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BIOC 3560 (Final) exam questions updated version, Exams of Advanced Education

Cheyney University of PennsylvaniaAdvanced Education

BIOC 3560 (Final) exam questions updated version

Typology: Exams

2025/2026

Available from 07/02/2026

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BIOC 3560 (Final) exam questions updated version
1. What glycolytic reaction is catalyzed by hexokinase? What 2
forms of hex-
okinase
exist?
How
are
these
enzymes
regulated?:
Hexokinase
catalyzes the conversion of
glucose to G6P (makes ATP).
Hexokinase I is expressed in the muscle and has a high aflnity for glucose (low Km). Hexokinase I is
inhibited by
increased [G6P].
Hexokinase IV is expressed in the liver and has a lower aflnity for glucose (enzyme activity more
highly influenced by increasing blood glucose). Hexokinase IV is regulated by F6P (made from G6P).
High [F6P] causes glucokinase
regulatory
protein
to
sequester
hexokinase
in
the
nucleus.
High
[glucose]
weakens
the
enzyme/regulator
interaction
of hexokinase IV-regulatory protein, encouraging
cytosolic localization of the enzyme.
2. What glycolytic reaction is catalyzed by phosphofructokinase-1
(PFK-1)? How
is
this
enzyme
regulated?:
PFK-1 catalyzes the reaction of F6P to
Fructose-1,6-bisphosphate (commits F6P to glycolysis).
1)
ATP
-->
binds
to
an
allosteric
site
on
PFK-1
and
lowers
aflnity
for
F6P
2)
ADP/AMP
-->
relieve
inhibition
by
ATP
3)
Citrate
-->
increases
inhibition
by
ATP
4)
Fructose 2,6 bisphosphate --> strong activator
3. What glycolytic reaction is catalyzed
by
pyruvate kinase? How is
this
enzyme
regulated?:
Pyruvate kinase catalyzes the conversion of phosphoenolpyruvate
to pyruvate.
High
levels
of
ATP,
acetyl
CoA,
LCFAs,
and
alanine
inhibit
PK.
F16BP
accumulation
stimulates
PK.
In
the
liver
only,
activation
of
PKA
by
glucagon
inactivates
PK.
4.
Gluconeogenesis is the metabolic process in which non-hexose
precursors are used to make glucose.
pf3
pf4
pf5
pf8
pf9
pfa
pfd
pfe
pff
pf12
pf13
pf14

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BIOC 3560 (Final) exam questions updated version

  1. What glycolytic reaction is catalyzed by hexokinase? What 2 forms of hex-okinase exist? How are these enzymes regulated?: Hexokinase catalyzes the conversion of glucose to G6P (makes ATP). Hexokinase I is expressed in the muscle and has a high aflnity for glucose (low Km). Hexokinase I is inhibited by increased [G6P]. Hexokinase IV is expressed in the liver and has a lower aflnity for glucose (enzyme activity more highly influenced by increasing blood glucose). Hexokinase IV is regulated by F6P (made from G6P). High [F6P] causes glucokinase regulatory protein to sequester hexokinase in the nucleus. High [glucose] weakens the enzyme/regulator interaction of hexokinase IV-regulatory protein, encouraging cytosolic localization of the enzyme.
  2. What glycolytic reaction is catalyzed by phosphofructokinase- (PFK-1)? How is this enzyme regulated?: PFK-1 catalyzes the reaction of F6P to Fructose-1,6-bisphosphate (commits F6P to glycolysis).
  1. ATP --> binds to an allosteric site on PFK-1 and lowers aflnity for F6P
  2. ADP/AMP --> relieve inhibition by ATP
  3. Citrate --> increases inhibition by ATP
  4. Fructose 2,6 bisphosphate --> strong activator
  1. What glycolytic reaction is catalyzed by pyruvate kinase? How is this enzyme regulated?: Pyruvate kinase catalyzes the conversion of phosphoenolpyruvate to pyruvate. High levels of ATP, acetyl CoA, LCFAs, and alanine inhibit PK. F16BP accumulation stimulates PK. In the liver only, activation of PKA by glucagon inactivates PK.
  2. Gluconeogenesis is the metabolic process in which non-hexose precursors are used to make glucose.

2 / 20 7/10 reactions in gluconeogenesis are the reverse reactions of glycolysis (3 irreversible steps are bypassed). In gluconeogenesis, what enzymes convert pyruvate back to phosphenolpyruvate (step 10 glycolysis)?: Mitochondria: Pyruvate carboxylase uses HCO3- + ATP to --> oxaloacetate + ADP + Pi. Mitochondrial malate dehydrogenase uses oxaloacetate + NADH + H+ --> L-malate + NAD+ Cytosol: Cytosolic malate dehydrogenase uses L-malate + NAD+ --> oxaloacetate + NADH + H+ Phosphoenolpyruvate carboxykinase uses oxaloacetate + GTP --> phosphenolpyruvate + CO2 + GDP

  1. Why is a malate intermediate used to export oxaloacetate from the mi-tochondria to the cytosol?: During gluconeogenesis the cytosolic reaction mediated by glyceralde-hyde-3-phosphate dehydrogenase consumes NADH. FA degradation occurring (need glycerol to produce glucose) in the mitochondria produces a surplus of NADH however this co-factor cannot be directly exported to the cytosol. Using a malate intermediate allows excess NADH from the mitochondria to move to the cytosol where it is needed. If lactate is the main substrate driving gluconeogenesis lactate dehydrogenase produces NADH and PEP carboxyki-nase will produce PEP directly (NADH not needed in the cytosol --> malate shuttle bypassed).
  2. Gluconeogenesis is the metabolic process in which non-hexose precursors are used to make glucose. 7/10 reactions in gluconeogenesis are the reverse reactions of glycolysis (3 irreversible steps are bypassed). In gluconeogenesis, what enzyme converts F16BP back to F6P (step 3 glycolysis)?: Fructose 1, bisphosphatase-1 (FBPase-1) uses F16BP + H2O --> F6P + Pi. This reaction is a phosphatase reaction (exergonic).
  3. Gluconeogenesis is the metabolic process in which non-hexose precursors are used to make glucose.

4 / 20 phosphatase.

  1. How are pyruvate carboxylase and PEP carboxykinase regulated? How does this relate to regulation of the hepatic form of pyruvate kinase?: Pyru-vate carboxylase (converts pyruvate to oxaloacetate in the mitochondria) --> stimulated by acetyl CoA and inhibited by ADP PEP carboxykinase (converts oxaloacetate to PEP in the cytosol) --> inhibited by ADP In the liver only, PK is phosphorylated by glucagon activated PKA and this slows glycolysis to save glucose for tissues that need it (liver may also begin initiating gluconeogenesis.
  2. Explain the oxidative phase of the pentose phosphate pathway. How is this pathway regulated?: The oxidative phase of the pentose phosphate pathway involves the oxidation of G6P to produce 2 NADPH (used for reductive biosynthesis) and ribulose-5-phosphate (used for nucleotide biosynthesis). The initial reaction of the oxidative phase of the pentose phosphate pathway is the conversion of G6P to 6-Phospho-gluconate by glucose-6-phosphate dehydrogenase. G6P dehydrogenase is stimulated by NADP+ and inhibited by NADPH and is therefore regulated by the redox state of the cytosol.
  3. Explain the non-oxidative phase of the pentose phosphate pathway.: The non-oxidative phase of the pentose phosphate pathway involves rearrangement of 5C molecules to 6C molecules by transaldolase/transketolase (6 5C --> 5 6C sugars). Overall the non-oxidative phase of the pentose phosphate shuttle replenishes G6P and glycolytic intermediates and generate xylulose-5-phosphate.
  4. How is glycogen synthesized?: 1) G6P is converted to G1P by phosphoglucomutase.
  1. G1P + UTP are converted to UDP-glucose + PPi by UDP-glucose pyrophosphorylase.
  2. UDP-glucose acts as an activated sugar donor and is added to the growing glycogen polymer.
  1. How is glycogen broken down?: Glycogen phosphorylase catalyzes the removal

5 / 20 of a single sugar residue (removed as G1P) from the glycogen polymer.

  1. How are glycogen synthase and glycogen phosphorylase reciprocally reg-ulated?: Glycogen synthase is converted to its inactive form when it is phosphorylated by GSK3. Glycogen phosphorylase is converted to its active form when it is phosphorylated by phosphorylase kinase. Protein phosphatase 1 mediates reciprocal regulation of glycogen synthase and glycogen phosphorylase. Protein phosphatase 1 removes phosphate groups from both enzyme and this activates glycogen synthase and deactivates glycogen phosphorylase.
  2. How is glycogen phosphorylase regulated?: Glycogen phosphorylase b kinase phosphory-lates and activates glycogen phosphorylase.

7 / 20 cis-Δ3 FAs are not substrates for acyl-CoA dehydrogenase because C3 is already in a double bond. The enzyme Δ3,

8 / 20 Δ2-enoyl-CoA isomerase moves the double bond and converts the cis-Δ3 FA to a trans-Δ2 FA. Trans-Δ FAs are a substrate for enoyl-CoA hydratase and beta oxidation proceeds normally (one fewer FADH produced).

  1. How does beta oxidation proceed when FAs have a 2 double bonds?: In linoleoyl-CoA the first double bond is in the 9 position, the second is at the 12 position. The reaction proceeds as with one double bond to produce a cis-Δ3, Δ6 FA. The cis-Δ3, Δ6 FA is converted to trans-Δ2 cis-Δ6 FA by Δ3, Δ2 enoyl-CoA isomerase. Trans-Δ2 cis-Δ6 FA is a substrate for hydratase and this beta-oxidation cycle completes normally yielding a cis Δ4 FA. With a cis-Δ4 FA acyl-CoA dehydrogenase produces a trans-Δ2, cis Δ4 FA and the resulting conjugated double bond cannot be hydrated by enoyl-CoA hydratase. Trans-Δ2, cis Δ4 FA is reduced by 2,4-dienoyl- CoA reductase yielding a trans-Δ3 FA. Trans-Δ3 FA is then converted to trans-Δ2 FA by Δ3, Δ2-enoyl-CoA isomerase and beta oxidation proceeds normally.
  2. What are the 3 types of ketone bodies? How are they formed?:
    1. Acetoacetate --> formed by condensing 3 acetyl-CoA molecules then cleaving one
  1. D-β-hydroxybutyrate --> formed by reducing acetoacetate
  2. Acetone --> minor product formed by the decarboxylation of acetoacetone that is exhaled
  1. Explain the acetyl group shuttle.: Acetyl-CoA is not directly transported from the mitochondria to the cytosol but is combined with oxaloacetate to produce citrate that is transported to the cytosol. Citrate lyase in the cytosol produces acetyl-CoA. Oxaloacetate is reduced to malate which can return to the mito-chondria directly or after decarboxylation to pyruvate. In the mitochondria malate/pyruvate is used to regenerate oxaloacetate.
  2. How is malonyl-CoA produced?: Malonyl-CoA is made from acetyl CoA and HCO3 in an ATP dependent reaction catalysed by acetyl-CoA carboxylase. Acetyl CoA carboxylase consists of a biotin carrier protein (carries biotin), biotin carboxylase (uses ATP to

10 / 20 During initiation of FA synthesis, Malonyl/acetyl-CoA ACP transferase (MAT) transfers acetyl from Acetyl-CoA to Acyl Carrier Protein (ACP). β-ketoacyl synthase (KS) than transfers acetyl from ACP to itself. MAT then transfers malonyl group to ACP and KS is ready for the first condensation step.

  1. β-ketoacyl-ACP synthase (KS) catalyzes the condensation reaction of an activated acyl group with malonyl CoA.
  2. β-ketoacyl-ACP reductase (KR) catalyzes the reduction of β-keto to β-alcohol
  3. β-hydroxyacyl-ACP dehydratase (DH) eliminates H2O to form a double bond between α and β carbons
  4. Enoyl-ACP reductase (ER) reduces the carbon double bond to form a saturated acyl group
  5. Butyryl group is translocated to Cys on KS and KS transfers the butyryl group from ACP to itself
  6. MAT transfers new malonyl group to ACP and KS condenses malonyl group with the butyryl group and another round of FA synthesis begins.
  1. Which enzyme releases palmitate from the FA synthase? How is palmitate used to make longer FAs? How are unsaturated FAs made?: Palmitate is released from FAS by cleavage by thioesterase. Elongation occurs 2 carbons at a time and malonyl CoA still used. Reactions are catalyzed by elongases and desaturases. In mammals, fatty acyl-CoA desaturases make cis doubles bonds at the 9 position. This enzyme requires O2 and cytochrome B5 which must be re-reduced using NADPH.
  2. How are TAGs assembled? Where are they assembled?: Acyl-CoA synthetases activate FA groups with CoA. Acyl transferases then transfer the activated FA to glycerol-3-PO4. TAGs are assembled in the liver and adipose tissue. In the adipose tissue TAGs are simultaneously synthesized and catabolized --> may help make system more responsive to quickly changing needs.
  3. How is fatty acid β-oxidation regulated?: Most important regulatory control is malonyl-CoA inhibition of carnitine acyltransferase I (transfer of FAs into the mitochondria = comitted step). In the mitochondria high [NADH]/[NAD+] inhibits β-hydroxyacyl-CoA dehydrogenase and acetyl CoA

11 / 20 inhibits thiolase.

  1. How is acetyl-CoA carboxylase regulated?: Acetyl-CoA carboxylase catalyzes the committed step of FA synthesis (synthesis of malonyl CoA). Palmitoyl-CoA (ultimate product) inhibits ACC while citrate (acetyl CoA precursor) activates ACC.

13 / 20 Phosphoglycerides - made up of a glycerol backbone, 2 FAs in an ester link, and a headgroup derived from alcohol

  1. Sphingolipids - made up of a sphingosine backbone and 1 FA in an amide link; similar shape to phosphoglycerides -> sphingosine mimics glycerol plus 1 FA. If headgroup is a CHO considered a glycolipid.
  2. Cholesterol - four fused rings with a hydroxyl polar group and alkyl side chain

14 / 20

  1. Membrane proteins are either classified as peripheral or integral. What techniques can be used to determine whether a membrane protein is integral or peripheral?: Peripheral membrane proteins interact with the polar head groups of membrane lipids via electrostatic interactions of H bonds. If changing pH or adding a chelator (removes stabilizing Ca++) releases a membrane protein this protein is classified as peripheral. If a detergent is needed to remove a membrane protein this protein is likely an integral transmembrane protein. If phospholipase releases a membrane protein this protein is an integral lipid-anchored protein.
  2. What are hydropathy plots used for?: Hydropathy plots index the mean hydrophobicity of a protein segment. If >20 (# of residues needed to cross membrane) successive residues have a high hydropathy index, this region is possibly a transmembrane segement.
  3. Where are tyrosine and tryptophan residues concentrated on membrane proteins?: Tyrosine and tryptophan residues are concentrated where polar head groups meet acyl chains. Charged residues (R, L, E, D) are almost always exclusively within the aqueous phase.
  4. What distinguishes N-linked and O-linked glycoproteins? Why are the sugar groups of glycoproteins and glycolipids important?: N-linked CHO chain --> Asn side chain O-linked CHO chain --> Ser or Thr side chain Sugar groups are important as the contribute to cell surface recognition and function as receptors.
  5. What are the 3 lipid bilayer states?: 1) Gel phase (cold) --> all motion of bilayer is constrained and lipids are ordered in a paracrystalline state
  1. Liquid-ordered state (physiological) --> intermediate thermal motion of acyl chains and atoms
  2. Liquid-disordered state (fluid) --> hydrocarbon chains are in constant motion, no regular organization
  1. How does membrane composition affect fluidity?: At physiologic temperatures, LCFAs pack well into a liquid-ordered state while unsatured/shorter chain FAs

16 / 20 when packed between cis FAs (eflcient packing of kinked chains) and at high temperatures (rigid cholesterol interacts with flexible acyl chains).

  1. Describe the actions of flippases, floppases, and scramblases.: Flippases --> uses ATP to move phospholipids from the outer leaflet to the inner leaflet Floppases --> uses ATP to move phospholipids from the inner leaflet to the outer leaflet Scramblases --> moves lipids in either direction towards equilibrium
  2. What is the role of spectrin in lipid and protein motion?: Spectrin is a component of the cytoskeleton and may act as a corral that keeps lipids from freely dittusing. Lipid rafts (microdomains) may also restrict the region in which lipids can dittuse freely.
  3. Explain how SNAREs mediate NT release.: 1) Extended helical domains of v- and t-SNARES bind to each other and draw the two membranes together.
  1. Zipping of these helical domains cause membrane curvature and lateral tension favouring the hemifusion between outer leaflets.
  2. Hemifusion creates an energetically unfavourable void space and influence inner leaflets to come into contact.
  3. Complete fusion of the outer and inner membranes create a fusion pore which widens and allows NT release.
  1. What are aquaporins? How do they work?: Aquaporins are H2O channels. His and Arg residues create elecrostatic repulsion and prevent H3O+ from passing through the channel. Asn residues create a dipole orientation that prevents H+ from passing.
  2. Explain transport by GLUT1.: GLUT1 is a passive transporter --> molecules still travel down a concentration gradient but rate of transport is highly selective, regulated, and saturable (unlike channels). Glucose binds to GLUT1 on one side of the membrane and this induces a conformational change. This conformational change opens up a site on the other side of the membrane and the substrate is released. Upon release transporter undergoes a conformational change.
  3. Explain how the Na+/K+ ATPase functions.: 1) Transporter binds 3 Na+ from inside the cell
  1. Phosphorylation (uses ATP) favours P-Enz II
  2. Transpoter releases 3 Na+ outside the cell and binds 2 K+ from outside the cell

17 / 20

  1. Dephosphorylation favours Enz I
  2. Transporter releases 2 K+ to the inside Overall creates (-)ve charge inside and (+)ve charge outside.

19 / 20 activity).

  1. Activated Gα dissociates from Gβγ and activates adenylyl cyclase

20 / 20

  1. Adenylyl cyclase catalyzes the formation of cAMP
  2. cAMP activates PKA which phosphorylates cellular proteins causing a cellular response to Epi.
  1. What drive the internalization of the epinephrine receptor?: Internalization of the epinephrine receptor is induced by phosphorylation of the receptor by β- adrenergic receptor kinase (βARK) and subsequent binding of β-arrestin.
  2. How does the active site of the insulin receptor open up in response to insulin binding?: When the insulin Rc is inactive, the tyrosine kinase catalytic site is blocked by the activation loop. This loop has 3 tyrosine including one that makes a key bond with an Asp. When insulin binds, the tyrosine kinase phosphorylates all 3 tyrosines and this stabilizes the loop in a conformation that no longer blocks the catalytic site.
  3. Explain the insulin signalling pathway.: 1) Phosphorylated IRS-1 is bound by SH2 (binds Y) domain of Grb
  1. Grb-2 binds Sos via SH3 (bind P) domain
  2. Grb2-Sos activate G-protein Ras
  3. GTP bound Ras activates a protein kinase cascade (Raf1 --> MEK --> ERK)
  4. Erk enters the nucleus and phosphorylates TFs also increase GLUT4 translocation, induce synthesis of hexokinase, and activate GS (by phosphorylating and inactivating GSK3)
  1. How does steroid hormone signalling take place?: Steroid hormones bind to and activate nuclear hormone receptors that act as TFs. Hormone binding induces a conformational change in the receptor. Zinc finger structures allow the receptor to bind to specific DNA element known as HREs.