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All Textbook Solutions for Biochemistry

RECALL State why the following terms are important in biochemistry: polymer, protein, nucleic acid, catalysis, genetic code.RECALL Match each entry in Column a with one in Column b; Column a shows the names of some important functional groups, and Column b shows their structures. Column a Column b Amino group CH3SH Carbonyl group (ketone) CH3CH=CHCH3 Hydroxyl group Carboxyl group CH3CH2NH2 Carbonyl group (aldehyde) Thiol group CH3CH2OCH2CH3 Ester linkage Double bond Amide linkage CH3OH Ether RECALL Identify the functional groups in the following compounds.REFLECT AND APPLY In 1828, Wohler was the first person to synthesize an organic compound (urea, from ammonium cyanate). How did this contribute, ultimately, to biochemistry?REFLECT AND APPLY A friend who is enthusiastic about health foods and organic gardening asks you whether urea is organic or chemical. How do you reply to this question?REFLECT AND APPLY Does biochemistry differ from organic chemistry? Explain your answer. (Consider such features as solvents, concentrations, temperatures, speed, yields, side reactions, and internal control.)REFLECT AND APPLY An earlier mission to Mars contained instruments that determined that amino acids were present on the surface of Mars. Why were scientists excited by this discovery?REFLECT AND APPLY Common proteins are polymers of 20 different amino acids. How big a protein (how many amino acid residues) would be necessary to have an Avogadros number of possible sequences?REFLECT AND APPLY Nucleic acids are polymers of just four different monomers in a linear arrangement. How many different sequences are available if one makes a polymer with only 40 monomers? How does this number compare with Avogadros number?REFLECT AND APPLY RNA is often characterized as being the first biologically active molecule. What two properties or activities does RNA display that are important to the evolution of life? Hint: Neither proteins nor DNA have both of these properties.REFLECT AND APPLY Why is the development of catalysis important to the development of life?REFLECT AND APPLY What are two major advantages of enzyme catalysts in living organisms when compared with other simple chemical catalysts such as acids or bases?REFLECT AND APPLY Why was the development of a coding system important to the development of life?REFLECT AND APPLY Comment on RNAs role in catalysis and coding in theories of the origin of life.REFLECT AND APPLY Do you consider it a reasonable conjecture that cells could have arisen as bare cytoplasm without a cell membrane?RECALL List five differences between prokaryotes and eukaryotes.RECALL Do the sites of protein synthesis differ in prokaryotes and eukaryotes?REFLECT AND APPLY Assume that a scientist claims to have discovered mitochondria in bacteria. Is such a claim likely to prove valid?RECALL Draw an idealized animal cell, and identify the parts by name and function.RECALL Draw an idealized plant cell, and identify the parts by name and function.RECALL What are the differences between the photosynthetic apparatus of green plants and photosynthetic bacteria?RECALL Which organelles are surrounded by a double membrane?RECALL Which organelles contain DNA?RECALL Which organelles are the sites of energy-yielding reactions?RECALL State how the following organelles differ from each other in terms of structure and function: Golgi apparatus, lysosomes, peroxisomes, glyoxysomes. How do they resemble each other?RECALL List the five kingdoms into which living organisms are divided, and give at least one example of an organism belonging to each kingdom.RECALL Which of the five kingdoms consist of prokaryotes? Which consist of eukaryotes?RECALL How does the five-kingdom classification differ from the one based only on plants and animals?REFLECT AND APPLY What are the advantages of being eukaryotic (as opposed to prokaryotic)?REFLECT AND APPLY Mitochondria and chloroplasts contain some DNA, which more closely resembles prokaryotic DNA than (eukaryotic) nuclear DNA. Use this information to suggest how eukaryotes may have originated.REFLECT AND APPLY Fossil evidence indicates that prokaryotes have been around for about 3.5 billion years, whereas the origin of eukaryotes has been dated at only about 1.5 billion years ago. Suggest why, in spite of the lesser time for evolution, eukaryotes are much more diverse (have a much larger number of species) than prokaryotes.RECALL Which processes are favored: those that require energy or those that release energy?RECALL Does the thermodynamic term spontaneous refer to a process that takes place quickly?BIOCHEMICAL CONNECTIONS For the process Nonpolarsolute+H2OSolution what are the signs of Suniv,SsysandSsurr? What is the reason for each answer? Ssurr refers to the entropy change of the surroundings, all of the Universe but the system.)RECALL Which of the following are spontaneous processes? Explain your answer for each process. (a) The hydrolysis of ATP to ADP and Pi Pi (b) The oxidation of glucose to CO2 and H2O by an organism (c) The phosphorylation of ADP to ATP (d) The production of glucose and O2 from CO2 and H2O in photosynthesis REFLECT AND APPLY In which of the following processes does the entropy increase? In each case, explain why it does or does not increase. (a) A bottle of ammonia is opened. The odor of ammonia is soon apparent throughout the room. (b) Sodium chloride dissolves in water. (c) A protein is completely hydrolyzed to the component amino acids. Hint: For Questions 37 through 39, consider the equation G=HT(S).REFLECT AND APPLY Why is it necessary to specify the temperature when making a table listing G values?REFLECT AND APPLY Why is the entropy of a system dependent on temperature?REFLECT AND APPLY A reaction at 23C has G=1kJmol1. Why might this reaction become spontaneous at 37C?REFLECT AND APPLY Urea dissolves very readily in water, but the solution becomes very cold as the urea dissolves. How is this possible? It appears that the solution is absorbing energy.REFLECT AND APPLY Would you expect the reaction ATPADP+Pi to be accompanied by a decrease or increase in entropy? Why?REFLECT AND APPLY The existence of organelles in eukaryotic cells represents a higher degree of organization than that found in prokaryotes. How does this affect the entropy of the Universe?REFLECT AND APPLY Why is it advantageous for a cell to have organelles? Discuss this concept from the standpoint of thermodynamics.REFLECT AND APPLY Which would you expect to have a higher entropy: DNA in its well-known double-helical form, or DNA with the strands separated?REFLECT AND APPLY How would you modify your answer to Question 29 in light of the material on thermodynamics?REFLECT AND APPLY Would it be more or less likely that cells of the kind we know would evolve on a gas giant such as the planet Jupiter?REFLECT AND APPLY What thermodynamic considerations might enter into finding a reasonable answer to Question 46?REFLECT AND APPLY If cells of the kind we know were to have evolved on any other planet in our solar system, would it be more likely to have happened on Mars or on Jupiter? Why?REFLECT AND APPLY The process of protein folding is spontaneous in the thermodynamic sense. It gives rise to a highly ordered conformation that has a lower entropy than the unfolded protein. How can this be?REFLECT AND APPLY In biochemistry, the exergonic process of converting glucose and oxygen to carbon dioxide and water in aerobic metabolism can be considered the reverse of photosynthesis, in which carbon dioxide and water are converted to glucose and oxygen. Do you expect both processes to be exergonic, both endergonic, or one exergonic and one endergonic? Why? Would you expect both processes to take place in the same way? Why?REFLECT AND APPLY Why is water necessary for life?REFLECT AND APPLY Contemplate biochemistry if atoms did not differ in electronegativity.RECALL What is a van der Waals force?RECALL What is an induced dipole?RECALL What is a salt bridge?RECALL Under what circumstance is a molecule that has a dipole not a polar molecule?REFLECT AND APPLY Which would you think would be a stronger interaction and why: an interaction between a sodium ion and the partial negative charge on the oxygen in ethanol (CH3CH2OH), or the interaction between two ethanol molecules?RECALL List the three types of van der Waals forces in decreasing order of strength.RECALL A hydrogen bond is a special case of what type of intermolecular force?REFLECT AND APPLY Why do you think that most textbooks do not consider a hydrogen bond to be an example of a van der Waals force?RECALL What are some macromolecules that have hydrogen bonds as a part of their structures?BIOCHEMICAL CONNECTIONS How are hydrogen bonds involved in the transfer of genetic information?REFLECT AND APPLY Rationalize the fact that hydrogen bonding has not been observed between CH4 molecules.REFLECT AND APPLY Draw three examples of types of molecules that can form hydrogen bonds.RECALL What are the requirements for molecules to form hydrogen bonds? (What atoms must be present and involved in such bonds?)REFLECT AND APPLY Many properties of acetic acid can be rationalized in terms of a hydrogen-bonded dimer. Propose a structure for such a dimer.REFLECT AND APPLY How many water molecules could hydrogen-bond directly to the molecules of glucose, sorbitol, and ribitol, shown here?REFLECT AND APPLY Both RNA and DNA have negatively charged phosphate groups as part of their structure. Would you expect ions that bind to nucleic acids to be positively or negatively charged? Why?RECALL Identify the conjugate acids and bases in the following pairs of substances: (a) (CH3)3NH+/(CH3)3N (b) +H3NCH2COOH/+H3NCH2COO (c) +H3NCH2COO/H2NCH2COO (d) OOCCH2COOH/OOCCH2COO (e) OOCCH2COOH/HOOCCH2COOH RECALL Identify conjugate acids and bases in the following pairs of substances:REFLECT AND APPLY Aspirin is an acid with a pKa of 3.5; its structure includes a carboxyl group. To be absorbed into the bloodstream, it must pass through the membrane lining the stomach and the small intestine. Electrically neutral molecules can pass through a membrane more easily than can charged molecules. Would you expect more aspirin to be absorbed in the stomach, where the pH of gastric juice is about 1, or in the small intestine, where the pH is about 6? Explain your answer.RECALL Why does the pH change by one unit if the hydrogen ion concentration changes by a factor of 10?MATHEMATICAL Calculate the hydrogen ion concentration, [H+], for each of the following materials: (a) Blood plasma, pH 7.4 (b) Orange juice, pH 3.5 (c) Human urine, pH 6.2 (d) Household ammonia, pH 11.5 (e) Gastric juice, pH 1.8 MATHEMATICAL Calculate the hydrogen ion concentration, [H+], for each of the following materials: (a) Saliva, pH 6.5 (b) Intracellular fluid of liver, pH 6.9 (c) Tomato juice, pH 4.3 (d) Grapefruit juice, pH 3.2 MATHEMATICAL Calculate the hydroxide ion concentration, [OH], for each of the materials used in Question 24.RECALL Define the following: (a) Acid dissociation constant (b) Acid strength (c) Amphipathic (d) Buffering capacity (e) Equivalence point (f) Hydrophilic (g) Hydrophobic (h) Nonpolar (i) Polar (j) Titration REFLECT AND APPLY Look at Figure 2.17. If you did this titration using TRIS instead of phosphate, how would the titration curve look compared to the figure? Explain.BIOCHEMICAL CONNECTIONS List the criteria used to select a buffer for a biochemical reaction.BIOCHEMICAL CONNECTIONS What is the relationship between pKa and the useful range of a buffer?MATHEMATICAL What is the [CH3COO]/[CH3COOH] ratio in an acetate buffer at pH 5.00?MATHEMATICAL What is the [CH3COO]/[CH3COOH] ratio in an acetate buffer at pH 4.00?MATHEMATICAL What is the ratio of TRIS/TRIS-H+ in a TRIS buffer at pH 8.7?MATHEMATICAL What is the ratio of HEPES/HEPES-H+ in a HEPES buffer at pH 7.9?MATHEMATICAL How would you prepare 1 L of a 0.050 M phosphate buffer at pH 7.5 using crystalline K2HPO4 and a solution of 1.0 M HCl?MATHEMATICAL The buffer needed for Question 35 can also be prepared using crystalline NaH2PO4 and a solution of 1.0 M NaOH. How would you do this?MATHEMATICAL Calculate the pH of a buffer solution prepared by mixing 75 mL of 1.0 M lactic acid (see Table 2.6) and 25 mL of 1.0 M sodium lactate.MATHEMATICAL Calculate the pH of a buffer solution prepared by mixing 25 mL of 1.0 M lactic acid and 75 mL of 1.0 M sodium lactate.MATHEMATICAL Calculate the pH of a buffer solution that contains 0.10 M acetic acid (Table 2.6) and 0.25 M sodium acetate.MATHEMATICAL A catalog in the lab has a recipe for preparing 1 L of a TRIS buffer at 0.0500 M and with pH 8.0: dissolve 2.02 g of TRIS (free base, MW=121.1 g/mol) and 5.25 g of TRIS hydrochloride (the acidic form, MW=157.6 g/mol) in a total volume of 1 L. Verify that this recipe is correct.MATHEMATICAL If you mix equal volumes of 0.1 M HCl and 0.20 M TRIS (free amine form; see Table 2.8), is the resulting solution a buffer? Why or why not?MATHEMATICAL What would be the pH of the solution described in Question 41?MATHEMATICAL If you have 100 mL of a 0.10 M TRIS buffer at pH 8.3 (Table 2.8) and you add 3.0 mL of 1 M HCl, what will be the new pH?MATHEMATICAL What would be the pH of the solution in Question 43 if you were to add 3.0 mL more of 1 M HCl?MATHEMATICAL Show that, for a pure weak acid in water, pH=(pKa2log[HA])/2.MATHEMATICAL What is the ratio of concentrations of acetate ion and undissociated acetic acid in a solution that has a pH of 5.12?BIOCHEMICAL CONNECTIONS You need to carry out an enzymatic reaction at pH 7.5. A friend suggests a weak acid with a pKa of 3.9 as the basis of a buffer. Will this substance and its conjugate base make a suitable buffer? Why or why not?48RE 49RE BIOCHEMICAL CONNECTIONS Which of the buffers shown in Table 2.8 would you choose to make a buffer with a pH of 7.3? Explain why.51RE REFLECT AND APPLY In Section 2-4, we said that at the equivalence point of a titration of acetic acid, essentially all the acid has been converted to acetate ion. Why do we not say that all the acetic acid has been converted to acetate ion?MATHEMATICAL Define buffering capacity. How do the following buffers differ in buffering capacity? How do they differ in pH? Buffer a: 0.01 M Na2HPO4 and 0.01 M NaH2PO4 Buffer b: 0.10 M Na2HPO4 and 0.10 M NaH2PO4 Buffer c: 1.0 M Na2HPO4 and 1.0 M NaH2PO4 BIOCHEMICAL CONNECTIONS If you wanted to make a HEPES buffer at pH 8.3, and you had both HEPES acid and HEPES base avail- able, which would you start with, and why?BIOCHEMICAL CONNECTIONS We usually say that a perfect buffer has its pH equal to its pKa. Give an example of a situation in which it would be advantageous to have a buffer with a pH 0.5 unit higher than its pKa.RECALL What quality of zwitterions makes them desirable buffers?57RE 58RE 59RE BIOCHEMICAL CONNECTIONS A frequently recommended treatment for hiccups is to hold ones breath. The resulting condition, hypoventilation, causes buildup of carbon dioxide in the lungs. Predict the effect on the pH of blood.RECALL How do D-amino acids differ from L-amino acids? What biological roles are played by peptides that contain D-amino acids?RECALL Which amino acid is technically not an amino acid? Which amino acid contains no chiral carbon atoms?RECALL For each of the following, name an amino acid in which the R group contains it: a hydroxyl group, a sulfur atom, a second chiral carbon atom, an amino group, an amide group, an acid group, an aromatic ring, and a branched side chain.RECALL Identify the polar amino acids, the aromatic amino acids, and the sulfur-containing amino acids, given a peptide with the following amino acid sequence: ValMetSerIlePheArgCysTyrLeu RECALL Identify the nonpolar amino acids and the acidic amino acids in the following peptide: GluThrValAspIleSerAla RECALL Are amino acids other than the usual 20 amino acids found in proteins? If so, how are such amino acids incorporated into proteins? Give an example of such an amino acid and a protein in which it occurs.MATHEMATICAL Predict the predominant ionized forms of the following amino acids at pH 7: glutamic acid, leucine, threonine, histidine, and arginine.MATHEMATICAL Draw structures of the following amino acids, indicating the charged form that exists at pH 4: histidine, asparagine, tryptophan, proline, and tyrosine.MATHEMATICAL Predict the predominant forms of the amino acids from Question 8 at pH 10.MATHEMATICAL Calculate the isoelectric point of each of the following amino acids: glutamic acid, serine, histidine, lysine, tyro- sine, and arginine.MATHEMATICAL Sketch a titration curve for the amino acid cysteine, and indicate the pKa values for all titratable groups. Also indicate the pH at which this amino acid has no net charge.MATHEMATICAL Sketch a titration curve for the amino acid lysine, and indicate the pKa values for all titratable groups. Also indicate the pH at which the amino acid has no net charge.MATHEMATICAL An organic chemist is generally happy with 95% yields. If you synthesized a polypeptide and realized a 95% yield with each amino acid residue added, what would be your overall yield after adding 10 residues (to the first amino acid)? After adding 50 residues? After 100 residues? Would these low yields be biochemically satisfactory? How are low yields avoided, biochemically?MATHEMATICAL Sketch a titration curve for aspartic acid, and indicate the pKa values of all titratable groups. Also indicate the pH range in which the conjugate acid-base pair +1 Asp and 0 Asp will act as a buffer.REFECT AND APPLY Suggest a reason why amino acids are usually more soluble at pH extremes than they are at neutral pH. (Note that this does not mean that they are insoluble at neutral pH.)REFECT AND APPLY Write equations to show the ionic dissociation reactions of the following amino acids: aspartic acid, valine, histidine, serine, and lysine.REFECT AND APPLY Based on the information in Table 3.2, is there any amino acid that could serve as a buffer at pH 8? If so, which one?REFECT AND APPLY If you were to have a mythical amino acid based on glutamic acid, but one in which the hydrogen that is attached to the -carbon were replaced by another amino group, what would be the predominant form of this amino acid at pH 4, 7, and 10, if the pKa value were 10 for the unique amino group?REFECT AND APPLY What would be the pI for the mythical amino acid described in Question 18?REFECT AND APPLY Identify the charged groups in the peptide shown in Question 4 at pH 1 and at pH 7. What is the net charge of this peptide at these two pH values?REFECT AND APPLY Consider the following peptides: PheGluSerMetandValTrpCysLeu. Do these peptides have different net charges at pH 1? At pH 7? Indicate the charges at both pH values.REFECT AND APPLY In each of the following two groups of amino acids, which amino acid would be the easiest to distinguish from the other two amino acids in the group, based on a titration? (a) gly, leu, lys (b) glu, asp, ser REFECT AND APPLY Could the amino acid glycine serve as the ba- sis of a buffer system? If so, in what pH range would it be useful?RECALL Sketch resonance structures for the peptide group.RECALL How do the resonance structures of the peptide group contribute to the planar arrangement of this group of atoms?REFECT AND APPLY Would the peptide group be planar if the amino group of amino acids was bonded to the carbon of the amino acid, rather than to the a carbon?27RE REFECT AND APPLY Consider the peptides SerGluGlyHisAlaandGlyHisAlaGluSer. How do these two peptides differ?REFECT AND APPLY Would you expect the titration curves of the two peptides in Question 28 to differ? Why or why not?REFECT AND APPLY What are the sequences of all the possible tripeptides that contain the amino acids aspartic acid, leucine, and phenylalanine? Use the three-letter abbreviations to express your answer.REFECT AND APPLY Answer Question 30 using one-letter designations for the amino acids.REFECT AND APPLY Most proteins contain more than 100 amino acid residues. If you decided to synthesize a 100-mer, with 20 different amino acids available for each position, how many different molecules could you make?REFECT AND APPLY If the amino acids alanine and glycine react to form a peptide bond, is there more than one reaction product? If so, what products?34RE REFECT AND APPLY Would the presence of a chiral center in an amino acid side chain affect the formation of a peptide bond?REFECT AND APPLY What might you infer (or know) about the stability of amino acids, when compared with that of other building- block units of biopolymers (sugars, nucleotides, fatty acids, etc.)?37RE REFECT AND APPLY Suggest a reason why the amino acids thyroxine and hydroxyproline are produced by posttranslational modification of the amino acids tyrosine and proline, respectively.REFECT AND APPLY Consider the peptides GlyProSerGluThr(open chain) and GlyProSerGluThr with a peptide bond linking the threonine and the glycine. Are these peptides chemically the same?40RE 41RE REFECT AND APPLY You are studying with a friend who draws the structure of alanine at pH 7. It has a carboxyl group (COOH) and an amino group (NH2). What suggestions would you make?43RE REFECT AND APPLY Suggest a reason (or reasons) why amino ac- ids polymerize to form proteins that have comparatively few covalent crosslinks in the polypeptide chain.45RE REFECT AND APPLY Speculate on the properties of proteins and peptides if none of the common amino acids contained sulfur.RECALL What are the structural differences between the peptide hormones oxytocin and vasopressin?RECALL How do the peptide hormones oxytocin and vasopressin differ in function?RECALL What is the role of the disulfide bond in oxytocin and vasopressin?RECALL Is it possible to form cyclic peptides without bonds between side chains of the component amino acids?51RE RECALL What types of experiments led to evidence regarding the effect of oxytocin and vasopressin on mammalian behavior?53RE THOUGHT QUESTION Imagine we identify a gene that is directly responsible for the effects of vasopressin on male mammals, including humans-we will call it trust1-that leads to the production of a vasopressin receptor in the brain, which we will call TRUST1. There are different versions of trust1, all of which lead to different levels of the behavior associated with this neuropeptide on male behavior. Give some examples where it would be a good idea to know a particular males genotype-that is, which of the trust1 genes he has. Give an example of when you think science has gone too far and this information should not be known.RECALL Match the following statements about protein structure with the proper levels of organization. (i) Primary structure (ii) Secondary structure (iii) Tertiary structure (iv) Quaternary structure (a) The three-dimensional arrangement of all atoms (b) The order of amino acid residues in the polypeptide chain (c) The interaction between subunits in proteins that consist of more than one polypeptide chain (d) The hydrogen-bonded arrangement of the polypeptide backbone.RECALL Define denaturation in terms of the effects of secondary, tertiary, and quaternary structure.RECALL What is the nature of random structure in proteins?REFLECT AND APPLY Suggest an explanation for the observation that when proteins are chemically modified so that specific side chains have a different chemical nature, these proteins cannot be denatured reversibly.REFLECT AND APPLY Rationalize the following observations. (a) Serine is the amino acid residue that can be replaced with the least effect on protein structure and function. (b) Replacement of tryptophan causes the greatest effect on protein structure and function. (c) Replacements such as LysArgandLeuIle usually have very little effect on protein structure and function.REFLECT AND APPLY Glycine is a highly conserved amino acid residue in proteins (i.e., it is found in the same position in the primary structure of related proteins). Suggest a reason why this might occur.REFLECT AND APPLY A mutation that changes an alanine residue in a protein to an isoleucine leads to a loss of activity. Activity is regained when a further mutation at the same site changes the isoleucine to a glycine. Why?REFLECT AND APPLY A biochemistry student characterizes the process of cooking meat as an exercise in denaturing proteins. Comment on the validity of this remark.RECALL List three major differences between fibrous and globular proteins.RECALL What are Ramachandran angles?11RE 12RE RECALL List some of the differences between the -helix and -sheet forms of secondary structure.RECALL List some of the possible combinations of -helices and -sheets in supersecondary structures.RECALL Why is proline frequently encountered at the places in the myoglobin and hemoglobin molecules where the polypeptide chain turns a corner?RECALL Why must glycine be found at regular intervals in the collagen triple helix?REFLECT AND APPLY You hear the comment that the difference between wool and silk is the difference between helical and pleated- sheet structures. Do you consider this a valid point of view? Why or why not?REFLECT AND APPLY Woolen clothing shrinks when washed in hot water, but items made of silk do not. Suggest a reason, based on information from this chapter.RECALL Draw two hydrogen bonds, one that is part of a secondary structure and another that is part of a tertiary structure.RECALL Draw a possible electrostatic interaction between two amino acids in a polypeptide chain.RECALL Draw a disulfide bridge between two cysteines in a polypeptide chain.RECALL Draw a region of a polypeptide chain showing a hydrophobic pocket containing nonpolar side chains.REFLECT AND APPLY The terms configuration and conformation appear in descriptions of molecular structure. How do they differ?REFLECT AND APPLY Theoretically, a protein could assume a virtually infinite number of configurations and conformations. Suggest several features of proteins that drastically limit the actual number.REFLECT AND APPLY What is the highest level of protein structure found in collagen?RECALL List two similarities and two differences between hemoglobin and myoglobin.RECALL What are the two critical amino acids near the heme group in both myoglobin and hemoglobin?RECALL What is the highest level of organization in myoglobin? In hemoglobin?RECALL Suggest a way in which the difference between the functions of hemoglobin and myoglobin is reflected in the shapes of their respective oxygen-binding curves.RECALL Describe the Bohr effect.RECALL Describe the effect of 2, 3-bisphosphoglycerate on the binding of oxygen by hemoglobin.RECALL How does the oxygen-binding curve of fetal hemoglobin differ from that of adult hemoglobin?RECALL What is the critical amino acid difference between the -chain and the -chain of hemoglobin?REFLECT AND APPLY In oxygenated hemoglobin, pKa=6.6 for the histidines at position 146 on the -chain. In deoxygenated hemoglobin, the pKa of these residues is 8.2. How can this piece of information be correlated with the Bohr effect?REFLECT AND APPLY You are studying with a friend who is describing the Bohr effect. She tells you that in the lungs, hemoglobin binds oxygen and releases hydrogen ion; as a result, the pH in- creases. She goes on to say that in actively metabolizing muscle tissue, hemoglobin releases oxygen and binds hydrogen ion and, as a result, the pH decreases. Do you agree with her reasoning? Why or why not?REFLECT AND APPLY How does the difference between the -chain and the -chain of hemoglobin explain the differences in oxygen binding between Hb A and Hb F?REFLECT AND APPLY Suggest a reason for the observation that people with sickle-cell trait sometimes have breathing problems during high-altitude flights.38RE REFLECT AND APPLY Why is fetal Hb essential for the survival of placental animals?BIOCHEMICAL CONNECTIONS Why might you expect to find some Hb F in adults who are afflicted with sickle-cell anemia?REFLECT AND APPLY When deoxyhemoglobin was first isolated in crystalline form, the researcher who did so noted that the crystals changed color from purple to red and also changed shape as he observed them under a microscope. What is happening on the molecular level? Hint: The crystals were mounted on a microscope slide with a loosely fitting cover slip.BIOCHEMICAL CONNECTIONS What is the direct cause of sickle- cell anemia (think primary structure)?BIOCHEMICAL CONNECTIONS What is the effect of the altered amino acid sequence in Hb S that causes the cells to form sickle shapes?BIOCHEMICAL CONNECTIONS Why do scientists believe that the sickle-cell trait has not evolved out of the human population yet considering how deadly it is to be homozygous for the sickle cell gene?45RE BIOCHEMICAL CONNECTIONS What is BCL11A and how is it related to hemoglobin?BIOCHEMICAL CONNECTIONS Given the purpose of hemoglobin, what could one envision as a downside to having all our hemoglobin as Hb F instead of Hb A?48RE REFLECT AND APPLY Comment on the energetics of protein folding in light of the information in this chapter.RECALL What is a chaperone?52RE 53RE 54RE RECALL What are some diseases caused by misfolded proteins?RECALL What causes protein aggregates to form?57RE 58RE BIOCHEMICAL CONNECTIONS What aspects of the transmission of scrapie or other spongiform encephalopathies act like genetic diseases? What aspects act like transmittable diseases?60RE 61RE RECALL What types of homogenization techniques are available for solubilizing a protein?RECALL When would you choose to use a PotterElvehjem homogenizer instead of a blender?RECALL What is meant by salting out? How does it work?RECALL What differences between proteins are responsible for their differential solubility in ammonium sulfate?RECALL How could you isolate mitochondria from liver cells using differential centrifugation?RECALL Can you separate mitochondria from peroxisomes using only differential centrifugation?RECALL Give an example of a scenario in which you could partially isolate a protein with differential centrifugation using only one spin.8RE REFLECT AND APPLY You are purifying a protein for the first time. You have solubilized it with homogenization in a blender followed by differential centrifugation. You wish to try ammonium sulfate precipitation as the next step. Knowing nothing beforehand about the amount of ammonium sulfate to add, design an experiment to find the proper concentration (% saturation) of ammonium sulfate to use.10RE RECALL What is the basis for the separation of proteins by the following techniques? (a) gel-filtration chromatography (b) affinity chromatography (c) ion-exchange chromatography (d) reverse phase HPLC RECALL What is the order of elution of proteins on a gel-filtration column? Why is this so?RECALL What are two ways that a compound can be eluted from an affinity column? What could be the advantages or disadvantages of each?14RE RECALL Why do most people elute bound proteins from an ion-exchange column by raising the salt concentration instead of changing the pH?RECALL What are two types of compounds that make up the resin for column chromatography?RECALL Draw an example of a compound that would serve as a cation exchanger. Draw one for an anion exchanger.RECALL How can gel-filtration chromatography be used to arrive at an estimate of the molecular weight of a protein?REFLECT AND APPLY Sephadex G-75 has an exclusion limit of 80,000 molecular weight for globular proteins. If you tried to use this column material to separate alcohol dehydrogenase (MW 150,000) from b-amylase (MW 200,000), what would happen?20RE RECALL What is the main difference between reverse phase HPLC and standard ion-exchange or gel filtration chromatography?RECALL How does HPLC differ from ion-exchange chromatography?REFLECT AND APPLY Design an experiment to purify protein X on an anion-exchange column. Protein X has an isoelectric point of 7.0.REFLECT AND APPLY Referring to Question 23, how would you purify protein X using ion-exchange chromatography if it turns out the protein is only stable at a pH between 6 and 6.5?25RE REFLECT AND APPLY You wish to separate and purify enzyme A from contaminating enzymes B and C. Enzyme A is found in the matrix of the mitochondria. Enzyme B is embedded in the mitochondrial membrane, and enzyme C is found in the peroxisome. Enzymes A and B have molecular weights of 60,000 Da. Enzyme C has a molecular weight of 100,000 Da. Enzyme A has a pI of 6.5. Enzymes B and C have pI values of 7.5. Design an experiment to separate enzyme A from the other two enzymes.REFLECT AND APPLY An amino acid mixture consisting of lysine, leucine, and glutamic acid is to be separated by ion-exchange chromatography, using a cation-exchange resin at pH 3.5, with the eluting buffer at the same pH. Which of these amino acids will be eluted from the column first? Will any other treatment be needed to elute one of these amino acids from the column?REFLECT AND APPLY An amino acid mixture consisting of phenylalanine, glycine, and glutamic acid is to be separated by HPLC. The stationary phase is aqueous and the mobile phase is a solvent less polar than water. Which of these amino acids will move the fastest? Which one will move the slowest?REFLECT AND APPLY In reverse-phase HPLC, the stationary phase is nonpolar and the mobile phase is a polar solvent at neutral pH. Which of the three amino acids in Question 28 will move fastest on a reverse-phase HPLC column? Which one will move the slowest?REFLECT AND APPLY Gel-filtration chromatography is a useful method for removing salts, such as ammonium sulfate, from protein solutions. Describe how such a separation is accomplished.RECALL What physical parameters of a protein control its migration on electrophoresis?RECALL What types of compounds make up the gels used in electrophoresis?RECALL Of the two principal polymers used in column chromatography and electrophoresis, which one would be most immune to contamination by bacteria and other organisms?RECALL What types of macromolecules are usually separated on agarose electrophoresis gels?RECALL If you had a mixture of proteins with different sizes, shapes, and charges and you separated them with electrophoresis, which proteins would move fastest toward the anode (positive electrode)?RECALL What does SDSPAGE stand for? What is the benefit of doing SDSPAGE?RECALL How does the addition of sodium dodecylsulfate to proteins affect the basis of separation on electrophoresis?RECALL Why is the order of separation based on size opposite for gel filtration and gel electrophoresis, even though they often use the same compound to form the matrix?RECALL The accompanying figure is from an electrophoresis experiment using SDSPAGE. The left lane has the following standards: bovine serum albumin (MW 66,000), ovalbumin (MW 45,000), glyceraldehyde 3-phosphate dehydrogenase (MW 36,000), carbonic anhydrase (MW 24,000), and trypsinogen (MW 20,000). The right lane is an unknown. Calculate the MW of the unknown.40RE 41RE 42RE 43RE REFLECT AND APPLY What would happen during an amino acid sequencing experiment using the Edman degradation if you accidentally added twice as much Edman reagent (on a per-mole basis) as the peptide you were sequencing?REFLECT AND APPLY A sample of an unknown peptide was divided into two aliquots. One aliquot was treated with trypsin; the other was treated with cyanogen bromide. Given the following sequences (N-terminal to C-terminal) of the resulting fragments, deduce the sequence of the original peptide. Trypsin treatment AsnThrTrpMetIleLysGlyTyrMetGlnPheValLeuGlyMetSerArg Cyanogen bromide treatment GlnPheValLeuGlyMetIleLysGlyTyrMetSerArgAsnThrTrpMet REFLECT AND APPLY A sample of a peptide of unknown sequence was treated with trypsin; another sample of the same peptide was treated with chymotrypsin. The sequences (N-terminal to C-terminal) of the smaller peptides produced by trypsin digestion were as follows: MetValSerThrLysValIleTrpThrLeuMetIleLeuPheAsnGluSeArg The sequences of the smaller peptides produced by chymotrypsin digestion were as follows: AsnGluSerArgValIleTrpThrLeuMetIleMetValSerThrLysLeuPhe Deduce the sequence of the original peptide.REFLECT AND APPLY You are in the process of determining the amino acid sequence of a protein and must reconcile contradictory results. In one trial, you determine a sequence with glycine as the N-terminal amino acid and asparagine as the C-terminal amino acid. In another trial, your results indicate phenylalanine as the N-terminal amino acid and alanine as the C-terminal amino acid. How do you reconcile this apparent contradiction?REFLECT AND APPLY You are in the process of determining the amino acid sequence of a peptide. After trypsin digestion followed by the Edman degradation, you see the following peptide fragments: LeuGlyArgGlySerPheTyrAsnHisSerGluAspMetCysLysThrTyrGluValCysMetHis What is abnormal concerning these results? What might have been the problem that caused it?49RE 50RE 51RE 52RE 53RE 54RE RECALL What is the basis for the technique called ELISA?56RE 57RE RECALL What are the main procedures involved in a western blot?RECALL Where did western blot get its name?60RE 61RE 62RE 63RE 64RE 65RE RECALL How does the catalytic effectiveness of enzymes compare with that of nonenzymatic catalysts?RECALL Are all enzymes proteins?MATHEMATICAL Catalase breaks down hydrogen peroxide about 107 times faster than the uncatalyzed reaction. If the latter required one year, how much time would be needed by the catalase- catalyzed reaction?REFLECT AND APPLY Give two reasons why enzyme catalysts are 103 to 105 more effective than reactions that are catalyzed by, for example, simple H+orOH.RECALL For the reaction of glucose with oxygen to produce carbon dioxide and water, Glucose+6O26CO2+6H2O the DG is 22880 kJ mol-1, a strongly exergonic reaction. However, a sample of glucose can be maintained indefinitely in an oxygen-containing atmosphere. Reconcile these two statements.REFLECT AND APPLY Would nature rely on the same enzyme to catalyze a reaction either way (forward or backward) if the DG were 0.8kcalmol1? If it were 5.3kcalmol1?REFLECT AND APPLY Suggest a reason why heating a solution containing an enzyme markedly decreases its activity. Why is the decrease of activity frequently much less when the solution contains high concentrations of the substrate?REFLECT AND APPLY A model is proposed to explain the reaction catalyzed by an enzyme. Experimentally obtained rate data fit the model to within experimental error. Do these findings prove the model?REFLECT AND APPLY Does the presence of a catalyst alter the standard free energy change of a chemical reaction?REFLECT AND APPLY What effect does a catalyst have on the activation energy of a reaction?REFLECT AND APPLY An enzyme catalyzes the formation of ATP from ADP and phosphate ion. What is its effect on the rate of hydrolysis of ATP to ADP and phosphate ion?REFLECT AND APPLY Can the presence of a catalyst increase the amount of product obtained in a reaction?

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