Download Bacterial Metabolism

Topic 11 (ch8)
Microbial Metabolism
Topics
– Metabolism
– Energy
– Pathways
– Biosynthesis
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Metabolism
• Catabolism
• Anabolism
• Enzymes
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Metabolic balancing act
Catabolism
Enzymes involved in
breakdown of
complex organic
molecules to extract
energy and form
simpler end
products
Anabolism
Enzymes involved in
the use of energy
from catabolism to
synthesize
macromolecules
and cell structures
from precursors
(simpler products)
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Catabolism and anabolism – simple model
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Enzymes – what are they?
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Function
Structure
Enzyme-substrate interaction
Cofactors
Action
Regulation
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Function
• Catalysts for
chemical reactions
• Lower the energy of
activation
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What Affects Enzymes?
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Unfolding Kills Enzymes
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Enzymes Inhibited by
Competition (more later…)
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Enzyme are Made of…
– Many protein enzymes are complete
without additions
– Apoenzymes are inactive if not bound to
non-protein cofactors (inorganic ions or
coenzymes)
– Binding of apoenzyme and its cofactor(s)
yields holoenzyme
– Some are RNA molecules called ribozymes
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Types of Enzyme
(Based on Structure)
• Simple enzyme
– protein alone
• Conjugated enzyme
– protein and nonprotein
• Three-dimensional features
– Enable specificity
• Active site or catalytic site
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A Conjugated Protein Enzyme
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Another Example of Conjugated Enzymes
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Enzymes in 3D
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Enzyme-substrate interactions
• Substrates specifically bind to the active
sites on the enzyme
– “lock-and-key”
– Induced fit
• Once the reaction is complete, the
product is released and the enzyme
reused
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Substrate Fit
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Lock-and-key model, and induced fit
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Cofactors
• Bind to and activate the enzyme
• Ex. Metallic cofactors
– Iron, copper, magnesium
• Coenzymes
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Coenzyme
• Transient carrier - alter a substrate by
removing a chemical group from one
substrate and adding it to another
substrate
• Ex. vitamins
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Example: coenzyme transfers chemical groups between
substrates
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Action
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Exoenzymes
Endoenzymes
Constitutive
Induction or repression
Types of reactions
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Exoenzymes vs. Endoenzymes
•Exoenzymes inactive inside the
cell, active after
release.
•Endoenzymes
remain in the cell and
are active
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Constitiutive and Regulated enzymes
Constitutive enzymespresent in constant
amounts
Regulated enzymes are
either induced or
repressed.
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Reaction types
• Condensation (associated with anabolic reactions)
• Hydrolysis (associated with catabolic reactions)
• Transfer reactions
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enzyme-catalyzed synthesis
and hydrolysis reactions
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Transfer reactions
• Transfer of electrons from one substrate to
another
– Oxidation
(add O2 to a compound with a loss of electrons, increase charge)
– Reduction
(add e- to a compound, decrease charge)
• Oxidoreductase
• Transfer of functional groups from one
molecule to another
– Transferases
• Aminotransferases
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How to remember re-dox?
• LEO goes GER
• Losing Electrons is Oxidation
• Gaining Electrons is Reduction
Image from http://library.thinkquest.org
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Examples of oxidoreductase, transferase, and hydrolytic enzymes
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Enzyme Regulation
• Metabolic pathways
• Direct control
• Genetic control
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Patterns of metabolism
Different metabolic
pathways are
regulated by the
enzymes that catalyze
the reactions.
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Two common direct control mechanismsCompetitive and Noncompetitive inhibitions
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Another Control Feedback Inhibition
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Genetic control
• Repression
• Induction
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Energy
• Cell energetics
– Exergonic
– Endergonic
• Redox reaction (change in oxidation number)
• Electron carrier
• Adenosine Triphosphate (ATP)
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Cell energy model (simplified)
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Redox Reaction (again)
• Reduction and oxidation reaction (LEO goes GER):
– Oxidation: loss of electrons, or gain of oxygen, gives
increase in oxidation number.
– Reduction: gain of electrons, or loss of oxygen, gives
decrease in oxidation number.
• Electron carriers transfer electrons and hydrogens
– Electron donor
– Electron acceptor
• Energy is also transferred and captured by the
phosphate in form of ATP
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Electron carriers
• Coenzymes
– Nicotinamide adenine dinucleotide (NAD)
• Respiratory chain carriers
– Cytochromes (protein)
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NAD reduction
simple
annotated
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Adenosine Triphosphate
(ATP - $$!)
• Temporary energy repository - energy
storage!
• Break phosphates bonds to release free
energy
• Three part molecule:
– Nitrogen base
– 5-carbon sugar (ribose)
– Chain of phosphates
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AMP grows to ATP, each stage higher in energy
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Carbohydrates – Most
Important
• Many organisms oxidize carbohydrates as
primary energy source for anabolic reactions
• Glucose most common carbohydrate used
• Glucose catabolized by two processes:
– Cellular respiration
– Fermentation
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Phosphorylation of glucose by ATP
ATP can phosphorylate an organic molecule like glucose during catabolism
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ATP can be synthesized by substrate-level phosphorylation.
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Various Pathways
• Catabolism
– Embden-Meyerhof-Parnas (EMP) pathway
or glycolysis
– Tricarboxylic acid cycle (TCA)
– Respiratory chain
• Aerobic
• Anaerobic
– Alternate pathways
– Fermentation
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Metabolism Summary of Glucose and Energy
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Aerobic respiration (O2)
Three stages:
• Glycolysis
• Tricarboxylic acid (TCA)
• Electron transport
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Basics of Glycolysis
• In cytoplasm for most cells
– Divided into three stages involving 10 total
steps
• Energy-investment stage
• Lysis stage
• Energy-conserving stage
(cont. next slide)
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Basics of Glycolysis
• In cytoplasm for most cells
• Oxidation of glucose
• Phosphorylation of some intermediates
(Uses two ATPs)
• Splits a 6 carbon sugar into two 3
carbon molecules
• Coenzyme NAD is reduced to NADH
• Substrate-level-phosphorylation
(Four ATPs are synthesized)
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(cont. next slide)
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Basic of Glycolysis (continued)
• Water is generated
• Net yield of 2 ATPs
• Final intermediates are two Pyruvic acid
molecules
(notice that it require 2 different, parallel pathways to finally
generate both pyruvic acid molecules…)
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Overview
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Glycolytic Steps:
Metabolism of Glucose
to 2 Pyruvic Acid
molecules (pyruvate)
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TCA cycle
• Each pyruvic acid is processed to enter the
TCA cycle (two complete cycles)
• CO2 is generated
• Coenzymes NAD and FAD are reduced to
NADH and FADH2
• Net yield of two ATPs
• Critical intermediates are synthesized
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TCA Cycle Steps
Each cycle handles
one 3 carbon
molecule.
This means it takes
two cycles to burn up
one 6 carbon glucose
molecule.
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Electron transport
• NADH and FADH2 donate electrons to
the electron carriers
• Membrane bound carriers transfer
electrons (redox reactions)
• The final electron acceptor completes
the terminal step (ex. Oxygen)
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Electron Transport (continued)
Driven by:
• Chemiosmosis
• Proton motive force (PMF)
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e- Transport
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Chemiosmosis and the electron transport system, with oxidative
phosphorylation e- transport and formation of a proton gradient
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Electron Transport Chain
Locations
• Eukaryotes
– mitochondria
• Prokaryotes
– Cytoplasmic membrane
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ATP Yield:
One glucose molecule, aerobic respiration
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Anaerobic respiration (No O2)
• Similar to aerobic respiration, except
nitrate or nitrite is the final electron
acceptor
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Fermentation
• Glycolysis only
• NADH from glycolysis is used to reduce the
organic products
• Organic compounds as the final electron
acceptors
• ATP yields are small (per glucose molecule),
compared to respiration
• Must metabolize large amounts of glucose to
produce equivalent respiratory ATPs
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Types of fermenters
• Facultative anaerobes
– Fermentation in the absence of oxygen
– Respiration in the presence of oxygen
– Ex. Escherichia coli
• Strict fermenters
– No respiration
– Ex. yeast
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Why Fermentation?
– Sometimes cells cannot completely oxidize
glucose by cellular respiration
– Cells require constant source of NAD+
• Cannot be obtained simply using glycolysis and
Krebs cycle
– Fermentation pathways provide cells with
alternate source of NAD+
• Partial oxidation of sugar (or other metabolites)
to release energy using an organic molecule
from within the cell as final electron acceptor
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Products of fermentation
• Alcoholic fermentation
• Acidic fermentation
• Mixed acid fermentation
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Fermentation of ethyl alcohol and lactic acid
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Pyruvate mixed acid fermentation diverse products
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Fermentation Products
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Respiration comparison
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Biosynthesis
• Anabolism
– Amphibolic (   )
– Gluconeogenesis
– Beta oxidation
– Amination
– Transamination
– Deamination
– Macromolecules
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Amphibolic
• Integration of the catabolic and anabolic
pathways
• Intermediates serve multiple purposes
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Overview of anabolic and catabolic relationships
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Gluconeogenesis
• Pyruvate (intermediate) converts to
glucose
• Occurs when the glucose supply is low
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Gluconeogenesis
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Beta oxidation
• Metabolism of fatty acids into acetylCoA  Krebs (TCA cycle)
• 4 steps:
– Oxidation by FAD
– Hydation of C2=C3 bond
– Oxidation by NAD+
– Thiol cleavage at C2-C3  Acetyl-CoA
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Production and Conversion of Amino Acids:
amination, transamination, deamination
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Fitting Cellular Together
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The Big Picture
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Macromolecules
• Cellular building blocks
– Monosaccharides
– Amino acids
– Fatty acids
– Nitrogen bases
– Vitamins
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Photosynthesis – free power!
6H2O + 6CO2  C6H12O6+ 6O2
2 independent reactions in the chloroplast
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Photosynthesis (cont.)
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