Microbiology: A Systems Approach, 2nd ed.

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Transcript Microbiology: A Systems Approach, 2nd ed.

Microbiology: A Systems
Approach, 2nd ed.
Chapter 8: Microbial Metabolismthe Chemical Crossroads of Life
8.1 The Metabolism of Microbes
• Metabolism: All chemical reactions and physical workings
of the cell
• Anabolism: also called biosynthesis- any process that
results in synthesis of cell molecules and structures (usually
requires energy input)
• Catabolism: the breakdown of bonds of larger molecules
into smaller molecules (often release energy)
• Functions of metabolism
– Assembles smaller molecules into larger macromolecules
needed for the cell
– Degrades macromolecules into smaller molecules and yields
energy
– Energy is conserved in the form of ATP or heat
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
How do Enzymes Work?
• Energy of activation: the amount of energy which
must be overcome for a reaction to proceed. Can be
achieved by:
– Increasing thermal energy to increase molecular velocity
– Increasing the concentration of reactants to increase the
rate of molecular collisions
– Adding a catalyst
• An enzyme promotes a reaction by serving as a
physical site upon which the reactant molecules
(substrates) can be positioned for various interactions
Enzyme Structure
• Most- protein
• Can be classified as simple or conjugated
– Simple enzymes consist of protein alone
– Conjugated enzymes contain protein and nonprotein molecules
• A conjugated enzyme (haloenzyme) is a combination of
a protein (now called the apoenzyme) and one or more
cofactors
• Cofactors are either organic molecules (coenzymes) or
inorganic elements (metal ions)
Figure 8.3
Figure 8.2
Apoenzymes: Specificity and the
Active Site
• Exhibits levels of molecular complexity called
the primary, secondary, tertiary, and
quaternary organization
• The actual site where the substrate binds is a
crevice or groove called the active site or
catalytic site
Enzyme-Substrate Interactions
• For a reaction to take place, a temporary
enzyme-substrate union must occur at the
active site. (Called an enzyme-substrate
complex.)
• “Lock-and-key” fit
• The bonds are weak and easily reversible
Figure 8.4
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
Classification of Enzyme Functions
• Site of action
• Type of action
• Substrate
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
Synthesis and Hydrolysis Reactions
Figure 8.7
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 Role of Microbial Enzymes in
Disease
• Many pathogens secrete unique exoenzymes
• Help them avoid host defenses or promote
multiplication in tissues
• These exoenzymes are called virulence factors
or toxins
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 are 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
Regulation of Enzymatic Activity and
Metabolic Pathways
• Metabolic Pathways
– Metabolic reactions usually occur in a multiseries
step or pathway
– Each step is catalyzed by an enzyme
– Every pathway has one or more enzyme
pacemakers that set the rate of a pathway’s
progression
Figure 8.8
Rate of Enzyme Production
• Enzymes are not all produced in the cell in
equal amounts or at equal rates
– Constitutive enzymes: production is continuous
and in relatively constant amounts
– Regulated enzymes: production is either induced
or repressed in response to a change in
concentration of the substrate
Control of Enzyme Activity
• Direct control of enzyme activity (constitutive
enzymes)
• Regulation of enzyme synthesis (regulated
enzymes)
Direct Controls on the Action of
Enzymes
• Competitive inhibition: The cell supplies a
molecule that resembles the enzyme’s normal
substrate, which then occupies and blocks the
enzyme’s active site
• Noncompetitive inhibition: The enzyme has
two binding sites- the active site and the
regulatory site; a regulator molecule binds to
the regulatory site providing a negative
feedback mechanism
Figure 8.9
Controls on Enzyme Synthesis
• Enzymes eventually must be replaced
• Enzyme repression: stops further synthesis of
an enzyme somewhere along its pathway
• Enzyme induction: The inverse of enzyme
repression
Regulated Enzymes
• Inducible enzymes- break down complex
substrates into simpler products; eg. lactose
to glucose; enzymes are only synthesized
(induced) when excess substrate is present.
Otherwise the enzymes are not synthesized.
• Repressible enzymes- synthesize products
such as tryptophan when the product is not
available in nutrient sources. Presence of
excess product represses enzyme production.
Figure 8.6
Figure 8.10
8.2 The Pursuit and Utilization of
Energy
• 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
Figure 8.11
A Closer Look at Biological Oxidation
and Reduction
• Biological systems often extract energy through redox
reactions
• Redox reactions always occur in pairs
– An electron donor and electron acceptor
– Redox pair
• Electron donor (reduced) + electron acceptor (oxidized) 
Electron donor (oxidized) + electron acceptor (reduced)
• This process leaves the previously reduced compound with
less energy than the now oxidized one
• The energy in the electron acceptor can be captured to
phosphorylate to ADP or some other compound, storing
the energy in a high-energy molecule like ATP
Electron Carriers: Molecular Shuttles
• Electron carriers repeatedly accept and
release electrons and hydrogens
• Facilitate the transfer of redox energy
• Most carriers are coenzymes that transfer
both electrons and hydrogens
• Some transfer electrns only
• Most common carrier- NAD
Figure 8.12
Adenosine Triphosphate: Metabolic
Money
•
•
•
•
ATP
Can be earned, banked, saved, spent, and exchanged
A temporary energy repository
The Molecular Structure of ATP
– Three-part molecule
• Nitrogen base (adenine)
• 5-carbon sugar (ribose)
• Chain of three phosphate groups
– The high energy originates in the orientation of the phosphate
groups
– Breaking the bonds between two successive phosphates of ATP
yields ADP
– ADP can then be converted to AMP
Figure 8.13
The Metabolic Role of ATP
•
•
•
•
Primary energy currency of the cell
When used in a chemical reaction, must be replaced
Ongoing cycle
Adding a phosphate to ADP replenishes ATP but it
requires an input of energy
• In heterotrophs, this energy comes from certain steps
of catabolic pathways
• Some ATP molecules are formed through substratelevel phosphorylation
– ATP is formed by a transfer of a phosphate group from a
phosphorylated compound (substrate) directly to ADP
Figure 8.14
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
8.3 The Pathways
• Pathway- a series of biochemical reactions
• Metabolism uses enzymes to catalyze reactions
that break down (catabolize) organic molecules to
materials (precursor molecules) that cells can
then use to build (anabolize) larger, more
complex molecules that are particularly suited to
them.
• Reducing power and energy are needed in large
quantities for the anabolic parts of metabolism;
they are produced during the catabolic part of
metabolism.
Catabolism: Getting Materials and
Energy
• Frequently the nutrient needed is glucose
• Most common pathway to break down glucose is glycolysis
• Three major pathways
– Respiration: series of reactions that convert glucose to CO2 and
allows the cell to recover significant amounts of energy
– Fermentation: when facultative and aerotolerant anaerobes
use only the glycolysis scheme to incompletely oxidize glucose
– Aerobic respiration: When oxygen is used as the final electron
acceptor at the end of the respiration scheme to produce H2O.
– Anaerobic respiration: Does not use molecular oxygen as the
final electron acceptor, but uses nitrogen or compounds of
nitrogen or sulfur or compounds of sulfur, or other inorganic
substances and the final electron acceptor.
Figure 8.15
Aerobic Respiration
• Series of enzyme-catalyzed reactions
• Electrons are transferred from fuel molecules to
oxygen as a final electron acceptor
• Principal energy-yielding scheme for aerobic
heterotrophs
• Provides both ATP and metabolic intermediates
for many other pathways in the cell
• Glucose is the starting compound
• Glycolysis enzymatically converts glucose through
several steps into pyruvic acid
Figure 8.16
Pyruvic Acid- A Central Metabolite
• Pyruvic acid from glycolysis serves an
important position in several pathways
• Different organisms handle it in different ways
• In strictly aerobic organisms and some
anaerobes, pyruvic acid enters the Krebs cycle
Figure 8.17
The Krebs Cycle: A Carbon and Energy
Wheel
• Pyruvic acid is energy-rich, but its hydrogens
need to be transferred to oxygen
• Takes place in the cytoplasm of bacteria and in
the mitochondrial matrix in eukaryotes
• Produces reduced coenzymes NADH and
FADH2, 2 ATPs for each glucose molecule
Insight 8.3
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
Figure 8.19
Potential Yield of ATPs from Oxidative
Phosphorylation
• Five NADHs (four from Krebs cycle and one
from glycolysis) can be used to synthesize:
– 3 ATP’s per electron pair from NADH
– 15 ATPs for ETS (5 X 3 per electron pair)
– 15 X 2 = 30 ATPs per glucose
• The single FADH produced during the Krebs
cycle results in
– 2 ATPs per electron pair
– 2 X 2 = 4 ATPs per glucose
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 for prokaryotes
• 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 atoms or 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 into 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 intermediates of either glycolysis or the Krebs cycle
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 – the
dominant type of photosynthesis on earth
• Other photosynthesizers such as green and purple
bacteria
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–
–
–
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