1. Important to recognize that metabolic need of individual cells is different from need of whole organism.
Brain needs glucose even when body is starving.
Liver will synthesize glucose via gluconeogenesis while brain uses glucose via glycolysis

2. FIGURE 15-1 Metabolism as a three-dimensional meshwork
FIGURE 15-1 Metabolism as a three-dimensional meshwork. A typical eukaryotic cell has the capacity to make about 30,000 different proteins, which catalyze thousands of different reactions involving many hundreds of metabolites, most shared by more than one "pathway." This overview image of metabolic pathways is from the online KEGG (Kyoto Encyclopedia of Genes and Genomes) PATHWAY database ( Each area can be further expanded for increasingly detailed information, to the level of specific enzymes and intermediates.

3. It is related to conc of substrate and product
Free energy
A-B + C --- B-C + A
If this reaction is displaced from equilibrium, some energy will be released as the reaction returns towards equilibrium.
The energy released could be lost as heat or made to do work (ATP)
Free energy (DG) of a chemical reaction is a measure of its capacity to do work.
It is related to conc of substrate and product
DG = -RTln[eqP]/[eqS]+RTln[initP]/[initS]
If initial conc =1M, RTln[initP]/[initS]=0
You get
DGo=-RTlnK
At equilibrium free energy change is zero
Higher the substrate conc, lower the product conc, greater the DG value.

4. Equilibrium
At equilibrium, rate of forward and reverse reaction is identical A --- B
No net flux in either direction A----- B----
At equilibrium No free energy change
Change in free energy as a reaction proceeds towards equilibrium is the key driving force in biological processes.
Equilibrium processes do not perform useful work (movement)
Equilibrium processes can not be easily regulated
Complex molecules (and processes) will not be made in large quantities under equilibrium conditions
Biological systems obtain energy to prevent equilibriums from reaching.

5. Open and closed systems
A-B + C --- B-C + A
In a closed system, heat released will equal heat absorbed
In an open system, heat released will be lost to environment, prevents the reaction from reaching equilibrium
Furthermore, all free energy change is not lost as heat. Some is captured as chemical bond energy (ATP)
A-B + C   B-C + A
/ \
ADP+Pi ATP
If all free energy change were captured as ATP, the reaction would be at equilibrium and there would be no net gain of ATP. However partial loss of energy as heat to the environment converts this reaction into a non equilibrium reaction allowing flux through the pathway towards ATP generation.

6. Dynamic steady state
Living cells are NOT AT EQUILIBRIUM
They maintain a DYNAMIC STEADY STATE
Glucose enters cells, and CO2 leaves cell, but mass and composition of cell do not change appreciably. Cells appear to be but are not at equilibrium with surroundings.
At molecular level each metabolic pathway is unidirectional and functioning.
Rate of metabolic flow (flux) through the pathway is high, but concentration of substrate/intermediates/products remains constant.
v1 v2
A S  P
v1=v2
If this steady state is disrupted, by external change in energy etc, temporarily the fluxes through the pathway will change and regulatory mechanisms will be triggered and the organism will arrive at a new steady state to achieve homeostasis.
Direction of flux in a pathway is dictated by position of equilibrium at each step of pathway

7. Steady state
Steady State- all flows/fluxes are constant and unchanging.
Living systems try and maintain a steady steady.
An open system at steady state is at maximum thermodynamic efficiency.
Changes in fluxes/flow require changes, which require energy.
Changes in the environment result in perturbation of the steady state, and the organism responds and re-obtains new steady state.
How are process maintained in non-equilibrium state?
Exchange of matter and energy between organism and environment
Substrates are derived from environment, products are returned to environment
(Metabolic processes only attain equilibrium at death)

8. Flux and equilibrium
10/sec 20/s ec 110/sec
A< B < C < D
0.1/sec 10/sec 100/sec
Some reactions are close to equilibrium other are obviously far from equilibrium
All the reactions are sufficiently away from equilibrium so that the process is not at equilibrium
While in theory all enzymes are regulated, activity of only certain enzymes regulate flux through the pathway
Reactions are usually limited by the substrate (intermediate) conc.
Therefore: Function of enzyme- Catalysis AND Monitoring state of pathway Via conc of substrates/products)

9. FIGURE 15-4 Near-equilibrium and nonequilibrium steps in a metabolic pathway. Steps 2 and 3 of this pathway are near equilibrium in the cell; for each step, the rate (V) of the forward reaction is only slightly greater than the reverse rate, so the net forward rate (10) is relatively low and the free-energy change, ΔG′, is close to zero. An increase in [C] or [D] can reverse the direction of these steps. Step 1 is maintained in the cell far from equilibrium; its forward rate greatly exceeds its reverse rate. The net rate of step 1 (10) is much larger than the reverse rate (0.01) and is identical to the net rates of steps 2 and 3 when the pathway is operating in the steady state. Step 1 has a large, negative ΔG′.

10. FIGURE 15-8 Flux control coefficient, C, in a branched metabolic pathway. In this simple pathway, the intermediate B has two alternative fates. To the extent that reaction B → E draws B away from the pathway A → D, it controls that pathway, which will result in a negative flux control coefficient for the enzyme that catalyzes step B → E. Note that the sum of all four coefficients equals 1.0, as it must for any defined system of enzymes.
In this simple pathway, the intermediate B has two alternative fates. To the extent that reaction B → E draws B away from the pathway A → D, it controls that pathway.

11. Product +ATP (equilibrium)
Enzymes and Equilibrium
Almost all steps in a pathway lose heat energy and are therefore displaced slightly from equilibrium.
Most enzyme catalyzed reactions in metabolism operate close to equilibrium.
In a few cases, they are not close to equilibrium. (Non equilibrium enzymes possess low catalytic activity so substrates accumulate and they will limit flux through pathway)
These reactions will generate the greatest free energy change and produce the most work
River—dam—sluice gate—work turbines
While to some extents all enzymes are regulated, the bottleneck enzymes are rate limiting and highly regulated.
Substrate energy
Product +ATP (equilibrium)
Energy loss as
reaction proceeds
Product +ATP + heat (non-equilibrium)
Product energy
Product + heat

12. A ---- B ---- C -------- D ---- E ---- F ---- G
Enzymes working farthest from equilibrium are often used in regulation of a pathway because the reverse reaction is not easily attainable (would require a very great increase in conc of D to reverse the reaction)
Natural bottlenecks!
A ---- B ---- C  D ---- E ---- F ---- G

13. Factors that affect flux
Flux through pathway are regulated by
1 Availability of substrate
2 Conc of enzymes responsible for rate limiting step
3 Allosteric regulation of enzyme (Feedback regulation)
4 Covalent modification of enzyme
5 Product removal
Reduction in substrate will decrease activity of enzyme (provided enzyme is not saturated by substrate- most biological pathways operate at suboptimal conc of substrate)
Removal of product enables reaction to proceed in a specific direction

14. Substrate concentration
FIGURE 15-9 Elasticity coefficient, ε, of an enzyme with typical Michaelis-Menten kinetics. At substrate concentrations far below the Km, each increase in [S] produces a correspondingly large increase in the reaction velocity, v. For this region of the curve, the enzyme has an ε of about 1.0. At [S] >> Km, increasing [S] has little effect on v; ε here is close to 0.0.
At substrate concentrations far below the Km, each increase in [S] produces a correspondingly large increase in the reaction velocity, v. For this region of the curve, the enzyme has an ε of about 1.0. At [S] >> Km, increasing [S] has little effect on v; ε here is close to 0.0.

15. FIGURE 15-7 Dependence of glycolytic flux in a rat liver homogenate on added enzymes. Purified enzymes in the amounts shown on the x axis were added to an extract of liver carrying out glycolysis in vitro. The increase in flux through the pathway is shown on the y axis.
Dependence of glycolytic flux in a rat liver homogenate on additional enzymes. Purified enzymes were added to an extract of liver carrying out glycolysis in vitro. The increase in flux through the pathway is shown on the y axis.

16. Mechanism of gene regulation by the transcription factor FOXO1.
Insulin activates a signaling cascade, leading to activation of protein kinase B (PKB). FOXO1 in the cytosol is phosphorylated by PKB, and the phosphorylated transcription factor is degraded by proteasomes.
Unphosphorylated FOXO1 can enter the nucleus, bind to specific gene promoters, and trigger transcription of the associated genes. Insulin therefore has the effect of turning off the expression of these genes, which include glucose 6-phosphatase.
FIGURE Mechanism of gene regulation by the transcription factor FOXO1. Insulin activates the signaling cascade shown in Figure 12-16, leading to activation of protein kinase B (PKB). FOXO1 in the cytosol is phosphorylated by PKB, and the phosphorylated transcription factor is tagged by the attachment of ubiquitin for degradation by proteasomes. FOXO1 that remains unphosphorylated or is dephosphorylated can enter the nucleus, bind to a response element, and trigger transcription of the associated genes. Insulin therefore has the effect of turning off the expression of these genes, which include PEP carboxykinase and glucose 6-phosphatase.

17. FIGURE The PEP carboxykinase promoter region, showing the complexity of regulatory input to this gene. This diagram shows the transcription factors (smaller icons, bound to the DNA) known to regulate the transcription of the PEP carboxykinase gene. The extent to which this gene is expressed depends on the combined input affecting all of these factors, which can reflect the availability of nutrients, blood glucose level, and other factors that go into making up the cell's need for this enzyme at this particular time. P1, P2, P3I, P3II, and P4 are protein binding sites identified by DNase I footprinting (see Box 26-1). The TATA box is the assembly point for the RNA polymerase II (Pol II) transcription complex.

19. FIGURE Regulation of hexokinase IV (glucokinase) by sequestration in the nucleus. The protein inhibitor of hexokinase IV is a nuclear binding protein that draws hexokinase IV into the nucleus when the fructose 6-phosphate concentration in liver is high and releases it to the cytosol when the glucose concentration is high.
Regulation of glucokinase by sequestration in the nucleus. The protein inhibitor of glucokinase is a nuclear protein that draws glucokinase into the nucleus when the enzyme is not required but releases it to the cytosol when the glucose concentration is high and the enzyme is required.

20. Protein phosphorylation and dephosphorylation.
FIGURE 15-3 Protein phosphorylation and dephosphorylation. Protein kinases transfer a phosphoryl group from ATP to a Ser, Thr, or Tyr residue in an enzyme or other protein substrate. Protein phosphatases remove the phosphoryl group as Pi.

21. Reversal of entire pathways
Reversal of entire pathway of glycolysis is difficult.
DGo’ for glycolysis (glucose to pyruvate is -73 kJ/mol
To do reverse reaction, you need to change product (pyruvate) conc many billion fold. Not feasible!
Also reversing reaction leads to loss of ATP

22. Glycolysis Vs Gluconeogenesis
Pyruvate
Glu
G6P
F6P
F1,6P2
PEP
Hexokinase
PFK1
Kinase
Regulation of three irreversible steps
Cell uses some enzymes from glycolysis in gluconeogenesis
Reactions with small DG are used by both pathways.
Reactions with large DG- regulated
Glucose 6-Phosphatase
Fru 1,6 bisphosphatese1
PEP-carboxykinase
Oxaloacetate
Pyruvate carboxylase

23. Factors affecting enzymes
FIGURE 15-2 Factors affecting the activity of enzymes. The total activity of an enzyme can be changed by altering the number of its molecules in the cell, or its effective activity in a subcellular compartment (1 through 6), or by modulating the activity of existing molecules (7 through 10), as detailed in the text. An enzyme may be influenced by a combination of such factors.

24. ATP requirement
FIGURE 15-5 Effect of ATP concentration on the initial velocity of a typical ATP-dependent enzyme. These experimental data yield a Km for ATP of 5 mM. The concentration of ATP in animal tissues is ~5 mM.
Effect of ATP concentration on the initial velocity of a typical ATP-dependent enzyme. These experimental data yield a Km for ATP of 5 mM. The concentration of ATP in animal tissues is ~5 mM.

25. Glucagon and insulin
The three enzymes catalyze irreversible steps
Concentration of these enzymes is regulated by hormones
Insulin is secreted from pancreas (b-cells) when glucose levels in blood increase (Insulin promotes storage of energy).
It induces transcription/translation of glucokinase, phosphofructokinase and pyruvate kinase (effects occur over hours)
Glucagon is secreted from pancreas (a-cells) when blood glucose is low. It has opposite effects (induces release of glucose into blood)

26. Rate of entry of glucose into cells is regulated by transporters.
Blood glucose level is 5mM
Basal Glucose transporter in most cells has Km of 1mM. Less than blood glucose and so glucose is taken up easily.
But in liver and pancreas glucose transporters have Km of ~15mM (close to blood glucose levels).
This allows pancreatic cells to monitor glucose levels and thereby regulate insulin secretion.
In liver cells, glucose is only taken up when it is very abundant. Then liver cells acquire glucose and convert it to glycogen and fatty acids.

27. Liver Muscle Regulation of glucose Blood glu high, (feeding)
Glut2 takes up glu,
Glucokinase induced
G6P produced and used in glycolysis or stored
Blood glu high, (feeding)
Glut4 takes up glu,
Hexokinase makes G6P
If glycogen stores are filled, high G6P inhibits hexokinase.
Blood glu low, (starving)
Glut2 not taking up glu
Glucokinase synthesis repressed
G6P not made
Blood glu low, (starving/resting)
Glut4 taking up glu (little)
Hexokinase is constitutively active
During exercise,
Blood glu low/high
Glut4 takes up glu (little/much)
Low G6P,
Hexokinase fully active
High glycolysis from glycogen stores or blood glucose

28. Glucokinase and Hexokinase
Glucokinase Hexokinase
Kinetic parameter
Km High (10mM) low (<0.1mM)
low affinity high affinity
Vmax high low
Tissue distn Liver, pancreas muscle and other tissues
Glucokinase activity increases with increased glucose but is not inhibited by increased glu6PO4. The levels of the protein are regulated by insulin.
Rate of reaction is driven by substrate-glucose not by demand for product-G6P. Allows all glu available to be converted to G6P and then if excess present, it is converted to glycogen and from there to triglycerides and fatty acids
Hexokinase activity increases with increased glucose but activity is inhibited by increased G6P. The levels of enzyme are constitutive. It only generates ATP when energy is required.
Glucokinase is not normally active because its Km is lower than normal blood glucose levels. Eating food increases glu in blood, activates glucokinase which converts glu to glycogen and fatty acids.
Blood glucose is 5mM

29. Note the sigmoidicity for glucokinase and the much lower Km for hexokinase I. When blood glucose rises above 5 mM, glucokinase activity increases, but hexokinase I is already operating near Vmax and cannot respond to an increase in glucose concentration.
FIGURE Comparison of the kinetic properties of hexokinase IV (glucokinase) and hexokinase I. Note the sigmoidicity for hexokinase IV and the much lower Km for hexokinase I. When blood glucose rises above 5 mM, hexokinase IV activity increases, but hexokinase I is already operating near Vmax and cannot respond to an increase in glucose concentration. Hexokinases I, II, and III have similar kinetic properties.

30. FIGURE Regulation of hexokinase IV (glucokinase) by sequestration in the nucleus. The protein inhibitor of hexokinase IV is a nuclear binding protein that draws hexokinase IV into the nucleus when the fructose 6-phosphate concentration in liver is high and releases it to the cytosol when the glucose concentration is high.

31. (nucleotides/cell div) Glycogen synthesis
Pyruvate
Kinase
Hexokinase
PFK1
Glu
G6P
F6P
F1,6P2
PEP
Pyruvate
Pentose phosphate
(nucleotides/cell div)
Glycogen synthesis

32. Control of glycogen synthesis from blood glucose in muscle.
Insulin affects three of the five steps in this pathway, but it is the effects on transport and hexokinase activity, not the change in glycogen synthase activity, that increase the flux toward glycogen.
FIGURE Control of glycogen synthesis from blood glucose in muscle. Insulin affects three of the five steps in this pathway, but it is the effects on transport and hexokinase activity, not the change in glycogen synthase activity, that increase the flux toward glycogen.

33. Liver Muscle Regulation of PFK1 Regulation of three irreversible steps
PFK1 is rate limiting enzyme and primary site of regulation
Liver
Muscle
Enzyme levels induced by insulin and reduced by starvation
Allosterically activated by
AMP (during exercise)
F2,6,BP
Allosterically inhibited by
ATP (high energy state/resting)
Citrate (high energy state- from Krebs cycle)
(fatty acid oxidation)
Constitutively on

34. PFK1 regulation by F2,6P2
PFK-2 catalyzes
F6P + ATP -> F2,6P2 + ADP
PFK-2 allosterically activated by F6P and insulin (insulin induced dephosphorylation)
High Glu- high F6P
Therefore PFK2 active-- high F2,6P2
F2,6P2 activates PFK1 and you get high glycolysis and fat synthesis
FBPase1

35. PFK2/FBPase2
F2,6P2 is made and degraded during metabolic transition
Its conc determines whether you get gylcolysis or gluconeogenesis
It is a positive allosteric effector of PFK1
It is a negative (inhibitor) of FBPase1
F2,6P2 is made and degraded by a SINGLE enzyme with two distinct domains having two distinct activities
-kinase (PFK2) synthesizes F2,6P2
-bisphosphatase (FBPase2) degrades F2,6P2
PFK2/FBPase2 is regulated by metabolic factors/hormones
F6P activates PFK2 and inhibits FBPase2 thus regulating level of F2,6P2

36. G6P F6P PFK2/FBPase2 PFK1 F2,6 P2 FBPase1 F1,6 P2 PEP In liver
Lots of glucose,
Lots of F6P made
F6P activates PFK2 (also inhibits FBPase2)
This makes more F2,6P2
F2,6P2 activates PFK1 (also inhibits FBPase1)
This now makes more F1,6P2
When glucose levels drop and decrease
F6P levels drop
Inhibition of FBPase2 is reduced, F2,6P2 levels reduce.
Lower levels of F2,6P2 reduced inhibition of FBPase1 and the reverse reaction now proceeds making more glucose.
PFK2/FBPase2 is also regulated by phosphorylation by PKA and PP2A
Phosphorylation- reduces PFK2 kinase activity and increases FBPase2 activity (generating more glucose)
PKA is regulated by AMP. More AMP in cell means less ATP energy (i.e. less glucose) so liver makes more glucose to secrete into blood for other organs.
G6P
F6P
PFK2/FBPase2
PFK1
F2,6 P2
FBPase1
F1,6 P2
PEP

37. FIGURE 15-6 Role of AMP-activated protein kinase (AMPK) in carbohydrate and fat metabolism. AMPK is activated by elevated [AMP] or decreased [ATP], by exercise, by the sympathetic nervous system (SNS), or by peptide hormones produced in adipose tissue (leptin and adiponectin, described in more detail in Chapter 23). When activated, AMPK phosphorylates target proteins and shifts metabolism in a variety of tissues away from energy-consuming processes such as the synthesis of glycogen, fatty acids, and cholesterol; shifts metabolism in extrahepatic tissues to the use of fatty acids as a fuel; and triggers gluconeogenesis in the liver to provide glucose for the brain. In the hypothalamus, AMPK stimulates feeding behavior to provide more dietary fuel.

38. Coordinated Regulation of PFK-1 and FBPase-1
Both are inducible, by opposite hormones (insulin and glucagon)
Both are affected by F2,6P2, in opposite directions

39. Pyruvate dehydrogenase
Pyruvate + CoA + NAD -> AcetylCoA + CO2 + NADH
Amino acids
Glucose
Lactate
PDH
Acetyl CoA
Oxaloacetate
CO2+H2O
Fatty acid
Ketone
TCA cycle
Gluconeogenesis

40. Regulation of PDH Muscle
Resting (don’t need energy)
Hi energy state
Hi NADH & AcCoA & ATP
Inactivates PDH
Hi ATP & NADH & AcCoA
Inhibits PDH
Exercising (need energy)
Low NADH, ATP, AcCoA

41. Regulation of PDH Liver
Just been Fed (high blood glucose)
Need to convert glucose to Fatty acids
Hi energy
Insulin activates PDH
Starved (don’t need PDH)
No insulin
PDH inactive

42. FIGURE 15-41 Regulation of carbohydrate metabolism in the liver
FIGURE Regulation of carbohydrate metabolism in the liver. Arrows indicate causal relationships between the changes they connect. For example, an arrow from ↓A to ↑B means that a decrease in A causes an increase in B. Pink arrows connect events that result from high blood glucose; blue arrows connect events that result from low blood glucose.