Biochemistry Review Flashcards

Biochemical Signaling

Matching Questions

• Receptors: Proteins that bind molecules and elicit a cellular response.
• Cyclic AMP: A molecule that often functions as a second messenger.
• Islets of Langerhans: The gland predominantly responsible for producing the hormone released in response to a meal high in carbohydrates.
• Adrenal Cortex: Isoproterenol functions as an agonist for receptors that bind hormones synthesized here.
• Insulin: A release of this would stimulate the liver to synthesize glycogen.
• Rhodopsin: The first G protein-coupled receptor (GPCR) to be structurally analyzed at the atomic level.
• Receptor Tyrosine Kinase (RTK): This signaling pathway undergoes autophosphorylation resulting in kinase activation.
• Adenylate Cyclase (AC): This signaling pathway relies on GTP-dependent hydrolysis for subsequent synthesis of cAMP.
• Phosphoinositide: Cytosolic calcium ion levels are altered by this signaling pathway.
• Cortisol: The hormone responsible for various actions, including the ability to cope with stress.

Multiple Choice Questions

• Insulin binds to a receptor that: Possesses tyrosine kinase activity; Interacts with proteins homologous to Src.
• Calcineurin: A phosphatase activated by Ca2+ essential for T cell proliferation.
• Desensitization: The ability of receptors to adapt to long-term stimulation by responding to changes in stimulation levels rather than absolute values of stimulation.
• Cancer-causing viruses often contain: oncogenes; genes encoding variant proteins; genes capable of inducing malignant transformation.
• The interaction (cross-talk) of various signaling pathways can be minimized by scaffold proteins.
• Phospholipase C cleaves PIP2, resulting in an increased cytosolic concentration of IP3 (inositolpolyphosphate-3) and Ca2+.
• β cells of the islets of Langerhans secrete insulin in response to elevated glucose levels in the muscle and/or adipose tissue.
• α cells of the islets of Langerhans secrete glucagon in response to low glucose levels in the liver.
• Heterotrimeric G proteins: consist of three subunits, Gα, Gβ, and Gγ; can function as a mediator to adenylate cyclase activity; are anchored to the cytoplasmic side of the membrane.
• The insulin signaling pathway includes autophosphorylation and phosphorylation of IRS-1 and/or IRS-2 proteins.
• Advantages of protein phosphorylation in biochemical signaling: Phosphorylation is rapid and specific; Phosphorylation is enzymatically reversible; Phosphorylation can be amplified by cascade systems; Phosphorylation results in covalent modification of enzymes.
• Results of insulin binding to its receptor: MAPK activation, which regulates gene expression via Fos, Jun, and Myc; PI3K activation leading to an increase in glucose transport; High affinity binding of SH2 domains to phosphorylated tyrosines; Autophosphorylation resulting in activation of tyrosine kinase.
• Ras is an example of: a protein anchored by prenylation; a kinase activated protein; a GTP dependent protein.
• Somatostatin inhibits the release of insulin and inhibits the release of glucagon.
• Catecholamines mediate their effects through α-adrenoreceptors and β-adrenoreceptors.
• Steroids function by binding to receptors that function directly as transcription factors.
• The following are produced in the adrenal cortex: Glucocorticoids, mineralocorticoids, androgens, estrogens.
• EF hand: structural motif found in calmodulin (CaM).
• Associated with cAMP binding to cAMP-dependent protein kinase A: cAMP binds to the regulatory subunits; Tetrameric regulatory subunits and catalytic subunits dissociate; Catalytic subunits phosphorylate multiple targets with specific serine and threonine residues.
• Some G proteins activate adenylate cyclase, while others inhibit it.
• The presence of an Arg residue deep in the binding pocket, increases the affinity of SH2 binding to phosphor-tyrosine.
• Considering UPS-1 through UPS-3, the possible conclusions given these results include that UPS-1 functions as a dimer; UPS-1 interacts with UPS-2; UPS-1 interacts with UPS-3; UPS-2 interacts with UPS-3.
• Considering UPS-1 through UPS-3, sugarish appears to solicit a similar insulin response to that expected from glucose."
• Based on the figure, "C" could be an inactive Ras protein.
• The virulent form of bubonic plague carries a protein called YopH, which functions as a protein tyrosine phosphatase.
• The following functions as a regulatory protein by dephosphorylating activated enzymes: phosphoprotein phosphatase.
• Anabolic steroids easily pass through the membrane and bind steroid receptors which migrate to the nucleus and function as a transcription factor.
• The following does not belong: autoinhibitor segment – receptor tyrosine kinase – SH2.
• The activity of protein kinase A is affected by caffeine, levels of cAMP, phosphodiesterases, and cholera toxin.
• The following are activated either directly or indirectly by a heterotrimeric G protein subunit: phospholipase C and calmodulin (CaM) sensitive kinase
• Oncogenes encode a protein which block cell cycle inhibition and can function as transcription factors.
• Scaffold proteins limit cross-talk.
• Autoinhibition in the SH2 and SH3 domains occurs when a SH2 phospho-Tyr binds a Pro segment on the SH3 domain, therefore blocking the active site and burying the required Tyr.
• Ca^{2+} binding to calmodulin (CaM) results in conformational change that exposes a hydrophobic patch capable of binding to calcium sensitive protein kinase
• DAG, cAMP, IP3 all function as second messengers.
• Sildenafil (Viagra®) increases the relative concentration of cGMP.
• Binding of a hormone to a receptor must signal the exchange of GDP for GTP in heterotrimeric G protein function.
• Increased activity of inositol polyphosphate 5-phosphatase would lead to a decrease in the level of IP3 in the cytosol.
• Anthrax toxin alters cAMP dependent cell signaling and calcium levels affect the function of the edema factor.
• Hormones elicit specific cellular responses.

Introduction to Metabolism

Matching Questions

• Autotrophs: Prokaryotes that are able to synthesize all of their cellular components from simple molecules such as CO2, H2O, NH3, and H2S.
• Obligate Aerobes: Organisms that require oxygen for nutrient breakdown.
• Anabolic Pathways: Biomolecules are synthesized from simpler components in these pathways.
• Acyl Phosphate: 1,3-Bisphosphoglycerate is an example of this.
• Pyrophosphatase: The enzyme that catalyzes the reaction, PPi 2 Pi.
• Adenylate Kinase: The enzyme that catalyzes the transfer of a phosphoryl group from ATP to AMP.
• Reduction Reaction: A metabolic reaction resulting in the formation of FADH_2 is an example of this.
• Oxidation Reaction: The reaction NADH NAD^+ is an example of this.
• The standard reduction potential under biochemical standard state conditions is symbolized as
• Proteomics: The study of the complete set of proteins synthesized in the cell in response to changing conditions.

Multiple Choice Questions

• Facultative Anaerobes: Organisms that can grow in either the presence or absence of oxygen.
• Correctly ranks the following compounds from lowest level of oxidation to highest level of oxidation:
  • 2 < 1 < 3 ($ CH2=CH2 < CH3CHO < CH3CO_2H$)
• Consider the following metabolic reaction:
  • Succinyl-CoA + Acetoacetate → Acetoacetyl-CoA + Succinate \Delta G°' = –1.25 \frac{kJ}{mol}
  • The K_{eq} for this reaction at 25°C is 1.66.
  • The \Delta G°' for the hydrolysis of Succinyl-CoA is –33.9 kJ/mol. What is the \Delta G°' for the hydrolysis of Acetoacetyl-CoA? Answer: -32.7 kJ/mol
  • This reaction is favorable under standard conditions.
• The K_{eq} is 0.503 at 25°C for the following reaction. What is the \Delta G°' for this reaction? D-Glucose-6-phosphate → D-Fructose-6-phosphate \Delta G°'= ? Answer: +1.70 kJ/mol
• Consider the following metabolic reaction:
  • 2-Phosphoglycerate → 3-Phosphoglycerate \Delta G°' = −4.40 \frac{kJ}{mol}
  • This reaction is at equilibrium under these conditions when the concentration of 2-phosphoglycerate is 0.490 mM and the concentration of 3-phosphoglycerate is 2.90 mM at 25°C.
• Consider the following metabolic reaction:
  • 3-Phosphoglycerate → 2-Phosphoglycerate \Delta G°' = +4.40 \frac{kJ}{mol}
  • The \Delta G for this reaction is –1.53 kJ/mol when the concentration of 2-phosphoglycerate is 0.290 mM and the concentration of 3-phosphoglycerate is 2.90 mM at 37°C. (using the equation \Delta G = \Delta G^o + RTlnK)
• The numbered arrow pointing toward a high-energy phosphoanhydride bond is 5.
• Given that the standard reduction potential of oxaloacetate is –0.166 V and the standard reduction potential of NAD^+ is –0.315 V, the \Delta \varepsilon°' for the oxidation of malate by NAD^+: Malate + NAD^+ → Oxaloacetate + NADH + H^+ is –0.149 V.
• Catabolism: The conversion of triacylglycerides into fatty acids for energy generation.
• ATP contains one phosphoester and two phosphoanhydride bonds.
• Pantothenic acid: The vitamin that is one of the components of coenzyme A, which is involved in acyl transfer.
• Flux: Is equal to the rate of synthesis minus the rate of breakdown of the metabolic intermediates.
• Cells control or regulate the flux through metabolic pathways by means of allosteric control of enzymes, covalent modification of enzymes, and genetic control of the concentrations of enzymes.
• The decrease in negative charge repulsion in the products compared to reactants are factors that contribute to the large negative standard free energy change for the reaction shown below: ATP → ADP + P_i
• The following are true regarding vitamins: They are essential organic molecules an organism is unable to synthesize; Some water-soluble vitamins mediate electron-transfer reactions; In humans, the water-soluble vitamins are converted into organic coenzymes.
• While NAD^+ is always involved in reactions that require the transfer of 2 electrons, flavin can participate in reactions that transfer either 1 or 2 electrons.
• Nutrition involves food intake and metabolic utilization of food.
• Obligate aerobes perish under conditions with O_2.
• In the catabolic pathway, major nutrients are exergonically broken down, resulting in the synthesis of ATP.
• In eukaryotes, glycolysis typically occurs in the cytosol.
• Carbon dioxide is in the highest oxidation state.
• Acyl phosphates such as 1,3-bisphosphoglycerate have a greater phosphoryl group transfer potential compared to ATP, which can be recognized by the more negative \Delta G°' values for hydrolysis.
• The reaction \ATP + creatine phosphocreatine + ADP \Delta G°' = +12.6 \frac{kJ}{mol} operates close to equilibrium in cells.
• The terminal electron acceptor in aerobic organisms is O_2.
• In redox half-reactions, a more positive standard reduction potential means the oxidized form has a higher affinity for electrons, and the greater the tendency for the oxidized form to accept electrons.
• Transcriptomics: The most reliable systems biology approach to assessing gene expression.
• Thioester: Acetyl-CoA contains this bond, which often provides the energy required for substrate-level phosphorylation.
• The enzyme inorganic pyrophosphatase catalyzes the hydrolysis of bonds in PP_i.
• Factors that increase the phosphate transfer potential of a compound: electrostatic repulsion between charged groups on the reactant; resonance stabilization of the hydrolysis products; greater energy of solvation of the hydrolysis products; the presence of an enol group in the reactants.
• A new metabolic enzyme which utilizes NAD^+ as a coenzyme, may be involved in a catabolic pathway.
• The correct coenzyme forms that correspond to X and Y in the following reaction as catalyzed by lactate dehydrogenase: Pyruvate + X → Lactate + Y are X = NADH Y = NAD^+.
• Negative feedback inhibition is one type of allosteric metabolic control.
• If Z = ATP formed via substrate level phosphorylation, Compound B contains a high-energy bond.
• If the diagram represents a catabolic pathway and enzyme 1 requires NAD^+, enzyme 1 catalyzes an oxidation.
• NADH is a derivative of niacin.
• The redox centers are ranked in order of increasing ability to produce a favorable electron flow as Q, F, C, D and Z
• A researcher is interested in determining if a long term change in the carbohydrate content of an individual's diet alters the levels of expression of carbohydrate metabolizing enzymes. DNA microarrays would address this question.
• If