Introduction to Metabolism

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Introduction to Metabolism
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Metabolism(The Acquisition and Utilization of
Free Energy)

• Catabolism exergonic oxidation
• Anabolism endergonic processes

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Anabolism and Catabolism
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ATP
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Sources of ATP

• Phototrophs photosynthesis
• Chemotrophs oxidation of organic compounds

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NADP
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NADPH
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Metabolic Pathways
A gt B gt C gt D gt E
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Potential Futile Cycles
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Properties of Metabolic Pathways

• Irreversible (overall) reversibility of
  individual steps
• Separate Anabolic and Catabolic Pathways
• First Committed (Exergonic) Step others close to
  equilibrium
• Regulation (usually first committed step) often
  rat-limiting
• Compartmentation transport

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Regulation of Metabolic Pathways

• Specific Controls
• General Controls

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Specific Controls

• Control of Enzyme Amount (153B)
• Constitutive Enzymes
• Inducible Enzymes
• Repressible Enzymes
• Control of Enzyme Activity (153A)
• Regulatory Enzymes
• Effectors (Ligands)

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General Controls(Integration of Cellular or
Organism Functions)

• Internal Effectors
• Catabolite Repression
• Energy Charge
• Reduction Potential
• External Effectors (e.g. hormones)

Significance Efficiency and Flexibility!
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Energy Charge(Daniel Atkinson)
Steady-State E.C. 0.93
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Types of Reactions
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Group Transfer Reactions
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Phosphoryl Group Transfer
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Oxidation-Reduction Reactions
SH2 NAD H2O gt S NADH H3O
SH2 Reduced Substrate S Oxidized Product NAD
Electron Acceptor
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NAD
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Alcohol Dehydrogenase(Oxidation-Reduction
Reaction)
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Elimination Reactions
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Isomerization Reactions(Intramolecular Hydrogen
Shifts)
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Racemization and Epimerization

• Racemization change stereochemistry of only
  chiral center
• Epimerization change stereochemistry of one
  chiral center of molecule with more than one
  chiral centers

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Rearrangements(altered carbon skeletons)
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Making C-C Bonds
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Breaking C-C Bonds
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Experimental Approachesto Metabolism
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Features of Metabolic Pathways
A gt B gt C gt D gt E

• Sequences and Energetics
• Enzymes and Mechanisms
• Control Mechanisms (Regulation)

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Elucidation of Metabolic Pathways
A gt B gt C gt D gt E
Metabolic Inhibitors accumulation of
intermediates Biochemical Genetics
mutants Pathway Labeling isotopes
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Metabolic Inhibitors(Accumulation of
Intermediates)

• Iodoacetate fructose-1,6-bisphosphate
• Fluoride 3-phosphoglycerate and
  2phosphoglycerate

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Biochemical Genetics(Mutants)

• Natural Genetic Defects
• Manipulation of Microorganisms

A gt B gt C gt D gt E
Accumulation of Intermediates Growth Requirements
(auxotrophic mutants)
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Pathway Labeling
A gt B gt C
Stable Isotopes Radioisotopes
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Detection of Isotopes

• Stable Isotopes
• Mass Spectropmetry
• NMR
• Radioisotopes
• Proportional Counting (Geiger Counter)
• Liquid Scintillation Counting
• Autoradiography

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Enzymes and Mechanisms

• Biochemistry

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Control Mechanisms (Regulation)

• Molecular Biology
• Biochemistry

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Compartmentation(Isolated Organs/Tissues, Cells
and Subcellular Organelles)

• Cell Biology
• Biochemistry

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ATP
Phosphoester Bonds acid and alcohol Phosphoanhydr
ide Bonds two acids
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Kinetic StabilityofPhosphoanhydride Bonds
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Coupled Reactions
?Go (kJ/mol)
---------- Fructose-6-P Pi gt
Fructose-1,6-bisP H2O 13.3
ATP H2O gt ADP Pi
-30.5 --------------------------------------------
----------------------------------- Fructose-6-P
ATP gt Fructose-1,6-bisP ADP -17.2
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Role of ATP

• Early stages of nutrient breakdown
• Glucose ATP gt Glucose-6-P ADP
• Interconverson of nucleoside triphosphtes
• NDP ATP gt NTP ADP
• Nucleoside Diphosphate Kinase
• Physiological processes
• Muscle contraction
• Active transport

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Role of ATP

• Additional phosphoanhydride cleavages in highly
  endergonic reactons
• (NMP)n NTP gt (NMP)n1 PPi
• PPi H2O gt 2 Pi
• Pyrophosphatase

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Formation of ATP

• Substrate-level phosphorylation XP ADP
  gt XH ATP
• Oxidative phosphorylation
• Photophosphorylation
• Adenylate Kinase reaction 2 ADP gt AMP
  ATP

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Substrate-level Phosphorylation
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Oxidative Phosphorylation
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Photophosphorylation
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Other High-Energy Compounds
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Steady State