Hmwk 6. Nucleic Acids

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1 The purpose of this homework exercise is Hmwk 6. Nucleic Acids 1). to recognize fundamental features of B-form DNA and A-form RNA 2). to view the folded structure of trna B-FORM DNA In aqueous solutions, double stranded DNA adopts the B form double helix. We will begin by considering the following fundamental features of that form : 1. relative orientation of strands (parallel vs antiparallel) 2. handedness 3. number of base pairs per turn 4. angle of the plane of the base pair relative to the helix axis 5. Chargaff's rule 6. major and minor grooves 7. hydrogen bonding Open JMol File - Open - "01 DNA sequence.rsm" (in folder "Exercise 06 v7 Nucleic acids") Load and run the script Nucleic.01.A.doc Do not rotate until Q2 is answered. Each nucleotide has been colored using the Shapely scheme. Q1. The two strands are. A. parallel B. antiparallel In the opening view, the 3' end (nucleotide 10) of the grey strand is at the bottom. Q2. In this view, when traveling from the bottom to the top, the grey helix is. A. right-handed B. left-handed Rotate the molecule 180 degrees so the 5' end (nucleotide 1) end of the grey strand is at the bottom. Q3. In this view, when traveling from the bottom to the top, the grey helix is. A. right-handed B. left-handed What you have learned is that the handedness is independent of your viewpoint of the helix. You wouldn't really have to know which end of a strand was 5' or 3', or the biological synthesis direction of the strand, to determine whether the spiral was right-handed or left-handed. Load and run the script Nucleic.01.B.doc. Do not rotate the structure until after questions 4 and 5 are answered.

2 Q4. The major groove of B-form DNA is. A. wide and deep B. narrow and deep Are the two grooves very different in depth, or are they approximately the same depth? Q5. The narrow minor groove of B-form DNA is. A. also deep B. very shallow Check your answers to Q4 and Q5 with Tbl 29-1 from Voet and Voet (next page). Load and run the script Nucleic.01.C.doc". Do not rotate the structure until after Q6 is answered. The structure has 10 nucleotides in each chain, so there are 10 base pairs in the drawing. After the animation, the view has the DNA oriented almost end-on. Nucleotides in one strand are labeled by residue number. Q6. The 10 base pairs constitute. A. approximately one complete turn B. significantly less than one complete turn C. significantly more than one complete turn Load and run the script Nucleic.01.D.doc. Do not rotate the structure until Q8 and Q9 are answered. This orients the molecule so the helix axis runs from floor to ceiling. This gives a side view of the double helix. Notice that the base pairs are almost perfectly perpendicular to the helix axis. They look very much like a stack of coins sitting on a desktop. In other words, if you consider the angle of tilt between the plane of each base pair and the plane of the desktop, that angle would be approximately 0 degrees. There is almost no tilt. Check table 29-1 (Voet & Voet) on the next page for B-form DNA. Q7. The angle is given as, which is close to 0. A. 2 degrees B. 6 degrees C. 10 degrees In its simplest form, Chargaff's rule states that in double stranded DNA, for every purine (large base) there is a pyrimidine (small base). This is because the distance from strand to strand across a base pair must be a constant, which is the sum of the distance across one large base and one small base. In this model purine sidechains on the blue chain are colored yellow, whereas purine sidechains on the red chain are colored white. Pyrimidine sidechains are colored green on both strands. Note that every base pair has a green pyrimidine component. There are 10 total base pairs.

3 Portions of TABLE 29-1 (Voet & Voet) : STRUCTURAL FEATURES OF IDEAL A AND B FORMS Property A-DNA or A-RNA B-DNA Helical sense Right-handed Right-handed Diameter 26 Angstroms 20 Angstroms Base pairs per helical turn Base tilt normal to the helix axis 20 degrees 6 degrees Major groove Narrow and very deep Wide and deep Minor groove Wide and shallow Narrow and deep Q8. The % of purines (white and yellow, out of 20 total nucleotides) in both strands combined is %. A. 30 B. 40 C. 50 D. 60 E. 70 Q9. The % of white purines (out of 10 total nucleotides) in the red strand is %. A. 30 B. 40 C. 50 D. 60 E. 70 Load and run the script Nucleic.01.E.doc. Do not rotate until Q10 and Q11 are answered. The labels MAJOR and MINOR mark the location of the major and minor grooves. The labels A and T identify adenosine and thymidine nucleotides. Q10. The AT base pair has the following numbers of nucleotide-to-nucleotide hydrogen bonds : NH to N: NH to O: OH to O: total A B C D E Why are there only two nucleotide-to-nucleotide H-bonds in AT and not three as in GC? The reason is that the potential hydrogen donor group for the third bond would be a ring C-H in A, which is nonpolar and does not quite reach the red O: in T.

4 Q11. The exposed AT groups which are not involved in base pairing and are therefore available for hydrophobic or hydrogen bonding interactions with proteins in the major groove are : hydrophobic H-bonding. group on base A. CH3 on T NH on T O: on A N: on A B. CH3 on T 2 nd : on :O: on T N: on A C. CH3 on T 2 nd : on :O: on T 2 nd H on NH2 on A N: on A D. CH3 on A NH on T O: on A N: on A E. CH3 on A NH on T 2 nd H on NH2 on A Load and run the script Nucleic.01.F.doc. Q12. The GC base pair has the following numbers of nucleotide-to-nucleotide hydrogen bonds : NH to N: NH to O: OH to O: total A B C D C Examine your answers to Q10 and Q12. Q13. The base-pairing hydrogen bonds between the strands in duplex DNA. A. always involve an NH donor. B. always involve an OH donor. C. include examples of both NH's and OH's as donors. B-FORM vs. A-FORM DOUBLE HELIX We next will make some distance measurements in the B-form of DNA in aqueous solution. We then will compare it with the A-form of RNA in aqueous solution (which also can be adopted by DNA in dry crystals). Open the structure 07 form-1.rsm. This is the B-form double helix. Load and run the script Nucleic.07.A.doc. This gives an animation ending with measurement of the double helix diameter. For the most part, the nucleic acids are colored white. Phosphorus is colored orange (its CPK color), and one of the oxygens on each phosphorus is colored red (its CPK color). In the B-form, those oxygens are like the tips of a snowflake, extending outwards from the main body of the cylinder. In the B-form, the base pairs reach straight across the axis of the double helix, so the center of the double helix is solidly packed with atoms. The diameter of the double helix, measured from outer red phosphate oxygen to outer red phosphate oxygen, is 20.7 Angstroms (2.07 nm).

5 In Tbl 29-1 (given earlier in this exercise), B-DNA is listed as having a diameter of 20 Angstroms, matching this model. Q14. In that same table, A-form RNA (which is like A-form dry DNA) has a diameter of Angstroms. A. 16 B. 20 C. 26 Open the structure 07 form-2.rsm. This is the A-form double helix. Load and run the script #07.B.1.doc. Do not reorient until you have read the following paragraph. In the A form double helix, there is a naturally occurring hole down the middle. The diameter of the A-form is the largest distance between CH groups on opposite sides of the cylinder. However x-ray diffraction of crystals does not give the positions of H s, so they are not in this structure. We can measure the distance between carbons across the ring, such as those colored green in the opening view, but that distance will be less than the actual diameter. As seen in the opening JMol view, the green C-to-C distance is 19.5 Angstroms (1.95 nm). The Voet and Voet table considered earlier reports that the true diameter of the A-form double helix is 26 Angstroms when hydrogen atoms are included. Q15. The double helix form with a hole down the middle is the. A. A form B. B form The antiparallel orientation of the two strands in the A-form is easily seen by inspecting the location of the phosphorus atoms. To see this, Load and run the script Nucleic.07.B.2.doc The phosphate groups on the white strand have a red phosphorus whose =O and O - which point upwards. The other two oxygens are part of the sugar-o-p-o-sugar backbone. The phosphate groups on the grey strand have an orange phosphorus whose =O and O - which point which point downwards. Four of these oxygens are colored light green. The green pairs point in opposite directions because the two strands of the A-form are antiparallel. Load and run the script Nucleic.07.B.3.doc After removing the atoms of the grey chain to help us see the white chain, you need to estimate where phosphate #1 would be located. It would come between phos-2 and phos-11 in the starting end-on view, but slightly closer to phos-2. Thus one complete turn from #1 to beyond #11 in the A form would be slightly larger than 11 nucleotides. Q16. In the end-on view of A-form, the labels 2-11 (which is 10 total labels) make. A. less than one complete turn B. one complete turn C. more than one complete turn Therefore since B-form is 10 residues per turn, A form requires more than 10 residues per turn.

6 Q17. In Table 29-1 of Voet and Voet, we note that the A form is about base pairs per turn. A. 12 B. 14 C. 16 Q18. Since B-form has a diameter of 20 Angstroms, we expect the diameter of A form to be 20 Angstroms because there are more nucleotides per turn. A. less than B. greater than This also can be checked in Table 29-1, and should be consistent with your answer to Q15. These extra nucleotides are needed to create a double helix with empty space in the center. Load and run the script Nucleic.07.B.4.doc. answered. Do not rotate by hand until Q19, Q20, and Q21 are One base pair at the end of the double helix is colored white. Q19. In the large-circumference large-diameter A-form, the white H-bonded partners of a base pair. A. are both close to the circumference of the circle in the end-on view, so there is a hole down the center of the helix B. span the distance across the circle of the end-on view (as in B form), so there is no hole down the center of the helix Compare the values of the A-form and B-form tilt angles in Table Do you see a distinct tilt for base pairs in the A-form structure on your screen? Q20. In A form, the white base pair is. A. identical to the B form (namely, almost no tilt) B. distinctly more tilted than in B form Q21. The A form is a double helix. A. right-handed B. left-handed Now you may rotate by hand to freely view the structure. Transfer RNA File - Open - "09 trna color by group.rsm" Load and run the script Nucleic.09.A.doc. A brief animation will run. Do not rotate until after Q23 is answered. We now will examine the structure of trna, which includes some double-stranded helix. The molecule is colored "by group", a coloring feature which uses blue at the 5' beginning of the polymer

7 (an "ice-cold" start at the beginning of the short race) and red at the 3' ending (a "red hot" finish to the race). Q22. The anticodon is at the of the polymer. A. blue end B. red end C. green middle Q23. The 5' and 3' ends of the polymer are relatively close to each other in three-dimensional space, but the end which sticks out a little further from the molecule is the. A. blue 5' end B. red 3' end (to which the amino acid will be attached) Two regions of double helix that are easy to see are the two "ends" of the L shaped molecule (here by "ends" we are referring to the ends of the folded L shape, not specifically the ends of the linear polymer). Look at the green geographical end of the L shape and the red/blue geographical end of the L shape. At both ends, view that portion end-on looking down the helix axis. The opening view is from the green end. Rotate the molecule to get a sense of grooves and the locations of the base pairs. Do the base pairs cross the helix axis as in solidly packed B-form, or are they closer to the circumference as in wide A-form? Q24. Based on the grooves and locations of base pairs relative to the central helix axis, the double helices in trna look like. A. A form double helix (an open twisted ribbon) B. B form double helix (a solidly packed cylinder) Load and run the script #Nucleic.09.B.doc There are four double helix regions in the three leaf clover, which are the stems of each individual leaf (green stem of leaf1, yellow stem of leaf2, and red stem of leaf3) and the stem of the whole assembly (colored blue). There are three hairpin turns, which are the tips of each of the three leafs. Note how the end of the hairpin turn of the 1st leaf in the sequence is adjacent in three-dimensional space to the end of the hairpin turn of the 3rd leaf. The tips of those two turns have exposed G and C sidechains respectively. Those bases hydrogen-bond to each other. We now will focus in on that base-pair, which stabilizes the tertiary structural folding of trna. These bases are far apart in the linear primary sequence but are close together and H-bond to each other in the folded tertiary structure. Q25. One of the bases in the base-pair is C56. The other is. A. G16 B. G17 C. G18 D. G19 E. G20 Hint : click on the bases and read their identity in the status bar or console window. Close JMol as follows : File - Exit