Biochem exam 3
(a) Why is it critical for maintaining flux through the metabolic pathway that NADH be oxidized to NAD+, and (b) how is that done under anaerobic conditions in human cells?
(a) NAD+ is required for the glyceraldehyde-3P dehydrogenase reaction; (b) by converting pyruvate to lactate.
Predict how oxygen transport is affected in individuals with a hexokinase deficiency as a result of decreased flux through the glycolytic pathway.
2, 3 BPG levels are reduced leading to higher oxygen affinity and reduced oxygen transport to the tissues
What is the appropriate order of the following steps? A. Glutamine binding to ur in idylyltransferase B. Adenylation of glutamine synthetase C. Deuridylation of glutamine synthetase adenylyltransferase
A, C, B
How can an extracellular signal be amplified a million-fold inside a cell? Choose the ONE correct answer
Activation of a single receptor can result in the production of 100 second messengers. Each of these second messengers can activate an enzyme that can act on 100 target enzymes. Each target enzyme can act on 100 other targets. 100 X 100 X 100 = 1,000,000
Choose the correct statements about the function and activity of arrestin.
Arrestin facilitates protein transport, which prevents a receptor from reassociating with the G protein complex. PKA phosphorylation also modifies GPCR, leading to arrestin binding to the receptor for endosomal transport.
Which amino acid is NOT a target for kinases?
Asp
What step of insulin-initiated signaling is shown in B in the figure below?
Autophosphorylation of tyrosine
Put the following steps in the correct order describing inhibition of glutamine synthetase by a metabolite allosteric effector. A. Adenylation of glutamine synthetase. B. Glutamine binding to uridylyltransferase C. Deuridylation of glutamine synthetase adenylyltransferase
B, C, A
Why is it critical to glucose homeostasis that glucokinase has a low affinity for glucose with regard to insulin release from the pancreas?
Because increased glucose concentrations in the blood lead to increased rates of metabolic flux through the glycolytic pathway, which is required for insulin release
Why is fructose toxic to liver cells, but not muscle cells, in individuals with a defect in the enzyme aldolase B?
Because liver cells, but not muscle cells, use up ATP converting fructose to fructose-1P, which cannot be further metabolized.
Once insulin has bound the α subunit of the insulin receptor, the β subunit of the receptor can bind to an insulin receptor substrate (IRS) protein, which acts as a membrane scaffold. What events happen next that enable the β subunit and the IRS protein to bind together?
Binding of insulin induces conformational changes in the β subunits, which enable them to autophosphorylate on tyrosine residues. These P-tyrosine residues are recognized by the phosphotyrosine binding sites (PTB domain) present in an IRS protein.
Both epinephrine (a tyrosine derivative) and glucagon (a peptide hormone) increase glucose export from the liver into the bloodstream. Each ligand binds a different receptor, but both lead to an activation of PKA. How does this happen?
Both receptors bind and activate the same Gα subunit, Gsα, which indirectly leads to PKA activation.
Place the following steps describing receptor tyrosine kinase (RTK) signaling in proper order: A. phosphorylation of RTK cytoplasmic tails B. activation of downstream signaling pathways C. ligand binding, receptor dimerization, and kinase activation D. protein binding to RTK phosphotyrosines and phosphorylation of target proteins
C, A, D, B
Which of the following is NOT a primary mechanism for affecting catalytic efficiency?
Cellular compartmentalization
Using the results of this experiment, select the correct answer or answers that describe the results of the experiment.
Compound X activates ERK through a PKA phosphorylation-mediated event. ERK phosphorylation is increased when compound X is added to the dish, indicating the activation of ERK. Loss of activation of ERK when PKA-I is added prior to compound X indicates that the drug is activating via a GPCR.
Put the following signal transduction pathway steps in the correct order: A. upstream signaling protein B. second messenger C. receptor protein D. first messenger E. target proteins F. downstream signaling protein
D, C, A, B, F, E
Whether a G alpha subunit is active or inactive depends on which guanine nucleotide is bound to it. Binding of GDP or GTP results in the protein switching between two conformational states. Which of the following answers 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, allowing for the association of G alpha with its effector proteins, such as adenylate cyclase.
Lysophosphatidic acid (LPA) is a water-soluble phospholipid derivative found in blood serum, where it binds to receptors throughout the body, inducing cell growth and other effects. This is an example of what kind of signaling system?
Endocrine
Which of the following activates a zymogen?
Enterokinase
Which protein is part of the TNF receptor-activated programmed cell death signaling pathway?
FADD
Glucose and fructose are both C6H12O6. What is the structural difference between them?
Fructose is a 5 membered ring, glucose is 6 membered
Which statements below describe 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
Beta-adrenergic receptor signaling must be terminated quickly or an extended metabolic shift could cause serious problems for the organism. Which best explains how receptors are "desensitized"?
G protein-coupled receptor kinases (GRKs) are protein kinases that phosphorylate receptors for internalization.
Signaling activity of G proteins is controlled by GTPase activating proteins (GAPs) and Guanine exchange factors (GEFs). What are the mechanisms by which GAPs and GEFs control G proteins (GPs)?
GAPs inhibit GPs by stimulating GTP hydrolysis; GEFs activate GPs by stimulating GDP-GTP exchange
You have a mystery hormone (agonist), and to test the nature of the agonist you add it to a dish of cultured liver cells. Shortly afterward you observe an increase in protein kinase activity. In a second experiment, you find the kinase is inhibited if you add an adenylate cyclase inhibitor to the cells prior to adding your mystery agonist. Which kind of receptor system is the agonist signaling through?
GPCR
If protein kinase A is activated in a liver cell in response to glucagon binding to the 2-adrenergic receptor, which of the following will result?
Glycogen degradation will be turned on
Glucagon binding to the glucagon receptor inhibits which of the following processes?
Glycogen synthesis
Levels of diacylglycerol increase in a cell on binding of a ligand to a taste receptor. Which trimeric G protein subunit is most likely to be bound to GTP?
Gqalpha
Which of the following 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.
Which of the following is the downstream signaling protein for the TRADD-associated complex in the cell survival path of TNF signaling?
IKK
Caffeine leads to a vasoconstriction, raises the epinephrine levels, and increases nervous signaling. A metabolite of caffeine blocks phosphodiesterase. What is the most likely impact of caffeine on cell signaling?
Inhibition of the phosphodiesterase results in an elevated cAMP levels and PKA activation, leading to increased glycogen breakdown and increased phosphorylation of events controlling the physiology of caffeine addiction.
Which of the following statements describe how the insulin receptor is activated?
Insulin binding to the insulin receptor induces a conformational change that stimulates tyrosine autophosphorylation of the beta subunits. The intracellular domain of the insulin receptor, specifically the tyrosines, must be phosphorylated to recruit the intracellular signaling partners.
When blood glucose levels are high in humans, the hormone ___________ stimulates metabolic flux through the __________ pathway and inhibits flux through the __________ pathway. The net effect of this hormone signaling is to increase ___________ of glucose.
Insulin, glycolysis, gluconeogenesis, influx
Kinase enzymes phosphorylate other proteins and enzymes. This is a common mechanism of covalently modifying enzymes in order to control their catalytic efficiency. Which of the following amino acids is not targeted for phosphorylation by kinases?
Leucine
Long-term activation by nuclear receptors differs from the more transient membrane receptor signaling for what reason?
Long-term activation occurs by nuclear receptors activating sets of genes, while membrane receptors involve small second messenger molecules responding quickly, as their signaling occurs by activation of kinases, phosphatases, and other enzymes already expressed in the cell.
Which of the following are characteristics of allosteric enzymes like ATCase? Choose the THREE that apply. Allosteric enzymes:
May have binding sites for regulatory molecules that are separate from active sites Tend to have a sigmoidal (S-shaped) curve of V0 vs. [S] Interconvert between a more active form and less active form
Which of the following is correct about the link between Ras and cancer?
Mutated Ras is an oncogene
One subtype of breast cancer involves the human epidermal growth factor receptor 2 gene (EGF receptor). One in every five breast cancers has a mutation in this gene. Understanding that this is a growth factor receptor gene, which of the answer choices best describes how this type of cancer develops?
Mutations that activate the kinase portion of the receptor result in a receptor that is constantly phosphorylated. This causes constitutive activation of downstream signaling and the resulting cell growth and proliferation.
Which one of the following molecules can function as a second messenger?
None
Which of the following are characteristics of allosteric enzymes such as aspartate transcarbamoylase. There are only three correct answers.
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.
A new protein is discovered that contains a pleckstrin homology domain. Which of the following is likely to bind to the protein?
PIP3
Signal transduction is part of a cell's response to an external signal. Although signal transduction pathways can differ in their details, there are some common elements. Determine which of the statements below accurately describe signal transduction pathways. Select the SIX correct statements.
Phosphatases remove phosphoryl groups from polypeptides, regulating a cell's response A second messenger may carry a signal from the cell membrane to an organelle. A receptor may pass on a signal by interacting with another protein or by acting as an enzyme. A ligand, such as a hormone, binds to a specific cell surface receptor on a target cell. A receptor changes conformation upon binding, transmitting a signal across the cell membrane. Signal transduction cascades, often involving protein kinases, amplify a signal intracellularly.
Which state of glycogen phosphorylase gives the enzyme its highest activity?
Phosphorylated glycogen phosphorylase
Redox enzymes commonly use electron carrier coenzymes such as NAD+/NADH, FAD/FADH2. Why are these coenzymes necessary? Choose the ONE correct answer.
Protein side chains are not chemically suited to reversibly bind electrons under a broad range of conditions.
Which of the following is NOT a primary mechanism used to regulate the catalytic efficiency of enzymes?
RNA synthesis
Which of the following is not a primary mechanism used to regulate the catalytic efficiency of enzymes?
RNA synthesis
Consider two reactions. Reaction 1 (P → Q) has ΔG = 2.3 kJ/mol. Reaction 2 (Q → R) has ΔG = 12.3 kJ/mol. Which reaction is more likely to require coupling to ATP or the equivalent in order to be spontaneous under cellular conditions?
Reaction 2 (Q → R). This reaction is nonspontaneous and operates far from equilibrium in the cell. It will not be able to proceed as written in the cell without coupling to a process with a large negative free energy change (such as ATP hydrolysis).
What can you deduce about the signaling mechanisms for sweet and salty?
Sweet utilizes the GPCR signaling pathway, activating phospholipase C. Sodium ions directly enter the cells, indicating the signal is transduced by an ion channel.
When ATCase is in the __________ state it indicates that ____________ is bound, and that ATCase is ______________ regulated.
T; CTP; down
TNF-alpha activation can lead to a cell survival mechanism as well as cell death. In the survival portion of TNF receptor signaling, TRADD recruits two adaptor proteins that function to initiate a downstream phosphorylation cascade. What is the role for one of these adaptor proteins called TNF receptor-associated factor 2 (TRAF2)?
TRAF2 recruits and activates NIK (NFkB inducing kinase) to the TNF receptor complex where NIK phosphorylates IKK, leading to the active transcription of anti-apoptotic genes.
Which of the following is correct about the binding of epidermal growth factor to its receptor?
The cytoplasmic tail of EGFR2 is phosphorylated before EGFR1.
What advantage is there to phosphoglycerate kinase having an open and closed protein configuration?
The induced-fit mechanism maximizes accessibility of active site without sacrificing hydrophobic environment
A mixture of enzyme and inhibitor is run through a size-exclusion chromatography column. The activity of the enzyme is assessed before and after the chromatography. The enzyme has more activity after the chromatography step. Which of the following is true?
The inhibitor is a reversible inhibitor.
Determine the relative proportions of secondary and quaternary structure(s). What best describes these structures?
The major secondary structures are beta sheets, and there is no quaternary structure.
What characteristic is true for both RTKs and GPCRs?
The receptor undergoes a conformational change on activation.
Retinoblastoma is a rare form of eye cancer where tumors grow in youth and young adults. For the most part, this cancer is due to one gene called the Rb1 gene. You have found that a father carries one of the genes with this mutation. He does not show symptoms of the disease. Genetic screening of the mother finds both copies of her genes are wild-type, not mutated. Of the four children, only one has retinoblastoma, but it did not show up until much later in the young man's life. Another family with both parents harboring one of the mutated copies had one of their four children with the disease, and the symptoms started much earlier.
The son whose father carried the mutated Rb1 gene likely developed a mutation in the Rb1 gene later in life, indicating this is a tumor suppressor gene. The requirement for both genes to mutate indicates a loss-of-function tumor suppressor gene mutation.
An enzyme undergoes a mutation that causes it to lose the ability to be regulated via phosphorylation. Which of the following mutations may lead to this loss of regulation? Assume that the overall structure is not altered by the mutation.
Tyr to Phe
An enzyme undergoes a mutation that causes it to lose the ability to be regulated via phosphorylation. Which of the following mutations may lead to this loss of regulation? Assume that the overall structure is not altered by the mutation and multiple kinases can phosphorylate the wild-type protein.
Tyr→ Phe
Why would mutation of a tyrosine residue to glutamate in the intracellular portion of a growth factor receptor lead to increased tumor formation?
Unlike tyrosine, a glutamate will leave the receptor "constitutively" active and no longer responsive to the phosphatases that shut off such signaling. A receptor with a glutamate in place of a tyrosine is a "phosphomimetic." That is, the protein mimics the phosphorylated state of tyrosine.
Which of the following statements are true about saquinavir and indinavir?
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. Saquinavir and indinavir both have a component that mimics the natural Phe-Pro dipeptide substrate of aspartate protease. The removal of the phenyl ring (six-membered carbon ring containing three double bonds and no attached functional groups) on indinavir and saquinavir would likely affect their inhibitory activity.
You are culturing mammalian brain cells with standard growth media that includes 10% fetal bovine serum (FBS). FBS has a number of hormones and other components that stimulate cell growth. Over a busy weekend you made a mistake and left the cells in media without FBS. These cells have begun apoptosis while normally cultured cells are growing and surviving just fine.
Withdrawal of a positive growth signal induced the cell death pathway of TNF-alpha
Which of the following mutations 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
A ligand binds to a transmembrane protein. This causes a conformational change in the protein that is detected by an intracellular protein. The intracellular protein is an enzyme that adds phosphate groups to target proteins. The phosphorylated proteins cause a physiological change within the cell. This is an example of
a signal transduction pathway
Procathepsin B is a lysosomal protease that is first translated as a proenzyme. On autocleavage it is fully activated. Procathepsin B is
a zymogen
The GS-alpha subunit of trimeric G proteins can function to
activate adenylate cyclase
Which of the following statements is true of procaspase 8?
activated by auto-cleavage
Which human disease states are treated by glucocorticoids based on the anti-inflammatory response of cells to glucocorticoid treatment? Choose the three most common (use a Google search).
arthritis, dermatitis, asthma
Why are Ras mutations so prevalent in certain types of cancers?
because a dominant mutation in Ras requires only one mutation to be a gain of function oncogene activation
Which of the following is not a biochemical process affecting the bioavailability of enzymes?
binding of a competitive inhibitor
Metabolism is best defined as a collection of
biochemical reactions that convert chemical energy into work.
What molecule, labeled "A" in the figure below, is responsible for protein kinase A activation?
cAMP
Which of the following statements is true concerning the role of cGMP in vasodilation?
cGMP is a secondary messenger that acts on protein kinase G. Tasting involves many different cell-signaling processes that ultimately generate nerve signals transduced by membrane depolarization. Sweet tastes result in PIP2 hydrolysis, while salty tastes allow sodium ions to directly alter the membrane potential.
The Lineweaver-Burk plot shown below is for a(n) __________ inhibitor.
competitive
Which of the following list includes ONLY first messengers?
cortisol, insulin, prostaglandins
A __________ inhibitor is a type of irreversible inhibitor.
covalent
The Lineweaver-Burk plot shows data obtained for an enzyme in the absence and presence of a noncompetitive inhibitor. If the [I] is increased significantly in the experiment, the Vmaxapp would __________ and the Kmapp would __________.
decrease; stay the same
Which of the following first messengers is unique because it is not water soluble and does not bind directly to a membrane receptor?
estradiol
In which of the following glycolytic pathway reactions is ATP phosphoryl transfer energy required to drive the reaction in the forward direction?
glucose -> glucose-6-phosphate
Which one of the following processes occurs after activation of the PI-3K pathway by insulin signaling?
glucose uptake rates increase and lower blood glucose levels
When compared with the T state of aspartate transcarbamoylase, the R state
has greater separation of the catalytic subunits.
Which of the following pairs correctly matches the type of interaction observed between an inhibitor and an enzyme with the type of inhibition?
hydrogen bonding; reversible
Acetylcholinesterase is an important enzyme in the nervous system. Acetylcholinesterase activity is blocked by the nerve agent sarin gas, which forms a covalent bond with a Ser in the active site of the enzyme. Sarin gas is a(n)
irreversible inhibitor
An estrogen-dependent breast cancer cell line is grown in a medium that contains estrogen. Cell proliferation is monitored over time. In a separate experiment, the cell line is grown in a medium that lacks estrogen but includes bisphenol A, a compound found in polycarbonate plastics. When monitored, cell proliferation is higher than in the presence of estrogen. A possible explanation of these results is that bisphenol A
is an agonist of the estrogen receptor.
How can an unfavorable reaction (∆G°' > 0) still occur in a metabolic pathway?
link it to a favorable reaction
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
Flux is defined as the rate at which __________is/are interconverted.
metabolites
Cultures of two different human cell types are exposed to the same steroid signaling molecule. Analysis of gene expression shows that only one of the cell types activated gene expression characteristic of the steroid signaling pathway. Which of the following is the most likely explanation for this difference?
only one of the cell types expresses the cognate steroid receptor
Which enzyme is responsible for terminating the activity of membrane-bound PIP3?
phosphatase and tensin homolog, PTEN
Which two of the following compounds are used to produce ATP by substrate-level phosphorylation in glycolysis?
phosphoenolpyruvate and 1, 3 biphosphoglycerate
Below is the molecular structure of a single bovine mc030-1.jpg-arrestin subunit. Two locations are indicated. What is most likely to interact with the protein at these locations?
phosphorylated GPCR
The catalytic acitivity and/or conformational stability of this protein is likely dependent upon ---- of peripheral amino acid side chains. These side chains are expected to have a ---- value.
protonation, low pKa
The catalytic acitivity and/or conformational stability of this protein is likely dependent upon ---- of peripheral amino acid side chains. These side chains are expected to have a ----- value.
protonation, low pka
A plot of vo versus [S] for aspartyl transcarbamoylase displays three sigmoidal lines. If the line in the middle represents the enzyme activity in the absence of any allosteric effectors, then the line to the __________ represents the enzyme in the __________ when bound to __________.
right; T state; CTP
Cyclic GMP is the __________ during vasodilation
second messenger
Muscle relaxation in response to neuronal stimualtion and nitric oxide signaling would be reduced if a(n) ______________was present.
stimulator of cGMP phosphodiesterase
In the reaction A→ B, what can be said about the directionality of the reaction if when starting with equal concentratios of A and B at time zero (T0), you find that at equilibrium 30 minutes (T30) later, that [B] >> [A]?
strongly favored in the forward direction
When protein kinase A (PKA) is inactive, which of the following is true?
the intrinsic pseudosubstrate peptide is bound to the active site
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
An inhibitor that binds only to the ES complex and not free enzyme is known as a(n) ___________ inhibitor.
uncompetitive
