CHEM 3653: AC8 Problems

The pKa of the hydrogen that is attached to N3 of the pyrimidine uracil is 9.5 (see underlined hydrogen in the figure below). If uracil is in a solution that has a pH of 12.0, then how many carbons, nitrogens, oxygens, and hydrogens does uracil predominantly have at this pH? If this was a “fill in the blank” question on Canvas, you would proceed as follows to enter your answer: if you determined that there were 4 carbons, 3 nitrogens, 1 oxygen, and 0 hydrogens, then you would enter “4C3N1O0H” (minus quotation marks). Make sure you use capital O for oxygen and the numeral 0 for zero, if necessary.

The pKa of the hydrogen that is attached to N3 of the pyrimidine uracil is 9.5 (see underlined hydrogen in the figure above). If uracil is in a solution that has a pH of 9.0, then what would be the ratio of the unprotonated form to the protonated form at this pH? Enter your answer to two figures.

The pKa of the hydrogen that is attached to N3 of the pyrimidine uracil is 9.5 (see underlined hydrogen in the figure above). If uracil is in a solution that has a pH of 9.0, then what would be the fraction of the unprotonated form to the total of possible forms at this pH? Enter your answer to two figures.

The pKa of the hydrogen that is attached to N3 of the pyrimidine uracil is 9.5 (see underlined hydrogen in the figure above). If uracil is in a solution that has a pH of 10.0, then what is the net charge of this molecule at this pH? Report your answer to two figures.

Adenylate is also called 5’ adenosine monophosphate (5’ AMP), and it is shown below. The hydroxyl that is part of the phosphoryl group and labeled “1” has a pKa of 0.9; the hydroxyl that is part of the phosphoryl group and labeled “2” has a pKa of 6.1; and the protonated N1 of the adenine moiety has a pKa of 3.8 (N1 is positively charged when protonated and neutral when unprotonated). Given this information, what will be the average net charge of 5’ AMP when the pH equals 0.9?

Hint: To calculate the average net charge, use the following equation: Net charge = ∑qifi, where qi is the charge on the ith group and fi is the fraction of the ith group that is in the charged form. To simplify, if the pH is 2 or more units from the pKa of a particular group, assume the group is completely protonated or unprotonated, as appropriate. If the pH is less than 2 units from the pKa of a particular group, use the Henderson-Hasselbalch equation to determine the ratio of charged to uncharged form of that group, then convert that ratio to a fraction.

Adenylate is also called 5’ adenosine monophosphate (5’ AMP), and it is shown above. The hydroxyl that is part of the phosphoryl group and labeled “1” has a pKa of 0.9; the hydroxyl that is part of the phosphoryl group and labeled “2” has a pKa of 6.1; and the protonated N1 of the adenine moiety has a pKa of 3.8 (N1 is positively charged when protonated and neutral when unprotonated). Given this information, what will be the average net charge of 5’ AMP when the pH equals 3.8?

Hint: To calculate the average net charge, use the following equation: Net charge = ∑q_if_i, where q_i is the charge on the i^th group and fi is the fraction of the i^th group that is in the charged form. To simplify matters, if the pH is 2 or more units from the pKa of a particular group, assume the group is completely protonated or unprotonated, as the case may be. If the pH is less than 2 units from the pKa of a particular group, use the Henderson-Hasselbalch equation to determine the ratio of charged to uncharged form of that group, then convert that ratio to a fraction.

Adenylate is also called 5’ adenosine monophosphate (5’ AMP), and it is shown above. The hydroxyl that is part of the phosphoryl group and labeled “1” has a pKa of 0.9; the hydroxyl that is part of the phosphoryl group and labeled “2” has a pKa of 6.1; and the protonated N1 of the adenine moiety has a pKa of 3.8 (N1 is positively charged when protonated and neutral when unprotonated). Given this information, what will be the average net charge of 5’ AMP when the pH equals 6.1?

Hint: To calculate the average net charge, use the following equation: Net charge = ∑qifi, where qi is the charge on the ith group and fi is the fraction of the ith group that is in the charged form. To simplify matters, if the pH is 2 or more units from the pKa of a particular group, assume the group is completely protonated or unprotonated, as the case may be. If the pH is less than 2 units from the pKa of a particular group, use the Henderson-Hasselbalch equation to determine the ratio of charged to uncharged form of that group, then convert that ratio to a fraction.

Adenylate is also called 5’ adenosine monophosphate (5’ AMP), and it is shown above. The hydroxyl that is part of the phosphoryl group and labeled “1” has a pKa of 0.9; the hydroxyl that is part of the phosphoryl group and labeled “2” has a pKa of 6.1; and the protonated N1 of the adenine moiety has a pKa of 3.8 (N1 is positively charged when protonated and neutral when unprotonated). Given this information, what will be the average net charge of 5’ AMP when the pH equals 5.0?

Hint: To calculate the average net charge, use the following equation: Net charge = ∑q_if_i, where q_i is the charge on the i^th group and fi is the fraction of the i^th group that is in the charged form. To simplify matters, if the pH is 2 or more units from the pKa of a particular group, assume the group is completely protonated or unprotonated, as the case may be. If the pH is less than 2 units from the pKa of a particular group, use the Henderson-Hasselbalch equation to determine the ratio of charged to uncharged form of that group, then convert that ratio to a fraction.

Draw, using chemical logic, the “curved-arrow” mechanism of the spontaneous deamination of cytosine as catalyzed by a general acid, A−H. Recall that the curved arrows represent electron flow. In particular, an arrow with a doubly barbed tip represents the movement of two electrons, whereas an arrow with a singly barbed tip (i.e., a fish-hook arrow) represents the movement of a single electron. Recall also that the base of the arrow starts at a site of excess electron density (e.g., a lone pair of electrons), and the tip of the arrow stops just short of the electrophile (i.e., a fully positive or partially positive species).

Diagram from memory the late-1920s experiment by Frederick Griffith, in which he used the nonvirulent, rough strain of a pneumococcal bacterium and the virulent, smooth strain of the same pneumococcal bacterium. Then diagram from memory the early 1940s experiment by Oswald Avery and co-workers, a modified version of the Griffith experiment that identified the molecule of heredity.

Diagram from memory the Waring Blendor Experiment (aka the Hersey-Chase Experiment) that corroborated the experimental findings of Oswald Avery and co-workers.

The nitrogenous base nicotinamide is shown below. Connect this nitrogenous base via a glycosidic bond to a D-ribofuranose that is itself connected to a 5’-phosphoryl group, which in turn is connected to another phosphoryl group and then to the 5’-carbon of a second D-ribofuranose that is connected via a glycosidic linkage to the nitrogenous base adenine. What molecule have you just drawn?

Draw adenine and the keto form of thymine, and then show how these two species could base pair via two hydrogen bonds. Next, draw adenine and the enol form of thymine and show how the hydrogen bonding pattern is altered (or eliminated).

Draw the keto forms of guanine and cytosine, then show how these two species can base-pair via three hydrogen bonds. Next, draw the enol forms of guanine and cytosine and show how the hydrogen-bonding pattern changes (or is eliminated).

Protein kinases regulate the activities of key enzymes through which of the following?

Which of the following is a pyrimidine base that is present in RNA but is NOT present in DNA?

In the DNA molecule, guanine on 1 strand is joined to cytosine on the complementary strand by which of the following bonds?

Which of the following are NOT produced by the hydrolysis of nucleic acids?

If the molar percentage of A (adenine) in a native DNA specimen is 22%, then what is the molar content of G (guanine)?

Which of the following bonds link the monomeric units of nucleic acids?

As DNA is denatured, each of the following events take place EXCEPT one. Which event is this EXCEPTION?

Which of the following is true of the T_m (melting temperature) of a given DNA double helix?

Which of the following is LEAST descriptive of lipids?

Which of the following substances represents an unsaturated fatty acid?

Upon complete hydrogenation, oleic, linoleic and linolenic acids yield

Neutral fats contain mixtures of one or more fatty acids esterified with

In addition to phosphoric acid, which of the following are the products of hydrolysis of lecithin?

Hint: lecithin comprises a number of glycerophospholipids.

Which of the following pairs of structureS depicts stereoisomers according to conventional rules of projection?

Imagine the adjacent reaction is conducted in a closed system containing gaseous CO₂ and a buffered aqueous solution. If the reaction reaches equilibrium, the final concentration of bicarbonate ions in the aqueous phase would most likely increase by ____.

Which of the following types of bonds or interactions are LEAST likely to be involved in stabilizing the three-dimensional folding of most proteins?

Which of the following is meant by the statement that glucose and mannose are epimers?

A solution contains DNA polymerase I, Me²⁺ salts of dATP, dGTP, dCTP, and dTTP, and an appropriate buffer. Which of the following DNA molecules would serve as a template for DNA synthesis when added to this solution?