1. Lecture 19 Quiz next Friday (Oct. 28) on glycolysis.
Metabolism and thermodynamics
(This material forward not on exam)

2. Summary: various methods to increase rate
Increase frequency of the correct group in the correct place e.g. proximity effect
Lower EA by specific catalysis -acid-base catalysis, nucleophile or electrophile
Raise energy of reactants (closer to EA) - ring distortion, transition state analog
Provide alternate low EA pathway - covalent catalysis.
Michaelis Menten vs. Allosterism
Lineweavear Burk
Eadie Hofstee
Competitive inhibition
Noncompetitive inhibition
Uncompetitive inhibition 2

3. Terms to review for enzymes
Cofactor
Coenzyme
Prosthetic group
Holoenzyme
Apoenzyme
Lock and Key
Transition analog model
Induced fit
Active site, binding site, recognition site, catalytic site 3

4. To be included on the quiz

5. Introduction to metabolism: Main Functions
To obtain energy for growth
From the degradation of energy rich compounds (chemotrophy)
Organotrophs-organism obtains H or e- from organic compounds
Lithotrophs-uses an inorganic substrate to obtain reducing equivalents.
From light (photosynthesis) Phototrophs
To use energy to assemble precursors into building blocks of the cell and to convert those building blocks into proteins, carbohydrates, lipids, etc.
Autotrophs (starting carbon source is CO2)
Heterotroph (use preformed complex organics)
To degrade and recycle unnecessary metabolites or compounds no longer in use by the cell.
03_12_Oxidation reduction.jpg

6. Metabolism
The sum of the chemical changes that convert nutrients into energy and the chemically complex products of cells
Hundreds of enzyme reactions organized into discrete pathways
Substrates are transformed to products via many specific intermediates
Metabolic maps portray the reactions
Intermediary metabolism

7. A Common Set of Pathways
Organisms show a marked similarity in their major metabolic pathways
Evidence that all life descended from a common ancestral form
There is also significant diversity

8. The Sun is Energy for Life
Phototrophs use light to drive synthesis of organic molecules
Heterotrophs use these as building blocks
CO2, O2, and H2O are recycled

10. Metabolism Metabolism consists of catabolism and anabolism
Catabolism: degradative pathways
Usually energy-yielding!
Anabolism: biosynthetic pathways
energy-requiring!

12. Metabolism is divided into 2 types
Catabolism - degradative metabolism to yield CO2, simple metabolites, and energy. Accompanied by the release of G stored in complex molecules - stored as ATP, NADPH (generate free energy)
Anabolism - Biosynthesis. Energy requiring step-uses building blocks, ATP and NADH/NADPH to form complex molecules.
Primary Metabolism - metabolism used for the construction of essential building blocks and energy metabolism.
Secondary Metabolisms - Other nonessential metabolism.
“Chemical reactions that create diverse byproducts often unique to a taxon and generally not essential for survival and have no known metabolic role.”
03_12_Oxidation reduction.jpg

13. Catabolism and Anabolism
Catabolic pathways converge to a few end products
Anabolic pathways diverge to synthesize many biomolecules
Some pathways serve both in catabolism and anabolism
Such pathways are amphibolic

14. Organization in Pathways
Pathways consist of sequential steps
The enzymes may be separate
Or may form a multienzyme complex
Or may be a membrane-bound system
New research indicates that multienzyme complexes are more common than once thought

15. Mutienzyme complex
Separate
enzymes
Membrane
Bound System

16. Organization of Pathways
Closed Loop
(intermediates recycled)
Linear
(product of rxns are substrates for subsequent rxns)
Spiral
(same set of enzymes used repeatedly)

17. 5 principal characteristics of metabolic pathways
Metabolic pathways are irreversible. (large negative free energy change)
Catabolic and anabolic pathways must differ.
Every metabolic pathway has a first committed step.
All metabolic pathways are regulated.
Metabolic pathways in eukaryotic cells occur in specific cellular locations.

18. Metabolism Proceeds in Discrete Steps
Enzyme specificity defines biosynthetic route
Controls energy input and output
Allow for the establishment of control points.
Allows for interaction between pathways

19. Regulation of Metabolic Pathways
Pathways are regulated to allow the organism to respond to changing conditions.
Most regulatory response occur in millisecond time frames.
Most metabolic pathways are irreversible under physiological conditions.
Regulation ensures unidirectional nature of pathways.
Flow of material thru a pathway is referred to as flux.
Flux is regulated by supply of substrates, removal of products, and activity of enzymes

20. Enzyme Regulation of Flux
Common mechanisms
Feedback inhibition – product of pathway down regulates activity of early step in pathway
Feedforward activation – metabolite produced early in pathway activates down stream enzyme

21. Metabolic Control Theory
Pathway flux is regulated by multiple enzymes in a pathway.
Control coefficient determined for each enzyme. =  activity /  enzyme concentration.
Enzymes with large control coefficients impt to overall regulation.
Recent finding suggest that the control of most pathways is shared by multiple pathway enzymes

22. Regulating Related Catabolic and Anabolic Pathways
Anabolic & catabolic pathways involving the same compounds are not the same
Some steps may be common to both
Others must be different - to ensure that each pathway is spontaneous
This also allows regulation mechanisms to turn one pathway and the other off

25. G = H -TS Gibb’s Free Energy
Useful to know how likely a reaction will occur. The measurement of driving force for all reactions is the decrease in G.
G = H -TS
Spontaneous reactions all have -G, but imply nothing about the rate! (G = 0 at equilibrium)
This is related to the G of the entire system.
For our purposes, dependent upon of formation for the reactants and products.
Gf

26. Oxaloacetate (OAA) + H+ CO2 (g) + pyruvate
Gibb’s Free Energy
Oxaloacetate (OAA) + H CO2 (g) + pyruvate
G for the reaction = Gf(products) - Gf(reactants)
Gf (kcal/mol)
OAA
Pyr
CO2(g)
H (-9.87)
pH 7 1M
G = ( ) - ( ) = kcal/mol
‘ indicates physiological conditions
In biochemistry-usually deal with physiological conditions (10-7M H+)
G ‘ = ( ) - ( ) = -7.4 kcal/mol

27. Gibb’s Free Energy
Since the spontaneity of a reaction is independent of the pathway, we can force G of an overall reaction to be negative even though it has a positive step by coupling it to a step with greater -Gf.
Reaction A C same as A B C
GAP
Gº = +1.5
1,3-BPG
Pi + NAD+
NADH
Glyceraldehyde-3-phosphate dehydrogenase
Gº = -4.5
MgADP
MgATP
3PG
3-phosphoglycerate kinase
Method A
(steps 6,7)
GAP
3PG
Gº = -3.0
Net reaction

28. Gibb’s Free Energy Method B C D B A Glucose + Pi G6P MgADP + Pi MgATP
(step 1) C D A B
Gº = +3.3
Glucose + Pi
G6P
MgATP
MgADP + Pi
Gº = -7.3
Net reaction
Glucose + Pi + MgATP
G6P + MgADP + Pi
Gº = -4.0

29. ATP ATP is the energy currency of cells
In phototrophs, light energy is transformed into the light energy of ATP
In heterotrophs, catabolism produces ATP, which drives activities of cells
ATP cycle carries energy from photosynthesis or catabolism to the energy-requiring processes of cells

30. ATP is the general “high energy” coupler molecule used in biochemistry
CH2-O-P-O-P-O-P-O- O N OH HO O-
Mg++
Gº
-7.3
-7.4
-3.0
MgATP
ADP + Pi
MgADP
AMP + Pi
MgATP
AMP + Pi
AMP
Adenosine
+ Pi
Mg Adenosine triphosphate (MgATP)

31. ATP O O
Why is the presence of the anhydride so energetically unfavorable?
P-O-P
(1) Ability of products to delocalize electrons (all phosphates) -O
P=O O O- O -O P O- O
Free ATP
(2) Close proximity of charges (bond strain)
Gº
7.89
9.56
-8.4
-7.7
-7.5 O
pH 6.0 O O
pH 9.0 + +
Adenosine-O-P-O-P-O-P-O-
0.0 M Mg O- O- O-
0.001 M Mg
pK2
0.01 M Mg
ATP-4

32. Phosphoric Acid Anhydrides
ADP and ATP are examples of phosphoric acid anhydrides
Large negative free energy change on hydrolysis is due to:
electrostatic repulsion
stabilization of products by ionization and resonance
entropy factors

33. Phosphoryl-group Transfer
Energy produced from a rxn can be coupled to another rxn that requires energy to proceed.
Transfer of a phosphate group from high energy phosphorylated compounds can activate a substrate or intermediate of an energy requiring rxn.
A-P + ADP -> A + ATP, ATP +C-> ADP + C-P
The ability of a phosphorylated compound to transfer a phosphoryl group is termed its phosphoryl-group-transfer-potential.

34. Phosphoryl-group Transfer

35. In addition to energetics -must balance redox chemistry
Glucose (C6H12O6) + 6 O2
6 CO2 + 6 H2O
Broken down into “half pathways”
Glycolysis
Active hydrogen 2H+ + 2e-
Glucose
2 pyruvate + 2 (2H)
Mitochondria
(2H) + 1/2 O2
H2O

36. Common carrier of (H) O N C-N-H2 N O O N CH2-O-P-O-P-CH2 N N (+) O OOH HO HO OH Pi
NAD(P) Nicotinamide adenine dinculeotide (phosphate)
(oxidized form)
NAD+ + 2e-
NADH + H+

37. Common carrier of (H) O H H N C-N-H2 N O O N CH2-O-P-O-P-CH2 N N O OPi
NAD(P) Nicotinamide adenine dinculeotide (phosphate)
(reduced form)
NADH + H+
NAD+ + 2e-
Eº ‘ = 0.31 volt

38. Gº ‘ = -nF Eº‘ Gº ‘ = -2( )131 volt) Gº ‘ = -56 kcal/mol
Thermodynamically
Eº’ = volt
2e- + 2H+ + 1/2 O2
H2O
NADH + H+
NAD+ + 2H+ + 2e-
Eº’ = volt
NADH + H+ + 1/2 O2
NAD+ + H2O
Eº’ = volt
Ease at which molecule donates electron(s)
aka electromotive force
Convert using the Nernst Equation
Gº ‘ = -nF Eº‘
F = faraday= 23,086 cal
n=mol e-
mol  e-  volt
23,086 cal
Gº ‘ = -2( )131 volt)
mol  e-  volt
Gº ‘ = -56 kcal/mol

39. ATP and NAD(P)H
So in metabolism, ATP formed in reaction sequences where
Gº‘ > Gº‘ hydrolysis of ATP (catabolism)
Used to drive reaction with Gº‘ < Gº‘ hydrolysis (<0)
NAD(P)H production and ATP production are usually coupled
ATP and NAD(P)H are coenzymes and therefore need to be recycled.

40. Thermodynamics and Metabolism
Standard free energy A + B <-> C + D
Go’ =-RT ln([C][D]/[A][B])
Go’ = -RT ln Keq
Go’ < 0 (Keq>1.0) Spontaneous forward rxn
Go’ = 0 (Keq=1.0) Equilibrium
Go’ > 0 (Keq <1.0) Rxn requires input of energy