Biochem Exam 2
Why does a competitive inhibitor not change Vmax?
A competitive inhibitor blocks binding, not catalysis.
What is the function of the protein kinase?
A kinase is an enzyme that phosphorylates a protein using a high-energy phosphate, such as ATP, as the phosphate donor.
Would you expect the structure of a noncompetitive inhibitor of a given enzyme to be similar to that of its substrate?
A noncompetitive inhibitor does not bind to the active site of an enzyme. its structure need bear no relation to that of the substrate.
Why does a pure noncompetitive inhibitor not change the observed Km?
A noncompetitive inhibitor does not change the affinity of the enzyme for its substrate.
What molecule acts as a positive effect (activator of ATCase? What molecule acts as an inhibitor?
ATP acts as a positive effector of ATCase, and CTP acts as an inhibitor.
Does the behavior of allosteric enzymes become more or less cooperative in the presence of activators?
Activators make the shape of the curve less sigmoidal.
What features distinguish enzymes that undergo allosteric control form those that obey the Michaelis-Menten equation?
Allosteric enzymes display sigmoidal kinetics when rates are plotted versus substrate concentration. Michaelis-Menten enzymes exhibit hyperbolic kinetics. Allosteric enzymes usually have multiple subunits, and the binding of substrates or effector molecules to one subunit changes the binding behavior of the other subunits.
Explain how a researcher makes an abzyme. What is the purpose of an abzyme?
An abzyme is created by injecting ghost animal with a transition-state analogue of a reaction of interest. The host animal makes antibodies to the foreign molecule, and these antibodies have specific binding points that mimic an enzyme surrounding a transition state. The purpose is to create an antibody with catalytic activity.
Define omega-3 fatty acid.
An omega-3 fatty acid has a double bond at the third carbon from the methyl end.
Write the structural formula for triacylglycerol, and name the component parts.
Any combination of fatty acids is possible.
Suggest a reason why the cell membranes of bacteria grown at 20C tend to have a higher proportion of unsaturated fatty acids than the membranes of bacteria of the same species grown at 37C. In other words, the bacteria grown at 37C have a higher proportion of saturated fatty acids in their cell membranes.
At the lower temperature, the membrane would tend to be less fluid. The presence of more unsaturated fatty acids would tend to compensate by increasing the fluidity of the membrane compared to one at the same temperature with a higher proportion of saturated fatty acids.
Suggest a reason why inorganic ions, such as K+, Na+, Ca2+, and Mg2+, do not cross biological membranes by simple diffusion.
Biological membranes are highly nonpolar environments. Charged ions tend to be excluded from such environments rather that dissolving in them, as they would have to do to pass through the membrane by simple diffusion.
Suggest a role for coenzymes based on reaction mechanisms.
Coenzymes can accomplish the same mechanisms that the amino acids do in a reaction. For example, a metal ion may act as a general acid or base. Parts of a coenzyme, such as the reactive carbanion of thiamine pyrophosphate, may act as a nucleophile to catalyze the reaction.
What conditions are necessary for the free energy change to be used to predict the spontaneity of a reaction?
Constant temperature and pressure.
How is the cooperative behavior of allosteric enzymes reflected in a plot of reaction rate against substrate concentration?
Enzymes that exhibit cooperativity do not show hyperbolic curves of rate versus substrate concentration. Their curves are sigmoidal. The level of cooperativity can be seen by the shape of the sigmoidal curve.
Suppose that you are studying a protein involved in transporting ions in and out of cells. Would you expect to find the nonpolar residues in the interior or exterior? Why? Would you expect to find the polar residues in the interior or the exterior? Why?
In a protein that spans the membrane, the nonpolar residues are the exterior ones; they interact with the lipids of the cell membrane. The polar residues are in the interior, lining the channel through which the ions enter and leave the cell.
How can competitive and pure noncompetitive inhibition be distinguished in terms of Km?
In the case of competitive inhibition, the value of Km increases, while the Km remains unchanged in noncompetitive inhibition.
Briefly describe the role of nucleophilic catalysis in the mechanism of the chymotrypsin reaction.
In the first step of the reaction, the serine hydroxyl is the nucleophile that attacks the substrate peptide bond. In the second step, water is the nucleophile that attacks the acyl-enzyme intermediate.
Does the behavior of allosteric enzymes become more or less cooperative in the presence of inhibitors?
Inhibitors make the shape of the curve more sigmoidal.
Why is it useful to plot rate data for enzymatic reactions as a straight line rather than as a curve?
It is easier to detect deviations of individual points from a straight line than from a curve.
Is it good (or bad) that enzymes can be reversibly inhibited? Why?
It is very good, in the case of noncompetitive inhibitors; much of metabolic control depends on feedback inhibition by downstream noncompetitive inhibitors. The question is perhaps moot in the case of competitive inhibitors, which are much less commonly encountered in vivo. Some antibiotics, however, are competitive inhibitors (good for the sick person, bad for the bacteria).
Why does the American Heart Association recommend the use of canola oil or olive oil rather than coconut oil in cooking?
Less heart disease is associated with diets low in saturated fatty acids.
Why is it important that energy released by exergonic reactions can be used to provide energy for endergonic reactions?
Many endergonic reactions are necessary for life processes. They need a source for the energy they require, and that source is the energy released by exergonic reactions.
Crisco is made from vegetable oils, which are usually liquid. Why is Crisco a solid?
Many of the double bonds have been saturated. Crisco contains "partially hydrogenated vegetable oils."
How are coenzymes related to vitamins?
Most coenzymes are derivatives of compounds we call vitamins. For example, nicotinamide adenine dinucleotide is produced from the B vitamin niacin. Flavin adenine dinucleotide comes from riboflavin.
Can the thermodynamic property ΔG° be used to predict the speed of a reaction in a living organism? Why or why not?
No, there is no relationship between the thermodynamic quantity ΔG° and the speed. The ΔG° reflects the thermodynamic possibility under states. Speed is a kinetic quantity that is based on the ability of an enzyme to catalyze the reaction and the real substrate concentrations in the cell.
Which is more hydrophilic, cholesterol or phospholipids? Defend you answer.
Phospholipids are more hydrophilic than cholesterol. The phosphate group is charged, and the attached alcohol is charged or polar these groups interact readily with water. Cholesterol has only a singular polar group, an -OH.
Do all proteins associated with membranes span the membrane from one side to another?
Proteins that are associated with membranes do not have to span the membrane. Some can be partially embedded in it, and some associate with the membrane by noncovalent interactions with its exterior.
Chapter 6
Question 26 + 30
Chapter 8
Question 3
What do the following indicators tell you about whether a reaction can proceed as written? a) the standard free energy change is positive b) the free energy change is positive Reaction would proceed only if coupled to an exergonic reaction. The reaction is exergonic.
Reaction A would take place only if it is coupled to an exergonic reaction. Reaction B would proceed only is coupled to an exergonic reaction. Reaction C would proceed as written.
What amino acids are often phosphorylated by kinases?
Serine, threonine, and tyrosine are the three most often phosphorylated amino acids in proteins that are acted upon by kinases. Aspartate is another one that is often phosphorylated.
Which of the following statements is (are) true about the modified standard state for biochemistry? For each, explain why or why not. a) [H+] = 1 X 10^-7 M, not 1 M b) The concentration of any solute is 1 x 10^-7 M
Statement A is true, but statement B is not. The standard state of solutes is normally defined as unit activity (1 M for all but the most careful work). In biological systems, the pH is frequently in the neutral range (i.e., H+ is close to 10^-7 M); the modification is a matter of convenience. Water is the solvent, not a solute, and its standard state is the pure liquid.
Which statements are consistent with the known facts about membrane transport? a) Active transport moves a substance from a region on which its concentration is lower to one in which its concentration is higher. b) Transport does not involve any pores or channels in membranes. c) Transport proteins may be involved in bringing substances into cells.
Statements A and C are correct; statement B is not correct because ions and larger molecules, especially polar ones, require channel proteins.
How does the structure of steroids differ from that of the other lipids discussed in this chapter?
Steroids contain a characteristic fused-ring structure, which other lipids do not.
Other things being equal, what is a potential disadvantage of an enzyme having a very high affinity for its substrate?
The ES complex would be in an "energy trough," with consequentially large activation energy to the transition state.
With respect to the concerted model, what os the L value? What is the c value?
The L value is the equilibrium ratio of the T/R form. The c value is the ratio of the dissociation constants for substrate and the two forms of enzyme, such that c = KR/KT.
Why does the apparent Km decrease in the presence go an uncompetitive inhibitor?
The binding of inhibitor to the ES complex to form EIS removes some of the ES. By LeChatelier's principle, this will tend to force the reaction to the right forming more ES. By stimulating the binding of E and S in this manner, the graph will show that the Km is reduced.
In biochemistry mechanisms, what group is often attacked by a nucleophile?
The carbon of a carbonyl group is often attacked by a nucleophile.
What is the role in vision of the cis-trans isomerization of retinal?
The cis-trans isomerization of retinal in rhodopsin triggers the transmission of an impulse to the optic nerve and is the primary photochemical event in vision.
How can you recognize an enzyme that does not display Michaelis-Menten kinetics?
The graph of rate against substrate concentration is sigmoidal for an allosteric enzyme but hyperbolic for an enzyme that obeys the Michaelis-Menten equation.
The ΔG°' for the reaction: Citrate -> Isocitrate is +6.64 kJ mol^-1 = +1.59 kcal mol^-1. The ΔG°' for the reaction: Isocitrate -> a-Ketoglutarate is -267 kJ mol^-1 = -63.9 kcal mol^-1. What is the ΔG°' for the conversion of citrate to a-ketoglutarate? Is that reaction exergonic or endergonic, and why?
The over all ΔG°' = -260.4 kJ mol^-1 or -62.3 kcal mol^-1. The reaction is exergonic, because it has a large, negative ΔG°'.
If only a few of the amino acid residues of an enzyme are involved in its catalytic activity, why does the enzyme need such a large number of amino acids?
The overall protein structure is needed to ensure the correct arrangement of amino acids in the active site.
Are the relative amounts of cholesterol and phosphatidylcholine the same in all the kinds of membranes found in a typical mammalian cell?
The relative amounts of cholesterol and phosphatidylcholine can vary widely in different types of membranes in the same cell.
Which allosteric model can explain negative cooperativity?
The sequential model can explain negative cooperativity, because a substrate binding to the T form could induce other subunits to switch to the T form, thereby reducing binding affinity.
Define steady state, and comment on the relevance of this concept to theories of enzyme reactivity.
The steady state assumption is that the concentration of the enzyme-substrate complex does not change appreciably over time in which the experiment takes place. The rate of appearance of the complex is set equal to its rate of disappearance, simplifying the equations for enzyme kinetics.
In lipid bilayers, there is an order-disorder transition similar to the melting of a crystal. In a lipid bilayer in which most of the fatty acids are unsaturated, would you expect this transition to occur at a higher temperature, a lower temperature, or the same temperature as it would in a lipid bilayer in which most of the fatty acids are saturated? Why?
The transition temperature is lower in a lipid bilayer with mostly unsaturated fatty acids compared with one with a high percentage of saturated fatty acids. The bilayer with the unsaturated fatty acids is already more disordered than the one with a high percentage of saturated fatty acids.
Why is it necessary to define a modified standard state for biochemical applications of thermodynamics?
The usual thermodynamic standard state refers to pH = 0. This is not very useful in biochemistry.
Which of the following lipids are NOT found in animal membranes? a) phosphoglycerides b) cholesterol c) triacylglycerols d) glycolipids e) sphingolipids
Triacylglycerols are not found in animal membranes.
How is the turnover number of an enzyme related to Vmax?
Turnover number = Vmax/[ET]
When does the kcat/Km value approximate the catalytic efficiency of an enzyme?
Under conditions of low substrate concentration.
List an important chemical property of vitamin E.
Vitamin E is an antioxidant.
What are the structural features of waxes? What are some common uses of compounds of this type?
Waxes are esters fo long-chain carboxylic acids and long-chain alcohols. They tend to be found as protective coatings.
Why is is necessary or advantageous for the body to make zymogens?
Zymogens are often seen with digestive enzymes that are produced in one tissue and used in another. If the enzyme were active immediately upon production, it would digest other cell proteins, where is would cause great damage. By having it produced as a zymogen, it can be safe made and then transported to the digestive tissue, such as the stomach or small intestine, where it can then be activated.
For the hydrolysis of ATP at 25C (298K) and pH 7, ATP + H20 -> ADP + Pi + H+, the standard free energy of hydrolysis (ΔG°') is -30.5 kJ mol ^-1 (-7.3 kcal mol^-1), and the standard enthalpy change (ΔH°') is -20.1 kJ mol^-1 (-4.8 kcal mol^-1). Calculate the standard entropy change (ΔS°') for the reaction in both joules and calories. Why is the positive sign of the answer to be expected in view of the nature of the reaction?
ΔG°' = ΔH°' - TΔS°' ΔS°' = 34.9 J mol^-1 K^-1 = 8.39 cal mol^-1 K^-1. There are two particles on the reactant side of the equation and three on the product side, representing an increase in disorder.