Cellular Metabolism

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Lecture 3

• Cellular Metabolism
• Kinetics

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Please join the UT BME Department for the
worldwide movie premiere of the BME377
Internship Documentary

• Come celebrate the achievements of our
  spectacular BME undergraduates - the stars of
  this years summer internship at The Texas
  Medical Center!

Date Sept. 15, 2004 Place ACES room 2.302
Time 5 oclock
Come see how a summer can change your life!
Be among the first to screen the BME 377
documentary! Enjoy BME377 student posters. A
reception will follow the screening. Refreshments
provided. More info and the movie (after 9/15)
are available at http//www.engr.utexas.edu/bme
/faculty/richards-kortum/BME377/mission/mission.ht
m
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Review of Lecture 2

• Introduction to Modeling
• Review of Electric Circuits

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Outline

• Biochemical reactions
• Enzymes and enzyme kinetics
• Cell metabolism and ATP production
• Synthetic pathways

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Outline

• Biochemical reactions
• Equilibrium concentrations
• Biochemical energetics
• ATP
• Oxidation-Reduction reactions
• Enzymes and enzyme kinetics
• Cell metabolism and ATP production
• Synthetic pathways

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Biochemical Reactions

• Metabolism
• Collection of chemical reactions in the body
• These reactions
• Extract energy from nutrient biomolecules
• Synthesize or break down molecules
• Catabolism
• Produce energy by breaking down large
  biomolecules
• Anabolism
• Consume energy by synthesizing large biomolecules

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Fig 4.4 Exergonic and endergonic
reactions Silverthorn 2nd Ed
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Metabolism

• Highly coordinated process
• Consists of a series of pathways
• Each step in the pathway is an enzymatically
  controlled reaction
• Many metabolic pathways couple
• exergonic reactions that release energy
• with endergonic reactions that consume energy

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Fig 4.21 Overview of aerobic pathways for ATP
production Silverthorn 2nd Ed
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Equilibrium Concentrations

• Law of mass action
• Rate of reaction
• rate of product formation
• dC/dt
• Rx rate collisions between reactants per
  unit time x probability that collision is
  energetic enough to overcome activation energy
• dC/dt ABk
• Useful model much like Ohms law

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Mass Action

• Reaction can proceed in both directions
• dA/dt k-C - kAB
• At equilibrium
• dA/dt 0
• Ceq (k/k-)AeqBeq
• Ceq (1/Keq)AeqBeq

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Mass Action

• If no other reactions are taking place
• A C Ao constant
• At equilibrium
• Ceq (1/Keq)AeqBeq
• Ceq AoBeq/(KeqBeq)

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Biochemical Energetics

• ATP
• ATP serves as carrier of energy
• Complex biomolecules serve as energy reservoirs
• ATP H20 ? ADP Pi H energy
• 3 phosphates have negative charge
• Requires energy to overcome Coulombic repulsion
• 7-12 kCal/mole of ATP

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Biochemical Energetics

• Oxidation Reduction reactions
• NADH H 1/2O2 ? NAD H20 energy
• Reduced form ? Oxidized form energy
• 52 kCal/mole
• FADH2 1/2O2 ? FAD2 H20 energy
• Reduced form ? Oxidized form energy

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Control of Metabolism

• Five ways cells regulate metabolism
• Control enzyme concentration
• Produce allosteric and covalent modulators
• Use two different enzymes to catalyze reversible
  reactions
• Isolate enzymes within intracellular organelles
• Maintain an optimum ratio of ATP to ADP

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Outline

• Biochemical reactions
• Enzymes and enzyme kinetics
• Enzymes as catalysts
• Enzyme kinetics
• Enzyme inhibition
• Cell metabolism and ATP production
• Synthetic pathways

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Enzymes

• Biological catalysts
• Speed up reaction rate, but are not changed in
  reaction
• Enzyme increases rate by decreasing activation
  energy
• Reaction rate
• 1 molecule/100s without enzyme
• 106 molecules/s with enzyme

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Fig 4.7 Enzymes lower the activation energy of
reactions Silverthorn 2nd Ed
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Enzymes

• Most enzymes are
• large proteins
• complex 3D shapes
• Small region known as active site
• binds substrates
• brings them close enough to react

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Fig 4.8 Enzymes bind substrate at the binding
site Silverthorn 2nd Ed
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Enzymes

• Nomenclature
• Most have ase at the end
• Prefix refers to type of reaction or substrate
• Factors affecting enzyme activity
• Some must be activated
• Some require cofactor binding
• Modulators alter enzyme activity
• Competitive inhibitors
• Allosteric modulators

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Fig 4.9 Silverthorn 2nd Ed
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Fig 4.10 Silverthorn 2nd Ed
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Fig 4.13 Competitive inhibition Silverthorn
2nd Ed
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Fig 4.14 Allosteric inhibition Silverthorn
2nd Ed
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Enzyme Kinetics

• Law of mass action
• One step reactions
• Most enzymatically catalyzed rxs dont follow
• Michaelis Menten kinetics
• Multi-step reaction
• Substrate and enzyme form complex? breaks down
  into product and enzyme

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Michaelis Menten Kinetics

• Equilibrium approximation
• Substrate is in instantaneous equilibrium with
  complex
• Reaction rate
• Linear at low substrate concentrations
• Saturates at high concentrations
• VmaxeoK2, Rx limited by amount of enzyme and K2

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Briggs Haldane Kinetics

• Quasi- steady state approximation
• Rates of formation and breakdown of complex are
  equal at all times (except at very beginning)
• Reaction rate
• Same form as Michaelis Menten
• VmaxeoK2, Rx limited by amount of enzyme and K2

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Michaelis Menten Eq. App.
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Enzymatic Control of Reactions

• Cofactor activation
• Cofactor binding required for enzyme to be active
• Competitive Inhibition
• Reaction stops when inhibitor binds to enzyme
• Allosteric Inhibition
• Inhibitor binds at an allosteric site
• Decreases maximal reaction rate

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Fig 4.10 Silverthorn 2nd Ed
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Fig 4.13 Competitive inhibition Silverthorn
2nd Ed
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Competitive Inhibition
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Fig 4.14 Allosteric inhibition Silverthorn
2nd Ed
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Outline

• Biochemical reactions
• Enzymes and enzyme kinetics
• Cell metabolism and ATP production
• Glycolysis
• Energy yield per glucose molecule
• Synthetic pathways

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ATP Production

• ATP transfers energy between rxs
• Characterize a metabolic pathway in terms of net
  yield of ATP
• ATP Production
• Aerobic pathways
• Require oxygen
• Yields most ATP
• Anaerobic pathways
• Dont require oxygen
• Yield less ATP

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Aerobic Pathways

• Input
• Carbohydrates (eg glucose)
• Proteins (amino acids)
• Lipids (Fatty acids)
• Output
• High energy electrons carried by NADH, FADH2
• ATP
• Overall
• C6H12O6 6O2 ? 6 CO2 6 H2O energy
• 30-32 ATP/glucose
• Common steps
• Glycolysis (occurs in cytosol)
• Citric acid cycle (occurs in mitochondria)
• Electron transport (mitochondria)

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Fig 4.21 Overview of aerobic pathways for ATP
production Silverthorn 2nd Ed
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Glycolysis

• Summary
• Glucose 2NAD 2ADP 2Pi ? 2 pyruvate 2 ATP
  2 NADH 2H 2 H2O
• Does not require oxygen
• Yields pyruvate in anaerobic process
• Then
• If low oxygen converts to lactate
• If sufficient oxygen pyruvate enters citric
  acid cycle

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Fig 4.22 - Glycolysis Silverthorn 2nd Ed
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Citric Acid Cycle

• Summary
• Pyruvate transported from cytosol to mitochondria
• Pyruvate converted to acetyl coA which enters
  citric acid cycle
• Yield
• 1 ATP
• 3 NADH, 1 FADH2 ? transfer their high energy
  electrons to ATP in electron transfer chain

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Fig 4.23 Pyruvate metabolism Silverthorn
2nd Ed
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Fig 4.24 The citric acid cycle Silverthorn
2nd Ed
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Electron Transport Chain

• Oxidative phosphorylation
• Occurs in mitochondrial membrane
• Facilitated by mitochondrial proteins
• High energy electrons pass through e- transport
  chain
• Their energy is used to transport H from
  mitochondrial matrix to intermembrane space
• Energy stored in concentration gradient, then
  transferred to ATP as H moves back across
  membrane

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Fig 4.25 The electron transport system and ATP
synthesis Silverthorn 2nd Ed
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Net Energetics
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Outline

• Biochemical reactions
• Enzymes and enzyme kinetics
• Cell metabolism and ATP production
• Synthetic pathways
• Lipid synthesis
• Protein synthesis

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Fig 4.21 Overview of aerobic pathways for ATP
production Silverthorn 2nd Ed
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Fig 4.26 Glycogen catabolism Silverthorn
2nd Ed
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Fig 4.27 Protein catabolism Silverthorn 2nd
Ed
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Fig 4.28 - Lipolysis Silverthorn 2nd Ed
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Summary

• Biochemical reactions
• Enzymes and enzyme kinetics
• Cell metabolism and ATP production
• Synthetic pathways

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Poem of the Day

• Billy Collins
• Former US Poet Laureate (2001-03)
• New York State Poet Laureate (2004-06)
• Professor of English, Lehman College, CCNY
• Another Reason Why I Dont Keep a Gun in the
  House

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Due Dates

• Tuesday, September 7th
• Homework 2