chymotrypsin to produce a Val-Ly Glu-Met-Ser Trp-Arg-Ala B Val-LYs-Glu-Met-Ser -Tr C Val-Lys-Glu-Met-Ser Trp-Arg-Ala d Val-LyS-Glu Met-Ser-Trp-Arg-Ala E Val-Lys-Glu-Met Ser-Trp-Arg-Ala 3. Hydrogen bonds in a-helices are a more numerous than van der Waals interactions B not present at Phe residues C analogous to the steps in a spiral staircase D roughly parallel to the helix axis E about 5? in length 4. In b-pleated sheet structures a neighboring chains lie in a flat plane B neighboring residues are hydrogen bonded c neighboring chains are connected by a- helic D neighboring residues have F& Y angles of about 90o E neighboring chains are hydrogen bonded. 5. If the F and Y angles of each peptide unit in a protein are known, the following will also be determined a complete secondary structure. B complete tertiary structure mplete quaternary structure d thermodynamic stability e Both the first and the second choices are correct ※<5> Which of the following is an example of tertiary structure in a protein? a polyalanine b a multimeric protei c an a-helix d a b-pleated sheet e a globular domain 2. An"oil drop with a polar coat"is a metaphor referring to the three dimensional structure of a fibrous proteins collagen globular proteins
chymotrypsin to produce: A Val-Lys + Glu-Met-Ser + Trp-Arg-Ala. B Val-Lys-Glu-Met-Ser-Trp + Arg-Ala. C Val-Lys-Glu-Met-Ser + Trp-Arg-Ala. D Val-Lys-Glu + Met-Ser-Trp-Arg-Ala. E Val-Lys-Glu-Met + Ser-Trp-Arg-Ala. 3. Hydrogen bonds in a-helices are A more numerous than Van der Waals interactions. B not present at Phe residues. C analogous to the steps in a spiral staircase. D roughly parallel to the helix axis. E about 5? in length. 4. In b-pleated sheet structures A neighboring chains lie in a flat plane. B neighboring residues are hydrogen bonded. C neighboring chains are connected by a-helices. D neighboring residues have F & Y angles of about 90°. E neighboring chains are hydrogen bonded. 5. If the F and Y angles of each peptide unit in a protein are known, the following will also be determined: A complete secondary structure. B complete tertiary structure. C complete quaternary structure. D thermodynamic stability. E Both the first and the second choices are correct. 5 ※<5> 1. Which of the following is an example of tertiary structure in a protein? A polyalanine. B a multimeric protein. C an a-helix. D a b-pleated sheet. E a globular domain. 2. An "oil drop with a polar coat" is a metaphor referring to the three dimensional structure of: A fibrous proteins. B collagen. C globular proteins
D silk protein e The first and the second choice are both correct 3. The portion of proteins having the highest mobility are a a-helices C peptide bonds. d surface side chains E aliphatic groups 4. Which of the following is most correct a Charged amino acids are never buried in the interior of a protein b Charged amino acids are seldom buried in the interior of a protein c All hydrophobic amino acids are buried when a protein folds d Tyrosine is only found in the interior of proteins e Glycine is rarely found in proteins because it is too destabilizing 5. Disulfide bonds most often stabilize the native structure of a extracellular proteins. b dimeric proteins c hydrophobic proteins D intracellular proteins E multisubunit proteins 6. Buried hydrophobic sidechains in a globular protein fit into a"hole"formed by the sidechains of a 1-3 other amino acid b precisely six other amino acids C 5-7 othe d 9-12 other amino acids E 13-15 other amino acids 7. The most important parameter relating to the energy of a H-bond in protein structure is: a whether it is found in an a-helix or a b-sheet b the angle between donor and accepter, i.e. 1800 +/-20 c the distance between donor and accepter i e. <3.2? D the peptide bond dipole, i.e.-370 D e the planarity of the peptide bond 8. All other things being equal, the free energy of favorable electrostatic interaction between two charges separated by 4?(-4kJ/mol) will a decrease 2-fold at 2? separation. b decrease 4-fold at 2? separation
D silk protein. E The first and the second choice are both correct. 3. The portion of proteins having the highest mobility are A a-helices. B b-sheets. C peptide bonds. D surface side chains. E aliphatic groups. 4. Which of the following is most correct: A Charged amino acids are never buried in the interior of a protein. B Charged amino acids are seldom buried in the interior of a protein. C All hydrophobic amino acids are buried when a protein folds. D Tyrosine is only found in the interior of proteins. E Glycine is rarely found in proteins because it is too destabilizing. 5. Disulfide bonds most often stabilize the native structure of: A extracellular proteins. B dimeric proteins. C hydrophobic proteins. D intracellular proteins. E multisubunit proteins. 6. Buried hydrophobic sidechains in a globular protein fit into a "hole" formed by the sidechains of A 1-3 other amino acids. B precisely six other amino acids. C 5-7 other amino acids. D 9-12 other amino acids. E 13-15 other amino acids. 7. The most important parameter relating to the energy of a H-bond in protein structure is: A whether it is found in an a-helix or a b-sheet. B the angle between donor and accepter, i.e. 180° +/- 20°. C the distance between donor and accepter, i.e. <3.2?. D the peptide bond dipole, i.e. - 3.70 D. E the planarity of the peptide bond. 8. All other things being equal, the free energy of favorable electrostatic interaction between two charges separated by 4? (-4kJ/mol) will A decrease 2-fold at 2? separation. B decrease 4-fold at 2? separation
C remain about the same D increase 2-fold at E increase 4-fold at 2? separation 9. Attractive van der Waals forces occur a between apolar molecules in the liquid state c between polar molecules in the solid state d only if other forces are less favorable e only in the gas ph 10. Unpaired H-bond donors and acceptors are found in the hydrophobic core of a protein a only at the ends of a-helices b only at the turns connecting b-strands d about once or twice/protein e only very rarely 11. All other things being equal, the free energy of an unfavorable electrostatic interaction between two charges separated by water(e=80)will a decrease 20-fold in benzene(e= 4) b decrease 400-fold in benzene C remain about the same d increase 20-fold in benzene E increase 400-fold in benzene ※<6 The strong conclusion from anfinsen's work on rnasea was that a 100%enzyme activity corresponds to the native conformation B disulfide bonds(s-s)in proteins can be reduced in vitro C Cys-sH groups are not found in vivo d the native conformation of a protein is adopted spontaneously. E irreversible denaturation of proteins violates the Thermody Hypothesis 2. Treatment of RNase A with 8M urea, but without add ing mercaptoethanol would a not have unfolded the protein B have simplified the experimental analysis c also denature the enzyme d have caused irreversible denaturation e also result in formation of Cys-SH residues
C remain about the same. D increase 2-fold at 2? separation. E increase 4-fold at 2? separation. 9. Attractive van der Waals forces occur A between apolar molecules in the liquid state. B between any pair of nearby atoms. C between polar molecules in the solid state. D only if other forces are less favorable. E only in the gas phase. 10. Unpaired H-bond donors and acceptors are found in the hydrophobic core of a protein A only at the ends of a-helices. B only at the turns connecting b-strands. C only on Pro residues. D about once or twice/protein. E only very rarely. 11. All other things being equal, the free energy of an unfavorable electrostatic interaction between two charges separated by water (e = 80) will A decrease 20-fold in benzene (e = 4). B decrease 400-fold in benzene. C remain about the same. D increase 20-fold in benzene. E increase 400-fold in benzene. 5 ※<6> 1. The strong conclusion from Anfinsen's work on RNaseA was that: A 100% enzyme activity corresponds to the native conformation. B disulfide bonds (S-S) in proteins can be reduced in vitro. C Cys-SH groups are not found in vivo. D the native conformation of a protein is adopted spontaneously. E irreversible denaturation of proteins violates the "Thermodynamic Hypothesis". 2. Treatment of RNaseA with 8M urea, but without adding mercaptoethanol would A not have unfolded the protein. B have simplified the experimental analysis. C also denature the enzyme. D have caused irreversible denaturation. E also result in formation of Cys-SH residues
3. If Anfinsen had not determined the location of the s-s bonds in renatured rnasea his result of >90% recovery of enzyme activity would a have proven his hypothesis b not have been believed c not have been possible d have been hard to believe e have gone unnoticed 4. The statement(from Campbell, p 127)that"the amino acid sequence of a protein contains all of the information required for the complete three dimensional structure a cannot be falsified by experiment; hence it is trivial B is strongly supported by denaturation-renaturation experiments C is called an"hypothesis"since its valid ity is sort of dicey D is called a"model"because it can be diagrammed in textbooks e has essentially been proven by recent theoretical work 5. Anfinsen probably chose RNase A for his experiments instead of say, trypsin or chymotrypsin, because a trypsin would digest itself to oligopeptides under mildly denaturing. conditions(slow removal of urea). b RNase A is less expensive than trypsin or chymotrypsin C Trypsin and chymotrypsin are intracellular enzymes(no S-s bonds) d RNase a has only 25 amino acid residues e RNase a does not have any interfering His residues 6. Which of the following occurred when RNase A refolded? a The primary structure of the protein was rearranged b Most of the charged residues were found buried in the protein C The entropy of the protein in d All of the above e None of ※<7> 1. Cleavage of an IgG molecule by the protease, papain, produces a an antigen -bind ing site and two constant regions B two heavy chain-light chain dimers C an inactive mixture of oligopeptides d two Fab fragments and one Fc fragment E an antibody without its N-linked oligosaccharide 2. Antibodies of the Igg class
3. If Anfinsen had not determined the location of the S-S bonds in renatured RNaseA, his result of >90% recovery of enzyme activity would A have proven his hypothesis. B not have been believed. C not have been possible. D have been hard to believe. E have gone unnoticed. 4. The statement (from Campbell, p.127) that "the amino acid sequence of a protein contains all of the information required for the complete three dimensional structure" A cannot be falsified by experiment; hence it is trivial. B is strongly supported by many denaturation-renaturation experiments. C is called an "hypothesis" since its validity is sort of dicey. D is called a "model" because it can be diagrammed in textbooks. E has essentially been proven by recent theoretical work. 5. Anfinsen probably chose RNaseA for his experiments instead of say, trypsin or chymotrypsin, because A trypsin would digest itself to oligopeptides under mildly denaturing conditions (slow removal of urea). B RNaseA is less expensive than trypsin or chymotrypsin. C Trypsin and chymotrypsin are intracellular enzymes (no S-S bonds). D RNaseA has only 25 amino acid residues. E RNaseA does not have any interfering His residues. 6. Which of the following occurred when RNaseA refolded? A The primary structure of the protein was rearranged. B Most of the charged residues were found buried in the protein. C The entropy of the protein increased. D All of the above. E None of the above. 5 ※<7> 1. Cleavage of an IgG molecule by the protease, papain, produces: A an antigen-binding site and two constant regions. B two heavy chain-light chain dimers. C an inactive mixture of oligopeptides. D two Fab fragments and one Fc fragment. E an antibody without its N-linked oligosaccharide. 2. Antibodies of the IgG class
a consist of four subunits B are glycoproteins c have inter- and intra-chain d sulfide crosslinks d are secreted into the blood stream E All four choices are correct 3. The immunoglobulin fold a found only in Igg molecules b composed of two antiparallel b-strands folded into a globular domain c a b-barrel composed of a three -and a four-stranded antiparallel b-sheet d found six times in the lgg molecule e The third and fourth choices are both correct 4. Antigenic determinants bind to which portions of an antibody? a variable regions B constant regions c only light chain d only heavy chains e the effector region 5. Monoclonal antibod ies produced in the laboratory a lack the constant regions of IgG b cannot be used for disease diagnosis yet c derive from human cancer patients d can be selected to bind to almost any known molecule e None of the above are correct 6. Antibodies in the human immune system can identify approximately 108 different molecules. Which one of the following is true? a This diversity is generated from 108 different immunoglobin genes b Most of these antibodies recognize self-antigens C Most of these antibodies recognize proteins. D Most of these antibodies recognize small organic molecules e There are really just a small number of antibodies, each of which can bind to many different antiger gon ※<8 1. The specificity of a ligand bind ing site on a protein is based on a the absence of competing ligands b the amino acid residues lining the bind ing site. c the presence of hydrating water molecules
A consist of four subunits. B are glycoproteins. C have inter- and intra-chain disulfide crosslinks. D are secreted into the bloodstream. E All four choices are correct. 3. The immunoglobulin fold is A found only in IgG molecules. B composed of two antiparallel b-strands folded into a globular domain. C a b-barrel composed of a three- and a four-stranded antiparallel b-sheet. D found six times in the IgG molecule. E The third and fourth choices are both correct. 4. Antigenic determinants bind to which portions of an antibody? A variable regions. B constant regions. C only light chains. D only heavy chains. E the effector region. 5. Monoclonal antibodies produced in the laboratory A lack the constant regions of IgG. B cannot be used for disease diagnosis yet. C derive from human cancer patients. D can be selected to bind to almost any known molecule. E None of the above are correct. 6. Antibodies in the human immune system can identify approximately 108 different molecules. Which one of the following is true? A This diversity is generated from 108 different immunoglobin genes. B Most of these antibodies recognize self-antigens. C Most of these antibodies recognize proteins. D Most of these antibodies recognize small organic molecules. E There are really just a small number of antibodies, each of which can bind to many different antigens. F have gone unnoticed. 5 ※<8> 1. The specificity of a ligand binding site on a protein is based on: A the absence of competing ligands. B the amino acid residues lining the binding site. C the presence of hydrating water molecules