemiosmosis
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Aerobic Respiration
Glycolysis – ( Embden-Meyerhof Pathway) – Fig 8.16
1. The first stage in both cell respiration and fermentation.
2. Anaerobic process – Can occur in the presence of oxygen, but No Oxygen is Used
3. Glucose ( C6H12O6) is oxidized into 2 molecules of pyruvic acid ( each with 3 carbons)
4. All 6 of the original Carbons are still present at the end of glycolysis.
5. 2 NAD+ are reduced to NADH
6. 4 ATP are produced ; 2 ATP are used : Net GAIN is 2 ATP
7. End product of glycolysis is 2 molecules of pyruvic acid
Pyruvic Acid – A central Metabolite – Fig 8.17 – pyruvic acid can be reduced into various products
by the process of fermentation, or it can be converted to acetyl-CoA to enter the Krebs (TCA) cycle
The Transition or Conversion of Pyruvic Acid to Acetyl Co-A – Fig 8.17
1. Pyruvic Acid ( 3 carbons) is split to yield acetyl ( 2 carbons) and CO2
2. This step also reduces 1 NAD+ to NADH
3. The acetyl group joins with coenzyme-A to produce acetyl Co-A
4. This 2 carbon compound ( acetyl-CoA) enters the Kreb cycle
5. Each glucose molecule produces 2 molecules of pyruvic acid and therefore 2 molecule sof
acetyl-CoA to enter the Kreb Cycle
The Tricarboxylic Acid (TCA) Cycle; also called the Krebs Cycle Fig 8.18
1. The 2 carbon Acetyl-CoA joins to a 4 carbon molecule ( oxaloacetic acid) that is already in the
cycle. This produces a 6 carbon compund ( citric acid)
2. A series of reactions occurs, each step controlled by its own enzyme.
3. For each acetyl CoA that enters the cycle and joins with oxaloacetic acid:
o The 6 carbon compound is oxidized ( electrons and H+ are removed)
o 3 NAD+ are reduced to NADH
o 1 FAD+ is reduced to FADH
o 1 ATP is produced by substrate level phosphorylation
o 2 Carbons are removed and are lost as CO2
4. the 4 carbon oxaloacetic acid is regenerated to accept another acetyl Co-A
5. Each glucose molecule produces 2 acetyl-CoA, enough to run the Kreb Cycle twice.
6. At the end of the Kreb cycle, most of the energy has been transferred to the reduced energy
carriers, NADH and FADH. These must transfer the electrons to the electron transport chain in
order to generate more ATP.
The Electron transport Chain Fig 8.19
1. A series of carrier proteins located on the plasma membrane ( in prokaryotes) and on the inner
mitochondrial membrane ( in eukaryotes)
2. As electrons move down the chain, each transfer of electrons releases energy.
3. Carriers on the electron transport chain
o Flavoproteins - contain flavins derived from riboflavin (Vit B2)
o Cytochromes - have in iron-containing heme group
o Coenzyme Q – small, nonprotein cofactor
4. The proteins on the chain vary greatly among different bacteria
Electron Flow down the Chain Fig 8.19, 8.20
1. The reduced energy carriers, NADH and FADH2 carry the electrons and H+ to the electron
transport chain.
2. NADH donates electrons to the flavoproteins at the top of the chain
3. FADH2 donates at a lower level ( less energy is produced)
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4. The electrons are passed down the chain from protein to protein ( a series of oxidation-reduction
reactions). Each electron transfer releases energy
5. In aerobic respiration the final electron acceptor is oxygen, which then combines with 2 H+
to produce water.
Chemiosmosis – Fig 8.19, 8.20
1. The energy carriers ( which donated electrons to the chain) also release H+
2. The energy released by electron transfer is used to pump H+ across the membrane
3. This results in a concentration gradient ( a buildup of H+ on one side of the membrane)
Remember – a concentration gradient represents a source of potential energy.
4. The excess hydrogen will diffuse back across the membrane to reach equilibrium, but the H +
ions can only cross the membrane through certain channels.
5. The ATP-synthase is a large protein complex. It allows the H+ to cross back through the
membrane. This proton flow releases energy which is used to make ATP from ADP and Pi. ( The
ATP synthase complex also contains enzymes for this reaction).
6. In eukaryotes this process occurs on the inner mitochondrial membrane or in chloroplasts. In
prokaryotes this occurs on the plasma membrane.
7. Each NADH produces enough energy to make 3 ATP
8. Each FADH produces enough energy to make 2 ATP
9. Chemiosmosis produces 34 molecules of ATP ( on average)
Summary of ATP produced – see fig 8.21
Glycolysis
4 ATP produced ( substrate level ) – 2 ATP used = Net Yield
2 NAD+  2 NADH -- go to the electron transport chain
2 ATP
6 ATP from chemiosmosis
Conversion of pyruvic acid to acetyl CoA
2 NAD+  2 NADH -- go to the electron transport chain
6 ATP from chemiosmosis
Krebs Cycle
6 NAD+  6 NADH - go to the electron transport chain
2 FAD+  2 FADH - go to the electron transport chain
2 ATP ( substrate level)
18 ATP from chemiosmosis
4 ATP from chemiosmosis
2 ATP
Total Net Yield
prokaryotes – 38 ATP
Eukaryotes -- 36 ATP ( 2 ATP are “spent” to take the reactions from the
cytoplasm into the mitochondria)
Anaerobic Respiration - The final electron acceptor is an inorganic ion other than oxygen
1. Nitrate: NO3-  NO2-, N2O, or N2 gas
2. Sulfate : SO42-  H2S ( hydrogen sulfide gas)
3. Carbonate: CO32-  CH4 ( methane gas)
Although the Krebs cycle and the electron transport chain function in anaerobic respiration, they don’t
produce as much energy as aerobic respiration. Anaerobes grow more slowly than aerobes.
Fermentation – Fig 8.22 ; Insight 8.4
1. Breaks down sugars, amino acids, organic acids, purines and pyrimidines.
2. Does not require oxygen, but can occur in its presence.
3. Does not use the Krebs Cycle or the electron transport chain.
4. Uses an organic molecule as the final electron acceptor.
5. only produces 1- 2 molecules of ATP / glucose
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6. Begins with glycolysis
 Glucose  2 pyruvic acid
 2 NAD+  2 NADH
 2 ADP + Pi  2 ATP
7. NAD+ must be regenerated; no electron transport chain functions to accept the electrons and H + from
NADH.
8. Instead, NADH donates electrons to pyruvic acid to form “fermentation end products”. NAD + is
regenerated ; glycolysis can continue.
Lactic Acid Fermentation
1. Substrate: glucose
2. End product: lactic acid
3. Organisms: Lactobacillus, Streptococcus
4. Food spoilage, dental caries, yogurt, sauerkraut, pickles, cheeses, etc.
Alcohol fermentation
1. Substrate: glucose
2. End product: ethanol and carbon dioxide
3. Organisms: Saccharomyces cerevesiae ( Baker’s yeast; Brewer’s yeast); some bacteria
4. Baking bread, wine, beer, liquors
Industrial Uses for Fermentation
1. Acetone
2. Acetic acid ( vinegar)
3. Organic acids
4. Alcohols – isopropyl ( rubbing); butanol; propanol
Biochemical Testing ( for identifying bacteria)
1. Test medium – contains protein and a single source carbohydrate for energy
2. PH indicator – changes color if acid is produced
3. Durham tubes – small glass tube will trap gas to detect gas production.
Lipid Catabolism fig 8-24
1. Lipids  glycerol and fatty acids
2. Glycerol is funneled into the Krebs cycle
3. Fatty acids are broken down by the Beta-oxidation cycle into acetyl CoA which can feed into the
Krebs cycle
4. Some bacteria actually degrade lipids like petroleum ( used for bioremediation)
Protein Catabolism Fig 8.23
1. proteins  amino acids ; There are 20 common amino acids
2. The amino acids are transported into the cell
3. Deamination : removes an amino group from an amino acid ; converts it to ammonia ; the rest of
the amino acid goes into the Krebs cycle.
4. Decarboxylation and dehydrogenation : removes a carboxyl group from an amino acid ;rest of the
amino acid feeds into the Krebs Cycle
Biosynthesis
Metabolic Pathways are Integrated – Fig 8.24
Catabolic Pathways release energy and produce intermediates and end products that can be used for
anabolic pathways. Anabolic Pathways synthesize the building blocks that can be used for other anabolic
pathways which synthesize macromolecules ( proteins, carbohydrates, lipids, nucleic acids)