Consider normal B-form DNA. It forms a regular antiparallel double-helical structure with Watson-Crick base-pairing mediated through hydrogen bonding. The base pairs all stack upon one another, with 3.4 Å spacing between them. DNA strands having a complementary sequence will spontaneously form a double-helix in an aqueous solution. In terms of energy, what primarily drives helix formation?
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- The hydrophobic effect explains why: O Water regulates pH in the interstitial fluid between eukaryotic cells. O Salt bridges form between oppositely charged histones and DNA in an aqueous environment. Nitrogenous bases are in the interior of the helix, when DNA is in an aqueous environment. Oil forms a homogenous mixture with polar solvents, like acetone.DNA contents of nitrogenous bases • %A = %T %C = %G • A+G = C+T %3D Example: if 35% of the bases of a DNA - molecule is thymine what the % of Cyosine?Fast please At 20 Celsius degree, protein-Z binds DNA with a free energy of –7 kJ/mole. Protein Z has an unfolding free energy of 11 kJ/mole without ligand bound and 15 kJ/mole with ligand bound. Does the unfolded/denatured form of protein Z bind to DNA, and if so – what is the "Delta G" of binding of the unfolded form?
- Assume the energy of hydrogen bonds per base pair to be 5.86 kJ•mol-1. Given two complementary strands of DNA containing 145 base pairs each, calculate the ratio of two separate strands to hydrogen-bonded double helix in solution at 319 K. ratio = Supnorting MatorialsUsing Fig. as a guide, draw the complete structure of a nucleoside triphosphate before and after it becomes incorporated into a polynucleotide chain. Draw the structure that would result if the newly formed phosphodiester bond were hydrolyzed.Would you expect the double helix in a short segment of DNA to be more stable in a storage solution of sodium phosphate buffer at pH 7.0 or in pure water? Why? pure water; because any cations in the storage solution would prevent complementary bases from forming ionic interactions sodium phosphate buffer at pH 7.0; because a neutral pH is required to maintain the covalent bonds between complementary bases O pure water; because the high dielectric constant of water is sufficient to stabilize the covalent bonds between deoxyriboses in the DNA backbone sodium phosphate buffer at pH 7.0; because the presence of water and sodium neutralizes the charge of phosphate groups in the DNA backbone
- This is DNA. Locate the nitrogen bases (nitrogens are blue). Where are they located in the molecule?Locate the sugars and phosphates, and describe their location. Adjacent nucleotides are linked by covalent phosphodiester bonds (-O-P-O-) produced by a condensation reaction. What parts of the adjacent nucleotides are linked by phosphodiester bonds?Two nitrogenous bases extending towards the middle of the double helix. Are there any covalent bonds between these bases?If there are no covalent bonds between these bases, what other kinds of bonds might hold the two strands of the double helix together?DNA has pKa ≈ 1.0. At normal pH what would the charge be for a double helix that is chain 50 angstroms long?Proflavine was used to treat wounded soldiers in the Far East during the second world war. Which of the following statements is false regarding proflavine! H₂N7 NH₂ Its target is located in the cell membrane. Its planar shape is important to intercalation. The primary amine groups are protonated and interact with phosphate groups of the DNA backbone. When inserted into DNA, the tricyclic system can form van der Waals interactions with base pairs above and below it.
- N. NH 2. One of the key pieces of information that Watson and Crick used in determining the secondary structure of DNA came from experiments done by E. Chargaff, in which he studied the nucleotide composition of DNA from many different species. O=P-OCH, N. `NH, HN он O= P- OCH, NH, Chargaff noted that the molar quantity of A_was always approximately equal to the molar quantity of T. and the molar quantity of C was always approximately equal to the molar quantity of G. How were Chargaff's results explained by the structural model of DNA proposed by Watson and Crick? N OH N. O= P-OCH, OH OHCAN YOU PLEASE ANSWER 1b 1a) The phosphate groups in the sugar-phosphate backbone of each strand of a DNA molecule have a pKa of ~2.14. Normal physiological pH in most cells is 7.0-7.5, which is significantly above the pKa for the phosphate groups, so every phosphate group in the backbone of both strands of a DNA molecule is deprotonated and carries a -1 charge - but DNA in cells is normally double-stranded. Briefly explain, in your own words, why the large negative charges on the backbones of the two strands of a double-stranded DNA molecule don't cause the strands to separate under normal cellular conditions. 1b) If you raise the pH to 12, but keep everything else about the solution in which the double-stranded DNA is dissolved the same, the two strands of DNA will separate/the DNA will denature. Briefly explain, in your own words, why this happens - why does DNA denature at pH 12 but not at pH 7?It is known that double stranded DNA is denatured at low pH. pKa values should allow the determination of whether this is due to perturbation of the hydrogen bonding in A-T and/or G-C base pairs. The table gives values for the pKas of different protonated groups in the nucleobases.Nucleobase Position & pKa A N1, 3.5 G N7, 1.6; N1, 9.2 C N3, 4.2 T N3, 9.7a) Draw the A-T and G-C base pairs. - Label the bases with the one-letter code. – - Number the atoms in the rings and label the atom that attaches to the sugar. - Mark the groups that interact in normal…