Yuan Provido

2065 AY2022-23
Chapter 18
1. Explain how glycogenolysis proceeds and how it is controlled (glycogen phosphorylase,
phosphorolysis, phosphoglucomutase, debranching enzymes)
- Glycogenolysis is an alternative pathway for glucose wherein it involves the
conversion of glycogen back into glucose if the cell needs it
- In this process it involves the Glycogen Phosphorylase Reaction involving the
Glycogen phosphorylase which is an enzyme that catalyzes the phosphorolysis
of glycogen to give glucose-1-phosphat

•
• Attack is by phosphate group, therefore also known as a
phosphorolysis instead of hydrolysis
1. Phosphorolysis refers to the addition of phosphoric acid
across a bond, such as the glycosidic bond in glycogen,
giving glucose phosphate and a glycogen remainder one
residue shorter; it is analogous to hydrolysis (addition of
water across a bond)
• G-1-P is converted to G-6-P by an enzyme called
phosphoglucomutase
1. Phosphoglucomutase is an enzyme that catalyzes the
isomerization of glucose-1-phosphate to glucose-
6phosphate
• In muscle cells, G-6-P proceeds to glycolysis
 • In liver cells, G-6-P is hydrolyzed to glucose and exported to other
tissues via the circulatory system
• G-6-P cannot escape the cell by itself
- Moreover, debranching enzymes also are involved in the process wherein these
enzymes hydrolyzes the linkages in a branched-chain polymer such as
amylopectin
• Limit Dextrins
1. The Highly branched polysaccharides left after amylase
activity
2. Degraded by debranching enzymes
1. Oligo-alpha(1,4->1,4)glucanotransferase
• Removes a trisaccharide unit (breaks down after 4 so it breaks down
a segment of three units) and transfers it to another existing
alpha(1->4) glycosidic linkage
1. This results into the chain becoming longer
2. Alpha and Beta-amylase can start to do its function again
until it reaches its limit
• Alpha(1->6)glucosidase removes the single glucose reside in an
Alpha(1->6) linkage to main chain
1. This enzyme comes in the remaining branch point thus it is
able to remove the chain and after this, the Alpha- or Beta-
amylase is now able to take over

•
2. Explain how glycogenesis proceeds and how it is controlled (glycogen synthase, roles of
UDP-glucose pyrhophosphorylase, glycogenin, branching enzyme)
- Glycogenesis is an alternative pathway for glucose wherein it involves the
conversion of glucose into glycogen

-
• Glucose is converted into G-6-P and in this state, it can branch off
to other pathways, specifically it can undergo isomerization thus
converting it into Glucose-1-phosphate
• G-1-P is then converted into glycogen
o This process also involves the UDP-Glucose synthesis
▪ Catalyzed by specific phosphorylase enzymes
▪ Reaction is reversible usually, but can be irreversible by hydrolysis of
pyrophosphate
▪
• 1st step: UTP experiences a nucleophilic attack on its phosphate
group by the G-1-P which is catalyzed by UDP-Glucose
pyrophosphate, which then releases a pyrophosphate o Optional –
the produced pyrophosphate can be hydrolyzed thus the whole
process is now irreversible
o UDP-glucose pyrhophosphorylase is an enzyme that
catalyzes the first stage of the synthesis of glycogen where
in glucose-1-phosphate (obtained from glucose-6phosphate
by an isomerization reaction) reacts with UTP to produce
uridine diphosphate glucose (also called UDPglucose or
UDPG) and pyrophosphate
• 2nd step: This produces UDP-Glucose o Importance of UDP-
Glucose – In glycogen, the formation of glucose polymers is
essential thus the production of UDP-Glucose and its process
showcases how the glucose units are added and formed into
glucose polymers
- Moreover, the enzyme Glycogen Synthase is also involved in this process
wherein this enzyme catalyzes the growth of glycogen chain – specifically it is
necessary for the elongation of glucose units in the glucose polymers
• It involves Glycogenin which is a protein and it forms the core of a
glycogen particle
1. A protein containing a specific tyrosine which has a
hydroxyl group that acts as the primer for the initiation of
glycogen synthesis
• Contains a specific tyrosine residue
• First glucose is linked to the tyrosine residue, tyrosine -OH
• The main purpose of Glycogen synthase is that it transfers glucosyl
units from UDP-glucose to C-4 hydroxyl at a nonreducing end of a
glycogen strand

•
1. First, we have UDP-glucose and the green figure is the
important glucosyl unit
2. The green labeled glucosyl unit is converted into an
Oxonium ion intermediate – the portion that contains the
 positive charge experiences an attack by the c4 hydroxyl
group of an existing glycogen strand
3. This this then elongates the glycogen strand by 1 more unit
(sticking the new one with the strand)
- Lastly, the formation of Glycogen Branches also occurs in this process
• Catalyzed by amylo-(1,4 -> 1,6)-transglycosylase also known as
branching enzyme
1. This enzyme catalyzes the reactions needed to introduce a
branch point during the synthesis of glycogen
• Involves a transfer of a six or seven residue segment from the non-
reducing end of a linear chain at least 11 residues long to the C-6
hydroxyl residue of the same or of another chain

•
• The strand highlighted in yellow is at least 11 residues long and it
is cut by the branching enzyme
• This strand is then transferred to another strand of glycogen
making a new branch
 • This process is repeated in order to form glycogen

3. Explain the logic as to why glycogen phosphorylase and glycogen synthase are under
reciprocal control
- Essentially, glycogen phosphorylase and glycogen synthase are subject to
reciprocal regulation or reciprocal control wherein one is activated and one is
inactivated in order to maintain the balance of blood glucose levels. • It is also
important to note that Glucose derived from glycogen breakdown also supplies
glucose for muscles
• Moreover, blood glucose levels must be maintained at 5mM.

4. Apply mechanisms of control (from previous chapters) to glycogen phosphorylase and

glycogen synthase

- Glycogen Phosphorylase is regulated allosterically

• Inorganic Phosphate is a positive homotropic effector of glycogen
phosphorylase
1. This means that the presence of an inorganic phosphate
allows the Glycogen Phosphorylase to have increased
activity

2.
• ATP and G-6-P are allosteric inhibitors of Glycogen Phosphorylase
 1.
2. ATP is end product of glycolysis (and CAC)
1. This indicates that the cell is in a high energy state
therefore there is no need to break down glycogen
3. G-6-P is converted from G-1-P ; G-6-P enters glycolysis
pathway
1. This indicates that the cell is in a high energy state
4. ATP and G-6-P are negative heterotopic effectors because
they reduce the affinity of enzyme to the inorganic
phosphate – deactivates glycogen phosphorylase
(compared to Inorganic Phosphate)
• AMP is an allosteric activator of glycogen phosphorylase

1.
1. High AMP levels in the cell implies the cell has low
energy – this leads to the usage of glycogen reserves in
order to enter the glycolytic pathway and CAC to start
producing ATPs
 2. AMP binds to same as ATP but stimulates rather than
inhibits the enzyme
1. Due to the AMP having a slightly different shape
• AMP and ATP concentrations in cell are inversely proportional
1. High AMP = Low ATP ; Low AMP = High ATP
2. Both AMP and ATP compete for the same site in the
enzyme with opposite effects, thus, manifesting rapid and
reversible control over glycogen phosphorylase
3. Production of ATP in the cell is commensurate/corresponds
to its needs
- Covalent modification of glycogen
phosphorylase • Glycogen phosphorylase
exists in 2 forms:
1. Phosphorylase a (active form)
2. Phosphorylase b (less active form)
• Conversion from Phosphorylase b to Phosphorylase a is achieved
by phosphorylation
• Phosphorylase a is less sensitive to allosteric regulation

•
1. Phosphorylase a (phosphorylated) is affected by glucose
and caffeine
 2. Phosphorylase b is affected by AMP, ATP, G-6-P, Glucose
and caffeine
3. Covalent modification of phosphorylase overrides allosteric
regulation
1. Which means that allosteric regulation or reactions
are no longer needed to activate the phosphorylases
5. Explain how gluconeogenesis proceeds and how it is controlled (pyruvate carboxylase,
PEP carboxykinase, fructose-1,6-bisphosphatase, glucose-6-phosphatase)

-
• Top to bottom is glycolysis while bottom to top is gluconeogenesis
• Steps 1,3 and 10 are control points in glycolysis
• The others are considered as reversible steps.
1. These reversible steps are shared in Gluconeogenesis
- Gluconeogenesis is the biosynthesis of glucose from simpler molecules,
primarily pyruvate and its precursors. The compounds that are involved in this
process are the following
• Pyruvate
• Lactate
 • Some amino acids (glucogenic)
• Tri-Carboxylic Acid / CAC cycle intermediates
• These molecules can be converted to form glucose
- Moreover this process highlights the need to produce glucose due to..
• Need to maintain glucose levels in narrow range in blood
• Some tissue – such as the brain, erythrocytes, and muscles in
exertion use glucose at a rapid rate and sometimes require glucose
in addition to dietary glucose
- The Gluconeogenesis pathway is similar to the reverse of glycolysis but differs
at critical sites (Pyruvate -> Lactate -> Pyruvate -> Glucose)
• Control of these opposing pathways is reciprocal so that
physiological conditions favoring one disfavor the other and vice
versa (glycolysis and gluconeogenesis are subject to reciprocal
control)
• General principles of metabolic control
1. Pathways are not simple reversals of
each other
2. Under reciprocal control
- Four unique reactions in Gluconeogenesis involve the following enzymes:
• Pyruvate carboxylase reaction
1. Pyruvate -> oxaloacetate
• Phosphoenolpyruvate (PEP) Carobxykinase reaction
1. Oxaloacetate -> phosphoenol pyruvate
• Fructose-1,6-bisphosphatase reaction
1. Fructose-1,6-bisphosphatase -> fructose-
6-phosphate
• Glucose-6-Phosphatase reaction
1. Glucose-6-Phosphate -> Glucose - In
terms of control
-
• G-6-Phosphatase: Km is large

1. This means that the

enzyme is not saturated with substrate under normal
conditions.
2. Activity is nearly linearly dependent on glucose-
6phosphate concentration.
3. This enzyme is said to be under substrate-level control.
• Acetyl-CoA is a potent allosteric effector of glycolysis AND
gluconeogenesis (glycolytic enzyme) ; it also inhibits pyruvate
kinase and pyruvate dehydrogenase but activates pyruvate
carboxylase (gluconeogenesis enzyme)
• Fructose-1,6-bisphosphatase - Inhibited by AMP and activated by
citrate
• Phosphofructokinase - Activated by AMP and inhibited by citrate
6. Indicate how substances other than pyruvate can enter the gluconeogenesis pathway
(lactate, certain amino acids, glycerol)

- Essentially, Sites of Gluconeogenesis are only found in the Liver and

Kidneys
o Source of precursors:
▪ Lactate from muscle – the primary source for pyruvate
• In muscle, lactate is produced in great quantities during exertion
• This excess lactate cannot be further oxidized in muscle
• Lactate is released from the muscles to the blood and travels to the
liver for conversion to pyruvate and to glucose
▪ Glucogenic amino acids from diet or breakdown of muscle protein during
starvation
▪ Propionate from breakdown of fatty acids and amino acids ▪ Glycerol from
fats

7. Explain why oxaloacetate is an intermediate in gluconeogenesis (role of biotin)

-
• The figure showcases the Pyruvate carboxylase reaction
mechanism which leads to the formation of Oxaloacetate
 • Step 1: Nucleophilic attack of a bicarbonate oxygen at the gammaP
(third phosphate of the phosphate group ; starting from right to
left)of ATP to form carbonylphosphate
• Step 2: Rapid reaction of carbonylphosphate with biotin to form N-
carboxybiotin
• Step 3: Abstraction of proton from C3 of pyruvate, forming a
carbanion that attacks C of N-carboxybiotin to form Oxaloacetate

-
- In the Pyruvate carboxylase reaction, Biotin is a coenzyme that is required for
the process.
• Biotin is a carrier of carbon dioxide; it has a specific site for
covalent attachment of CO2
- The Pyruvate Carboxylase enzyme is found only in matrix of mitochondria
 • Oxaloacetate (if present in mitochondria) cannot cross the
mitochondrial membrane
• The enzyme that acts on Oxaloacetate (in gluconeogenesis) is
found in the matrix, the cytosol or both (phosphoenolpyruvate
carboxykinase - PEPCK)
• Matrix: convert oxaloacetate to malate, aspartate or PEP (in order
to move across the mitochondrial membrane)
• Cytosol: exported malate or aspartate must be converted back to
oxaloacetate
1. Based on the figure, once the pyruvate is converted into
oxaloacetate – it is then converted into malate, aspartate or
PEP in order to move across the mitochondrial membrane,
once it is finished crossing – it is again reconverted back
into oxaloacetate thus being able to participate in the
Gluconeogenesis process
- To conclude, during the Pyruvate carboxylase reaction pyruvate is essentially
converted into Oxaloacetate. Since oxaloacetate cannot cross the mitochondrial
membrane, it is converted into malate, aspartate or PEP in order to move across
the mitochondrial membrane and once it is able to fully cross the membrane, it
is again converted back into its original form thus being able to continue the
overall process of gluconeogenesis. Hence its intermediate nature.
• The purpose of the roundabout way of getting oxaloacetate out of the
mitochondria via malate dehydrogenase is to produce NADH in the
cytosol so that gluconeogenesis can continue.

8. Cite the two possible fates of oxaloacetate produced in the mitochondria in

gluconeogenesis (direct conversion to PEP then exported to the cytosol, conversion to
malate then exported to the cytosol then converted back to oxaloacetate)
- 1st: It can continue to form PEP, which can then leave the mitochondria via a
specific transporter to continue gluconeogenesis in the cytosol.
 - 2nd: The other possibility is that the oxaloacetate can be turned into malate via
mitochondrial malate dehydrogenase, a reaction that uses NADH.
• With the newly formed malate, it is then able to leave the and have the
reaction reversed by cytosolic malate dehydrogenase
9. Explain the role of sugar phosphates in gluconeogenesis
- In gluconeogenesis, the Dephosphorylation of Sugar Phosphates occurs in two
reactions that differ from glycolysis, specifically these reactions have a
phosphate-ester bond to a sugar-hydroxyl group is hydrolyze - both reactions
are catalyzed by phosphatases and are exergonic.
- The first reaction is the hydrolysis of fructose-1,6-bisphosphate to produce
fructose-6-phosphate and phosphate ion, essentially this reaction is a control
point in the pathway
- While the second reaction is the hydrolysis of glucose-6-phosphate to glucose
and phosphate ion
• In gluconeogenesis, the organism can make direct use of the fact that
the hydrolysis reactions of the sugar phosphates are exergonic,
hence its importance and role.

10. Explain the logic why glycolysis and gluconeogenesis are under reciprocal control
- Nearly all reactions in glycolysis and in gluconeogenesis occur in the cytosol
• Thus the 2 processes are under reciprocal control
- They exhibit reciprocal control to essentially lessen wasting resources and
energy
• If uncontrolled, both processes would operate simultaneously with
considerable consumption of AT
11. Explain the logic of enzymatic cascade in the activation of glycogen phosphorylase
- Phosphorylase Cascade (way of enzyme activity is controlled)
• Upon binding to cell receptors, a cascade mechanism is induced
 -
• 1st - Hormones are introduced which activates an adenylyl cyclase
• 2nd - Adenylyl cyclase helps converts ATP to cAMP
• 3rd – cAMP activates cAMP-dependent protein kinase
• 4th - cAMP-dependent protein kinase helps activates Active
phosphorylase kinase
• 5th - Active phosphorylase kinase then phosphorylates glycogen
phosphorylase
- The logic of enzymatic cascade in the activation of glycogen phosphorylase
essentially presents that these series of reactions allow for the fine tuning of the
enzymatic activity.

12. Explain how hormones control glycogen metabolism (insulin, glucagon, epinephrine)

o Hormonal Control: Insulin

• Released as a response to increased blood glucose levels
• Produced by islets of Langerhans (specialized cells in the pancreas)
and secreted to the pancreatic vein, which empties into the portal vein
system
• Stimulates transport of glucose into muscle and adipose tissue (fat
cells)
 • Stimulates enzymes that are responsible for glycogen synthesis and
inhibits glycogen breakdown
• Activates glucokinase, phosphofructokinase, and pyruvate kinase
• Inhibits enzymes of glucogenesis
o Hormonal Control: Glucagon
• Released by alpha-cells in pancreatic islets of Langerhans
• Released in response to decreased blood glucose levels
• Peptide hormone
• Active in liver and adipose tissues only
• Involved in long-term maintenance of blood sugar levels
o Hormonal Control: Epinephrine
• Released by adrenal glands in response to central nervous system
signals
• Fight or Flight hormone
• Acts in liver and muscles
• Not involved in long-term maintenance of blood sugar levels.

13. Explain how substrate cycling regulates metabolism

- Substrate cycling refers to the control process in which opposing reactions are
catalyzed by different enzymes
- Two opposing reactions, such as formation and breakdown of a given
substance, are catalyzed by different enzymes, which can be activated or
inhibited separately.
• (Responds rapidly to external stimuli.)
- An example would be Glycolysis and Gluconeogenesis
14. Explain how the Cori cycle recycles lactic acid (dead-end in metabolism) is recycled -
The Cori Cycle is essentially a process wherein the lactate is produced under
anaerobic conditions in the muscles and the produced lactate would be converted back
into Glucose - Steps:
 • Transported into the liver
• Converted to pyruvate
• Eventually back into Glucose
• The Glucose is then re-exported back to the muscles
1. Glucose then undergoes glycolysis
2. If still under anaerobic conditions, it will produce lactic acid
thus proceeding to back into the blood then to the liver and
from there, it undergoes gluconeogenesis which then
transforms into glucose and this is reported back into the
muscles….. vice versa

-
15. Explain the roles of the pentose phosphate pathway PPP in metabolism to produce
pentoses and NADPH (importance of pentoses, metabolic role of NADPH, oxidative
reactions, nonoxidative reactions; you don’t need to worry too much about the
individual reactions)
- PPP or also known as the pentose phosphate pathway is a pathway in sugar
metabolism that gives rise to five-carbon sugars and NADPH
 • The general purpose of this process is to produce NADPH which a
biomolecule needed for biosynthetic purposes and to produce
ribose which is a component of nucleic acids
- Control of the pathway allows the organism to adjust the relative levels of
production of five-carbon sugars and of NADPH according to its needs.
• If the cell just needs Ribose-5-Phosphate and NADPH
1. Only the oxidative branch is active
2. Products: Glucose-6-P -> Ribose-5-P + 2 NADPH

3.
• If the cell only needs Ribose-5-Phosphate
1. The oxidative branch is bypassed and glycolytic
intermediates enter the non-oxidative branch branch
2. Products: 5 glucose-6-P -> 6-ribose-5-P

3.
• If the cell only needs NADPH
1. Ribulose-5-P is all converted back into G-6-P
 2. It passes through the whole cycle both oxidative and
nonoxidative branches
3. Products: 6Ribulose-5-P -> 5Glucose-6-P

4.
• If the cell needs NADPH and ATP
1. Ribulose-5-P is all converted to pyruvate
2. Products: 3 Glucose-6-P -> 3 CO2 + 6 NADPH + 5
pyruvate
3.