CH. 3 Molecular and Cell bio Q&As
Isomerization of glucose 1-phosphate to glucose 6-phosphate is energetically favorable. At 37°C, ΔG° = -1.42 log10K. What is the equilibrium constant for this reaction if ΔG° = -1.74 kcal/mole at 37°C?
16.98
Arrange the following molecules in order with respect to their relative levels of oxidation (assign 5 to the most oxidized and 1 to the most reduced). _______ CH2O (formaldehyde) _______ CH4 (methane) _______ CHOOH (formic acid) _______ CH3OH (methanol) _______ CO2 (carbon dioxide)
3, 1, 4, 2, 5 More oxygen=more oxidized More hydrogens=more reduced
The small molecule cyclic AMP (cAMP) takes about 0.2 second to diffuse 10 µm, on average, in a cell. Suppose that cAMP is produced near the plasma membrane on one end of the cell; how long will it take for this cAMP to diffuse through the cytosol and reach the opposite end of a very large cell, on average? Assume that the cell is 200 µm in diameter
80 seconds
During respiration, energy is retrieved from the high-energy bonds found in certain organic molecules. What, in addition to energy, are the ultimate products of respiration?
CO2, H2O
Oxidation is a favorable process in an aerobic environment, which is the reason cells are able to derive energy from the oxidation of macromolecules. Once carbon has been oxidized to _______________, its most stable form, it can only cycle back into the organic portion of the carbon cycle through __________________.
CO2, photosynthesis.
Fill in the blanks, selecting from the choices below. Light + _________ + _________ --> _________ + heat + sugars CO, CO2, O2, H2, H2O, N2, NO
H20, CO2, O2
If you weigh yourself on a scale one morning, then eat four pounds of food during the day, will you weigh four pounds more the next morning? Why or why not? (Hint: What happens to the atoms from the food you ingested?)
No, you will not weigh four pounds more the next morning because only a small portion of the mass of the food will form components of the body. Much of the mass of food is either released as CO2 and H2O that are breathed out into the atmosphere or converted into materials excreted as waste products
Hydrolysis reactions are commonly used inside the cell to split high-energy covalent bonds. For each of the three reactions below, use the ΔG° for each reaction to determine the equilibrium constants (K). Assume that each reaction occurs independently of the other two. ΔG° (kcal/mole) Reaction 1: acetyl-P ! actetate + P -10.3 Reaction 2: ATP ! ADP + P -7.3 Reaction 3: glucose 6-P ! glucose + P -3.3
Reaction 1: K = 107.25 Reaction 2: K = 105.14 Reaction 3: K = 102.32
Chemical reactions that lead to a release of free energy are referred to as "energetically favorable." Another way to describe these reactions is: _____________.
Spontaneous
Which of the following statements would not be true of a favorable binding equilibrium? (a) The free-energy change is negative for the system. (b) The concentration of the complex remains lower than the concentration of the unbound components. (c) The complex dissociation rate is slower than the rate for component association. (d) The binding energy for the association is large and negative.
The concentration of the complex remains lower than the concentration of the unbound components.
Oxidation is the process by which oxygen atoms are added to a target molecule. Generally, the atom that is oxidized will experience which of the following with respect to the electrons in its outer shell?
a net loss
Which of the pair is more reduced? a) Fe^3+ or Fe^2+ b) H2C==CH2 or H3C--CH3 c) H-O-O-H or H-O-H
a) Fe^2+ b) H3C--CH3 c) H-O-H "More reduced" means having more electrons; gain of electrons can result in an increased negative charge or a decreased positive charge and can be due to an increase in the number of hydrogen atoms in a molecule.
When there is an excess of nutrients available in the human body, insulin is released to stimulate the synthesis of glycogen from glucose. This is a specific example of a(n) __________ process, a general process in which larger molecules are made from smaller molecules.
anabolic
Chemical reactions carried out by living systems depend on the ability of some organisms to capture and use atoms from nonliving sources in the environment. The specific subset of these reactions that break down nutrients in food can be described as _____________.
catabolic Memorization Trick: Cats eat food = CATabolic break down food
The energy used by the cell to generate specific biological molecules and highly ordered structures is stored in the form of _____________.
chemical bonds
The equilibrium constant (K) for the reaction Y!X can be expressed with respect to the concentrations of the reactant and product molecules. What is the correct relationship between K, [Y], and [X]?
K = [X]/[Y]
The second law of thermodynamics states that the disorder in any system is always increasing. In simple terms, you can think about dropping NaCl crystals into a glass of water. The solvation and diffusion of ions is favored because there is an increase in _____________.
entropty
A chemical reaction is defined as spontaneous if there is a net loss of free energy during the reaction process. However, spontaneous reactions do not always occur rapidly. Favorable biological reactions require ______________ to selectively speed up reactions and meet the demands of the cell.
enzymes
ΔG° indicates the change in the standard free energy as a reactant is converted to product. Given what you know about these values, which reaction below is the most favorable?
glucose --> CO2 + H2O. ΔG°= -686
At first glance, it may seem that living systems are able to defy the second law of thermodynamics. However, on closer examination, it becomes clear that although cells create organization from raw materials in the environment, they also contribute to disorder in the environment by releasing _____________.
heat
In the first stage of photosynthesis, light energy is converted into what other form of energy?
kinetic or electrical
Seed oils are often dehydrogenated and added back into processed foods as partly unsaturated fatty acids. In comparison with the original oil, the new fatty acids have additional double carbon-carbon bonds, replacing what were once single bonds. This process could also be described as _____________.
oxidation
When elemental sodium is added to water, the sodium atoms ionize spontaneously. Uncharged Na becomes Na+. This means that the Na atoms have been _____________.
oxidizied
By definition, catalysis allows a reaction to occur more __________________. Chemical reactions occur only when there is a loss of __________________ energy. Enzymes act more __________________ than other catalysts. A catalyst decreases the __________________ energy of a reaction.
rapidly, free, selectively, activation
The net distance a molecule travels through the cytosol via diffusion is relatively short in comparison with the total distance it may need to travel. This is because movement governed by diffusion alone is a ________________ process that is most effective for the dispersion of small molecules over short distances.
slow
Even though cellular macromolecules contain a large number of carbon and hydrogen atoms, they are not all spontaneously converted into CO2 and H2O. This absence of spontaneous combustion is due to the fact that biological molecules are relatively __________ and an input of energy is required to reach lower energy states
stable
What does the Km value indicate with the respect to enzyme--substrate interactions?
the enzyme-substrate binding affinity
The study of enzyme kinetics is usually performed with purified components and requires the characterization of several aspects of the reaction, including the rate of association with the substrate, the rate of catalysis, and _____________.
the regulation of the enzyme activity
Oxidation and reduction states are relatively easy to determine for metal ions, because there is a measurable net charge. In the case of carbon compounds, oxidation and reduction depend on the nature of polar covalent bonds. Which of the following is the best way to describe these types of bond?
unequal sharing of electrons across a covalent bond
The potential energy stored in high-energy bonds is commonly harnessed when the bonds are split by the addition of _______________ in a process called _____________.
water, hydrolysis
For the reaction Y!X at standard conditions with [Y] = 1 M and [X] = 1 M, ΔG is initially a large negative number. As the reaction proceeds, [Y] decreases and [X] increases until the system reaches equilibrium. How do the values of ΔG and ΔG° change as the reaction equilibrates?
ΔG becomes less negative and ΔG° stays the same.
ΔG measures the change of free energy in a system as it converts reactant (Y) into product (X). When [Y] =[X], ΔG is equal to _____________.
ΔG°
Which of the following is true for a reaction at equilibrium? (a) ΔG = ΔG° (b) ΔG° + RT ln [X]/[Y] = 0 (c) RT ln [X]/[Y] = 0 (d) ΔG + ΔG° = RT ln [X]/[Y]
ΔG° + RT ln [X]/[Y] = 0
In the case of a simple conversion reaction such as X-->Y, which value of ΔG° is associated with a larger concentration of X than Y at equilibrium? (Hint: How is ΔG° related to K?) (a) ΔG° = -5 (b) (c) ΔG° = 0 (d) ΔG° = 1
ΔG° = -1
Indicate whether the following statements about enzymes are true or false. If a statement is false, explain why it is false. A. Enzymes alter the equilibrium point of a reaction. B. Vmax can be determined by measuring the amount of product accumulated late in the reaction. C. Competitive inhibitors bind irreversibly to the enzyme active site, lowering Vmax.
A. False. An enzyme catalyzes its reaction in both directions, lowering the energy of activation for both the forward and reverse reactions. Enzymes do not affect the free energy of the reactants and products are the same, and thus they do not affect the reaction equilibrium. B False. Initial reaction velocities are measured to determine Vmax. C. False. Competitive inhibitors bind reversibly to an enzyme's active site.
Which of the following statements are true or false? If a statement is false, explain why it is false. A. Enzymes lower the free energy released by the reaction that they facilitate. B. Enzymes lower the activation energy for a specific reaction. C. Enzymes increase the probability that any given reactant molecule will be converted to product. D. Enzymes increase the average energy of reactant molecules.
A. False. Enzymes do not affect the initial energy of the reactants nor the final energy of the products after the reaction is complete, which are the values that determine the change in free energy of a reaction. B. True. C. True. D. False. By lowering the energy of activation, enzymes increase the number of molecules in a population that can overcome the activation barrier.
Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. When two macromolecules form a complex, the free energy of the system increases because there is a net increase in the amount of order in the cell. B. Sequential pathways can help drive unfavorable reactions by siphoning off the products into the next energetically favorable reaction in the series. C. The cytosol is densely packed with molecules, creating what is more an aqueous gel than a solution. D. The diffusion rates for smaller molecules in the cytosol are much lower than what is observed for the same molecules in water.
A. False. Even nonspecific interactions between macromolecules can be favorable if there is a large number of water molecules and ions displaced at the interaction interface. This would lead to an overall increase in disorder, even though the two larger molecules become associated and more ordered. B. True. C. True. D. False. Small molecules diffuse through the cytosol nearly as rapidly as they diffuse in water.
pIndicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Photosynthetic organisms release only O2 into the atmosphere, while nonphotosynthetic organisms release only CO2. B. The cycling of carbon through the biosphere first requires the incorporation of inorganic CO2 into organic molecules. C. The oxidation of one molecule is always coupled to the reduction of a second molecule. D. During cellular respiration, carbon-containing molecules become successively more oxidized until they reach their most oxidized form, as CO2.
A. False. Plants, as well as photosynthetic algae and bacteria, perform both photosynthesis and respiration. This means that photosynthetic organisms release both O2 and CO2 into the atmosphere. B. True. C. True. This forms the basis for redox pairs. D. True.
Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. The second law of thermodynamics states that the total amount of energy in the Universe does not change. B. The ultimate source of energy for living systems is chlorophyll. C. CO2 gas is fixed in a series of reactions that are light-dependent. D. H2 is the most stable and abundant form of hydrogen in the environment.
A. False. The second law of thermodynamics states that components of any system move toward greater disorder. B. False. The ultimate source of energy for living organisms is sunlight. C. False. The fixation of carbon from CO2 occurs independently of light. D. False. The most stable form of hydrogen is H2O.
Consider the reaction X!Y in a cell at 37°C. At equilibrium, the concentrations of X and Y are 50 µM and 5 µM, respectively. Use this information and the equations below to answer questions A-E. ΔG° = -0.616 ln Keq ΔG = ΔG° + 0.616 ln [Y]/[X] Recall that the natural log of a number z will have a negative value when z < 1, positive when z > 1, and 0 when z = 1. ! X-X-X... + H2O Æ X + X-X... X + ATP Æ X-P + ADP ATP + H2O Æ ADP + P DG° = - 4.5 kcal/mole DG° = - 2.8 kcal/mole DG° = - 7.3 kcal/mole A. What is the value of Keq for this reaction? B. Is the standard free-energy change of this reaction positive or negative? Is the reaction X!Y an energetically favorable or unfavorable reaction under standard conditions? C. What is the value of the standard free energy? Refer to Table 3-1 in the textbook or use a calculator. D. Imagine circumstances in which the concentration of X is 1000 µM and that of Y is 1 µM. Is conversion of X to Y favorable? Will it happen quickly? E. Imagine starting conditions in which the reaction X!Y is unfavorable, yet the cell needs to produce more Y. Describe two ways in which this may be accomplished.
A. Keq = [Y]/[X] = 5 µM/50 µM = 0.1 B. The standard free-energy change, ΔG°, is positive because Keq is less than 1. Under standard conditions (equal concentrations of X and Y), the reaction X!Y is unfavorable. C. ΔG° = -0.616 ln Keq = -0.616 ln 0.1 = (-0.616) (-2.3) = 1.4 kcal/mole. D. Yes, the conversion is favorable because the value of [Y]/[X] is less than the equilibrium value. However, the speed of the reaction cannot be determined from the free-energy difference. For example, combustion of this piece of paper is a highly favorable reaction, yet it will not happen in our lifetime without a catalyst. E. The cell may directly couple the unfavorable reaction to a second, energetically favorable reaction whose negative ΔG has a value larger than the positive ΔG of the X!Y reaction; the coupled reaction will have a ΔG equal to the sum of the component reactions. Alternatively, more X will be converted to Y if the concentration of Y drops; this may happen if Y is converted to Z in a second reaction or if Y is exported from the cell or compartment where the X!Y reaction occurs.
On the basis of the two reactions below, decide which of the following statements are true and which are false. If a statement is false, explain why it is false. 1: ATP + Y --> Y-P + ADP ΔG = -100 kcal/mole 2: Y-P + A --> B ΔG = 50 kcal/mole A. Reaction 1 is favorable because of the large negative ΔG associated with the hydrolysis of ATP. B. Reaction 2 is an example of an unfavorable reaction. C. Reactions 1 and 2 are coupled reactions, and when they take place together, reaction 2 will proceed in the forward direction. D. Reaction 2 can be used to drive reaction 1 in the reverse direction.
A. True. B. True. C. True. D. False. This is false for two reasons: (1) reaction 2 is unfavorable, as indicated by the positive free-energy change associated with the reaction; (2) the reverse reaction, although possibly more favorable, will yield the product for reaction 1, not reactants to help drive it forward.
Consider a description of an enzymatic reaction pathway that begins with the binding of substrate S to enzyme E, and ends with the release of product P from the enzyme. In many circumstances, Km = [E][S]/[ES] A. What proportion of enzyme molecules is bound to substrate when [S] = Km? B. Recall that when [S] = Km, the reaction rate is ½Vmax. Does your answer to part A make sense in the light of this rate information?
A. When [S] is substituted for Km in the equation, it becomes clear that [E] = [ES]. Thus, half of the enzyme molecules are free and half are bound to the substrate. B. Yes. If half of the enzyme molecules are bound to the substrate, it makes intuitive sense that the reaction rate is half of the maximum possible rate, or half of the rate observed when all of the enzyme molecules are bound to the substrate.
The equilibrium constant for complex formation between molecules A and B will depend on their relative concentrations, as well as the rates at which the molecules associate and dissociate. The association rate will be larger than the dissociation rate when complex formation is favorable. The energy that drives this process is referred to as ___________.
Binding Energy
Which of the values listed below is used to calculate the enzyme turnover number? (a) ½Vmax (b) Km (c) Vmax (d) Vmax - Km
Vmax
If proteins A and B have complementary surfaces, they may interact to form the dimeric complex AB. Which of the following is the correct way to calculate the equilibrium constant for the association between A and B? (a) kon/koff = K (b) K = [A][B]/[AB] (c) K = [AB]/[A][B] (d) (a) and (c)
D
Although the biochemical study of reaction rates and free energies is important for understanding each biological reaction individually, these studies do not provide an accurate picture of what is happening to reactants and products inside the cell. Why not?
Chemical reactions inside the cell do not reach a state of equilibrium because both reactants and products are typically used in more than one set of reactions, which means their concentrations are constantly fluctuating. As a result, the forward and reverse reaction rates are almost never identical.
Protein E can bind to two different proteins, S and I. The binding reactions are described by the following equations and values: E + S -> ES Keq for ES = 10 E + I -> EI Keq for EI = 2 Given the equilibrium constant values, which one of the following statements is true? (a) E binds I more tightly than S. (b) When S is present in excess, no I molecules will bind to E. (c) The binding energy of the ES interaction is greater than that of the EI interaction. (d) Changing an amino acid on the binding surface of I from a basic amino acid to an acidic one will probably make the free energy of association with E more negative.
Choice (c) is true. The binding energy is the standard free energy of the binding reaction, and thus is proportional to ln Keq. As the binding energy increases, the equilibrium constant for the association reaction becomes larger. Choices (a) and (b) are false, because although E binds S more tightly than it does I, some E molecules will still be bound to I molecules. Choice (d) is false; although not enough information is given to be certain, it is more likely that binding would be weakened by this change, making the free energy of association more positive.
Catalysts are molecules that lower the activation energy for a given reaction. Cells produce their own catalysts called _____________.
Enzymes
Your body extracts energy from the food you ingest by catalyzing reactions that essentially "burn" the food molecules in a stepwise fashion. What is another way to describe this process?
Oxidation
explain how enzymes catalyze reactions
The presence of enzyme in the mixture of reactant molecules does not change the energy distribution of the population of molecules. Their average energy will remain the same, and there still will be only a very small proportion of the molecules with high energy. Enzyme catalysis increases the total number of molecules that have sufficient energy to participate in the reaction because the total energy required per molecule that reacts is lowered.
In the cytoplasm, materials are organized, separated, and sorted by membranes. Cells exploit the selective permeability of these membranes to partition populations of molecules and generate chemical energy for the cell. Use the principles of the first and second laws of thermodynamics to explain how membranes can be used to produce chemical energy.
The second law of thermodynamics indicates that, if allowed to do so, the molecules would move across the membrane until there is an equal distribution of molecules on either side. The accumulation of molecules on one side of the membrane represents a store of potential energy. The first law of thermodynamics tells us that this energy will not be lost, but rather converted into a different type of energy.
Assume that the average human adult requires 2000 kilocalories per day to sustain all normal processes and maintain a constant weight. If manufactured solar panels could somehow provide power directly to the human body, what size solar panel would be required (in cm2)? Assume there are 10 hours of sunlight per day, and that the usable energy output for a typical solar panel is 850 kJ/ft2 per hour. Note: 1 kcal = 4.184 kJ 1 ft2 = 929.03 cm2
X = 914.57 cm2