Microbial Metabolism- the

Chemical Crossroads of Life

Figure 8.1
 Enzymes
 Catalyze the chemical reactions of life
• Enzymes: an example of catalysts, chemicals
that increase the rate of a chemical reaction
without becoming part of the products or being
consumed in the reaction
Activation energy is the energy required to bring all
molecules in a chemical reaction into the reactive state
Enzymes overcome activation energy
 How Enzymes Lower Ea
 By increasing concentrations of substrates at active site
of enzyme
 By orienting substrates properly with respect to each
other in order to form the transition-state complex
 Increasing thermal energy to increase molecular
velocity
 Induced fit model for enzyme-substrate interaction

6
 Enzyme Structure
 Most- protein
 Can be classified as simple or conjugated
– Simple enzymes- consist of protein alone
– Conjugated enzymes- contain protein and non-
protein molecules
 Conjugated enzyme/Holoenzyme
 Apoenzyme
– protein component of an enzyme
 Cofactor
– nonprotein component of an
enzyme
 prosthetic group – firmly attached
 coenzyme – loosely attached, can

act as carriers/shuttles
 Holoenzyme = apoenzyme +
cofactor
8
 Cofactors: Supporting the Work of
Enzymes
 Metallic cofactors
– Include Fe, Cu, Mg, Mn, Zn, Co, Se
– Metals activate enzymes, help bring the active site and
substrate close together, and participate directly in
chemical reactions with the enzyme-substrate complex
 Coenzymes
– Organic compounds that work in conjunction with an
apoenzyme to perform a necessary alteration of a
substrate
– Removes a chemical group from one substrate
molecule and adds it to another substrate
– Vitamins: one of the most important components of
coenzymes
conjugated enzyme (holoenzyme)
 Location and Regularity of Enzyme
Action
 Either inside or outside of the cell
 Exoenzymes break down molecules outside
of the cell
 Endoenzymes break down molecules inside
of the cell
Figure 8.5
 Rate of Enzyme Production
 Enzymes are not all produced in the cell in
equal amounts or at equal rates
– Constitutive enzymes: always present and in
relatively constant amounts
– Regulated enzymes: production is either
induced or repressed in response to a change in
concentration of the substrate
Figure 8.6
15
Synthesis and Hydrolysis Reactions
 Transfer Reactions by
Enzymes
 Oxidation-reduction reactions
– A compound loses electrons (oxidized)
– A compound receives electrons (reduced)
– Common in the cell
– Important components- oxidoreductases
 Other enzymes that play a role in necessary
molecular conversions by directing the transfer of
functional groups:
– Aminotransferases
– Phosphotransferases
– Methyltranferases
– Decarboxylases
 The Sensitivity of Enzymes to Their
Environment
 Enzyme activity is highly influenced by the
cell’s environment
 Enzymes generally operate only under the
natural temperature, pH, and osmotic pressure
of an organism’s habitat
 When enzymes subjected to changes in normal
conditions, they become chemically unstable
(labile)
 Denaturation: the weak bonds that maintain
the native shape of the apoenzyme are broken
 Energy in Cells
– Exergonic reaction: a reaction that releases
energy as it goes forward
– Endergonic reaction: a reaction that is driven
forward with the addition of energy
20
Figure 8.13
How does a cell produce
ATP?
 3 types of Phosphorylation
 Substratelevel phosphorylation
 Oxidative phosphorylation
– Series of redox reactions occurring during the
final phase of the respiratory pathway
 Photophosphorylation
– ATP is formed through a series of sunlight-
driven reactions in phototrophic organisms
Oxidative phosphorylation and
Photophosphorylation use the
Electron Tranport Chain via proton
motive force to produce ATP
 Electron Carriers
 located in plasma membranes of
chemoorganotrophs in bacteria and archaeal
cells
 located in internal mitochondrial
membranes in eukaryotic cells
 examples of electron carriers include NAD,
NADP, and others

25
 Electron Transport Chain
 Electron carriers
(ETC)
organized into ETC
– first electron carrier
having the most negative
E’o
– the potential energy
stored in first redox
couple is released and
used to form ATP
– first carrier is reduced
and electrons moved to
the next carrier and so on
26
Electron Carriers
 NAD
– nicotinamide
adenine
dinucleotide
 NADP
– nicotinamide
adenine
dinucleotide
phosphate

27
Electron Carriers
 FAD
– flavin adenine
dinucleotide
 FMN
– flavin
mononucleotide
– riboflavin phosphate
 coenzyme Q (CoQ)
– a quinone
riboflavin
– also called
28 ubiquinone
Electron Carriers
 Cytochromes
– use iron to transfer
electrons
 iron is part of a heme
group
 Nonheme iron-sulfur
proteins
– e.g., ferrodoxin
– use iron to transport
electrons
 iron is not part of a
29 heme group
Figure 8.15
 The Embden-Meyerhof
Pathway
 Occurs in cytoplasmic matrix of most
microorganisms, plants, and animals
 The most common pathway for glucose
degradation to pyruvate in stage two of
aerobic respiration
 Function in presence or absence of O 2
 Two phases
– Six carbon phase
– Three carbon phase

31
32
 Summary of Glycolysis
glucose + 2ADP + 2Pi + 2NAD+

2 pyruvate + 2ATP + 2NADH + 2H+

33
Figure 8.17
 The Tricarboxylic Acid Cycle
 Also called citric acid cycle and Kreb’s
cycle
 Common in aerobic bacteria, free-living
protozoa, most algae, and fungi
 Major role is as a source of carbon
skeletons for use in biosynthesis

35
36
 The Respiratory Chain: Electron
Transport and Oxidative
Phosphorylation
 The final “processing mill” for electrons and
hydrogen ions
 The major generator of ATP
 A chain of special redox carriers that receives
electrons from reduced carriers (NADH and
FADH2) and passes them in a sequential and
orderly fashion from one redox molecule to the
next
Figure 8.18
Glycolysis
2 ATPs
2 NADH Total net ATPs
Bacteria = 32
Kreb‘s Cycle
2 ATPs
Eukaryotes = 30
8 NADH
2 FADH2

ETC
10 NADH X 2.5 = 25 ATPs
2 FADH2 X 1.5 = 3 ATPs
ATP Yield During Aerobic Respiration

 Maximum ATP yield can be

calculated
– includes P/O ratios of
NADH and FADH2
– ATP produced by substrate
level phosphorylation
 The theoretical maximum total
yield of ATP during aerobic
respiration is 38
– the actual number closer to
30 than 38

40
 Factors Affecting ATP Yield
 Bacterial ETCs are shorter and have lower
P/O ratios
 ATP production may vary with
environmental conditions
 PMF in bacteria and archaea is used for
other purposes than ATP production
(flagella rotation)
 Precursor metabolite may be used for
biosynthesis

41
42
 5.14 Catabolic Diversity

 Microorganisms demonstrate a wide range of

mechanisms for generating energy
– Fermentation

– Aerobic respiration

– Anaerobic respiration

– Chemolithotrophy

– Phototrophy
Catabolic Diversity

Figure 5.23
Catabolic Diversity

Figure 5.23
Catabolic Diversity

Figure 5.23
 5.14 Catabolic Diversity

 Anaerobic Respiration
– The use of electron acceptors other than oxygen

– Examples include nitrate (NO 3-), ferric iron (Fe3+), sulfate

(SO42-), carbonate (CO32-), certain organic compounds

– Less energy released compared to aerobic respiration

– Dependent on electron transport, generation of a proton

motive force, and ATPase activity

 5.14 Catabolic Diversity
 Chemolithotrophy

– Use of inorganic chemicals as electron donors

– Examples include hydrogen sulfide (H 2S), hydrogen gas

(H2), ferrous iron (Fe2+), ammonia (NH3)

– Typically aerobic

– Begins with oxidation of inorganic electron donor

– Uses electron transport chain and proton motive force

– Autotrophic; uses CO2 as carbon source

 5.14 Catabolic Diversity

 Phototrophy: metabolism that uses light as energy

source
– Photophosphorylation: light-mediated ATP synthesis

– Photoautotrophs: use ATP for assimilation of CO 2 for

biosynthesis
– Photoheterotrophs: use ATP for assimilation of organic carbon

for biosynthesis
 Summary of Aerobic
Respiration
 The total possible yield of ATP is 40
– 4 from glycolysis
– 2 from the Krebs cycle
– 34 from electron transport
 But 2 ATPs are expended in early glycolysis, so a
maximum yield of 38 ATPs
 6 CO2 molecules are generated during the Krebs cycle
 6 O2 molecules are consumed during electron transport
 6 H2O molecules are produced in electron transport and
2 in glycolysis; but 2 are used in Krebs cycle for a net
number of 6
 The Terminal Step
 Oxygen accepts the electrons
 Catalyzed by cytochrome aa3 (cytochrome
oxidase)
 2 H+ + 2 e- + 1/2O2  H2O
 Most eukaryotic aerobes have a fully
functioning cytochrome system
 Bacteria exhibit wide-ranging variations
which can be used to differentiate among
certain genera of bacteria
 Anaerobic Respiration
 Functions like the aerobic cytochrome system
except it utilizes oxygen-containing ions rather
than free oxygen as the final electron acceptor
 The nitrate and nitrite reduction systems are
best known, using the enzyme nitrate reductase
 Denitrification: when enzymes can further
reduce nitrite to nitric oxide, nitrous oxide, and
nitrogen gas- important in recycling nitrogen in
the biosphere
 Fermentation
 The incomplete oxidation of glucose or other
carbohydrates in the absence of oxygen
 Uses organic compounds as the terminal electron
acceptors and yields a small amount of ATP
 Many bacteria can grow as fast using fermentation
as they would in the presence of oxygen
– This is made possible by an increase in the rate of
glycolysis
– Permits independence from molecular oxygen
 Products of Fermentation in
Microorganisms
 Products of Fermentation in Microorganisms
– Alcoholic beverages
– Organic acids
– Dairy products
– Vitamins, antibiotics, and even hormones
– Two general categories
 Alcoholic fermentation

 Acidic fermentation
 Alcoholic Fermentation
Products
 Occurs in yeast or bacterial species that
have metabolic pathways for converting
pyruvic acid to ethanol
 Products: ethanol and CO2
Figure 8.20
 Acidic Fermentation Products
 Extremely varied pathways
 Lactic acid bacteria ferment pyruvate and reduce it
to lactic acid
 Heterolactic fermentation- when glucose is
fermented to a mixture of lactic acid, acetic acid,
and carbon dioxide
 Mixed acid fermentation- produces a combination
of acetic, lactic, succinic, and formic acids and
lowers the pH of a medium to about 4.0
 Catabolism of Noncarboyhdrate
Compounds
 Polysaccharides can easily be broken down into their
component sugars which can enter glycolysis
 Microbes can break down lipids and proteins to produce
precursor metabolites and energy
– Lipases break apart fats in to fatty acids and glycerol
 The glycerol is then converted to DHAP

 DHAP can enter step 4 of glycolysis

 The fatty acid component goes through beta oxidation

 Can yield a large amount of energy (oxidation of a 6-carbon fatty acid

yields 50 ATPs)
– Proteases break proteins down to their amino acid components
 Amino groups are then removed by deamination

 Results in a carbon compound which can be converted to one of

several Krebs cycle intermediates
Figure 8.21
 8.4 Biosynthesis and the Crossing
Pathways of Metabolism
 The Frugality of the Cell- Waste Not, Want Not
– Most catabolic pathways contain strategic
molecular intermediates (metabolites) that can be
diverted into anabolic pathways
– Amphibolism: the property of a system to
integrate catabolic and anabolic pathways to
improve cell efficiency
– Principal sites of amphibolic interaction occur
during glycolysis and the Krebs cycle
Figure 8.22
 Amphibolic Sources of Cellular
Building Blocks
 Glyceraldehyde-3-phosphate can be diverted away from glycolysis and
converted into precursors for amino acid, carbohydrate, and triglyceride
synthesis
 Pyruvate also provides intermediates for amino acids and can serve as the
starting point in glucose synthesis from metabolic intermediates
(gluconeogenesis)
 The acetyl group that starts the Krebs cycle can be fed into a number of
synthetic pathways
 Fats can be degraded to acetyl through beta oxidation
 Two metabolites of carbohydrate catabolism that the Krebs cycle produces
are essential intermediates in the synthesis of amino acids
– Oxaloacetic acid
– Α-ketoglutaric acid
– Occurs through amination
 Amino acids and carbohydrates can be interchanged through
transanimation
Figure 8.23
 Anabolism: Formation of
Macromolecules
 Monosaccharides, amino acids, fatty acids, nitrogen
bases, and vitamins come from two possible sources
– Enter the cell from outside as nutrients
– Can be synthesized through various cellular pathways
 Carbohydrate Biosynthesis
– Several alternative pathways
 Amino Acids, Protein Synthesis, and Nucleic Acid
Synthesis
– Some organisms can synthesize all 20 amino acids
– Other organisms (especially animals) must acquire the
essential ones from their diets
 Assembly of the Cell
 When anabolism produces enough
macromolecules to serve two cells
 When DNA replication produces duplicate
copies of the cell’s genetic material
 Then the cell undergoes binary fission
 8.5 It All Starts with the Sun
 Photosynthesis
– Proceeds in two phases
 Light-dependent reactions

 Light-independent reactions
 Light-Dependent Reactions
 Solar energy delivered in discrete energy packets called photons
 Light strikes photosynthetic pigments
– Some wavelengths are absorbed
– Some pass through
– Some are reflected
 Light is absorbed through photosynthetic pigments
– Chlorophylls (green)
– Carotenoids (yellow, orange, or red)
– Phycobilinss (red or blue-green)
 Bacterial chlorophylls
– Contain a photocenter- a magnesium atom held in the center of a complex
ringed molecule called a porphyrin
– Harvest the energy of photons and converts it to electron energy
 Accessory photosynthetic pigments trap light energy and shuttle it to
chlorophyll
Figure 8.24
Figure 8.25
 Light-Independent Reactions
 Occur in the chloroplast stroma or the
cytoplasm of cyanobacteria
 Use energy produced by the light phase to
synthesize glucose by means of the Calvin
cycle
Figure 8.26
Other Mechanisms of Photosynthesis
 Oxygenic (oxygen-releasing) photosynthesis that
occurs in plants, algae, and cyanobacteria- dominant
type on earth
 Other photosynthesizers such as green and purple
bacteria
– Possess bacteriochlorophyll
– More versatile in capturing light
– Only have a cyclic photosystem I
– These bacteria use H2, H2S, or elemental sulfur rather than
H2O as a source of electrons and reducing power
– They are anoxygenic (non-oxygen-producing); many are
strict anaerobes