Oefenvragen, proeftentamen en oude tentamen PDF

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Q1. Out of four types of macromolecules found in the cell, which one forms branched polymers? a. Glycans b. RNA c. DNA d. Proteins Q2. How many kinds of nucleotides (not taking into account modified bases) are found in DNA and RNA? a. 4 b. 5 c. 6 d. 20 Q3. The acronym ADMET stands for: a. Absorption...

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Q1. Out of four types of macromolecules found in the cell, which one forms branched polymers? a. Glycans b. RNA c. DNA d. Proteins Q2. How many kinds of nucleotides (not taking into account modified bases) are found in DNA and RNA? a. 4 b. 5 c. 6 d. 20 Q3. The acronym ADMET stands for: a. Absorption, distribution, metabolism, Excretion, Toxicity b. Administration, disintegration, Metabolism, efficacy, Toxicity c. Absorption, diffusion, metabolism, efficacy, Toxicity d. Absorption, distribution, metabolism, excretion, toxicity Q4. Choose the polar AA (one letter code) in the list below; a. L b. K c. V d. F Q5. The formation of Hoogsteen bases helps to create which RNA element? a. Tetraloop b. Double helix c. Triple helix d. Wobble base pair Q6. A linear binding curve indicates a simple binding equilibrium, whereas a hyperbolic binding curve indicates that the system contains a receptor that is allosteric or contains multiple binding sites with different affinities a. True b. False Q7. The B-form DNA has a sugar pucker in a. C2’ endo b. C2’ exo c. C3’ exo d. C3’ endo Q8. The central dogma of molecular biology states that RNA is translated from proteins a. True b. False Q9. The space group of a protein crystal structure describes a. The symmetry of the crystal lattice b. The shape and dimensions of the unit cell c. The shape and dimensions of the asymmetric unit d. Which parts of a protein 3D group together to form a single domain Q10. Find a false statement about big data a. Big data has arisen in structural biology because of increased data volume, velocity, variety and veracity b. The role of big data in the pharmaceutical industry is rapidly increasing c. The only big data repository relevant for the structural biology is PDB d. In structural biology big data arises because researches are generating and storing a lot of useful and redundant information

Q11. An N-H …O=C hydrogen bond has optimal energy when it? a. Is bent b. Has a donor-acceptor distance of 4 A c. Is linear d. Has a donor-acceptor distance of 2 A Q12. How many codons are used in the genetic code? a. 4 b. 20 c. 44 d. 64 Q13. Which of the following is NOT a stabilizing force for the structure and stability of doublestranded nucleic acids? a. Electrostatic forces b. Disulfide bonds c. Base stacking d. Hydrogen bonding Q14. Which of the following statements about the Hill coefficient are true? I. It is the steepnesss of the log-log binding isotherm at the half saturation point II. Allosteric systems have a Hill coefficient of exactly 1 III. The maximum value for a dimeric protein is 2 a. Only I is true b. Both I and III are true c. Both II and III are true d. All the statements are true Q15. Interface residues that do not contribute greatly to binding affinity are also generally unimportant for specificity a. True b. False Q16. Which of the following is not a unit of structure found in proteins? a. A helices b. B sheets c. Y strand d. ω loop Q17. Ionic interactions are stronger in water than in vacuum because water forms strong hydrogen bonds with polar molecules a. true b. False Q18. What is the best definition of a precipitant in protein crystallization? a. A chemical compound which causes precipitation of the protein molecules b. A chemical compound which stabilizes the protein molecules during crystallization c. A chemical compound which crosslinks the protein molecules thereby forming a crystal d. A chemical compound which lowers the solubility of the protein molecules Q19. In allosteric proteins, ligand binding can only result in positive cooperativity a. True b. False Q20. Which of the following statements regarding interfacial waters is true? a. There are typically fewer water-mediated hydrogen bonds than direct hydrogen bonds at protein-protein interfaces b. They contribute only to affinity, but not the specificity of protein-protein recognition c. They help to optimize the packing at the contact surface d. They contribute favorably to the entropy of protein-protein recognition

Q21. The least restricted ϕ and ψ angles are found in polypeptides in which type of secondary structure? a. Left-handed α helix b. B sheet c. Right handed α helix d. Loop Q22. The phenomenon of relaxation in NMR describes: a. The process of excited spines returning to their equilibrium state b. The desire of NMR spectroscopists to take a break after analyzing a lot NMR theory c. The mechanism by which can we understand the effect of radio frequency pulses on a sample d. The process of generating enhanced NMR signals via so-called pulse sequences Q23. Which of these types of molecules serves as a template for messenger RNA? a. Ribosome b. DNA c. Transfer RNA d. PROTEIN Q24. Atomic structures obtained by NMR are based on: a. Measurement of inter-atomic distances using multidimensional NMR spectra b. Measurement of dihedral (torsion) angles that define the protein backbone, based on the NMR chemical shifts of the AA c. Knowledge of the primary sequence of the protein under study d. All the above Q25. The hydrogen atoms are normally not observed in protein crystal structures. Why is this? a. Hydrogen atoms are used to form hydrogen bonds b. Hydrogen atoms are too mobile to be observed c. Hydrogen atoms are very weak X-ray scatterers d. All of the above Q26. Metal ions, such as K+, Na+, and Mg2+ typically interact which part of RNA/DNA a. With the phosphate backbone group b. With the C2’-OH group of sugar c. With the base d. There is no preferential binding site Q27. The secondary structure of a protein refers to the extent and order of it’s a helices and B sheets a. True b. False Q28. Which of the following is not a process governed by molecular recognition? a. The fidelity of DNA replication b. Passive diffusion c. Active transport d. Translation by the ribosome Q29. Proteins fold with their hydrophobic AA on the surface and their hydrophilic AA in the core a. True b. False Q30. The value of KD corresponds to: a. The reciprocal of KA b. The concentration of ligand at half-saturation of receptor c. The ration of [P][L] over [PL] d. All of the above Q31. Crystals of human cyclin-dependent kinase 2 with a bound drug were grown using the hangingdrop vapour diffusion method, with the following reservoir solution; 20% (w/v) PEG 3000, 100 nm HEPES (pH 7.5), 200 nm NaCl. Which component in the reservoir solution acts as the precipitant?

a. PEG-3000 b. HEPES c. NaCl d. All of above Q32. The affinity of a macromolecular interaction reflects the strength of an interaction for one receptor relative to all other possible receptors a. True b. False Q33. A Ramachandran plot of a protein structure can reveal a. Which AA residues show large deviations in bonds length and bond angles b. Which AA residues have wrong backbone conformations c. Which AA residues have wrong side chain conformations d. Which AA residues show a bad fit to the electron density map Q34. In general, higher affinity of a ligand is achieved by a. Increasing its concentration b. The introduction of charged groups c. Increasing its hydrophobicity d. Increasing the number of donors / acceptors of H-bonds Q35. When two atoms approach closer than their van der Waals radii the interaction energy a. Goes up very sharply b. Drops insignificantly c. Goes down very sharply d. Stays the same Q36. Specificity depends on the concentration of ligand, whereas affinity is independent of ligand concentration a. True b. False Q37. The R-factors of protein crystal structure describe a. The quality of the model relative to other protein crystal structures b. How well the model fits the observed diffraction data c. How the quality of model depends on the resolution of the diffraction data d. The deviation of the model from ideal geometry Q38. What is the reason for the so-called “size limit” in solution NMR studies of proteins? a. As proteins get larger beyond a certain size, they tumble ever more slowly causing increasingly broader lines b. As proteins get larger, they tumble more slowly. This allows the NMR signals of large protein to be narrower, as is needed for high resolution NMR c. Very large proteins have reduced NMR signals due to the difficulty of the magnetic field to penetrate into the protein d. Due to small number of AA, very small proteins give NMR signals that are too weak, making it difficult to apply NMR to proteins below a certain “size limit” Q39. Which of the following can result in an allosteric modulation of activity? a. Covalent modification such as phosphorylation or acetylation b. Oligomerization c. Binding of a ligand d. All of above

Q40. When a system is ultrasensitive, the response to an input is a. Sharper than expected b. Broader than expected

c. Same as in linear response d. Hyperbolic Q41. The tertiary structure of functional RNA molecules is easily predicted a. True b. False Q42. Which nonstandard base pair is most likely to form a wobble base pair? a. U-U b. G-G c. G-U d. G-A Q43. The only genetically encoded amino acid without a stereoisomer is a. P b. W c. G d. A Q44. Genomic DNA can become deformed from its normal B-form by DNA binding proteins, such as the histone proteins and the TATA box binding protein a. True b. False Q45. Select a true statement a. The direction of the drug development process is; lead  hit  drug b. Pharmacophore is a cavity on the surface or in the interior of a protein that possesses suitable properties for binding a ligand c. Allosteric modulator is a noncompetitive inhibitor or activator d. All of the statements are true Q46. A by-product of forming a peptide bond from 2 AA is water a. True b. False Q47. How many AA are universally (i.e. present in all kingdoms of life) genetically coded? a. 19 b. 20 c. 21 d. 22 Q48. Noncovalent interactions, such as ionic and hydrophobic interactions, are generally much stronger than covalent interactions a. True b. False Q49. Which of the following would lead to a decrease in binding affinity? a. Releasing more protein-bound water molecules upon binding b. Decreasing the number of rotational degrees of freedom of the ligand binding c. Adding more hydrophobic interactions to the ligand-protein interface d. Increasing the number of hydrogen bonds between the ligand and protein Q50. Globular proteins are generally embedded in the interior of a lipid bilayer a. True b. False

Q1. A Q2. B Q3. A

Q4. B Q5. C Q6. B Q7. A Q8. B Q9. A Q10. C Q11. C Q12. D Q13. B Q14. B Q15. B Q16. C Q17. B Q18. A Q19. B Q20. C Q21. D Q22. A Q23. B Q24. D Q25. C Q26. A Q27. A Q28. B Q29. B Q30. D Q31. A Q32. B Q33. B Q34. C Q35. A Q36. A Q37. B Q38. A? Q39. D Q40. A Q41. B Q42. C Q43. C Q44. A Q45. C Q46. A Q47. C but B is also good Q48. B Q49. B Q50. B...