CZ5211 Topics in Computational Biology Lecture 7: Biological Pathways II: Metabolic Pathways Prof. Chen Yu Zong Tel: [phone] Email: [e-mail] http://xin.cz3.nus.edu.sg Room 07-24, level 7, SOC1, NUS

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CZ5211 Topics in Computational Biology Lecture
7 Biological Pathways II Metabolic
PathwaysProf. Chen Yu ZongTel
6874-6877Email yzchen_at_cz3.nus.edu.sghttp//xin.
cz3.nus.edu.sgRoom 07-24, level 7, SOC1, NUS
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Some key concepts about metabolism
All metabolism may be thought of as the coupling
of energy production and energy use.
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Some key concepts about metabolism
Certain biochemical reactions occur spontaneously
Net release of energy
Other must be forced to occur
coupling
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Energy and Chemical Reactions
Figure 4-5 Energy transfer and storage in
biological reactions
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Enzymes speed biochemical reactions

• Lower activation E
• Specificity
• Activation
• Cofactors
• Modulators
• Acidity
• Temperature
• Competitive inhibitors
• Allosteric
• Concentrations

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Enzymes speed biochemical reactions
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Law of Mass Action

• Defined
• Equlibrium
• Reversible

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Types of Enzymatic Reactions

• Oxidationreduction
• Hydrolysisdehydration
• Additionsubtraction exchange
• Ligation

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Cell Metabolism

• Pathways
• Intermediates
• Catabolic - energy
• Anabolic - synthesis

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Metabolic Pathways

• Catabolic Pathways
• Those that convert energy into biologically
  useful forms are called catabolic pathways
• Fuels (carbs fats) ? CO2 H2O useful
  energy catabolism
• Examples degradation, pathways by which
  nutrients and cellular components are broken down
  for reuse or to generate energy

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Metabolic Pathways

• Anabolic Pathways
• Those that require inputs of energy to proceed
  are called, anabolic pathways
• Useful energy small molecules ? complex
  molecules anabolism
• Biosynthesis, building up of biomolecules from
  simpler components
• Pathways that can be either anabolic or catabolic
  are referred to as amphibolic pathways

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Coupling favorable unfavorable reactions

• A pathway must satisfy minimally two criteria
• Reaction must be specific, yielding only one
  particular product or set of products. Enzymes
  provide specificity
• Whole set of reactions in a pathway must be
  thermodynamically favored. A reaction can occur
  spontaneously only if ?G, the change in free
  energy, is negative
• 3. An important thermodynamic fact the overall
  free energy change for a chemically coupled
  series of reactions is equal to the sum of the
  free-energy changes of the individual steps

A ? B C ?G0 5 kcal mol-1 B ? D
?G0 - 8 kcal mol-1
A ? C D
?G0 - 3 kcal mol-1
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Control of Metabolic Pathways

• Feedback inhibition
• Enzyme modulators
• No enzyme
• Enzyme isolation
• Energy availability - ATP

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ATP is the Universal Currency of Free Energy
Metabolism is facilitated by the use of a common
energy currency Part of the free energy derived
from the oxidation of foodstuffs and from light
is transformed into ATP - the energy currency A
large amount of free energy is liberated when ATP
is hydrolyzed to ADP Pi, or ATP to AMP PPi
ATP H2O ? ADP Pi ?G0 -7.3 kcal
mol-1 ATP H2O ? AMP PPi ?G0 -10.9
kcal mol-1
Under typical cellular conditions, the actual ?G
for these hydrolyses is approximately -12 kcal
mol-1
ATP hydrolysis drives metabolism by shifting the
equilibrium of coupled reactions by a factor of
approximately 108
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Structures of ATP, ADP, AMP
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Structures of ATP, ADP, AMP
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Coupled Reactions Involving ATP
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Coupled Reactions Involving ATP
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Coupled Reactions Involving ATP
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ATP Production

• Glycolysis
• Phosphorylation
• Pyruvate
• Anaerobic respiration
• Lactate production
• 2 ATPs produced

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Pyruvate Metabolism

• Aerobic respiration
• In mitochondria
• Acetyl CoA and CO2
• Citric Acid Cycle
• Energy Produced
• 1 ATP
• 3 NADH
• 1 FADH
• Waste2 CO2s

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Pyruvate Metabolism
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Electron Transport

• High energy electrons
• Energy transfer
• ATP synthesized from ADP
• H2O is a byproduct

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Electron Transport
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Biomolecules Catabolized to make ATP

• Complex Carbohydrates
• Glycogen catabolism
• Liver storage
• Muscle storage
• Glucose produced

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Protein Catabolism

• Deamination
• Conversion
• Glucose
• Acetyl CoA

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Lipid Catabolism

• Higher energy content
• Triglycerides to glycerol
• Glycerol
• Fatty acids
• Ketone bodies - liver

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Lipid Catabolism
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Stages of Catabolism from Foodstuffs
Extraction of energy from foodstuffs can be
divided into three stages
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Synthetic (Anabolic) pathways

• Glycogen synthesis
• Liver storage
• Glucose to glycogen
• Gluconeogenesis
• Amino acids
• Glycerol
• Lactate

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Lipogenesis

• Acetyl Co A
• Glycerol
• Fatty acids
• Triglycerides

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Protein Synthesis

• 20 Amino acids
• DNA code sequence
• mRNA transcription processing
• Translation by ribosomes
• Chain (polymer) of amino acids

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Embden-Meyerhof Pathway (EM, glycolysis)
Major pathway for the conversion of hexose sugars
into pyruvate.

• It results in the formation of
• two NADH
• two ATP

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(from Glyceraldehide-3-P to Pyruvate) Gain of 4
ATP
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The Embden-Meyerhof Pathway (EM, glycolysis)
It results in the formation of six of the
critical biosynthetic intermediates
Which ones? (look at the table provided)
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(from Glyceraldehide-3-P to Pyruvate) Gain of 4
ATP

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The Hexose Monophosphate (HM) Pathway (also known
as oxidative pentose, OM, or pentose phosphate
pathway)
It provides all the key intermediates not
provided by the EM pathway.
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The Entner-Doudoroff Pathway
It may be considered an alternate hexose
monophsphate pathway.

• It provides a minimum of five of the critical
  biosynthetic intermediates
• glucose-6-P
• triose phosphate
• 3-phosphoglycerate
• phosphoenol pyruvate (PEP)
• pyruvate

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The Entner-Doudoroff Pathway
It begins the same as the HM pathway up to
phosphogluconic acid. Then, instead of being
converted to pentose and carbon dioxide, it is
dehydrated yielding 2-keto-3, dehydro, 6
phosphogluconic acid.
pyruvate
Glyceraldehyde-3-P
The top half of the molecule of glucose
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The Entner-Doudoroff Pathway
Both the EM and the ED pathway convert a glucose
molecule to two molecules of pyruvate.
In the EM pathway, pyruvate arises by the
intermediate formation of glyceraldehyde-3-P. In
the ED pathway, from the top half of the molecule
of glucose.
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Cyclic Metabolic Pathway
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Multiple Metabolic Pathways
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Multiple Metabolic Pathways
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Multiple Metabolic Pathways
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Post Translational Protein Modification
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Metabolic Engineering
Cells developed optimal use of their resources
for their survival. Metabolic pathways are
networks, regulated to optimally distribute their
fluxes for best use of resources Metabolic
engineering is to overcome the cellular
regulation to produce product of our interest or
to create a new product that the host cells
normally dont need to produce.
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Scope of Metabolic Engineering
Modify host cells, host multicellular organisms,
or product Improved production, in selectivity
or in quantity, of chemicals already produced by
the host organism Extended substrate range for
growth and product formation Addition of new
catabolic activities for degradation of toxic
chemicals Production of chemicals new to the
host organism Modification of cell properties
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Methods of Metabolic Engineering
Repeated mutations were necessary to create
strains of the mold Penicillium chrysogenum which
produce high titers of penicillin that became
the foundation of a commercial process and
changed human health care. Radiation and
chemical agents were employed by investigators to
induce mutations in the microorganism.
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Methods of Metabolic Engineering

• Identify the target phenotype or trait
• Increase the frequency of occurrence of gene(s)
  that may confer the phenotype
• Increase the mutation frequency in producing
  cells
• by Mutagen treatment (UV, X-ray, chemical
  mutagen) (Classical method)
• Introduce additional gene(s) (that may already
  exist or absent in the host
• cell) known to give cells the desired
  properties (Genetic Engineering)
• Introduce genetic element to inactivate or
  activate the gene by random
• insertion of extra sequence
• Identify the mutants (clones) that have the
• Desired trait.
• Two general means
• Screening
• Selection

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Methods of Metabolic Engineering
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Methods of Metabolic Engineering
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Methods of Metabolic Engineering
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Metabolic Engineering
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Metabolic Engineering
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Thermodynamics of Metabolic Pathways
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Thermodynamics of Metabolic Pathways
Thermodynamics, as Related to Metabolism Reaction
s near equilibrium Easily switch direction
depending on relative concentrations of reactants
and products Enzymes act to restore
equilibrium Reactions far from equilibrium
Irreversible Enzymes act as dams have
insufficient activity to allow reaction to
approach equilibrium reactants build up changes
in activity of enzyme change flux
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Thermodynamics of Metabolic Pathways
Three Major Implications of Thermodynamics for
Metabolism Metabolic pathways are
irreversible. Biological systems are governed by
thermodynamics! For a process to be spontaneous
?G must be negative Every metabolic pathway
has a committed step. Usually the first
irreversible step unique to a pathway. Usually an
important site of regulation Catabolic and
anabolic pathways differ