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1. Which is true? 12. What is the number of proteins in a bacterial ribosome (E. coli)? a) Four-helix bundle is an example of the globin fold a) 21 b) Four-helix bundle is part of the glo...

1. Which is true? 12. What is the number of proteins in a bacterial ribosome (E. coli)? a) Four-helix bundle is an example of the globin fold a) 21 b) Four-helix bundle is part of the globin fold b) 32 c) The helices in four-helix bundle are parallel c) 53 d) The helices in four-helix bundle are antiparallel d) 250 2. Which of the following amino acids contains sulphur? 13. In how many directions the propagating light is not split into two rays a) Serine in orthorhombic, monoclinic, and triclinic crystals? b) Cysteine a) there is no such direction c) Tryptophan b) 1 d) Arginine c) 2 d) in any direction 3. What is the orientation of the side chains in Z-DNA? a) pyrimidines: gauche-gauche, purines: trans-gauche 14. In what system the following Bravais lattices are possible: P, I, F, C ? b) pyrimidines: trans-gauche, purines: gauche-gauche a) triclinic c) pyrimidines: gauche-trans, purines: gauche-gauche b) monoclinic d) pyrimidines: gauche-gauche, purines: gauche-trans c) orthorhombic d) cubic 4. How many protein structures have been determined by the X-ray diffraction method? 15. What reagents are used in the dauterization method of protein a) about 50 crystal derivatization? b) about 100 a) Cations of heavy metals c) about 1000 b) Deuterium d) over 10,000 c) Halides (Br-, I-) d) Selenomethionine (Se-Met) 5. The conformation of the glycosidic bond is defined as: a) cis-trans 16. Which quadrant of the Ramachandran Plot is the alpha-helix region b) syn-anti located in? c) egzo-endo a) upper left d) gauche-trans b) upper right c) lower right 6. What lattice centering are the following nodes characteristic of: 0,0,0; d) lower left 1/2,1/2,0; 1/2,0,1/2; 0,1/2,1/2 ? a) P 17. Which statement about the alpha helix is false? b) I a) are typically longer than 75 A c) F b) can contain more than 36 residues d) C c) their surface can have a hydrophobic side and a hydrophilic side 7. What system does the crystal class 422 belong to? d) they have a dipole moment a) monoclinic b) orthorhombic 18. Choose the smallest amino acid: c) tetragonal a) glycine d) cubic b) alanine c) valine 8. How many times during one full rotation between crossed polarizers d) proline will an optically anisotropic crystal brighten the field? a) 4 19. Which of the following is a pyrimidine deoxyribonucleoside? b) 8 a) adenosine c) the field will remain bright b) guanosine d) the field will remain dark c) thymidine d) uridine 9. What is the conformation of the 2'-deoxyribose rings in Z-DNA? a) C2'-endo 20. C3' deviates from the ribose plane in the same direction as C5'. What b) C3'-endo sugar conformer is this? c) pyrimidines: C3'-endo, purines: C2'-endo a) C3'-endo d) pyrimidines: C2'-endo, purines: C3'-endo b) C2'-endo c) C3'-egzo 10. One of the point groups below includes two-fold rotation. Which d) C2'-egzo one? a) 1 21. A crystal placed between crossed polarizers does not brighten the b) -1 field when rotated 360 deg in any of two different orientations on the c) mmm microscope stage. What system does the crystal belong to? d) 3 a) triclinic b) cubic 11. What is the relative orientation of the polarization directions of the c) tetragonal, trigonal, or hexagonal Ordinary and Extraordinary rays? d) orthorhombic, monoclinic, or triclinic a) parallel b) perpendicular 22. Crystals are generally optically anisotropic. The exception are crystals c) can be any with what symmetry? d) at least one of these rays is not polarized a) triclinic b) tetragonal c) hexagonal d) cubic 1 23. Crystals from one of the systems below are not uniaxial. Find this 34. What system does the crystal class 6/m mm belong to? system. a) triclinic a) tetragonal b) tetragonal b) trigonal c) hexagonal c) hexagonal d) cubic d) cubic 35. Which of the proteins has alfa/beta structure? 24. What is positive salt effect? a) Papain a) Precipitation of protein as a result of interaction with salt b) Triosephosphate isomerase ions c) gamma-crystallin b) Precipitation of salt from mother liquor d) Myoglobin c) Precipitation of protein as a result of dehydration by salt ions 36. What is the conformation of ribose in double-helical A-RNA? d) Precipitation of protein as a result of attraction of a) C2'-endo uncompensated charges on the surface of protein molecules b) C2'-egzo c) C3'-endo 25. What is the distance (in Å) between the planes of the successive base d) C3'-egzo pairs stacked in the B-DNA double helix? a) 2.6 37. Which of the types of lattice centering below is not possible in the b) 3.4 cubic system? c) 3.6 a) P d) 33.8 b) I c) F 26. Which of the statements characterizing protein crystals is false: d) C a) They are easily dried and lose crystallinity b) Ionizing radiation triggers degradation by free radicals 38. Find the type (fold) that is impossible for a crystallographic axis: c) They are unstable because the surface of protein molecules a) 1 is hydrophobic b) 3 d) For stability, they require the presence of the mother liquor c) 5 d) 6 27. What is Nicol's prism made of? a) glass 39. What is the relation between Bijvoet pairs and Friedel pairs? b) quartz a) Bijvoet pairs are special cases of Friedel pairs c) plexiglass b) Friedel pairs are special cases of Bijvoet pairs d) calcium carbonate c) they are the same thing d) they are unrelated 28. A repeating motif of main-chain torsion angles and a repeating motif of hydrogen bonds is characteristic of: 40. In an alanine molecule viewed along the N->C direction, the a) only of alpha helices substituents at the C atom form a clockwise sequence: H-> CH3 -> CO. b) only of beta sheets What stereoisomer is this? c) of secondary structures a) L-alanine d) this is an impossible situation b) D-alanine c) alanine is not chiral 29. Which statement about synchrotron radiation is false? d) it is not possible to decide because the viewing direction is a) It is very intense incorrect b) It is polarized c) It is coherent 41. cis peptide bonds are most likely to be found between the following d) Allows tuning of the wavelength amino acids: a) Proline - any 30. What system does the crystal class 1 belong to? b) Any - proline a) triclinic c) Any - any b) monoclinic d) Peptide bonds are never cis c) orthorhombic d) cubic 42. In most forms of nucleic acids the glycosidic bonds are anti. In what types of nucleotides has the syn form been observed? 31. The number of base pairs per one helical turn of the Z-DNA double a) purine-ribose helix is: b) purine-deoxyribose a) 3.6 c) pyrimidine-ribose b) 10 d) pyrimidine-deoxyribose c) 12 d) 33.8 43. Which of the following space group symbols is wrong? a) Cccm 32. What is the range of wavelengths (A) in the visible light? b) B4 a) 40-70 c) P622 b) 400-700 d) I23 c) 4000-7000 d) 40000-70000 44. Which of the statements about the helix-turn-helix motif is false? a) can be found in DNA binding proteins 33. Which form of DNA double helix has the largest diameter? b) can be found in calcium binding proteins (EF hand) a) A-DNA c) can be found in zinc binding proteins b) B-DNA d) is not present in gamma-crystallin c) Z-DNA d) All forms have the same diameter 2 45. How many Bravais lattices are there in the triclinic system? d) they are not possible in double-helical DNA a) 1 55. Which of the rays, Extraordinary (E) or Ordinary (O), has the same b) 2 speed in all directions in a birefringent crystal? c) 7 d) 14 a) E b) O 46. What symmetry element and in what location is represented by the c) none following transformation: x,y,z -> x,-y,z d) both a) it's an illegal operation 56. Find the true statement: b) center of inversion at 000 c) a dyad (2) along y a) the core of globular proteins is formed through interactions d) a mirror plane (m) perpendicular to y between the main chain and the side chains b) the core of globular proteins is formed by hydrophobic side 47. Which of the following space group symbols is wrong? chains a) P2(1) c) the core of globular proteins is formed by hydrophilic side b) I222 chains c) F1 d) in the protein core, the main chain is unable to form d) R32 hydrogen bonds 48. What vectors of the direct lattice is the reciprocal lattice vector a* 57. Tridymite and cristobalite are polymorphic forms of: normal to? a) quartz a) b, c b) carbon b) a, b c) magnesium c) a, c d) silicon d) only to a 58. What is anticodon? 49. What is the difference between linearly polarized and unpolarized a) A triplet of nucleotides coding one amino acid light? b) A triplet of nucleotides (in tRNA) that is complementary to a a) In polarized light the electric vector vibrates along the codon propagation direction, in unpolarized light it is perpendicular c) The triplet of nucleotides of a codon written in the reverse to it order (3' -> 5') b) in polarized light the electric and magnetic vectors vibrate in d) A triplet of nucleotides that is meaningless (does not code one plane, in unpolarized light they are perpendicular any information) c) in polarized light there is no magnetic vector 59. Linus Pauling discovered: d) in linearly polarized light the electric vector vibrates in one plane a) the DNA double helix b) the alpha helix 50. What system does the crystal class m3m belong to? c) penicillin a) triclinic d) vitamin C b) orthorhombic 60. What is the pitch (in A) of A-DNA double helix? c) trigonal d) cubic a) 26.0 b) 28.2 51. Which form of DNA double helix has the smallest diameter? c) 33.8 a) A-DNA d) 45.0 b) B-DNA 61. What is the orientation of the glycosidic bonds in Z-DNA? c) Z-DNA d) All forms have the same diameter a) syn b) anti 51. How many optic axes have orthorhombic, monoclinic, and triclinic c) pyrimidines: anti, purines: syn crystals? d) pyrimidines: syn, purines: anti a) none 62. What crystal class does the space group P6(4)22 belong to? b) 1 c) 2 a) 6 d) infinity b) 6/m mm c) 622 52. What is the number of three-dimensional point groups (crystal d) 422 classes)? 63. Which statement about isomorphous derivatives is true: a) 11 b) 14 a) They have the same space group but very different unit cell c) 32 parameters d) 230 b) They have the same unit cell parameters but different space groups 53. The "corn" rule has to do with: c) They have the same space group and unit cell parameters a) The structure of the proteins isolated from the corn kernel d) They represent different crystal forms of the same protein b) The absolute configuration of amino acids 64. The valence angles around a C(sp3) atom are (deg): c) The directionality of the peptide chain d) The isomerism of the peptide bond a) 60.0 b) 90.0 54. In what form of double-helical DNA are syn glycosidic bonds possible? c) 109.5 a) A-DNA d) 120.0 b) B-DNA c) Z-DNA 3 65. Which of the space groups is suitable for protein crystallization: 75. What system does the space group P212121 belong to? a) P21/c a) triclinic b) C2221 b) monoclinic c) Pmm2 c) orthorhombic d) I-4 d) trigonal 66. The first three-dimensional protein structure was determined for: 76. Which of the crystal classes below is not possible for protein crystals? a) Hemoglobin a) 2/m b) Myoglobin b) 32 c) Pepsin c) 23 d) Insulin d) 1 67. What system does the crystal class 222 belong to? 77. What is aminoacyl-tRNA synthetase? a) monoclinic a) Enzymatic tRNA molecule catalyzing the synthesis of an b) orthorhombic amino acid c) trigonal b) An enzyme synthesizing tRNA d) cubic c) An enzyme attaching an amino acid to the 5'-end of a 68. The first crystallographic determination of a protein structure was corresponding tRNA molecule made for: d) An enzyme attaching an amino acid to the 3'-end of a corresponding tRNA molecule a) Hemoglobin (Max Perutz) b) Myoglobin (John Kendrew) 78. The valence angles around a C(sp2) atom are (deg): c) Pepsin (Dorothy Hodgkin) a) 60.0 d) Insulin (Dorothy Hodgkin) b) 90.0 69. A crystal placed between crossed polarizers and rotated 360 deg c) 109.5 does not brighten the field in one orientation but brightens it as many as d) 120.0 four times in another orientation. What system does the crystal belong 79. One of the nucleosides below does not belong to the pyrimidine to? series. Which one? a) monoclinic a) cytidine b) cubic b) adenosine c) tetragonal, trigonal, or hexagonal c) thymidine d) orthorhombic, monoclinic, or triclinic d) uridine 70. Find the true statement: 80. What is the approximate mass (kDa) of bacterial ribosome (E. coli)? a) the structure of DNA is more diversified than the structure a) 25 of proteins b) 250 b) the information about the three-dimensional structure of c) 2500 biomolecules has been derived mainly from crystallographic d) 25000 studies c) today, the three-dimensional structure of a protein can be 81. Which of the DNA double helices is left-handed? easily predicted by theoretical methods d) a protein's function is not related to its structure a) A-DNA b) B-DNA 71. Find the false statement about the up-and-down barrel: c) Z-DNA d) DNA is always right-handed a) It consists of antiparallel beta chains b) It contains hairpin motifs 82. How many RNA molecules are there in the small ribosomal subunit? c) It has hydrophobic core d) It has hydrophilic core a) none b) 1 72. Who and when discovered the structure of the DNA double helix? c) 2 d) 3 a) Chargraff, 1938 b) Linus Pauling, 1952 83. The major groove is wide and deep, the minor groove is small, c) Francis Crick & James Watson, 1953 narrow, and deep. What form of DNA double helix is this? d) John Kendrew, 1959 a) A-DNA 72. What is the diameter (in Å) of B-DNA double helix? b) B-DNA c) Z-DNA a) 3.4 d) No unique answer exists b) 16 c) 20 84. Repeated peptide units having phi=-119 deg and psi =113 deg will d) 26 form: 73. The conformational difference between A-DNA and B-DNA lies in: a) an alpha helix b) a beta strand in 'antiparallel' conformation a) sugar conformation c) a beta strand in 'parallel' conformation b) the glycosidic bond d) no regular secondary structure will be formed c) the side chain d) the phosphate group 85. How many different amino acids are proteins built from: 74. Find the screw axis that is not neutral. a) 4 b) 16 a) 21 c) 20 b) 31 d) 252 c) 63 d) more than one are not neutral 4 86. A crystal placed between crossed polarizers and rotated 360 deg 97. Which DNA double helix has the shortest distance between the brightens the field in all orientations. What system does the crystal planes of the successive base pairs? belong to? a) A-DNA a) any b) B-DNA b) cubic c) Z-DNA c) tetragonal, trigonal, or hexagonal d) It's the same in all forms of double-helical DNA d) orthorhombic, monoclinic, or triclinic 98. What system does the crystal class m belong to? 87. What is Nicol's prism used for? a) triclinic a) to split light b) monoclinic b) to focus light c) orthorhombic c) to filter light d) cubic d) to polarize light 99. The region of the uv-vis spectrum characteristic for the absorption of 88. Can natural proteins crystallize in the crystal class 222? aromatic side chains is: a) Never a) Near 190 nm b) Yes, it is a popular class b) Near 280 nm c) Yes, but only in very rare cases c) Near 595 nm d) Yes, but only when the crystals are twinned d) Aromatic side chains do not absorb in the uv-vis region 89. Find the false statement about small proteins (up to 100 amino 100. Which of the following space group symbols is wrong? acids): a) Pacb a) Their structure is frequently stabilized by disulfide bridges b) P21/c b) Their structure is frequently stabilized by coordinated metal c) P32 ions d) Aba2 c) They can only exist in oligomeric form d) They are usually unable to form stable hydrophobic core 101. How many RNA molecules are there in the large ribosomal subunit? a) 1 90. Fatty-acid binding proteins have the following structure: b) 2 a) Up-and-down barrel c) 3 b) Greek-key barrel d) 6 c) Jelly-roll barrel d) alpha/beta barrel 102. Which statement characterizing the diffraction of X-rays on crystals is false? 91. Sugars: C2'-endo, glycosidic bonds: anti, side chains: gauche-gauche. a) The information about the crystal structure is encoded in What form of double helical DNA is it? the reflection intensities. a) A-DNA b) The X-rays are scattered by the electrons. b) B-DNA c) The number of possible reflections is proportional to the c) Z-DNA volume of the unit cell. d) There is no such form d) The number of possible reflections is inversely proportional to the crystal size. 92. Cubic crystals, amorphous materials, and gases are always: a) optically isotropic 103. Repeated peptide units having phi=-139 deg and psi=135 deg will b) optically anisotropic form: c) optically active a) an alpha helix d) optically inactive b) a beta strand in 'antiparallel' conformation c) a beta strand in 'parallel' conformation 93. What is the pitch (A) of the left-handed Z-DNA double helix? d) no regular secondary structure will be formed a) 26.0 b) 28.2 104. What is the number of ribosomal subunits? c) 33.4 a) 2 d) 45.0 b) 3 c) 4 94. Can natural proteins crystallize in the crystal class -4? d) 6 a) Never b) Yes, it is a popular class 105. How many space groups are available for protein crystallization? c) Yes, but only in very rare cases a) 11 d) Yes, but only when the crystals are twinned b) 32 c) 65 95. The solvent content, by volume, in protein crystals is usually: d) 230 a) Below 30% b) 30 - 80% 106. Which of the following screw axes is left-handed? c) More than 80% a) 21 d) There is no solvent in protein crystals b) 32 c) 42 96. During protein crystallization, sodium azide is used as: d) 62 a) precipitant b) reducing agent 107. What is essentially plotted on the Ramachandran diagram? c) buffer a) The relation between the phi and psi angles d) antibacterial agent b) The dependence of the phi and psi angles on the secondary structure c) Conformational energy as a function of the phi/psi angles d) The phi/psi angles in function of conformational energy 5 108. Among the DNA double-helical forms, gauche-trans sugar side c) cubic chains are possible in: d) the symbol is wrong a) A-DNA 119. Repeated peptide units having phi=-57 deg and psi=─47 deg will b) B-DNA form: c) Z-DNA d) gauche-trans conformation is not possible a) an alpha helix b) a beta strand in 'antiparallel' conformation 109. Which is true: c) a beta strand in 'parallel' conformation a) The value of the torsion angle A-B-C-D depends on the d) no regular secondary structure will be formed viewing direction (B-C or C-B) 120. When ammonium sulphate is used as the precipitant, what happens b) The torsion angles in optical isomers are the same during hanging-drop crystallization? c) The absolute configuration of any chiral molecule can be defined through torsion angles a) The drop shrinks d) The absolute value of any torsion angle must be less or b) The drop volume increases equal 180 deg c) The drop volume does not change d) The drop volume may increase or decrease 121. What direct lattice vector is normal to the b* and c* vectors of the 110. Choose the biggest amino acid (most non-H atoms): reciprocal lattice? a) tryptophan a) a b) tyrosine b) b c) arginine c) c d) methionine d) none 111. Which statement about the alpha helix is true? 122. Argand diagram is used to illustrate: a) Its handedness in the N->C direction is opposite to that in a) The Ewald construction the C->N direction b) The Laue construction b) The hydrogen bonds within an alpha helix are formed c) The structure factor in the complex plane between the N-H group of unit n and the C=O group of unit d) The method of isomorphous replacement n+4 c) The C=O groups in an alpha helix point in the C->N direction 123. What is the number of nucleotides in a typical tRNA molecule? d) The main-chain fragment closed by a hydrogen bond a) 35 contains 12 non-H atoms b) 75 c) 150 112. Find the true statement: d) 750 a) all proteins have quaternary structure b) myoglobin does not have tertiary structure 124. Which of the classes (point groups) below does not belong to the c) myoglobin does not have quaternary structure orthorhombic system? d) hemoglobin does not have quaternary structure a) 2/m b) 222 113. Can natural proteins crystallize in the crystal class 4? c) mm2 a) Never d) mmm b) Yes c) Yes, but only when the crystals are twinned 125. a=b, c - any; alpha=beta=gamma=90. What crystallographic system d) There is no such class is this? a) monoclinic 114. In the hanging-drop method, the protein crystals are formed: b) orthorhombic a) in the drop c) tertragonal b) on the cover slide near the drop d) hexagonal c) in the reservoir cell d) in the space between the reservoir and the drop 126. poly(dG.dC) crystallized from high ionic strength has the form: a) A-DNA 115. A typical single C-C bond in organic molecules has the length: b) B-DNA a) 1.52 E-12 cm c) Z-DNA b) 1.08 E-10 cm d) the form will depend on humidity c) 3.34 E-10 cm d) 1.54 E-8 cm 127. Four peptide chains 1,2,3,4 are connected by hydrogen bonds in the following fashion: 116. What system(s) do the crystal classes 32 and 23 belong to? 4 - 1 - 2 - 3. What motif is this? a) both trigonal a) Beta hairpin b) both cubic b) Greek key c) 32 - cubic, 23 - trigonal c) Jelly-roll fold d) 32 - trigonal, 23 - cubic d) Such an arrangement is not possible 117. How many different Bravais lattices are there? 128. How many four-fold axes are missing from this list: 4, 41, 42, 43? a) 4 a) none b) 7 b) 1 c) 14 c) 2 d) 230 d) 3 118. What system does the space group I2(1)3 belong to? a) monoclinic b) trigonal 6 129. A typical Mg-O coordinative bond has the following length: c) tertiary structure a) 1Å d) quaternary structure b) 2Å 140. The number of base pairs per one helical turn of the B-DNA double c) 3.6 Å helix is: d) 10 Å a) 3.6 130. At low ionic strength, what humidity is preferred by B-DNA? b) 10 a) low c) 12 b) high d) 33.8 c) humidity is not important 141. What is the form of double-helical RNA? d) B-DNA does not exist in low ionic strength a) A-RNA 131. a, b, c - any; alpha=gamma=90, beta -any. What crystallographic b) B-RNA system is this? c) Z-RNA a) monoclinic d) RNA never assumes double-helical structure b) orthorhombic 142. What is the pitch (in Å) of B-DNA double helix? c) trigonal d) hexagonal a) 1.54 b) 3.4 132. What coordinates are generated from x,y,z by a two-fold axis along c) 20 y? d) 33.8 a) -x,-y,-z 143. Find the false statement b) -x,y,-z c) x,-y,z a) all amino acids occurring in proteins are L stereoizomers d) y,x,z b) some natural amino acids contain sulfur c) the peptide bond usually takes the trans form 133. What is the wavelength (Å) of the characteristic X-ray radiation d) some amino acids have aromatic side chains generated from a copper tube? 144. A typical N...O distance in N-H...O hydrogen bonds is: a) 0.15 b) 0.7 a) 1.0 Å c) 1.5 b) 1.5 Å d) 15 c) 2.7 Å d) 3.6 Å 134. Only in one of the sets below, all five symmetry planes can appear as normal to z. Find this set. 145. What is the conformation of the sugar rings in double helical B- DNA? a) m, a, b, n, d b) a, b, c, n, d a) C2'-endo c) m, a, b, c, d b) C2'-egzo d) m, a, b, c, n c) C3'-endo d) C3'-egzo 135. What is the fraction of RNA in ribosome mass? 146. What symmetry element and in what location is represented by the a) 15% following transformation: x,y,z -> -x,-y,z b) 33% c) 50% a) it's an illegal operation d) 66% b) a dyad (2) along z c) a mirror plane (m) perpendicular to x 136. How many crystallographic systems are missing from this list: d) a mirror plane (m) perpendicular to y monoclinic, orthorhombic, tetragonal, trigonal, hexagonal? 147. The image plate operates on the principle of: a) none b) 1 a) Gas ionization c) 2 b) Semiconducting effect d) 7 c) Photostimulated luminescence d) Video camera 137. Protein crystallization requires: 148. What system does the crystal class 3 belong to? a) formation of crystallization nuclei in the labile region and their growth in metastable region a) triclinic b) formation of crystallization nuclei in the metastable region b) orthorhombic and their growth in the labile region c) trigonal c) formation of crystallization nuclei in the unsaturated region d) cubic and their growth in the supersaturated region d) formation of crystallization nuclei in the supersaturated 149. Radiation of one wavelength is called: region and their growth in the unsaturated region a) monochromatic b) polychromatic 138. Which of the following space group symbols is wrong? c) polarized a) P43m d) coherent b) C432 c) Fddd 150. Which is false? d) I212121 a) A protein can consist of only one domain b) A protein can consist of multiple domains 139. The arrangement of simpler structural motifs in the three- c) Single-domain proteins cannot form quaternary structure dimensional protein structure is known as: d) "Domain" and "subunit" have different meaning a) primary structure b) secondary structure 7 151. Hydrophobic groups in water tend to cluster together because: a) There are attractions between polar and hydrophobic groups b) Their ordered structure is favored entropically c) Ordered structure of water is favored entropically d) This way more water can be released to the disordered bulk 152. Which of the rays, Ordinary (O) or Extraordinary (E), is polarized in uniaxial crystals in the plane of the propagation direction and the optic axis? a) E b) O c) none d) both 153. Which of the glide planes cannot appear as normal to x? a) a b) c c) n d) d 8