153C Final Exam Study Guide

Below are topics that you need to know for the final exam. The following questions and comments are meant
to guide your studying for the final exam. The final exam will be somewhat comprehensive. Those topics from
the first two midterms will be listed. The final will emphasize the material covered after the second midterm;
lipid metabolism, sterol metabolism, hormonal integration and tissue specialization and neuronal control of
metabolism. You will have 3 hours to complete the exam.

1) What are the five types of biochemical reactions? Give an example of each type from the pathways we
have learned about and any use of critical R groups in the active site that allow the reaction to occur.
a) Group-transfer reactions:
i) Common groups transferred: acyl, phosphoryl, glycosyl
ii) Mediated via nucleophile-electrophile reactions and formation of intermediates
b) Oxidation-reduction reactions:
i) Biological reduction and oxidation reactions mediated by use of electron carriers.
ii) Ex: FAD+/FADH2, NAD+/NADH mediate one-electron and two-electron transfer vs. electron
transport chain (ETC): molecular oxygen can only accept one-electron.
iii) Dehydrogenase: removal of hydrogen on substrate; effectively oxidizing substrate
c) Elimination, isomerization, and rearrangements:
i) Eliminations, common: dehydration (removal of water)
ii) Isomerization, common: intramolecular shift of a H like in tautomerization
iii) Rearrangements, common: break/reform carbon skeleton mediated by additions of nucleophilic
carbanion to electrophilic carbocation
(1) Requires stabilization of the carbanion either via Schiff base formation (positively charged
nitrogen acts a electron withdrawing group towards negatively-charged carbanion, promoting
charge spreading) and/or resonance.
d) Reactions that synthesize and destroy double bonds: (see elimination reactions)
2) What are the five principles of metabolic pathways? Please give an example that illustrates each of the
five principles from the pathways and enzymes we have covered in this class.
a) Metabolic pathways are irreversible
i) Large negative dG is indicative that a reaction is irreversible as well as spontaneous.
ii) Reaction steps where dG ~ 0 indicates equilibrium steps.
b) Catabolic and anabolic pathways must differ.
i) Ex: catabolic paths: glycolysis, beta-oxidation vs. anabolic paths: gluconeogenesis, fatty acid
synthesis
c) Every metabolic pathway has a first committed step.
i) One of the irreversible steps (i.e. large, negative dG)
ii) If successfully proceeds through step, then overall reaction proceeds to completion.
d) All metabolic pathways are regulated: for example, negative feedback loops.
i) Rate limiting step (RLS) or rate-determining step (RDS) = slowest (kinetics, large activation
energy) as well as irreversible (thermodynamics; large, negative dG)
e) Metabolic pathways are localized in specific cells and tissues (recall that prokaryotes have no cellular
compartments, organelles)
i) Ex: liver performs glycogen, gluconeogenesis whereas muscle, adipose perform glycolysis
3) List the enzyme co-enzymes/co-factors that we learned about in the course noting an enzyme/pathway
they are associated with and the type of biochemical reaction they function in.
a) Glycolysis (cytosol): hexokinase (HK), phosphoglucose isomerase (PGI), phosphofructokinase (PFK),
aldolase, triose phosphate isomerase (TIM), glyceraldehyde-3-phosphate dehydrogenase (GADPH),
phosphoglycerate kinase (PGK), phosphoglycerate mutase (PGM), enolase, pyruvate kinase (PK),
b) Homolactate fermentation (cytosol): lactate dehydrogenase (LD)
c) Alcoholic fermentation (cytosol): pyruvate decarboxylase (PD), alcohol dehydrogenase (AD)
 d) Pyruvate decarboxylation (matrix): pyruvate dehydrogenase (E1), dihydrolipoyl transacetylase (E2),
dihydrolipoyl dehydrogenase (E3); summation: pyruvate decarboxylation complex (PDC)
e) Citric acid cycle (CAC): citrate synthase, aconitase, isocitrate dehydrogenase (ID), alpha-
ketoglutarate dehydrogenase [similar to PDC], succinyl-CoA synthetase, succinate dehydrogenase,
fumarase, malate dehydrogenase
f) Electron transport chain (ETC): complex I (NADH-hydrogenase), complex II (succinate
dehydrogenase), complex III (CoQ-Cyt C oxidoreductase), complex IV (Cyt C oxidase), complex V (ATP
synthase)
g) Gluconeogenesis: pyruvate carboxylase, PEP carboxykinase (PEPCK), fructose-1-6-BP (F-1,6-BPase),
glucose-6-phosphatase
h) Glycogen mobilization (glycogenolysis): glycogen phosphorylase, glycogen debranching enzyme,
phosphoglucomutase, phosphorylase kinase (PhK), phosphoprotein phosphatase-1 (PP1),
phosphoprotein phosphatase inhibitor 1 (inhibitor-1)
i) Glycogen biosynthesis: UDP-glucose pyrophosphorylase, glycogen synthase, glycogen-branching
enzyme
j) Glyoxylate pathway: citrate synthase, aconitase, malate dehydrogenase, isocitrate lyase, malate
synthase
k) Pentose phosphate pathway: glucose-6-phosphate dehydrogenase, lactonase, 6-phosphogluconate
dehydrogenase, phosphopentose isomerase, transketolase, transaldolase
l) Transamination: aminotransferase
m) Deamination: glutamate dehydrogenase (GDH)
n) Urea cycle: carbamoyl phosphate synthetase I, ornithine transcarbamoylase, arginosuccinate
synthetase, arginase
o) Amino acid biosynthesis: glutamate synthase, glutamine synthetase, glutamine amidotransferase,
aspartokinases (I, II, III)
p) Heme biosynthesis: porphobilinogen deaminase (PBG)
q) Beta-oxidation: acyl-CoA synthetases, acyl-CoA dehydrogenase, enoyl-CoA hydratase, 3-L-
hydroxyacyl-CoA dehydrogenase, beta-ketoacyl CoA thiolase, 2,4-dienoyl-CoA reductase, 3,2-enoyl-
CoA isomerase
4) Why is glycolysis the preferred catabolic route for ATP production in the cell? Also explain when and why
the citric acid cycle is used in the production of ATP in tissues such as the nervous system and cardiac
muscle?
a) Glycolysis (cytosol, either under anaerobic, aerobic):
i) Hexokinase (HK), phosphoglucoisomerase (PGI), PFK-1, Aldolase, GADPH
b) Citric acid cycle (matrix, aerobic):
5) Explain what is meant when the term amphibolic is used to describe the citric acid cycle?
a) Amphibolic, describes biochemical pathway involving both catabolic and anabolic steps.
b) CAC does contain both catabolic and anabolic steps;
i) Citrate to succinyl-CoA: catabolic
ii) Succinyl-CoA to oxaloacetate (OAA): anabolic
6) How do the cofactors, CoQ and cytochrome C of in the electron transport chain facilitate the transfer of
electrons from NADH to the redox centers of the electron transport chain complexes?
a) Co-enzyme CoQ can participate in either one- or two-electron transfers whereas cytochrome C can
only participate in one-electron transfers at a time. The semiquinone form of co-enzyme CoQ
manifests its ability to stably mediate one-electrons in that one electron radical in the structure is
resonance-stabilized. Therefore, the transfer of electron from CoQ to Cyt C can be achieved vis the
semiquinone form of CoQ.
7) What are the enzymes that make gluconeogenesis thermodynamically favorable?
a) Gluconeogenesis (cytosol; reverse of glycolysis) is the opposite of glycolysis; however, recall that
metabolic pathways must differ from each other. Energy consideration enforces this principle as
glycolysis is net exergonic; and so, if glycolysis ran exactly in the opposite direction with the same
 reactions but in reverse, this net pathway would be net endergonic. Just the mere fact that a
metabolic pathway is net endergonic violates the principle of metabolic pathways being irreversible
and thus net exergonic. Therefore, satisfying both principles can be achieved by circumventing the (3)
irreversible steps in glycolysis with using different enzymes that will also catalyze irreversible steps in
gluconeogenesis. Other intermediates will be employed as well too, ensuring that both glycolysis and
gluconeogenesis are different and that both pathways are net irreversible (i.e. net exergonic).
b) Gluconeogenesis:
i) Pyruvate carboxylase: biotin-mediated addition of carbon dioxide to pyruvate to form
oxaloacetate (OAA, recall: citric acid cycle intermediate)
ii) PEP carboxykinase (PEPCK): OAA decarboxylates, forming a carbanion that tautomerizes to the
enol form; negatively-charged oxygen of enol performs a nucleophilic attack on GTP to form PEP
(recall: glycolytic intermediate; bypasses pyruvate kinase step)
iii) Fructose-1-6-BP (F-1,6-BPase): converts F-1,6-BP to F6P and bypasses glycolytic PFK-1.
iv) Glucose-6-phosphatase converts G6P to glucose; bypasses hexokinase.
8) Be able to explain what chemical properties of the PLP cofactor allow it to mediate the same reaction but
result in the cleavage of different bond positions.
a) Pyridoxal-5’-phosphate (PLP) exhibits a carbonyl group that can participate in the formation of a
Schiff base as well as a conjugated ring (i.e. benzene). Both components can stabilize the formation of
carbanion on the substrate for an enzyme.
b) PLP cofactor in glycogen mobilization (i.e. glycogenolysis): a component in glycogen phosphorylase
and linked to the enzyme as Schiff base; facilitates the inorganic phosphate in its role as an
electrophile and subsequent nucleophile by first being a proton donor and then a proton acceptor.
c) Similar to PLP: thiamin pyrophosphate (TPP) exhibits a thiazolium ring that has an acidic proton,
granted by the resonance-stabilization that can occur upon carbanion formation; in addition, the in-
ring positively-charged nitrogen augments the stabilization provide by resonance by functioning as an
electron-withdrawing group, spreading the negative charge from the carbanion towards the
positively-charged nitrogen.
9) Amino acids are classified as what two types depending on their α-ketoacid carbon skeletons?
a) Following the removal of amino group from amino acid, the remaining carbon skeleton (i.e. the alpha-
keto acid) dictates whether it will enter a gluconeogenic precursor pool or a ketogenic precursor pool.
b) Carbon skeletons that gluconeogenic can be converted into pyruvate (3-carbon alpha-keto acid) and
oxaloacetate (OAA, alpha-keto diacid) whereas carbon skeletons that are ketogenic can be converted
into acetyl-CoA.
c) Note that there are two strategies for the removal of the alpha- amino group: transamination and
deamination. Transamination simply exchanges the alpha-amino group of one amino group to an
alpha-keto acid (e.g. alpha-ketoglutarate), resulting in the alpha-keto acid of the former amino acid
and the amino acid (e.g. glutamate) of the former alpha-keto acid.
i) PLP-linked aminotransferase forms a Schiff base with the addition of an alpha-amino group of an
amino acid. The resulting PLP—linked-aminotransferase Schiff base is subsequently hydrolyzed
with the PLP-linked aminotransferase (i.e. PMP-enzyme) now containing the amino group that
was once the alpha-amino group of the initial amino acid. Now, the PMP-enzyme reacts with an
alpha-keto acid (i.e. alpha-ketoglutarate) in efforts of not only regenerating its catalytic active site
but also in generating the corresponding amino acid (e.g. glutamate).
ii) However, to truly eliminate the alpha-amino group of the initial amino acid, the deamination
reaction is required following the production of the amino group (i.e. glutamate) produced from
the aminotransferase-catalyzed transamination reaction. In this case, the removal of the alpha-
amino group of glutamate is catalyzed by glutamate dehydrogenase (GDH) that facilitates the
conversion of glutamate to alpha-iminoglutarate (i.e. Schiff base) and then to alpha-ketoglutarate
with the hydrolysis of Schiff base. The hydrolysis of the Schiff base forms the free amino group in
the form of ammonia.
10) What enzyme is the major control point for amino acid biosynthesis in the cell and how is it regulated?
 a) Recall that glutamine (i.e. note the side chain amino group) is the preferred amino group donor for a
wider variety of biosynthetic processes whereas glutamate (i.e. note the alpha-amino group) is the
amino group donor for most other amino acids. Glutamine amidotransferase
b) Glutamine synthetase (GS): facilitates the formation of glutamine; activity of GS is controlled via
adenylylation by an adenylyltransferase that is complexed to a regulator protein; GS adenylylation
lowers the GS activity whereas GS de-adenylylation increases the GS activity.
i) Covalent regulation:
(1) Sufficient energy supply leads to storage of energy stores (i.e. high [ATP]) and thus promote
higher GS activity: regulatory protein uridylated => promotes GS de-adenylylation => increases
GS activity
(2) Insufficiency energy supply leads to mobilization of energy stores (i.e. high [AMP]) and thus
lower GS activity: regulatory protein de-uridylated => promotes GS adenylylation => lower GS
activity
ii) Allosteric regulation:
(1) Inhibitors: histidine, tryptophan, CPS II, glucosamine-6-phosphate, AMP, CTP, alanine, serine,
glycine
c) Glutamate synthetase: Composed of 3 active sites where electrons from NADPH are transferred to
FAD, thereby reducing FAD in active site 1. Simultaneously, glutamine gets deaminated, releasing a
free amino group (i.e. its side chain amino group) that travels from active site 2 to active site 3 via a
tunnel. At active site 3, a free alpha-ketoglutarate is converted into alpha-iminoglutarate (Schiff base)
via the addition of the free amino group generated from active site 2. Alpha-iminoglutarate is later
reduced to glutamate using the electrons carried from active site 1 in active site 2 (i.e. electrons from
FADH2 transferred to FMN; and then FMNH2 transferred to alpha-iminoglutarate).
d) Glutamine amidotransferase: (after glutamine has been synthesized) facilitates the transfer of the
side chain amino group of a glutamine to an activated substrate (i.e. alcohol or keto).
11) What is the function of carnitine in β-oxidization of fatty acids? Why is this a major target of regulation in
controlling the balance between fatty acid synthesis and fatty acid β -oxidation?
a) The function of carnitine in beta-oxidation of fatty acid is to facilitate transport of fatty acyl-CoA (i.e.
activated fatty acid) from the cytosol into the mitochondria matrix.
b) Acyl-CoA is transferred to carnitine in the cytosol by carnitine palmitoyl transferase I. The resulting
acyl-carnitine is permitted to pass through the inner membrane into mitochondrial matrix. Once in the
matrix, acyl group from acyl-carnitine is transferred to CoA (within in the mitochondrial matrix pool),
resulting in the carnitine-palmitoyl transferase II-mediated formation of acyl-CoA. Carnitine is
subsequently transported back into the cytosol.
12) Odd chain fatty acids are first degraded to what and then converted to what? Is this final product used by
the citric acid cycle to produce NADH?
a) Odd-numbered fatty acids chains are degraded to propionyl-CoA and then succinyl-CoA. Although
succinyl-CoA is an intermediate in the citric acid and succinyl-CoA produced here can enter the citric
acid cycle, NADH cannot be obtained from succinyl-CoA involvement in the CAC. In fact, for succinyl-
CoA to be utilized, it must be converted into malate
13) What is the function of ACC and what is the importance for the two isoforms of the gene?
a) Acetyl-CoA carboxylase (ACC) contains a biotin component that facilitates carboxylation of acetyl-
CoA to malonyl-CoA (i.e. in this case) and promotes fatty acid synthesis.
b) There are two isoforms of ACC where ACC1 is expressed in lipogenic tissues such as adipose tissues
and ACC2 is expressed in oxidative tissues (i.e. energy mobilization) such as skeletal and cardiac
muscles. Both ACC1 and ACC2 are present in the liver and the ratio [ACC1]/[ACC2] determines
whether fatty acid biosynthesis occurs is more prevalent than beta-oxidation or vice versa. A lower
ratio promotes fatty acid biosynthesis whereas a higher ratio promotes beta-oxidation.
c) Regulation:
i) Counter-regulatory molecules such as E, NE, and glucagon promote the mobilization of energy
stores; NE, E bind to beta-adrenergic receptors that activate 2nd messengers such as cAMP that
 promote the activation of protein kinase A (PKA). Phosphorylation by PKA onto ACC suppresses
fatty acid biosynthesis. However, phosphorylation by AMPK is usually observed.
ii) Insulin promotes energy stores; insulin activates a phosphatase that dephosphorylate an active,
phosphorylated ACC in the goal of suppressing fatty acid synthesis.
14) What is unique about the structure function relationship of FAS-1. Be sure that you know each of the
associated functions of the enzyme.
a) FAS-1 is a megasynthase enzyme, containing all enzymatic activities for biosynthesis on one single
polypeptide.
b) Components:
i) Malonyl/acetyl-CoA-ACP transaceylase (MAT): transfers an ACP (acyl carrier protein) to acetyl-
CoA and also to malonyl-CoA, forming acetyl-ACP and malonyl-ACP.
ii) Beta-ketoacyl-ACP synthase (KS): facilitates the condensation of acetyl-ACP and malonyl-ACP,
forming acetoacetyl-ACP in a decarboxylation-mediated reaction.
iii) Beta-ketoacyl-ACP reductase (KR): Reduces the beta-keto group to a hydroxy group.
iv) Beta-ketoacyl-ACP dehydratase (DH): Performs a beta-elimination reaction, forming an alpha-
beta unsaturated double bond.
v) Enoyl-CoA-ACP reductase (ER): Catalyzes the reduction of the resulting double bond, forming
butyryl-ACP, which is the 2-carbon extended product of acetyl-ACP. Butyryl-ACP can then
undergo subsequent condensation with malonyl-ACP for further elongation.
vi) Palmitoyl-CoA thioesterase (TE): Catalyzes the termination of elongation of the fatty acid with
facilitating the hydrolysis of fatty acid from ACP.
15) What is the source of acetyl-CoA for fatty acid biosynthesis? Where does it originate from within the cell?
How does it transit between those two compartments?
a) The source of acetyl-CoA is via the tricarboxylic acid transport system, where citrate is broken down
into oxaloacetate and acetyl-CoA, which is utilized in fatty acid biosynthesis.
16) What are the differences between fatty acid synthesis and fatty acid β -oxidation that allow the two
pathways satisfy the principle “catabolic and anabolic pathways must differ”?
a) CoA is the acyl group carrier for beta-oxidation whereas ACP is the acyl group carrier for fatty acid
biosynthesis
b) FAD and NAD+ are the electron acceptors for beta-oxidation whereas NADPH is the electron donor
for fatty acid biosynthesis.
c) The C2 unit product in beta-oxidation is acetyl-CoA whereas the C2 unit donor in fatty acid
biosynthesis is malonyl-CoA.
17) What is the function of increased cardiolipin concentration in the mitochondrial membrane?
18) What is the starting molecule for prostaglandin biosynthesis and where is it stored in the cell?
19) PGH synthase contain two enzymatic activities, what are there associated functions and prosthetic
groups?
20) What is the molecular target of aspirin and other NSAIDS and how do they differ in the mechanism by
which they inhibit PGH synthase?
21) What molecule is cholesterol derived from?
22) Cholesterol is built from shorter five carbon units called what?
23) How are the isoprenoid units synthesized and subsequently linked together to form squalene, i.e. what is
unique about the reaction mechanism FPP reaction?
24) At what stage in cholesterol biosynthesis does the molecule reside in the ER membrane?
25) What is the rate-limiting step in the cholesterol biosynthetic pathway and how is it regulated? Be sure to
know the hormonal regulation and the lanosterol regulated mechanism.
26) How is SREBP regulated by the sterol content of the cell?
27) How do statins work? What is the target for the drug? What is the consequence on the regulation of the
sterol content in the cell? Why does it lower plasma cholesterol levels? Why does this drug not work in
patients with familial hypercholesterolemia?
28) What is the function of Phosphofructokinase 2/Fructose-2,6-bisphophatase in the liver and muscle tissue?
What is the key difference in how this single polypeptide is regulated in the liver and muscle tissue that
allows it to be a major integrator of the fasting response?
29) Define and give an explanation of how each of these hormones regulate cellular metabolism. Note you
need to state what proteins they regulate and how this affects the various pathway they regulate but
mainly with respect to glycogen pyrophosphorylase and carbohydrate metabolism:
a) Insulin
b) Glucagon
c) Norepinephrine and Epinephrine (catecholamines): increase energy
d) Fructose-2,6-bisphate
30) In addition to glycogen phosphorylase and glycogen synthase know the other target molecules of AMP-
kinase, PKA and PPase1/2 (i.e. enzymes of fatty acid metabolism and sterol metabolism that are target of
these proteins regulation).
a) Glycogen phosphorylase facilitate mobilization of glycogen (i.e. mobilization of energy stores) in
response to inadequate energy supply and thus:
i) Activators: AMP
ii) Inhibitors: ATP, G6P
b) Glycogen synthase: facilitate storage of glycogen (i.e. storage of energy stores) in response to high or
sufficient energy supply and thus:
i) Activators: ATP, G6P
ii) Inhibitors: AMP
c) AMP-kinase phosphorylates acetyl-CoA carboxylase (ACC) to inactivate and suppress fatty acid
synthesis; AMP-kinase serves to monitor the energy balance between fatty acid synthesis and fatty
acid utilization
d) Protein kinase A (PKA) becomes activated upon a signaling transduction pathway that also sees the
adenylyl-cyclase-conversion of AMP to cAMP.
31) What are the functions of ghrelin, NPY, PYY, leptin, insulin in the neuronal control of metabolism?
a) NPY/AgRP: promotes obesity by stimulating food intake and inhibiting energy expenditure.
b) POMC/CART neurons: inhibits obesity by inhibiting food intake and stimulating energy expenditure
c) Ghrelin: stimulates appetite
d) Leptin: fights again obesity; promotes fatty acid metabolism & mobilization; suppress/inhibit fat
storage/fat synthesis
32) What is the importance of neuronal control of metabolism? What are the neuronal pathways involved in
this response, the hormones involved, and the tissues that are involved?
33) As a final note/question please know each of the rate limiting steps for the pathways we discussed in the
course and the substrates, key intermediates, and products of those pathways.