Homework Week 3

1. What are the enzymes of gluconeogenesis? With respect to glycolysis what is the significance of
these enzymes? (2 pts.)
a. The enzymes of gluconeogenesis are pyruvate carboxylase, PEP carboxykinase (PEPCK),
fructose-1,6-biphosphatase (FBPase), and glucose-6-phosphatase. The significance of such
gluconeogenic enzymes is that such enzymes provides catalysis to revert from pyruvate to
glucose in a separate metabolic pathway. Given that every metabolic pathway is irreversible,
there is no possible way for the product of glycolysis (i.e. pyruvate) to revert back to glucose
using the exact same enzymes and/or metabolic intermediates in the reverse direction. The
irreversibility of the glycolytic reaction enforces a single-direction tending to the production
of pyruvate only.
b. However, an independent pathway for the reversion of pyruvate to glucose is possible if this
independent pathway is able to differ from the glycolytic pathway. The gluconeogenic
pathway is, in fact, an independent pathway from the glycolytic pathway with being
compromised of previously-mentioned enzymes that are not present in the glycolytic pathway.
In addition, there is a metabolic intermediate, oxaloacetate, not present in the glycolytic
pathway, further enforcing a difference between the two independent pathways. Such
independent pathways also allow for independent controls given by their independence. The
glycolytic pathway can be controlled independently without affecting the gluconeogenic
pathway and vice versa.
c. Furthermore, given that the irreversible glycolytic pathway tends to the production of
pyruvate, yielding a net exergonic, and thus favorable, Gibbs free energy, driving the
glycolytic pathway in reverse from pyruvate to glucose would require free energy (i.e.
endergonic), thereby not being thermodynamically favorable. Typically, metabolic pathways
can avoid this net energy uphill by differing in the enzymes and metabolic intermediates used,
such as in the case of the net-exergonic gluconeogenic pathway, even though you
interchange between the same two substrates (i.e. in glycolysis and gluconeogenesis, pyruvate
and glucose).
2. What is the cofactor for pyruvate carboxylase and what type of reaction does it perform? (1 pt.3)
a. Biotin is the cofactor for pyruvate carboxylase and is CO2 carrier. Biotin facilitates a
carbanion-mediated carboxylation of pyruvate. Biotin does this by being carboxylated at its
N1 position, forming an enzyme-linked carboxybiotinyl structure that carries a CO2 molecule.
b. The enzyme-linked carboxybiotinyl structure subsequently decarboxylates, forming a
resonance-stabilized carbanion that abstracts alpha proton of pyruvate and induces the
formation of a resonance-stabilized carbanion pyruvate molecule (i.e. pyruvate enolate). The
CO2 that the enzyme-linked carboxybiotinyl structure had previously expelled is attacked by
the nucleophilic pyruvate enolate, forming oxaloacetate.
3. PEP carboxykinase decarboxylates oxaloacetate without the use of a cofactor, how does this occur?
(2 pts.)
a. PEP carboxykinase (PEPCK) decarboxylates oxaloacetate without the use of a cofactor given
that beta-keto acids, such as oxaloacetate, are considered “higher-energy” compounds. The
principle of molecules favoring lower-energy state is applied here in that due to oxaloacetate
being a higher-energy compound, it will tend to react in order to convert to a lower-energy
compound and thus lower-energy state. Indeed, decarboxylation fulfills this principle as the
decarboxylated products of beta-keto acids are lower in energy than their starting beta-keto
acids.
4. What property of glycogen makes it an ideal storage molecule? (1 pts.)
 a. The alpha-1-6 branching exhibited by glycogen permits for glycogen’s rapid degradation
through the simultaneous release of glucose units at the end of every branch. The rapid
degradation and simultaneous release provide for an enhanced mobilization of glucose for
efficient energy production.
5. The cofactor pyridixal-5’ phosphate is used in the glycogen phosphorylase reaction. What is its
function in breaking the glycosidic bond? (2 pts.)
a. Pyridoxal-5’-phosphate (PLP) is an essential cofactor for phosphorylase that essentially acts as
a proton donor for the phosphate group that has donated its single proton to the C4-oxygen of
the sugar upstream of the non-reducing end and subsequently accepts a proton from PLP. The
alpha-1-4 linkage is broken with the phosphate group donating its single proton and
effectively acting as an acid. Following this phosphate-acid catalyst, the lone pairs of the C4-
oxygen engages in a nucleophilic attack on C1, forming an oxonium ion. Conversely, the
phosphate group now acts a conjugate base performing a nucleophilic attack on the resulting
oxonium ion at its C1 position in order to form glucose-1-phosphate.
6. What is the role of cAMP in the regulation of glycogen phosphorylase? In your response please
explain (map out) the route to the regulation of glycogen phosphorylase. (2pts.)
a. Cyclic AMP (cAMP), which is synthesized via an adenylate-mediated conversion from ATP,
acts to regulate the activity of protein kinase A (PKA). Specifically, cAMP acts to activate and
upregulate the activity of protein kinase A (PKA). PKA subsequently phosphorylate the
inactive phosphorylase kinase b to convert it to the active phosphorylase kinase a.
Phosphorylase kinase a then acts to convert the inactive glycogen phosphorylase b to the
active glycogen phosphorylase a as well as to convert the active glycogen synthase a to the
inactive glycogen synthase b. The PKA-mediated, simultaneous activation of glycogen
phosphorylase a and inactivation of glycogen synthase b ensures that net glycogenolysis
proceeds. In addition, the cAMP-dependent PKA further ensures net glycogenolysis by
activating the phosphoprotein phosphatase inhibitor, preventing the removal of activating
phosphorylations performed by the PKA itself as well as by the active phosphorylase kinase a.