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Microbial Metabolism-The Chemical Crossroads of Life
Microbial Metabolism-The Chemical Crossroads of Life
Microbial Metabolism-The Chemical Crossroads of Life
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+
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
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
– 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
– Typically aerobic
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
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