Term
| The active site of an enzyme usually occupies only a small fraction of its surface. |
|
Definition
| True. Only a few amino acid side chains contribute to the active site. The rest of the protein is required to maintain the polypeptide chain in the correct position, provide additional binding sites for regulatory purposes, and localize the protein in the cell. |
|
|
Term
| Catalysis by some enzymes involves the formation of a covalent bond between an amino acid side chain and a substrate molecule. |
|
Definition
| True. Some enzymes form covalent intermediates with their substrates; however, in all cases the enzyme is restored to its original structure after the reaction. |
|
|
Term
| A Beta sheet can contain up to five strands, but no more. |
|
Definition
| False. Beta sheets can, in principle, contain any number of strands because the two strands that form the rims of the sheet are available for hydrogen bonding to other strands. |
|
|
Term
| The Specifity of an antibody molecule is contained exclusively in loops on the surface of the folded light chain domain. |
|
Definition
| D) False. It is true that the specifity of an antibody molecule is exclusively contained in loops on its surface; however, these loops are contributed by both the folded light and heavy chain domains. |
|
|
Term
| The possible linear arrangements of amino acids are so vast that new proteins almost never evolve by alternation of old ones. |
|
Definition
| E) False. The possible linear arrangements of amino acids that lead to a stably folded protein domain are so few that most new proteins evolve by alteration of old ones. |
|
|
Term
| Allosteric enzymes have two or more binding sites |
|
Definition
| F) True. Allosteric enzymes generally bind one or more molecules that function as regulators at sites that are distinct from the active site. |
|
|
Term
| Noncovalent bonds are too weak to influence the three dimensional structure of macromolecules |
|
Definition
| False. Noncovalent bonds are a major contributor to the three dimensional structure of macromolecules. |
|
|
Term
| Affinity chromatography separates molecules according to their intrinsic charge. |
|
Definition
| H) Flase. Affinity chromatography separates specific macromolecules because of their interactions with specific ligands, not because of their charge. |
|
|
Term
| Upon centrifugation of a cell homogenate, smaller organelles experience less friction and thereby sediment faster than larger ones. |
|
Definition
| ) False. The larger an organelle is, the more centrifugal force it experiences and the faster it sediments, despite an increased frictional resistance from the fluid through which it moves. |
|
|
Term
| Protein structure is determined solely by a protein’s amino acid sequence. Should a genetically engineered protein in which the order of all amino acids is reversed therefore have the same structure as the original protein? |
|
Definition
| No. It would not have the same or even a similar structure, because the peptide bond has a polarity. Looking at two sequential amino acids in a polypeptide chain, the amino acid that is closer to the N terminal end contributes the carboxyl group and the other amino acid contributes the amino group to the peptide bond that links the two. Changing their order would put the side chains into a different position with respect to the peptide backbone and therefore change their chemical environment. |
|
|
Term
| enzyme reactions often conform to the equation. |
|
Definition
E + S <--> ES -> EP <--> E + P
Where E, S, and P are enzyme, substrate, and product, respectively |
|
|
Term
What does ES represent in this equation?
E + S <--> ES -> EP <--> E + P |
|
Definition
| ES represents the enzyme-substrate complex. |
|
|
Term
Why is the first step shown with bidirectional arrows and the second step as a unidirectional arrow?
E + S <--> ES -> EP <--> E + P |
|
Definition
| B) Enzyme and substrate are in equilibrium between their free and bound states; once bound to the enzyme, a substrate molecule may either dissociate again (hence bidirectional arrows) or be converted to product. As substrate is converted to product, however, a reaction often proceeds strongly in the forward direction, as indicated by the unidirectional arrow. |
|
|
Term
Why does E appear on both ends of the equation?
E + S <--> ES -> EP <--> E + P |
|
Definition
| C) The enzyme is a catalyst and is therefore liberated in an unchanged form after the reaction; thus, E appears at both ends of the equation. |
|
|
Term
| one often finds that high concentrations of P inhibit the enzyme. Suggest why this might occur. |
|
Definition
| D) Often the products of a reaction resemble the substrates sufficiently that they can also bind to the enzyme. Any enzyme molecules that are bound to product are unavailable for catalysis; excess P therefore inhibits the reaction by lowering the concentration of free E. |
|
|
Term
| Compound X resembles S and binds to the active site of the enzyme but cannot undergo the reaction catalyzed by it. What effects would you expect the addition of X to the reaction to have? Compare the effects of X and of accumulation of P. |
|
Definition
| Compound X is an inhibitor of the reaction and works similarly by forming an EX complex. However, since P has to be made before it can inhibit the reaction, it takes longer to act than X, which is present from the beginning of the reaction. |
|
|
Term
| Which of the following amino acids would you expect to find more often near the center of a folded globular protein? Which ones would you expect to find more often exposed to the outside? Explain your answers. Ser, Ser-P, Leu, Lys, Gln, His, Phe, Val, Ile, Met, Cys-S-S-Cys, and Glu. Where would you expect to find the most N-terminal amino acid and the most C-terminal amino acid? |
|
Definition
| The polar amino acids Ser, Ser-P, Lys, Gln, His, and Glu are more likely to be found on a proteins surface, and the hydrophobic amino acids Leu, Phe, Val, Ile, and Met are more likely to be found in its interior. The oxidation of two cysteine residues to form a disulfide bond eliminates their potential to form hydrogen bonds and therefore makes them even more hydrophobic. Disulfide bonds are usually found in the interior of proteins. Irrespective of the nature of their side chains, the most N terminal amino acid and the most C terminal amino acid each contain a charged group and hence are usually found on the proteins surface. |
|
|
Term
| An enzyme isolated from a mutant bacterium grown at 20 degrees Celsius works in a test tube at 20 degrees Celsius but not at 37 degrees Celsius. Furthermore, once the enzyme has been exposed to the higher temperature, it no longer works at the lower one. The same enzyme isolated from the normal bacterium works at both temperatures. Can you suggest what happens at the molecular level to the mutant enzyme as the temperature increases? |
|
Definition
| The heat inactivation of the enzyme suggests that the mutation causes the enzyme to have a less stable structure. For example, a hydrogen bond that is normally formed between two amino acid side chains might no longer be formed because the mutation replaces on of these amino acids with a different one that cannot participate in the bond. Lacking such a bond that normally helps to keep the polypeptide chain folded properly, the protein unfolds at a temperature at which it would normally be stable. Polypeptide chains that are denatured when the temperature is raised often aggregate, and they rarely refold into active proteins when the temperature is decreased. |
|
|
Term
| Gel-Filtration chromatography separates molecules according to size. Smaller molecules diffuse faster in solution than larger ones, yet smaller molecules migrate more slowly through a gel filtration column than larger ones. Explain this paradox. What should happen at very rapid flow rates? |
|
Definition
| The slower migration of small molecules through a gel filtration column occurs because smaller molecules have access to many more spaces in the porous beads that are packed into the column than do larger molecules. However, it is important to give the smaller molecules sufficient time to diffuse into the spaces inside the beads. At very rapid flow rates, all molecules will move rapidly around the beads, so that large and small molecules will now tend to exit together from the column. |
|
|
Term
| Describe the different methods that cells use to restrict proteins to specific regions of the plasma membrane. is a membrane with many anchored proteins still fluid? |
|
Definition
| The different ways in which membrane proteins can be restricted to different regions of the membrane are summarized in figure 11-33. the mobility of the membrane proteins is drastically reduced if they are bound to other proteins such as those of the cytoskeleton or the extracellular matrix. some membrane proteins are confined to membrane domains by barriers, such as tight junctions. the fluidity of the lipid bilayer is not significantly affected by the anchoring of membrane proteins; the sea of lipid molecules flows around anchored membrane proteins like water around the posts of a pier. |
|
|
Term
The structure of a lipid bilayer is determined by the particular properties of its lipid molecules. What would happen if
A. Phospholipids had only one hydrocarbon chain instead of two? |
|
Definition
| True. The lipid bilayer is fluid because the lipid molecules in the bilayer can undergo these motions. A |
|
|
Term
The structure of a lipid bilayer is determined by the particular properties of its lipid molecules. What would happen if
B. The hydrocarbon chains were shorter than normal, say, about 10 carbon atoms long? |
|
Definition
| True. The lipid bilayer is fluid because the lipid molecules in the bilayer can undergo these motions. B |
|
|
Term
The structure of a lipid bilayer is determined by the particular properties of its lipid molecules. What would happen if
C. All of the hydrocarbon chains were saturated? |
|
Definition
| True. The lipid bilayer is fluid because the lipid molecules in the bilayer can undergo these motions. C |
|
|
Term
The structure of a lipid bilayer is determined by the particular properties of its lipid molecules. What would happen if
D. All of the hydrocarbon chains were unsaturated? |
|
Definition
| True. The lipid bilayer is fluid because the lipid molecules in the bilayer can undergo these motions. D |
|
|
Term
| Lipid molecules exchange places with their lipid neighbors every 10^-7 second. a lipid molecule diffuses from one end of a 2-microliter long bacterial cell to the other in about 1 second. are these two numbers in agreement (assume that the diameter of a lipid head group is about 0.5nm)? if not, can you think of a reason for the difference? |
|
Definition
| When lined up, there are about 4000 lipid molecules (each 0.5 nm wide) between a lipid molecule at one end of the bacterial cell and one at the other end. thus, if one of these molecules started to move toward the other, exchanging places with neighboring molecule every 10^-7 sec, it would take only 4 x 10^-4 sec to reach the other end. in reality, however the lipid molecule would move in a random path rather than in a defined direction, so it would take considerably longer (1 sec) to reach the other end. if a 4cm ping pong ball exchanged places with a neighbor every 10^-7 sec, it would travel at a speed of 1,440,000 km/hr. if its movement were only in one direction, it would reach the other wall in 1.5 x 10^-5 sec and, if it kept going, it would circle the earth in approximately 2 minutes. in a random walk it would take considerably longer to reach the other side of the room (~2msec) |
|
|
Term
| why does a red blood cell membrane need proteins? |
|
Definition
| Membrane proteins anchor the lipid bilayer to the cytoskeleton, strengthening the plasma membrane so that it can withstand the forces on it when the red blood ecll is pumped through small blood vessels. membrane proteins also transport nutrients and ions across the plasma membrane. |
|
|
Term
| Predict which of the following organisms will have the highest percentage of unsaturated phospholipids in their membranes. Explain your answer. |
|
Definition
| Antarctic fish live at sub-zero temperatures and are cold-blooded. to keep their membranes fulid at these temperatures, they have a high percentage of unsaturated phospholipids. |
|
|
Term
| The diagram in figure 12-6 shows a passive transporter that mediates the transfer of a solute down its concentration gradient across the membrane. how would you need to change the diagram to convert the transporter into a pump that moves the solute up its electrochemical gradient by hydrolyzing ATP? explain the need for each of the steps in your new illustration. |
|
Definition
|
|
Term
| The plasma membrane is highly impermeable to all charged molecules |
|
Definition
|
|
Term
| channels must first bind to solute molecules before they can select those that they allow to pass. |
|
Definition
|
|
Term
| transporters allow solutes to cross a membrane at much faster rates than do channels |
|
Definition
|
|
Term
| Certain H+ pumps are fueled by light energy |
|
Definition
|
|
Term
| The plasma membrane of many animal cells contains open K+ channels, yet the K+ concentration in the cytosol is much higher than outside the cell |
|
Definition
|
|
Term
| A symport would function as an antiport if its orientation in the membrane were reversed (if the portion of the molecule normally exposed to the cytosol faced the outside of the cell instead) |
|
Definition
|
|
Term
| The membrane potential of an axon temporarily becomes more negative when an action potential excites it |
|
Definition
|
|
Term
| List the following compounds in order of increasing lipid bilayer permeability: RNA, Ca^2+, glucose, ethanol, N2, water |
|
Definition
|
|
Term
| Discuss the following statement: "the differences between a channel and a transporter are like the differences between a bridge and a ferry" |
|
Definition
|
|
Term
| The neurotransmitter acetylcholine is made in the cytosol and then transported into synaptic vesicles, where its concentration is more than 100 fold higher than in the cytosol. when synaptic vesicles are isolated from neurons, they can take up additional acetylcholine added to the solution in which they are suspended, but only when ATP is present. Na+ ions are not required for acetylcholine uptake, but, curiously, raising the pH of the solution in which the synaptic vesicles are suspended increases the rate of acetylcholine uptake. furthermore, transport is inhibited when drugs are added that make the membrane permeable to H+ ions. suggest a mechanism that is consistent with all of these observations. |
|
Definition
|
|
Term
Phospholipid bilayers form sealed spherical vesicles in water. assume you have constructed lipid vesicles that contain Na+ -K+ pumps as the sole membrane protein, and assume for the sake of simplicity that each pump transports one Na+ one way and one K+ the other way in each pumping cycle. all of the Na+ -K+ pumps have the portion of the molecule that normally faces the cytosol oriented toward the outside of the vesicles. with the help of figure 12-11, determine what would happen if:
A. Your vesicles were suspended in a solution containing both Na+ and K+ ions and had a solution with the same ionic composition inside them. |
|
Definition
|
|
Term
Phospholipid bilayers form sealed spherical vesicles in water. assume you have constructed lipid vesicles that contain Na+ -K+ pumps as the sole membrane protein, and assume for the sake of simplicity that each pump transports one Na+ one way and one K+ the other way in each pumping cycle. all of the Na+ -K+ pumps have the portion of the molecule that normally faces the cytosol oriented toward the outside of the vesicles. with the help of figure 12-11, determine what would happen if:
B: You add ATP to the suspension described in (A: Vesicles suspended in a solution containing both Na+ and K+ ions and had a solution with the same ionic composition inside them) |
|
Definition
|
|
Term
Phospholipid bilayers form sealed spherical vesicles in water. assume you have constructed lipid vesicles that contain Na+ -K+ pumps as the sole membrane protein, and assume for the sake of simplicity that each pump transports one Na+ one way and one K+ the other way in each pumping cycle. all of the Na+ -K+ pumps have the portion of the molecule that normally faces the cytosol oriented toward the outside of the vesicles. with the help of figure 12-11, determine what would happen if:
C: You add ATP, but the solution outside as well as inside the vesicles contains only Na+ ions and no K+ ions |
|
Definition
|
|
Term
Phospholipid bilayers form sealed spherical vesicles in water. assume you have constructed lipid vesicles that contain Na+ -K+ pumps as the sole membrane protein, and assume for the sake of simplicity that each pump transports one Na+ one way and one K+ the other way in each pumping cycle. all of the Na+ -K+ pumps have the portion of the molecule that normally faces the cytosol oriented toward the outside of the vesicles. with the help of figure 12-11, determine what would happen if:
D: Half of the pump molecules embedded in the membrane of each vesicle were oriented the other way around so that the normally cytosolic portions of these molecules faced the inside of the vesicles. you then add ATP to the suspension. |
|
Definition
|
|
Term
Phospholipid bilayers form sealed spherical vesicles in water. assume you have constructed lipid vesicles that contain Na+ -K+ pumps as the sole membrane protein, and assume for the sake of simplicity that each pump transports one Na+ one way and one K+ the other way in each pumping cycle. all of the Na+ -K+ pumps have the portion of the molecule that normally faces the cytosol oriented toward the outside of the vesicles. with the help of figure 12-11, determine what would happen if:
E: you add ATP to the suspension described in (A: vesicles suspended in a solution containing both Na+ and K+ ions and had a solution with the same ionic composition inside them), but in addition to Na+ -K+ pumps, the membrane of your vesicles also contains K+ leaks channels. |
|
Definition
|
|
Term
| Amino acids are taken up by animal cells using a symport in the plasma membrane. What is the most likely ion whose electrochemical gradient drives the import? Is ATP consumed in the process? If so, how? |
|
Definition
|
|
