Biochemistry Topoisomerases Ribose

Biochemistry I. MULTIPLE CHOICE. (45 points; 3 points each) Choose the BEST answer to the question and write the letter in the appropriate box. 1. Topoisomerases: A. B. C. D. E. 2. The compound that consists of ribose linked by an N -glycosidic bond to N-9 of adenine is: A. B. C. D. E. 3. The genome is 10.5% guanosine. The genome is 21% guanosine. The genome is 29% guanosine. The genome is 58% guanosine. The base percent composition of guanosine in the genome cannot be determined from the information given. Which of the following is not a reducing sugar? A. B. C. D. E. 5. a purine nucleotide. a pyrimidine nucleotide. adenosine. AMP. a deoxyribonucleoside. Which of the following is true about a circular double-stranded DNA genome that is determined by chemical means to be 21% adenosine? A. B. C. D. E. 4. are important for generating positive supercoils that help in replication and transcription to open up double-stranded DNA. can sometimes use NAD+ to seal nicks in DNA. such as DNA gyrase (E. coli topoisomerase II), in the presence of ATP, will decrease the linking number of a covalently closed, circular DNA molecule. always change the linking number in steps of one. occur in all bacteria, but not in eukaryotes. ribose glucose fucose glyceraldehyde sucrose Stereoisomers that are non-superimposable, complete, mirror images of each other are known as: A. enantiomers. B. diastereoisomers. C. chiral compounds. D. anomers. E. cis-trans isomers. 6. Which of these statements about alternate forms of DNA is false ? A. B. C. D. E. 7. B. C. D. E. peptide prolyl isomerase carbonic anhydrase protein disulfide isomerase GroEL Hsp70 Which of the following statements about heme structure is true? A. B. C. D. E. 11. N-term of the a-subunits, C-term His of the b-subunits, and in the cleft between the two b-subunits the cleft between the two b-subunits, N-term of the a-subunits, and the C-term His of the b-subunits the heme, C-term His of the b-subunits, and in the cleft between the two b-subunits the C-term His of the b-subunits, the heme, and in the cleft between the two b-subunits C-term His of the b-subunits, N-term of the a-subunits, and in the cleft between the two b-subunits Which one of the following enzymes is not useful for protein folding in the cell? A. B. C. D. E. 10. deprotonation of N7 base pairing with thymidine A:T Æ G:C mutations A:T Æ A:G mutations A:T Æ T:A mutations The allosteric binding sites for the three heterotropic negative effector molecules for hemoglobin, CO2, H+, and BPG are located at the _____, respectively. A. 9. B-form DNA predominates in aqueous solution; dehydration favors the A-form. Z-form DNA has a helical sense (left-handed) that is opposite that for A-form DNA. B-form DNA has 3.6 base pairs per turn A major difference between the A-form and the B-form is in the "pucker" of the ribose ring. Nucleotide sequence affects whether DNA takes the Z-form. At pH 7.0, the rare protonation of adenine at N1 (pK a=3.8) can lead to: A. B. C. D. E. 8. Page 2 Heme contains a tetrapyrrole ring with four methyl, four vinyl, and four propionate side chains. The iron atom in the heme may be present in the ferrous or the ferric state. The iron in free heme has six ligands. In deoxyhemoglobin, the iron atom is absolutely coplanar with the tetrapyrrole ring (porphorin) The axial coordination positions of heme are occupied by tyrosine residues in hemoglobin. The notation: Glc α(1-->4) Glc best describes which polysaccharide? A. B. C. D. E. Glycogen Starch Hyaluronic acid Amylose Amylopectin 12. Page 3 Which sugar would give a negative Benedict's or Nelson test (reducing sugar test)? A. B. C. D. E. F. G. H. 13. Which of the following statements about protein structure is true ? A. B. C. D. E. 14. Three-dimensional protein structure is principally stabilized by hydrogen bonds. Hydrophobic interactions are responsible for the greatest amount of stabilizing energy, while hydrogen bonding and polar interactions are responsible for specificity in protein-protein interactions, as well as enzyme-substrate interactions. Because proteins are compact, detergents are unable to disrupt protein stability. All salts denature proteins by neutralizing the charged amino-acid side chains. By studying protein-protein interactions we have learned that the most optimal binding interactions occur when two proteins rely upon extensive intermolecular hydrogen bonding, and very little on hydrophobic interactions between the two molecules. The ribose-sugar pucker affects DNA structure in drastic ways. explanation below best describes how this occurs? A. B. C. D. E. 15. maltose lactose a-methylglucoside sucrose galactose all of the above both C and D both B and E Which The 3'-endo pucker leads to a conformational change from anti to syn for the purine and pyrimidine bases. The 5'-exo pucker leads to a decrease in the distance between phosphates in attached to the 5' and 3' hydroxyl groups in the DNA polymer. The 3'-endo pucker leads to a decrease in the distance between phosphates in attached to the 5' and 3' hydroxyl groups in the DNA polymer. The 2'-exo pucker leads to a decrease in the distance between phosphates in attached to the 5' and 3' hydroxyl groups in the DNA polymer. The 2'-endo pucker leads to a decrease in the distance between phosphates in attached to the 5' and 3' hydroxyl groups in the DNA polymer. DNA rich in G/C base pairs has a higher Tm than DNA that is rich in A/T base pairs because __________ A. B. C. D. E. G/C base pairs have 3 hydrogen bonds, whereas A/T base pairs have only 2 hydrogen bonds. G/C base pairs have 2 hydrogen bonds, whereas A/T base pairs have 3 hydrogen bonds. G/C base pairs can form very strong Hoogsteen base pairs, whereas A/T base pairs cannot. G/C base pairs have much more van der Waals interactions in B-DNA than do A/T base pairs. The stacking energy for A/T base pairs is lower (larger negative ∆H) than for G/C base pairs, which results in strand repulsion. Page 4 II. STRUCTURE. 16. (10 points) Draw the structure of a C:G base pair, including dashed lines for the H-bonds between the two bases (4 pts). This is a base-pair found in DNA or RNA 17. Carbohydrate structures (6 pts): a.. DRAW the structure of Gal in a Fisher projection. c. Gal is the C__ epimer of Glc d. Man is the C__ epimer of Glc e. Circle the correct structure of α-D-glucose b. DRAW the structure of b-DGlcNAc in the Haworth projection. III. 18. SHORT ANSWER. Complete this protein purification table from the data provided from measurements AFTER each step, including any missing units . (4 pts) Specific Extent of activity purificat. Overall Total (fold from yield Activity protein (%) start) (units) (mg) 1. Crude homogenate 2. Ammonium sulfate precipitation Affi-gel Blue chromatography 3. 19. Page 5 (13 points) 100 1000 90 300 75 ( ) (1.0) 100 7.5 In the molecular-modeling laboratory, the program used to visualize protein structures was The . files used for this contain the x.y.z. coordinates of each atom in the protein structure (2 pts). 20. Place the events in the proper order for dioxygen binding to hemoglobin that results in a T-state to R-sate transition (3 pts) - - - - - - 1. Salt bridges with the C-term residue of one α/β-subunit and other residues on the other α/β dimer are destablized. 2. the H-bond between Val on helix F and Tyr near the C-term of either subunit breaks 3. Helix F moves 4. the two α/β dimers shift by 15° 5. the proximal His residue, which is bound to the Fe2+, moves 0.6 Å 6. BPG is released 7. dioxygen binds to the Fe2+ in the heme 21. In the box, place the letter corresponding to a graph that shows the correct process of protein unfolding (2 pts). 22. Write out the proper name of this oligo-saccharide in the box below (2 pts). IV. MATCHING 23. Match each item on the left with the best answer on the right. Only one choice per blank and choices on the right are only used once or not at all. (6 points) 1. 2. 3. 24. 25. Page 6 (32 points) transition between native and dentured states prevents protein aggregation in the cell catalyzes proper disulfide bond formation 4. small molecule that stabilizes the native state 5. small molecule that stabilizes the stabilizes denatured state 6. Scientist that showed the primary structure of proteins dictates its teriary structure A. Anfinsen B. GroEL/GroES C. PDI D. Crick E. 2-mercaptoethanol F. proteosome G. (NH4)2SO4 H. urea I. linear J. sigmoidal K. PPI DNA structure. Write the DNA structure type (A, B, or Z) in the blanks to the left of the descriptions. (6 points) 1. 10 base pairs (bp) per turn 2. 11 base pairs (bp) per turn 3. rise of 3.4 Å per bp 4. relatively de-hydrated 5. C2'-endo sugar pucker 6. C3'-endo sugar pucker 7. left-handed helix 8. propeller twist of 20° 9. Diameter of 26 Å 10. Diameter of 20 Å 11. Diameter of 18 Å 12. major and minor grooves are deep Place an "X" in the box next to the condition wherein a DNA duplex would have the higher Tm. Unless stated, all other conditions are identical. (5 pts) 1. 2. 3. 4. 5. GC content of 50% 1X SSC 50% formamide 5X SSC, pH 12 1X SSC, pH 1 OR OR OR OR OR AT content of 60% 0.1X SSC no formamide 5X SSC, pH 7 1X SSC, pH 7 26. The following phrases in the left-hand column best match an answer, feature, or completion in the right-hand column. Put the letter corresponding to the best answer in the box to the left of each phrase. An answer may be used once or not at all. (5 pts) 1. Hemoglobin is a tetrameric protein best described as a ____. 2. oxygen binding to Hb eventually leads to the 3. Hill coefficient for hemoglobin with BPG bound. 4. 5. 27. Hill coefficient for hemoglobin without BPG bound. Page 7 A. 2.8 B. a2b2 structure C. (ab)2 structure D. 1.0 E. Transition from the R-state to the Tstate F. breaking of several hydrogen bonds and salt-bridges at the in helices A and C G. Transition from the T-state to the Rstate H. Caused by mutation substituting Val, which finds a binding pocket in deoxyHb of another tetramer. I. Caused by mutation substituting Val, which finds a binding pocket in oxy-Hb of another tetramer. Sickle-cell anemia The following phrases in the left-hand column are best matched with an answer, feature, or completion in the right-hand column. Put the letter corresponding to the best answer in the BOX to the left of each phrase. An answer may be used only once or not at all. (10 pts) 1. Hexoses, with four chiral carbons, have ______ possible stereoisomers (open-chain only). A. disaccharide containing two glucoses 2. The smallest aldose is ______. B. deoxy 3. The monosaccharides a-D-galactose and b-D-galactose are ______. C. chondroitin sulfate D. axial 4. Bulky ring substituants preferentially occupy ______ positions in the chair conformation. E. anomers F. two G. lactose H. glyceraldehyde I. starch 7. Both a(1Æ4) and a(1Æ6) bonds can be found in the plant product______. J. epimers K. sixteen 8. The main component of one proteoglycan is a _____. L. glycogen 9. An example of a homopolysaccharide in liver and muscle is ______. M. equatorial N. disaccharide containing a sugar acid O. eight 5. The ______ sugars are monosaccharides in which a hydroxyl group is replaced with a hydrogen. 6. The disaccharide commonly found in dairy products is ______. 10. The main component of a glycosaminoglycan is a ______. Page 1 No. on Test Correct Answer 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 23 C C C E A C C A B A D G B C D a. 1. 2. 3. 4. 5. 6. 26. 1. 17 CHO b. c. 4 CH2OH OH HO OH HO OH O X X 27. O OH 1. Crude homogenate 2. Ammonium sulfate precipitation Affi-gel Blue chromatography 19 Pymole / .pdb 20 7-5-3-2-1-4-6 21 A d. 2 e. OH NAc Ac = C-CH3 CH2OH 3. 25. DNA a. 18 B A B A B A Z Z A B Z B C G A D H 2. 3. 4. 5. b. 24 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. J B C G H A Activity (units) 100 90 75 22 Total protein (mg) 1000 Specific Extent of activity purificat. Overall (fold from yield (%) start) (U/mg) 300 7.5 0.1 (1.0) 0.3 3 10 100 100 90 75 X X X 1. K 2. H 3. E 4. M 5. B 6. G 7. I 8. C 9. L 10. N