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.