EXAM 3 Flashcards
Which state of glycogen phosphorylase gives the enzyme its highest activity?
phosphorylated glycogen phosphorylase
What best describes the ribbon structure of pepsin?
The major secondary structures are beta sheets, and there is no quaternary structure.
The catalytic activity and/or conformational stability of this protein is likely dependent upon ____________ of peripheral amino acid side chains.
protonation
The peripheral amino acid side chains are expected to have a ______________ value.
low pKa
Which of the following correctly describes the biochemistry of the amino acids at the termini of pepsin?
two nonpolar amino acids at the N-terminus and one polar amino acid at the C-terminus
What is a characteristic of a competitive inhibitor?
Does not affect the vmax of the reaction
What does a competitive inhibitor bind to?
the active site of an enzyme
Higher concentrations of substrate can reduce the effect of which type of inhibitor?
competitive inhibitor
What remains the same in the y-axis intercept of the Lineweaver-Burk plot with a competitive inhibitor?
remains the same with or without this inhibitor
What is the effect of an uncompetitive inhibitor?
decreases both the vmax and the Km
What does a mixed inhibitor do?
Can bind to the free enzyme or the enzyme-substrate complex
What is the function of kinase enzymes?
phosphorylate other proteins and enzymes
Which amino acid is not targeted for phosphorylation by kinases?
leucine
Which enzyme activates a zymogen?
Enterokinase
What does PKA phosphorylation modify in GPCR?
leads to arrestin binding to the receptor for endosomal transport
What are the signaling mechanisms for sweet and salty tastes?
Sodium ions directly enter the cells; sweet utilizes the GPCR signaling pathway
What type of receptor system is the agonist signaling through if it increases protein kinase activity?
GPCR
Glucagon binding to the glucagon receptor inhibits which process?
Glycogen synthesis
What is a shared component of the signaling pathways for glucagon and epinephrine?
Adenylate cyclase activation
When ATCase is in the __________ state it indicates that ____________ is bound.
T; CTP
What kind of chemical catalysis is identified in a certain reaction?
Acid-Base catalysis
Which amino acid can act as X in the reaction?
TYR
What are characteristics of allosteric enzymes?
- Often have a sigmoidal (S-shaped) curve of Vo versus [S]
- Undergo conformational changes between the R and T state
- Can have a regulatory subunit and catalytic subunit
What do GAPs and GEFs control in G proteins?
- GAPs inhibit GPs by stimulating GTP hydrolysis
- GEFs activate GPs by stimulating GDP-GTP exchange
What is the nature of sarin gas regarding acetylcholinesterase?
irreversible inhibitor
Which characteristics apply to allosteric enzymes?
- Tend to have a sigmoidal (S-shaped) curve of V0 vs. [S]
- Interconvert between a more active form and less active form
- May have binding sites for regulatory molecules that are separate from active sites
What happens when protein kinase A is activated in a liver cell in response to glucagon?
Glycogen degradation will be turned on
What is the correct order of steps for inhibition of glutamine synthetase by a metabolite allosteric effector?
- Glutamine binding to uridylyltransferase
- Deuridylation of glutamine synthetase adenylyltransferase
- Adenylation of glutamine synthetase
What is the correct order of signal transduction pathway steps?
- first messenger
- receptor protein
- upstream signaling protein
- second messenger
- downstream signaling protein
- target proteins
Muscle relaxation in response to neuronal stimulation would be reduced if a(n) ______________ was present.
stimulator of cGMP phosphodiesterase
What can the GS-alpha subunit of trimeric G proteins do?
activate adenylyl cyclase
What is cross talk in signaling pathways?
One signaling pathway can activate a different receptor’s signaling pathway
What does the loss of activation of ERK when PKA-I is added indicate?
the drug is activating via a GPCR
Which protein is the downstream signaling protein for the TRADD-associated complex in TNF signaling?
IKK
What is the role of TRAF2 in TNF receptor signaling?
recruits and activates NIK to the TNF receptor complex
What is likely to explain the results of retinoblastoma cases in a family?
The requirement for both genes to mutate indicates a loss-of-function tumor suppressor gene mutation
When protein kinase A (PKA) is inactive, what is true?
the intrinsic pseudosubstrate peptide is bound to the active site
What is the most likely cause of resistance to cell death by TNF-alpha in breast cancer cells?
loss or mutational inactivation of caspase 8
What is the correct order for receptor tyrosine kinase (RTK) signaling?
- ligand binding
- receptor dimerization
- kinase activation
- phosphorylation of RTK cytoplasmic tails
- protein binding to RTK phosphotyrosines
- activation of downstream signaling pathways
Why are Ras mutations prevalent in certain types of cancers?
Because a dominant mutation in Ras requires only one mutation to be a gain of function oncogene activation
What occurs after activation of the PI-3K pathway by insulin signaling?
Glucose uptake rates increase and lower blood glucose levels
What is likely to bind to a protein containing a pleckstrin homology domain?
PIP3
Which protein prevents glucocorticoid receptors from binding to glucocorticoid response elements (GREs)?
Hsp90
How does long-term activation by nuclear receptors differ from membrane receptor signaling?
Long-term activation occurs by nuclear receptors activating sets of genes
Which ligand is most likely to bind the receptor shown in B?
Vitamin D
Which enzyme’s activity is controlled by glucose-6-P and fructose-6-P levels?
Phosphoglucoisomerase
Which parameter does not govern the cell-specific physiological responses controlled by nuclear receptors?
Organism-wide expression of coregulatory proteins
If GRB2 were truncated so that the N-terminal domain was missing, the truncated protein would be
Which enzyme’s activity is controlled by the levels of glucose-6-P and fructose-6-P in the cell?
Phosphoglucoisomerase
Which of the following is not a parameter that governs the cell-specific physiological responses controlled by nuclear receptors?
Organism-wide expression of coregulatory proteins
If GRB2 were truncated so that the N-terminal domain was missing, what would it be unable to bind?
none of these answers are correct
What is the function of growth factor receptor-bound 2 (GRB2) protein in RTK signaling?
It is an adaptor protein that binds to phosphotyrosine residues in RTKs and also binds to GEF proteins.
Choose THREE reasons why caspases function as ‘executioners’ in the cell death pathway.
- Caspases have preferred substrate recognition sites for cleavage
- Caspases must be activated by proteolytic cleavage to convert the inactive zymogen to the active form
- Caspases are enzymes that function catalytically
The subunit of trimeric G proteins can function to:
activate adenylate cyclase
If a technique isolated EGFR1 and EGFR2 at discrete steps along their activation pathway, what would be isolated?
A dimer in which EGFR2 contains phosphotyrosines but EGFR1 does not.
Caspase 3 is responsible for:
degrading key regulatory molecules.
Place the following steps in proper order: ligand binding, receptor dimerization, and kinase activation, phosphorylation of RTK cytoplasmic tails, protein binding to RTK phosphotyrosines and phosphorylation of target proteins, activation of downstream signaling pathways.
- ligand binding, receptor dimerization, and kinase activation
- phosphorylation of RTK cytoplasmic tails
- protein binding to RTK phosphotyrosines and phosphorylation of target proteins
- activation of downstream signaling pathways
Which of the following captures the sequence of biochemical events by which GPCRs link extracellular information with intracellular changes?
Extracellular ligand binding to GPCR: causes a conformational change that leads G± to release GDP and bind GTP; GTP-bound G± releases G²³; and instead binds to downstream signaling molecules.
What is the shared intermediate in the following series of reactions?
fructose-6-P
If a mutation occurred in SODD that prohibited its interaction with the DD of TNF receptor, what would happen?
The TNF receptor would bind TRADD, even in the absence of TNF-a.
What is a distinguishing characteristic specific to all G-protein-coupled receptors?
contain seven transmembrane helices.
Why are shared intermediates used effectively in coupled reactions?
limit product diffusion and allow intermediates to channel from one enzyme to the next.
Which protein in the insulin receptor signaling pathway is capable of autophosphorylation?
insulin receptor (IR)
Which protein is part of the TNF receptor-activated programmed cell death signaling pathway?
FADD
Which statement is true of procaspase 8?
It is activated by auto-cleavage.
What is the most likely explanation for why only one of two cell types activated gene expression characteristic of the steroid signaling pathway?
Only one of the cell types expresses the cognate steroid receptor.
Which human disease states are treated by glucocorticoids based on their anti-inflammatory response? Choose the three most common.
- asthma
- dermatitis
- arthritis
Flux is defined as the rate at which __________ is/are interconverted.
metabolites
Metabolism is best defined as a collection of:
biochemical reactions that convert chemical energy into work.
Which end is responsible for a positive result in Benedict’s test?
B
Identify the correct structure of L-arabinose.
A
Determine the secondary structure(s) exhibited in this polypeptide.
both alpha helices and beta sheets
What is the immediate impact on aldolase if phosphofructokinase experiences a mutation that interferes with substrate binding?
aldolase
In which situation is glycolysis alone likely to be a major contributor to ATP generation?
In erythrocytes
What is the coupled ΔG°’ of the last reaction in glycolysis?
-31.4 kJ/mol
How does coupling phosphoenolpyruvate hydrolysis with ATP synthesis change the relationship between Q and Keq?
Q < Keq for both reactions; Q/Keq uncoupled < Q/Keq coupled
What can be said about the directionality of the reaction A B if ΔG’ is negative?
strongly favored in the forward direction
How can an unfavorable reaction (ΔG°’ > 0) still occur in a metabolic pathway?
link it to a favorable reaction
What is the structural difference between glucose and fructose?
Fructose is a five-membered ring and glucose is a six-membered ring.
Name the following disaccharide using the common name and descriptive nomenclature.
Lactose; Gal(Beta 1 -> 4)Glc
Which of the following can enter glycolysis without additional reactions?
Both products from maltose after maltase treatment
What would be the expected results if a physician tested lactate levels during exercise before and after administering glycerol?
Lactate levels would be low after intense exercise and would increase after glycerol was administered if the patient has a deficiency in muscle phosphofructokinase-1.
Will ingesting additional glucose gel improve athletic performance?
No
Label the effect of high ATP, ADP, or fructose-2,6-bisphosphate on phosphofructokinase-1 (PFK-1) activity.
- Yellow (top): fructose-2,6-bisphosphate
- Green (middle): ADP
- Red (bottom): ATP
What best describes the effect of ADP on the activity of PFK-1?
High concentrations of ADP block the inhibitory effect of ATP by competing for the same allosteric site on PFK-1.
What metabolite will be elevated in cancer cells as compared to noncancerous cells even under normal oxygen saturation?
lactate
In which glycolytic pathway reaction is ATP phosphoryl transfer energy required?
glucose -> glucose-6-phosphate
Which two compounds are used to produce ATP by substrate-level phosphorylation in glycolysis?
- phosphoenolpyruvate
- 1,3-bisphosphoglycerate
A __________ inhibitor is a type of irreversible inhibitor.
covalent
Which of the following is not a biochemical process affecting the bioavailability of enzymes?
binding of a competitive inhibitor
Which amino acid is NOT a target for kinases?
Asp
What is true regarding the roles of adenylylation and uridylylation in the control of glutamine synthetase?
High levels of ATP and α-ketoglutarate result in more deadenylylated glutamine synthetase.
The Lineweaver-Burk plot shown below is for a(n) __________ inhibitor.
competitive
Which of the following is NOT a primary mechanism for affecting catalytic efficiency?
D. Cellular compartmentalization
Which of the following activates a zymogen?
D. Enterokinase
Which of the following is not a primary mechanism used to regulate the catalytic efficiency of enzymes?
B. RNA synthesis
Which of the following statements are true about saquinavir and indinavir?
- Saquinavir and indinavir both have a component that mimics the natural Phe-Pro dipeptide substrate of aspartate protease.
- Very high local concentrations of proteins with Phe-Pro or Tyr-Pro peptide bonds would reduce the effectiveness of saquinavir and indinavir in limiting HIV’s infectivity of new cells.
- The removal of the phenyl ring on indinavir and saquinavir would likely affect their inhibitory activity.
Which mutation would most impact PKA, leading to a constitutively active enzyme?
a mutation in the catalytic subunit where the kinase can still bind its target but no longer binds the regulatory subunit.
How do epinephrine and glucagon lead to PKA activation?
Both receptors bind and activate the same G± subunit, Gs±.
What kind of signaling system is lysophosphatidic acid (LPA)?
endocrine
What best describes the structural changes that occur in a G alpha subunit due to guanine nucleotide binding?
Dissociation of GDP for GTP with the G alpha subunit structurally shifts the switch II helix region.
What is true concerning the role of cGMP in vasodilation?
cGMP is a secondary messenger that acts on protein kinase G.
Which first messenger is unique because it is not water soluble?
estr
What causes the structural shift in the switch II helix region of the G alpha subunit?
Dissociation of GDP for GTP
What is the role of cGMP in vasodilation?
cGMP is a secondary messenger that acts on protein kinase G
Which first messenger is unique for not being water soluble and not binding directly to a membrane receptor?
estradiol
What molecule is responsible for protein kinase A activation?
cAMP
What is the most likely impact of caffeine on cell signaling?
Leads to vasoconstriction and raises epinephrine levels
How are G protein-coupled receptors desensitized?
Phosphorylation by G protein-coupled receptor kinases (GRKs)
What is cross talk in signaling pathways?
When one signaling pathway activates a different receptor’s signaling pathway
What does the loss of activation of ERK when PKA-I is added indicate?
The drug activates via a GPCR
What is phosphorylated before EGFR1 when epidermal growth factor binds its receptor?
The cytoplasmic tail of EGFR2
What is the most likely cause of resistance to cell death by TNF-alpha in breast cancer cells?
Loss or mutational inactivation of caspase 8
What is the relationship between mutated Ras and cancer?
Mutated Ras is an oncogene
What event allows the ²subunit of the insulin receptor to bind to an insulin receptor substrate (IRS)?
Insulin binding induces conformational changes enabling autophosphorylation
Which enzyme terminates the activity of membrane-bound PIP3?
Phosphatase and tensin homolog, PTEN
What type of receptor does insulin bind to?
A unique class of receptors with a tyrosine kinase intracellular domain
How does the insulin receptor become activated?
Tyrosines must be phosphorylated to recruit intracellular signaling partners
How do mutations in the human epidermal growth factor receptor 2 gene lead to breast cancer?
Mutations cause constitutive activation of downstream signaling
What might cause apoptosis in mammalian brain cells when cultured without FBS?
Withdrawal of a positive growth signal
Why would a mutation of tyrosine to glutamate in a growth factor receptor lead to increased tumor formation?
It mimics the phosphorylated state, leaving the receptor constitutively active
What step of insulin-initiated signaling is indicated by autophosphorylation of tyrosine?
B
What is the net reaction when coupling Reaction 1 (A + B → C) and Reaction 2 (C → D)?
A + B → D
What is the value of ΔG for the net reaction of A + B → D?
-6.7 kJ/mol
What is the relationship between Q and K for spontaneous reactions A’B and C’D?
Q < K for both reactions
Which reaction requires coupling to ATP to be spontaneous under cellular conditions?
Reaction 2 (Q → R)
How does Rosiglitazone enhance insulin effects?
It binds to a nuclear receptor, activating transcriptional regulatory function
What happens when more A is added to a metabolic pathway operating within a cell?
It will increase the amount of B and C in the system
Under what condition would adding more A not increase the flux of the pathway from A to E?
An allosteric inhibitor of the enzyme that catalyzes C → D is present
What is least likely to affect the metabolic flux of a pathway?
Steady-state substrate concentrations
What secondary structure is exhibited in a selected polypeptide?
Not specified in provided content
How does oxygen saturation of hemoglobin compare in individuals with bisphosphoglycerate mutase deficiency?
Increased compared to normal individuals
Erythrocytes deficient in pyruvate and bisphosphoglycerate mutase would have levels of 2,3-bisphosphoglycerate similar to what?
Unaffected erythrocytes
Why is a hydrophobic environment necessary for phosphoglycerate kinase activity?
To prevent hydrolysis of 1,3-bisphosphoglycerate
What is true about glucose and fructose?
- Both are hexose sugars
- Glucose found in common disaccharides, fructose in only one
- Glucose can form furanose and pyranose, fructose only furanose
Which relationship is correctly defined?
D-Ribose and D-Xylose are epimers
What is necessary for optimal activity of phosphoglycerate kinase?
A hydrophobic environment
Why is the oxidation/reduction reaction necessary in glyceraldehyde-3-phosphate dehydrogenase?
To form an intermediate with a large free energy of hydrolysis
How does hexokinase deficiency affect oxygen transport?
Reduces 2,3-BPG levels leading to higher oxygen affinity
Why can’t glucose phosphorylation occur without ATP investment?
One or both substrates would exceed solvent capacity
Can the reverse reaction of glucose phosphorylation be used for substrate-level phosphorylation?
No
(A) What is ΔG’ for phosphorylation of glucose without ATP? (B) What is ΔG’ when coupled with ATP hydrolysis?
13.8 kJ/mol
-16.7 kJ/mol
What does the phosphorylation of glucose tell about Q and Keq?
Without ATP, Q > Keq; with ATP, Q < Keq
What is the IUPAC name of the nonnutritive sweetener sucralose?
1,6-dicholoro-1,6-dideoxy-²-D-fructofuranosyl-4-chloro-4-deoxy-±–D-galactopyranoside
What is the IUPAC name of the molecule discussed?
1,6-dicholoro-1,6-dideoxy-²-D-fructofuranosyl-4-chloro-4-deoxy-±–D-galactopyranoside
What are the hydrolysis products of sucralose?
- 1,6-dichloro-1,6-dideoxyfructose
- 4-chloro-4-deoxygalactose
Is 1,6-dichloro-1,6-dideoxyfructose a reducing sugar?
No
Is 4-chloro-4-deoxygalactose a reducing sugar?
Yes
Which enzyme converts glucose to fructose in the production of HFCS?
Glucose isomerase
Why is HFCS preferred over corn syrup for sweetening?
HFCS is sweeter than corn syrup
A net yield of _______________ ATP would be produced from the conversion of three molecules of glucose into pyruvate.
6
Which reactions depend only on substrate availability?
- dihydroxyacetonephosphate ↔ glyceraldehyde-3-phosphate
- glucose-6-phosphate ↔ fructose-6-phosphate
What can be concluded about irreversible reactions in glycolysis?
- Enzyme activity can be increased or decreased
- Enzymes are not shared in opposing pathways
- They operate far from equilibrium
What condition is caused by a deficiency in the lactase enzyme?
Lactose intolerance
Why does lactase deficiency lead to lactose retention within the small intestine?
Lactose is a polar molecule and cannot cross the intestinal membrane without a transport protein
Should Jamal try the lactase pill to see if it will work for his galactosemia?
No
What is the balanced reaction for the catabolism of glucose to lactate?
Glucose + 2 ADP + 2 Pi → 2 Lactate + 2 ATP + 2 H2O
Which allosteric regulator is responsible for curve C in PFK-1 activity?
ATP
Which enzyme acts as the rate-limiting step to regulate entry of products from dietary disaccharides into glycolysis?
Phosphofructokinase-1
What condition do individuals with a deficiency in the aldolase B enzyme have?
Hereditary fructose intolerance
How does glucokinase affect blood glucose levels in individuals with aldolase B deficiency?
Blood glucose levels would be lower than normal
Why is it critical that glucokinase has a low affinity for glucose?
It regulates insulin release from the pancreas
List three regulatory mechanisms in the glycolytic pathway.
- Fructose-1,6-bisphosphate is an allosteric activator of pyruvate kinase
- Fructose-2,6-bisphosphate is an allosteric activator of phosphofructokinase-1
- ATP is an allosteric inhibitor of phosphofructokinase-1
Why is fructose toxic to liver cells in individuals with aldolase B deficiency?
Liver cells use ATP to convert fructose to fructose-1P, which cannot be further metabolized
What advantage does phosphoglycerate kinase having an open and closed configuration provide?
Maximizes accessibility of active site without sacrificing hydrophobic environment
Calculate the actual free energy change (deltaG) for a reaction with deltaGº’ of +5.5 kJ/mol and Q of 0.001.
-12.3 kJ/mol
What best defines substrate-level phosphorylation?
Direct transfer of a Pi to an ADP
(a) Why is it critical for maintaining flux that NADH be oxidized to NAD+, and (b) how is this done under anaerobic conditions?
(a) NAD+ is required for the glyceraldehyde-3P dehydrogenase reaction; (b) by converting pyruvate to lactate
What is the linkage between the two monosaccharide units and is this a reducing sugar?
alpha1->beta2, nonreducing
List the conditions that stimulate liver PFK-1 activity.
- Increased fructose-2,6-bisphosphate levels
- Shift toward increased amounts of R state structure
- AMP bound to allosteric site and ATP bound to catalytic site
- Low energy charge in the cell
- Increased levels of ADP and AMP
What reaction in glycolysis is a redox reaction?
glyceraldehyde-3-P → 1,3-bisphosphoglycerate
What is the correct order of the glycolytic reactions listed?
- Phosphorylation reaction generating a hexose sugar
- An isomerization reaction converting an aldose sugar into a ketose sugar
- Phosphorylation reaction converting a hexose monophosphate into a hexose bisphosphate
- Cleavage reaction converting a diphosphate sugar into two monophosphate metabolites
- A redox reaction utilizing inorganic phosphate and a coenzyme
- A substrate level phosphorylation reaction generating ATP
- A dehydration reaction generating a high energy phosphorylated compound
- Substrate level phosphorylation reaction generating net ATP
How does phosphoglycerate kinase make glycolysis energy neutral at this step?
It produces 2 ATP along with 3-phosphoglycerate
Are glucose and galactose epimers of each other?
Yes
List three ways in which flux is controlled through glycolysis.
- Regulation of glucokinase
- PFK-1
- Supply and demand of intermediates
An infant with galactosemia is unable to convert:
galactose-1-P to glucose-1-P
What is required for the reaction of fructose-1,6-bisphosphate cleaved by aldolase to proceed?
Formation of Schiff base intermediate
