If you want it to be done, do yourself Mr. Zorg, “Fifth Element” Search for natural compounds with a — Analytical Chemistry Chemistry Question
Unusual amino acids: search for new properties
If you want it to be done, do yourself
Mr. Zorg, “Fifth Element”
Search for natural compounds with anti-cancer potential is one of rapidly developing branches of modern science. Results of a recent research will be considered below.
X is a potential antineoplastic drug. In order to study mechanisms of its formation from different precursors, a mixture of three synthesized in the laboratory compounds A, B and С was administered orally to rats at doses of 63.5, 58.5 and 39.6 µg per kg of body weight, respectively. A and B are stable α-amino acids found in nature. Residue of one of these compounds is detected in proteins. Information about A, B, and С is summed up in the table below:
[VISUAL]
It is also known that:
* A, B and С have molar mass of less than 250 g mol-1 each;
* A, B and С contain C, H, N and O (not obligatory all these elements) in usual (native) isotopic ratios;
* The number of nitrogen atoms obeys the following inequality: Nnitrogen (B)≥Nnitrogen(A).
Considering all possibilities for the number of nitrogen atoms in A and B, determine their elemental composition.
Model Answer
Calculation of molar ratios of carbon, hydrogen and oxygen in A – C allows determining their minimal molar masses corresponding to the net formulae (note that isotopic ratios of C, H, N and O are native):
- Compound A: (C) : (H) : (O) = 5 : 11 : 2. Minimal molar mass M = 193.1 g mol-1.
- Compound B: (C) : (H) : (O) = 4 : 9 : 2. Minimal molar mass M = 180.1 g mol-1.
- Compound C: (C) : (H) = 1 : 4. Minimal molar mass M = 130.0 g mol-1.
With the upper bound (M < 250 g mol-1), the true and minimal molecular weights coincide. The residual molecular weights available for the other two elements (besides C, H, and O) in A and B are 90.0 and 91.0 g mol-1, respectively.
All possible variants of the number of nitrogen atoms (cannot exceed 6) in A are considered in the table:
- 1 N atom: 76 g mol-1 left for the 5th element.
- 2 N atoms: 62 g mol-1 left (e.g. 2 P).
- 3 N atoms: 48 g mol-1 left (e.g. 1 Ti?, 2 Mg?, 3 O?, 4 C? - all impossible/lack biochemical sense).
- 4 N atoms: 34 g mol-1 left.
- 5 N atoms: 20 g mol-1 left.
- 6 N atoms: 6 g mol-1 left.
With the inequality given in the problem text, 2 nitrogen atoms in A would correspond to 1 or 2 nitrogen atoms in B, leaving 75 or 63 g mol-1 for the 5th element in B, respectively. No reasonable biochemical variants agree with these values, indicating a dead end unless isotopes are considered.
If you failed to get the answer in i. 1, take advantage of an additional hint: A and B contain the same number of nitrogen atoms.
Model Answer
A difference of 1 g mol-1 in the molecular weights of the 5th element in A and B suggests the presence of stable isotopes of the same element (since A, B, and C are precursors of the same compound X).
Considering the equal number of nitrogen atoms in A and B, the stable isotope combinations matching the residual mass difference include: 20-21, 34-35, 48-49, 62-63, 76-77. The difference of 1 g mol-1 indicates exactly one atom of this 5th element in each compound.
Formally fitting stable isotope pairs are 48Ti-49Ti and 76Se-77Se. Since titanium is not found in native amino acids, the 5th element is selenium (Se). Thus, the elemental composition of A and B includes C, H, N, O, and Se.
Draw all possible structures of B (without stereochemical details).
Model Answer
As determined, the molecular formula of B is C4H9SeNO2. Four alpha-amino acid structures can be proposed:
1. COOH-CH(NH2)-Se-CH2-CH3 (unstable alpha-seleno compound)
2. COOH-CH(NH2)-CH2-CH2-SeH (selenohomocysteine)
3. COOH-CH(NH2)-CH(SeH-CH3 (contains two chiral centers, thus invalid as B has only 1 chiral atom)
4. COOH-CH(NH2)-CH2-Se-CH3 (methylselenocysteine)
Thus, the two valid, stable structures with exactly one chiral center are selenohomocysteine and methylselenocysteine [VISUAL].
If the provided data is sufficient, indicate the absolute configuration (R or S) at the stereocenters of the structures in i.3.
Model Answer
Both R- and S-amino acids are found in nature. Since it is not mentioned in the problem text which exactly of A and B is found in proteins, it is impossible to unambiguously assign configurations of α-carbon atoms without additional information.
During the experiment, samples of air exhaled by test animals were collected at definite time intervals. The following substances (in addition to other metabolites) were detected:
[VISUAL]
Draw the structures of A1 and B1, if it is known that A1 has only identical atoms of hydrogen and does not contain π-bonds.
Model Answer
Gases A1, B1, and C1 have molar masses of 106, 107, and 112 g mol-1, respectively. The difference in molecular weights of A and B (1 g mol-1) is retained in their metabolites, confirming A1 and B1 are isotopologues.
Excluding selenium, the residual molecular weight of A1 and B1 is 106 - 76 = 30 g mol-1. Feasible chemical formulas are C2H6Se or CH2SeO. Since A1 contains only identical hydrogen atoms and has no pi-bonds, the structure is dimethyl selenide, (CH3)2Se.
Thus, A1 is (CH3)2^76Se and B1 is (CH3)2^77Se.
Formation of С1 from С in rats proceeds via two enzymatic stages: reduction of C giving intermediate X is followed by its transformation into С1.
Determine the structures of C, С1, and antineoplastic metabolite X, if it is known that C does not contain C–O bonds.
Model Answer
The atomic weight of the selenium isotope in C1 is 82 (112 - 30 = 82 a.u.). Residual molecular weight left for the fourth element in C (which consists of only 4 elements) is 130 - 16 (for H_4) - 82 = 32 g mol-1, corresponding to two oxygen atoms. The molecular formula of C is CH4O2^82Se.
Because C1 contains methyl groups and C lacks C-O bonds, C must be methylseleninic acid, CH3Se(O)OH.
Intermediate X is methylselenol (CH3SeH), which undergoes enzymatic methylation to yield C1, dimethyl selenide, (CH3)2^82Se.
Formation of A1 and B1 from A and B, respectively, also occurs in two steps, the latter being catalyzed by the same enzyme as was involved in transformation of X into С1.
Determine the structures of A and B.
Model Answer
Methylation is the second step of the pathways. Highly specific methyltransferase enzymes require substrates very similar to X. Thus, the isotopologues of X (CH3^76SeH and CH3^77SeH) are the intermediates on the way from A and B to A1 and B1, respectively. These intermediates can only originate from precursors containing a CH3-Se- residue.
Therefore, A is methylselenocysteine (CH3-Se-CH2-CH(NH2)-COOH) and B is selenomethionine (CH3-Se-CH2-CH2-CH(NH2)-COOH).
Comment on the choice of A, B, and C masses in the mixture administered to rats.
Model Answer
To study pathways of selenium metabolism, the masses of selenium in each administered compound should be comparable. Calculating the mass of selenium in each compound based on their molecular weights (M_A = 193.1, M_B = 180.1, M_C = 130.0 g mol-1) and administered doses (63.5, 58.5, and 39.6 µg) reveals that the mixture contains exactly 25 µg of selenium from each isotope.
One of the amino acids discussed above can be found in proteins. It is also know that this amino acid does not have its own transfer RNA (tRNA).
Decide the residue of which amino acid (A or B) can be found in proteins. From the variants listed below, choose one explaining how it appears in proteins.
[VISUAL]
Model Answer
Variant 2 is correct. Selenomethionine (B) is structurally similar to methionine, which leads to mistakes during translation and false insertion of the selenium-containing amino acid instead of methionine. Since the 76Se isotope is natural, selenomethionine with 76Se is found (rarely) in proteins.
Variant 1 is incorrect because post-translational modification leading to A would involve methylation of selenohomocysteine, which also lacks its own tRNA.
Variants 3 and 5 are biochemically impossible since ribosome-mediated translation requires aminoacyl-tRNA.
Variant 4 is incorrect because methylselenocysteine (A) is structurally similar to S-methylcysteine, which is not a canonical amino acid and lacks its own tRNA.