Bioenergetics and Metabolism

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Part II and Chapter 13
Bioenergetics and Metabolism
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Bioenergetics and Reactions
Key topics Learning Goals

• Thermodynamics applies to biochemistry
• Organic chemistry principles at work
• Some biomolecules are high energy with respect
  to their hydrolysis and group transfers
• Energy stored in reduced organic compounds can be
  used to reduce cofactors such as NAD and FAD,
  which serve as universal electron carriers

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Metabolic Pathways Cooperate To

• Obtain Chemical Energy by
• a. Capturing Solar Energy, or
• b. Oxidizing Energy Rich Chemicals from the
  Environment.
• Convert Nutrient Molecules to metabolic
  intermediates, then monomers or waste products.
• Polymerize monomers to polymers (proteins,
  carbohydrates, nucleic acids, lipids).
• Synthesize and Degrade (turnover) biomolelcules.

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Anabolism and Catabolism
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Linear and Circular Pathways
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Metabolic Pathways
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Auto-Pathways
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Pathways Arranged as Multi-Protein Modules
Flagella LPS Outer Membrane Peptidoglycan Cytoplas
mic Membrane Glycolysis
ATPase RNA
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5 Main Classes of Metabolic Reactions

1. Oxidation-Reduction Reactions
2. Reactions that Make or Break Carbon-Carbon Bonds
3. Internal Rearrangements, Isomerizations,
   Eliminations.
4. Group Transfer Reactions.
5. Free Radical Reactions.

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Chapter 13 Bionergetics ATP
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Showed that Respiration Was Oxidation of Carbon
and Hydrogenthus began Thermodynamics
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Laws of Thermodynamics
First Law for any change, the energy of the
universe remains constant energy may change form
or it may be transported, but can not be created
or destroyed. Second Law The Entropy Law can be
stated 3 ways 1. Systems tend from ordered to
disordered. 2. Entropy can remain the same for
reversible processes but increases from
irreversible processes. 3. All processes tend
towards equilibrium. Everything ? Equilibrium
Death. Third Law Entropy goes to zero when
ordered substances approach absolute zero 0oK
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Thermodynamics
Gibbs Free Energy G and ?G Enthalpy H and
?H Entropy S and ?S ?G ?H - T?S
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Biochemistry Uses ?Go Not ?Go
Standard Conditions (all reactants and products
at 1M, gases at 1 atm, Temp 25C) are Not
Biological Conditions So, ?Go takes out water
(55.5M), and H is set at pH 7 (not 1M which
would be pH0) and for humans ?Go uses 37oC
(310 K), but for bacteria ?Go uses 25oC (298
K).or the temperature of the environment. ?Go
- RT ln Keq You should be able to do EOC
Problems 2 and 3 easily EOC Problem 6 the
difference between ?Go and ?G.
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Free energy, or the equilibrium constant, measure
the direction of processes
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?Gos Are Additive
Hexokinase Rxn Glucose ATP ? Glucose-6-P
ADP Glucose Pi ? Glucose-P H2O ?Go
13.8 kJ/mole ATP H2O ? ADP Pi
?Go -30.5 kJ/mole Overall ?Go -16.7
kJ/mole Exergonic ! So Keq 7.8 x
102 EOC Problems 9 and 12 the ?Go for 2
coupled reactions.
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Biochemical Pathways Have Evolved To

• Use reactions that are relevant to metabolic
  systems
• Makes use of available substrates with
  reaction rates that are NOT slow (have too high
  activation energies even with enzymes!) to
  produce useful products (which are themselves
  substrates). And,
• Maximize Rates
• Evolutions Toolbox reactions that work.
• circumvent impossible
  reactions.
• most reactions in organic
  chemistry occur in biology,
  except one, the Diels Alder Rxnbut we will
  see about that.

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You be a radical ! You be inonic !
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Rich in electrons ? donate electrons
Electron poor ? suck up electrons from donors
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The Importance of Carbonyls
Nucleophile Electrophile
Imines are like carbonyls
Here the carbonyl is an electrophile
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Making and Breaking Single Bonds
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Isomerations are Internally Complex
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The Classic Redox Reaction
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ATP Hydrolysis
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Energy Charge
ATP ½ ADP ATP ADP AMP
Energy Charge
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Energy Charge
Why the ½ ADP ??? It is because of Adenyl
Kinase ADP ADP ? ATP AMP
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Nucleotide Intracellular Concentrations
Nucleotide Conc, µM Nucleotide Conc, µM
ATP 3,000 GTP 923 ADP 250 GDP 128 AMP
105 GMP 20 dATP 175 dGTP 122 dTTP
77 dCTP 65 UTP 894 CTP 515 cAMP
6 cGMP nd ppGpp 31 NAD
790 NADP 54 NADH 16 NADPH 146 FAD
51 FMN 88 AcCoA 231 SuccCoA 15
in Salmonella enterica subsp Typhimurium from
Bochner and Ames, 1982, J. Biol. Chem
2579759-9769
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Magnesium Stabilizes Tri- and Di-phosphates
EOC Problem 19 How much ATP is used in a
human/day.
EOC Problem 20 About turn over of the a and ß
phosphates (can you located them above?).
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Pyruvate Kinase
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1,3-Bisphosphoglycerate has More Energy Than ATP
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Phosphocreatine Is Store of Energy in Muscle
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What About Actual ?G ?
?G ?Go RT ln(products/substrates) This
is the real, biological ?G in a cell !! At 25oC
RT 2.48 kJ/mole (2.5 kJ/mole) At 37oC RT
2.58 kJ/mole (2.6 kJ/mole) We will be doing
this a lot later on !
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Doing Worked Example 13-2
Using E. coli ?G ?Go RT ln
ADPPi/ATP ?G -30.5 kJ/mole (8.315
J/mole.K)(310K) ln(1.04mM)(7.9mM)/7.9 mM ?G
-30.5 kJ/mole 2.58 kJ/mole (-6.8) ?G -30.5
kJ/mole (-17.6) ?G -48.1 kJ/mole Note
Calculate mM such as 1.04mM 1.04 x 10-3M In
the text for the Human Erythrocyte it works out
to ?G -52 kJ/mole
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Acetyl-CoA (Thiol-ester) Has the Energy of ATP!
EOC Problem 21 Cleavage of ATP to AMP
PPi..why is this different (see Table 13-6
above). (What DNA enzyme did the same? Its in
Chapter 8)
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Enzyme Reaction Phosphorylation Intermediates
Used to form C-N Bonds
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Phosphates Ranking by the Standard Free Energy
of Hydrolysis
Phosphate can be transferred from compounds with
higher ?G? to those with lower ?G?.
Reactions such as PEP ADP gt Pyruvate
ATP are favorable, and can be used to synthesize
ATP.
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Nucleoside Diphosphate Kinase makes NTPs from
ATP and NDPs
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Carbon Redox Watch the Red Dots (Electrons)
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Emf or Eh or Eo
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EOC Problem 24 Respiratory chain thermodynamics
(we will do this in Chapter 19)learn it well now!
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Calculations
Differences between half cellsExample of
electron transfer from NADH to cytochrome-b NADH
Eo -.32 v Cyt-b Eo 0.077 v ?Eo
Eooxidized Eo reduced 0.077v
(-0.32v) ?Eo 0.397v
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Further Calculations
What is the ?Go for oxidation of NADH by
cytochrome-b ?Go - nF ?Eo Faraday Constant
96,480 J/v.mole F 96.5
kJ/v.mole ?Go - (2) 96.5 kJ/v.mole (0.397v)
- 77 kJ/mole
What about the real ?E ?...and then ?G !
?E ?Eo (RT/nF) ln (products/substrates) E
OC Problem 25 and 26 are all about this.
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NAD 2e- 2H ? NADH H
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Lactic Acid Dehydrogenase LDH
Rossmann fold, a structural motif in
Dehydrogenases
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Vitamin Niacin is Made from W and Needs to be
Amidated for NAD
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FMN and FAD
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Enzyme Reactions have a Yield of 1.0The Perfect
Catalysts
Assume Metabolism worked on each step in the
metabolic pathway having a yield of 0.9
(tremendously high for organic chemistry
reactions!!). Then look at a 10 reaction pathway
such as Glycolysis if you start with 100 mg of
glucose the pathway would only produce less than
39 mg of pyruvate.AND, the cell would fill up
with 61 mg of side reaction products! ? The
message is that metabolism and life would be
tremendously inefficient motionless, wasteful
BLOBS filled with junk. Most enzymes have a
yield of 0.9990 to 0.99990 (that is they make a
mistake reaction 1 in a 1,000 to 10,000
reactions).
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What is the BEST Yielding Enzyme?
Answer DNA polymerase makes an error 1 in 107
to 109 reactions. Why? It is the one of the
few enzymes to have a proof- reading function
to correct the 1 in 103 to 104 mistakes. Check
it out in Molecular Biology!
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Things to Know and Do Before Class

• The basic laws of thermodynamics.
• Be able to calculate ?G, ?Go from concentrations
  or Keq.
• Be able to calculate over all ?Go from summed
  reactions.
• Principles that make some bonds high energy.
• EOC Problems (2, 3), 6, 7, 9, 12, 14, 20, 21,
  24-26.
• Two Class periods for this chapter.