Chapter 10: Regulatory Strategies: Enzymes and Hemoglobin

• Chapter 10 is about the regulation of function.
• Allosteric control, isozymes, reversible covalent modification, and proteolytic activation are some of the regulatory mechanisms discussed.
• The authors used examples to show the structure-function relationships involved in the control mechanisms.
• The first step in the synthesis of pyrimidine is the condensation of carbamoylphosphate and aspartate.
• Its activity is regulated both positively and negatively.
• The ability to efficiently transport oxygen in blood and release it to myoglobin is dependent on coorperative binding of oxygen to hemoglobin.
• Hb is regulated by H+, CO2, and 2,3-biphosphoglycerate.

• After the section on allosteric control, the authors show how isozymes can be used to regulate enzymes in a tissue specific manner.
• The authors talk about the regulation of enzymes with modifications such as acetylation and ubiquination.

• The authors use the example of the cAMP dependent protein kinase (PKA) as an example of how a target can be regulated.
• The authors turn to proteolytic cleavage.
• The active forms of chymotrypsin, trypsin, and pepsin come from their inactive zymogens.
• Chapter 9 presented the mechanisms of action.
• The authors conclude Chapter 10 with a discussion of the blood clotting cascade, a series of proteolytic activations of clotting factors that lead to the formation of fibrin clot.
• The proteolytic enzymes are linked to several stimulating and inhibiting proteins.

• You should be able to complete the objectives once you have mastered this chapter.

• List the four major regulatory mechanisms that control activity.

• Give examples of ways in which a given isozyme can be different.

• List the modifications used to regulate the activity of the proteins.

• Phosphory is an effective control mechanism.

• Examples of zymogens and their biological processes can be given.

• A shift to curve B could be caused by the addition of an irreversible inhibitor.

• Homotropic activation is the allosteric effect of CTP.

• The allosteric effects that result from the interaction of hemoglobin with O2, CO2, H+, and BPG are reflected in the oxygen dissociation curve for hemoglobin.

• A phosphoryl group is transferred from oneprotein to another.

• There is a human being that is activated by a molecule.

• The source of trypsin is the pancreas.

• The chymotrypsinogen needs the cleavage of at least two bonds by trypsin.

• The zymogens are listed in the left column and the enzymes are listed in the right column.

• An allosteric inhibition is involved in the inactivation of trypsin.

• When the synthesis of pyrimidine nucleotides is available, the activation of ATCase occurs.
• The overproduction of pyrimidine nucleotides is prevented by feedback inhibition.

• a, c, d 7.
• Fetal hemoglobin is composed of different parts than adult hemoglobin.
• Fetal hemoglobin's affinity for oxygen is higher, and the fetus can extract O2 from maternal blood.

• The change in the environment of His 146 increases its affinity for protons because of the attraction between the negative charge of the aspartate and the protons.

• Two negative charges are introduced to a phosphoryl group.
• A phosphoryl group can form hydrogen bonds to adjacent H-bond partners.
• Local effects can be transmitted to more distant parts of theprotein in a similar way toosteric effects.

• Because trypsin is the common activator of the zymogens, it will produce the carboxyl-terminal residues.

• Ca2+ is chelators of g-carboxyglutamate.
• The elec trostatic anchor is Ca2+ and it brings interdependent clotting factors into close proximity.

• A study was conducted to understand the mechanism of the allosteric transi tion in ATCase.

• The nitrotyrosine reporter group was contained in the modified catalytic subunits.

• The first step in the biosynthetic pathway leads to the synthesis of cytidine triphosphate.
• When the cell has an ample supply of CTP, it shuts off the biosynthetic pathway.
• The first step in a pathway may not be the main regulatory step.

• The investigation of the properties of ATCase has been done with the use ofphosphonacetylL-aspartate.

• An effective respiratory carrier needs to be able to pick up oxygen from the lungs.

• Patients suffering from pneumonia have a portion of their lungs filled with fluid, and therefore have reduced lung surface area available for oxygen exchange.
• Standard hospital treatment of these patients involves placing them on a ventilating machine set to deliver enough oxygen to keep their blood pressure under control.

• Predict if each of the following sequence is likely to be phosphorylated.
• Explain your answers and tell which one would be phosphorylated.

• The steady-state [B]/[A] ratio can be increased by an increase in intracellular cAMP levels.

• Trypsin's primary structure has 13 and 2 arginine residues.

• Although thrombin has many properties in common with trypsin, the conversion of prothrombin to thrombin is not autocatalytic.

• Direct Chem ical measurements can't be used to determine if the factors are within normal concentrations or deficient because many of them are present in small concentrations.
• If a deficiency has been established, the affected person's blood can be used to screen for it in other people.
• A deficiency in Factor XII prolongs the time it takes to clot.
• If you have blood from someone who has a Factor XII deficiency, you should design a test that can help determine if another person has a Factor XII deficiency.

• Reactions that are far from equilibrium are the ones that are irreversible in cells.

• Amplification cascades are important in a number of regulatory processes.
• There is a catalyst for the activation of the enzyme B.
• Each pathway has a turnover number of 103.

• Both thrombin and trypsin are serine proteases that can leave the bond on the carboxyl side of arginine.

• The system would behave like a single form if the R and T forms were equal in affinities.
• The plot of the reaction speed versus the concentration would be hyperbolic.

• The aim of the experiment was to show that the reporter group undergoes a change in its structure because it is bound to a different part of the enzyme.
• If the experiment was to give meaningful results, binding of the substrate to the reporter group had to be stopped.

• There would be no control over the production of X from B if regulation were to occur at step 1 only.
• There would be no regulation over the production of X from A if only step 2 were regulated.
• Control of the amount of X produced from both A and B is provided by regulation at step 3.
• The main regulatory step is usually after the branch point.

• PALA is a bisubstrate analog, that is, it resembles a combination of both substrates, and it is a transition state analog for the carbamoylphosphate-aspartate complex.
• The location of the active site has been revealed by the X-ray analysis of ATCase.
• Comparisons of structures with and without PALA have shown the large structural changes that ATCase undergoes.

• The active site of ATCase is an analog of PALA.
• At low concentrations, the distribution of ATCase molecule to the R is shifted.
• This increases the activity of the enzyme.

• BPG interacts with hemoglobin.
• The interaction between the negatively charged phosphates of BPG and the positively charged residues of hemoglobin is stronger in the interior environment than it would be on the surface.
• The force of interactions is proportional to the medium's dielectric constant.
• It is possible that the dielectric constant is as low as 2.

• The surface has a dielectric constant of 80, but the electrostatic interactions there are much more stable.

• Substance A wouldn't let oxygen into peripheral tissues.
• Oxygen wouldn't be loaded in the lungs with Substance B.
• An effective carrier has an oxygen dissociation curve between substance A and substance B.
• It would have a lot of oxygen in the lungs and less in the peripheral tissues.

• Administering enough oxygen to give saturation levels greater than 92 would be wasteful because one reaches the point of diminishing returns.

• The risk of compromising oxygen delivery to the tissues is caused by giving oxygen in amounts less than required.

• According to the model, a mixture of fully oxygenated and fully deoxygenated molecules is posed with all of the components in the R form.
• According to the sequential model, some of the molecule's parts are oxygenated in the R form and others are deoxygenated in the T form.

• There is a consensus that the Arg-Arg-X-Ser-Z is large and small.
• The site is either Ser or Thr.

• The activity of en zyme 1 should be decreased by phosphorylation.
• The steady-state ratio of [B]/[A] could be increased by an increase in cAMP levels.
• The control of opposing metabolic sequence is observed frequently in cells.

• The activation of trypsinogen is an autocatalytic process.
• trypsinogen can be cleaved as the process occurs.
• The activation of chymotrypsinogen corresponds to Curve II.
• The chymotrypsinogen is not autocatalytic.
• Tryspin can convert chymotrypsinogen to p-chymotrypsin.
• The time course is initially linear.

• The active site of trypsin needs to be partially buried.

• Thrombin cleaves bonds.
• When pro thrombin is converted to thrombin, there are two bonds that are broken.
• The conversion cannot be autocatalytic.

• Prepare two blood samples for testing.
• Factor XII deficiency is probably not involved if clotting time is restored to normal.
• Factor XII deficiency can be suspected if the addition of normal plasma restores normal time but the addition of Factor XII deficiency does not.

• The reaction is at equilibrium.
• Nothing would happen if the reaction was made more active.
• The reaction is still at equilibrium.
• If the reaction is displaced far from equilibrium, more product will be produced.
• If a regulatory enzyme is to increase the flux rate through a pathway, it must make an irreversible step.

• One molecule of active A will lead to the activation of more than one molecule of D. 103 molecule of active B will be produced by Active A.
• Each of the 103 molecule of active B will make 103 molecule of C. The total of active C and B is 106 and 103, respectively.

• Both thrombin and trypsin have an oxyanion hole at the active site.
• Both sites have a negatively charged pocket that can be binding.
• thrombin has enough space to accommodate a Gly residue next to the Arg binding site in contrast to trypsin, which has no restrictions as to the amino acid residue that can be accommodated at the corresponding position.

• The positive charge on the carbonyl oxygen in the transition state is thought to be stable by histidine 134.

• Whether one proceeds R - T -TS or R -RSTS, S is the same.

• The constant for the conversion of R to T and R toRS is 103.
• The constant for the conversion of T toTS is 10 since the affinity of R for S is 100 times that of T. The constant for the conversion ofRS toTS is 10.
• The R to T ratio is changed by the binding of the substrate with a hundredfold tighter binding to R.

• The ratio in the fully liganded molecule will be 10 if there is no substrate.

• L is the ratio of T to R in the sence of ligand, and L is the number 105.

• The fraction of the molecule in the R state is either [R]/([R] + [T]) or [R]/([R] + [R]Lj).

• The concerted model can't be counted for negative cooperativity due to the fact that the binding of substrate promotes a conformational transition of all subunits to the high-affinity R state.

• If the model holds, allosteric interactions must be cooperative.
• In the sequential model, the binding of ligand changes the structure of the subunit to which it is bound, but not that of its neighbors.

• The binding of PALA ATCase switches from the T to the R state.
• There are fewer free catalytic sites for an empty molecule than there are for a bound one.
• The R state of the PALA- containing enzyme makes it more affinity for the substrates.
• The binding affinities of the R and T states are for the analog.

• All of the time, the R state would be occupied by the Mutant enzyme.
• According to a classical saturation curve, the reaction rate depends on the fraction of active sites occupied by the substrate.

• A molecule with a high density of negative charge is needed to replace 2,3-BPG.
• The best candidate is (b) inositol hexaphosphate, an analogue of a major natural hemoglobin effector.

• The zymogens are activated by the cleavage of one or more bonds.
• The pepsin moities are hydrolyzed when the catalytic site is exposed.
• The time required for half the pepsinogen molecule to be activated is dependent on the number of molecules present.

• A mixture of the two bloods will not clot if both patients have a Factor VIII deficiency.

• If the second patient's bleeding disorder is caused by the deficiency of another factor, a mixture of the two bloods should clot.

• Factor X is used to convert prothrombin to thrombin on blood platelets.
• The proteolytic activation removes the fragment of prothrombin that contains Ca+2-binding sites and releases thrombin.
• Factor X can be activated by other prothrombin molecule if it remains bound to the platelets.

• It is thought that antithrombin III is not good for thrombin.
• Many en zyme inhibitors have high affinity for active sites.
• Thrombin can react with antithrombin III because it has a fully formed active site.

• Chapter 3 of your textbook introduces a coiled coil.
• Since this is a long molecule made up of repeating units, one would expect to see side chains at regular intervals.

• The binding of elastase by a1-antitrypsin is dependent on the side chain of methionine 358, which is most susceptible to oxidation by cigarette smoke.
• A side chain with a strong binding affinity for elastase is needed.
• The side chain of leucine is more stable than the side chain of methionine but has the same volume.

• The sequential model predicts that the fraction in the R state should be equal to the fraction in the Y.

• A conformational change in response to a distant site is reported by the change in the absorbance.
• The structure of a different trimer that carries the reporter nitrotyrosine group is altered by the binding of succinate to the active sites of a native trimer.

• Allosteric activators drive the catalytic subunits into the active state.
• The effect of CTP is to drive the catalytic subunits into an inactive state and decrease the absorbance.

• The effect is working here.
• The valine side chain on the surface tries to avoid water by making favorable van der Waals interactions with the leucine and phenylalanine side chains.
• The effect is to cause long fibers to crystallize and distort the shapes of red blood cells.

• In step 1, the aspartate smino group carries out a nucleophilic attack on the carbonyl carbon.
• The negatively charged oxyanion can be mitigated by the histidine in the active site.

• The serine- OH group takes the role of water and accepts the g-phosphate in the reaction.
• During the attack on the g-phosphate in step 1, the active site will need a group to accept the protons from the serine oxygen.
• The extra negative charge on the intermediate between steps 1 and 2 would be stable if there was a functional group at the active site.