chapter 15

Question 1

Metabolic Pathways

Answer 1

-The biochemical reactions in the living cell―metabolism―are organized into metabolic pathways
-The pathways have dedicated purposes:
–Extraction of energy
–Storage of fuels
–Synthesis of important building blocks
–Elimination of waste materials

-The pathways can be represented as a map
–Follow the fate of metabolites and building blocks
–Identify enzymes that act on these metabolites
–Identify points and agents of regulation
–Identify sources of metabolic diseases

Question 2

Metabolic regulation

Answer 2

Maintain homeostasis at the molecular level

Metabolic control-process that leads to a change in the output of a pathway over time in response to a signal or change in circumstances in the cell

Question 3

Metabolic Pathways

Answer 3

-The pathways are intertwined in a multidimensional network of reactions, e.g. some of the possible fates of glucose 6-phosphate:

-passage into glycolysis for ATP production
-passage to the pentose phosphate pathway for NADPH production
-removal of phosphate to replenish blood glucose
-used to synthesize other sugars such as neuraminic acid for use in protein glycosylation
-partially degraded to make acetyl-CoA for fatty acid and sterol synthesis
-Remember E. coli can use glucose to make the carbon skeleton of every one of its molecules. When glucose is shuttled into one pathway, other pathways may be affected either directly or indirectly

Question 4

Homeostasis
-Cells and organisms maintain a
-When the steady state is disturbed
-Organisms maintain homeostasis by
-In steady state, the rate of synthesis of a metabolite equals the
-Pathways are at steady state unless
-After perturbation a NEW steady state

Answer 4

-Cells and organisms maintain a dynamic steady state
-When the steady state is disturbed, fluxes through the pathways are changed to return the organism to a new steady state. This is called homeostasis
-Organisms maintain homeostasis by keeping the concentrations of most metabolites at steady state
-In steady state, the rate of synthesis of a metabolite equals the rate of breakdown of this metabolite
-Pathways are at steady state unless perturbed
-After perturbation a NEW steady state will be established

Question 5

Regulatory mechanisms that have been selected that
-maximize fuel utilization by preventing
-partition metabolites appropriately between
-use fuel best suited for the immediate needs of the organism-
-shut down biosynthetic pathways when their

Answer 5

-maximize fuel utilization by preventing simultaneous operation of pathways that work in opposite directions- e.g. glycolysis and gluconeogenesis
-partition metabolites appropriately between alternative pathways- e.g. glycolysis and the pentose phosphate pathway
-use fuel best suited for the immediate needs of the organism- glucose, fatty acids, glycogen, amino acids
-shut down biosynthetic pathways when their products accumulate

Question 6

Principles of Regulation
-Regulatory mechanisms have evolved to
-The flow of metabolites through the pathways is regulated to
-Sometimes, the levels of required

Answer 6

-Regulatory mechanisms have evolved to ensure that metabolites move through each pathway in the correct direction and at the correct rate to match the organism’s requirements
-The flow of metabolites through the pathways is regulated to maintain homeostasis
-Sometimes, the levels of required metabolites must be altered very rapidly
–Need to increase the capacity of glycolysis during action
–Need to reduce the capacity of glycolysis after the action
–Need to increase the capacity of gluconeogenesis after successful action

Question 7

Feedback Inhibition

Answer 7

In many cases, ultimate products of metabolic pathways directly or indirectly inhibit their own biosynthetic pathways
–ATP inhibits the commitment step of glycolysis

Question 8

Rates of a Biochemical Reactions

Answer 8

-Rates of a biochemical reactions depend on many factors:
-Concentration of reactants vs. products

-Activity of the catalyst
Concentration of the enzyme
-Rate of translation vs. rate of degradation
Intrinsic activity of the enzyme
-Could depend on substrate, effectors or phosphorylation state

-Concentrations of effectors
–Allosteric regulators
–Competing substrates
–pH, ionic environment

Temperature

Question 8

Rates of a Biochemical Reactions

Answer 8

-Rates of a biochemical reactions depend on many factors:
-Concentration of reactants vs. products

-Activity of the catalyst
Concentration of the enzyme
-Rate of translation vs. rate of degradation
Intrinsic activity of the enzyme
-Could depend on substrate, effectors or phosphorylation state

-Concentrations of effectors
–Allosteric regulators
–Competing substrates
–pH, ionic environment

Temperature

Question 9

Proteins have a _____ lifespan

Answer 9

finite

Different proteins in the same tissue have very different half-lives
–Less than an hour to about a week for liver enzymes
–Stability correlates with the sequence at N-terminus

Some proteins are as old as you are
-Crystallins in the eye lens

Question 10

Phosphorylation of enzymes affects their activity
-Most common type of
-Phosphorylation is catalyzed by
-Dephosphorylation is catalyzed by
-Typically, proteins are phosphorylated on the
-Mechanism is to alter the
-Rapid changes due to

Answer 10

-Most common type of modification
-Phosphorylation is catalyzed by protein kinases
-Dephosphorylation is catalyzed by protein phosphatases, or can be spontaneous
-Typically, proteins are phosphorylated on the hydroxyl groups of Ser, Thr or Tyr
-Mechanism is to alter the active site or to force conformational changes the affect Vmax or Km
-Rapid changes due to allosteric changes that are triggered locally by the concentration of a particular metabolic in the cell

Question 11

Enzymes are also regulated
by

Answer 11

regulatory proteins

Binding of regulatory protein subunits affects specificity.

Question 12

Rate of reaction depends on the concentration of substrates
-The rate is more sensitive to concentration at
-The rate becomes insensitive at

Answer 12

The rate is more sensitive to concentration at low concentrations
–Frequency of substrate meeting the enzyme matters

The rate becomes insensitive at high substrate concentrations
–The enzyme is nearly saturated with substrate

Question 13

Km vs. [Metabolite]

Answer 13

-Many enzymes have a Km that is near or greater than the physiological concentration of their substrate
–Especially those utilizing ATP, or NAD(H)

Question 14

Reactions far from equilibrium are common points of regulation
-Within a metabolic pathway most reactions operate near
Key enzymes operate
-To maintain steady state all enzymes operate at

Answer 14

-Within a metabolic pathway most reactions operate near equilibrium
-Key enzymes operate far from equilibrium
–These are the sites of regulation
–Control flow through the pathway
-To maintain steady state all enzymes operate at the same rate

Question 15

ATP and AMP are key cellular regulators

Answer 15

-A 10% decrease in [ATP] can greatly affect the activity of ATP utilizing enzymes
-A 10% decrease in [ATP] leads to a dramatic increase in [AMP]
–AMP can be a more potent allosteric regulator

Question 16

AMP differentially affects pathways

Answer 16

in different tissues via AMPK

Question 17

Some enzymes in the pathway limit the flux of metabolites more than others

-Enzymes that are
-Not all regulated enzymes have the
-Hexokinase and phosphofructokinase are appropriate targets for

Answer 17

-Enzymes that are far from equilibrium (regulated)
-Not all regulated enzymes have the same affect on the entire pathway
–Some control flux through the pathway
–Others regulate steady state concentrations of metabolites in response to changes in flux

Hexokinase and phosphofructokinase are appropriate targets for regulation of glycolytic flux
–Increased hexokinase activity enables activation of glucose
–Increased phosphofructokinase-1 activity enables catabolism of activated glucose via glycolysis

Question 18

Hexokinase affects flux

Answer 18

glycolysis more than phosphofructokinase

Question 19

Glucose regulation at the organismal level
-Certain tissues do not maintain a glucose
-If blood [glucose] falls from
-Two hormones
-Once glucose arrives at the cell, it must be
-This also helps to illustrate another level of control-

Answer 19

-Certain tissues do not maintain a glucose reserve. E.g. brain needs a supply from blood.
-If blood [glucose] falls from 4 to 5 mM to half level, result in mental confusion and a fivefold reduction results in coma or even death
-Two hormones, insulin and glucagon with opposite effects are used to maintain blood glucose
-Once glucose arrives at the cell, it must be transported across the membrane into the cell. This is a point that can be regulated
-This also helps to illustrate another level of control- that is entry of molecules into cells or cellular compartments can be controlled by the action of molecules that transport them across the membrane

Question 20

Three reactions of glycolysis are irreversible

Answer 20

1. hexokinase
2. PFK-1 (phosphofructokinase-1)
3. pyruvate kinase
   -All three reactions have a large negative ΔG’
   -If the forward and reverse of these reactions were catalyzed at the same time, the net effect would be to waste ATP without useful work being done- a large amount of energy would be dissipated as heat and a futile cycle would occur

Question 21

Hexokinase- a regulatory enzyme
-catalyzes the entry of
-Four isozymes (different proteins that cayalyze the same reaction)
-In muscle the predominant form is
-Blood glucose concentration is about
-Muscle hexokinase I and II are inhibited by
-If cellular concentration of glucose 6-phosphate rises above

Answer 21

-catalyzes the entry of free glucose into glycolysis
-Four isozymes (different proteins that cayalyze the same reaction) I-IV occur each encoded by a different gene
-In muscle the predominant form is hexokinase II which has a high affinity for glucose and is half saturated at 0.1mM.
-Blood glucose concentration is about 4-5 mM so hexokinase II is saturated and is able to work maximally
-Muscle hexokinase I and II are inhibited by their product glucose 6-phosphate.
-If cellular concentration of glucose 6-phosphate rises above normal levels, the isozymes are temporarily inhibited to reestablish the steady state

Question 22

Glucose commitment to glycolysis is regulated by PFK-1
-The change of fructose 6-phosphate to fructose 1,6-bisphosphate is
-PFK-1 is a complex enzyme with
-ATP is a substrate for
-When [ATP] high= ATP production is
-Conversely when [ADP] or [AMP] increase in the cell, the inhibition of

Answer 22

-The change of fructose 6-phosphate to fructose 1,6-bisphosphate is irreversible and commits glucose to glycolysis
-PFK-1 is a complex enzyme with several regulatory sites where allosteric activators or inhibitors can bind
-ATP is a substrate for PFK-1 and is also an end product of glycolysis and it is used as a regulator for the activity of PFK-1
-When [ATP] high= ATP production is faster than ATP consumption, then ATP binds PFK-1 at an allosteric site and lowers the affinity for fructose 6-phosphate
-Conversely when [ADP] or [AMP] increase in the cell, the inhibition of ATP is released and enzyme activity increases

Question 23

Other regulators affect PFK-1
-Citrate, a key intermediate in the
-High [citrate] increases the inhibition of
-Citrate serves as an intracellular signal that the cell is meeting its
Fructose 2,6-bisphosphate is also an

Answer 23

-Citrate, a key intermediate in the aerobic oxidation of pyruvate, fatty acids and amino acids also allosterically regulates PFK-1.
-High [citrate] increases the inhibition of ATP, reducing the flow of glucose into glycolysis
-Citrate serves as an intracellular signal that the cell is meeting its current energy needs by oxidation of fats and proteins
-Fructose 2,6-bisphosphate is also an allosteric regulator of PFK-1 in liver

Question 24

The relative amounts of ATP, ADP and AMP regulate the activity of

Answer 24

The relative amounts of ATP, ADP and AMP regulate the activity of PFK-1

Question 25

Regulation of Phosphofructokinase 1 
and Fructose 1,6-Bisphosphatase

Answer 25

Go glycolysis if AMP is high and ATP is low
Go gluconeogenesis if AMP is low

Question 26

Fructose 2,6-bisphosphate
-NOT a glycolytic intermediate, only a
-Produced specifically to regulate
-Insulin has the
-Fructose 2,6-bisphosphate bind to its
-PFK-1 is virtually inactive in the absence of

Answer 26

-NOT a glycolytic intermediate, only a regulator.
-Produced specifically to regulate glycolysis and gluconeogenesis
–activates phosphofructokinase (glycolysis)
–inhibits fructose 1,6-bisphosphatase (gluconeogenesis)
-Insulin has the opposite effect
-Fructose 2,6-bisphosphate bind to its allosteric site on PFK-1 to increase its affinity for its substrate fructose 6-phosphate and reduce its affinity for its inhibitors ATP and citrate.
-PFK-1 is virtually inactive in the absence of fructose 2,6-bisphosphate

Question 27

Activity of fructose 2,6-bisphosphate in liver
-Formation of fructose 2,6-bisphosphate is done by
-The activities of PFK-2 and FBPase-2 are distinct activities of a
-So levels of fructose 2,6-bisphosphate are
-Glucagon reduces the amount of

Answer 27

-Formation of fructose 2,6-bisphosphate is done by PFK-2 acting on fructose 6-phosphate and breakdown is done by fructose 2,6- bisphosphatase (FBPase-2)
-The activities of PFK-2 and FBPase-2 are distinct activities of a bifunctional protein whose relative activities is regulated by hormones
-So levels of fructose 2,6-bisphosphate are regulated by hormones.
-Glucagon reduces the amount of fructose 2,6-bisphosphate by causing decrease in PFK-2 activity and increase in FBPase-2 activity.

Question 28

Pyruvate kinase regulation
-Pyruvate kinase exists in
-All isozymes are inhibited by
-In liver, pyruvate kinase is sensitive to
The muscle form is influenced by

Answer 28

-Pyruvate kinase exists in 3 isozymes that differ in tissue distribution and modulation
-All isozymes are inhibited by high [ATP], acetyl-CoA and long chain fatty acids( signs of abundant energy)
-In liver, pyruvate kinase is sensitive to [cAMP] but differently. Low [glucose], causes [cAMP] to rise. cAMP acts on cAMP-dependent protein kinase to phosphorylate the liver isozyme of pyruvate kinase thereby inactivating it. This reduces the use of glucose as fuel in the liver so that the glucose can be exported to brain as fuel.
-The muscle form is influenced by [cAMP], but glycolysis is stimulated to provide energy for the flight or fight response