Oxidative destruction of fatty acids is a universal biochemical process inherent in all living syste — Organic Chemistry Chemistry Question
Unusual pathways of fatty acid oxidation: Alpha-oxidation
Oxidative destruction of fatty acids is a universal biochemical process inherent in all living systems. The so-called β–oxidation is the dominating pathway of fatty acid degradation in mitochondria. It can be described by the following scheme:
[VISUAL]
At all stages of β-oxidation, acyl residues are linked with coenzyme A by thioester bond. On the above scheme, classes and subclasses (numbers beyond the arrows) of enzymes catalyzing corresponding reactions are given in accordance with IUB classification. Note that substituent R remains unchanged within one cycle turnover.
Phytanic acid A is a saturated fatty acid which is found in nature as a mixture of two diastereomers. It is not involved in β-oxidation due to peculiar features of its structure. Nevertheless, mammals metabolize it into pristanic acid B with retention of configuration of chiral atoms. The latter process (usually referred to as α-oxidation) occurs in special cellar organelles, peroxisomes. Reaction equations on the scheme below illustrate metabolism of A:
[VISUAL]
NMP and NTP are mono– and triphosphates of ribonucleoside N (A, C, G or U), respectively, PPi – pyrophosphate, CoA-SH – coenzyme A, NAD+ and NADH – oxidized and reduced forms of nicotine amide adenine dinucleotide, respectively, E1-E4 – enzymes catalyzing corresponding reactions.
Biosynthesis of A1 catalyzed by E1 is a two-stage process. The intermediate formed contains phosphorus and oxygen in a molar ratio of 1 : 8.
Draw structures (without stereochemical details) of metabolites X, Y and Z using symbol “R” for the unchanged part of acyl residue.
Model Answer
According to the IUB classification, the enzymes and steps of the β-oxidation cycle are:
- X: β-unsaturated acyl-CoA, represented as R-CH=CH-CO-SCoA.
- Y: 3-hydroxyacyl-CoA, represented as R-CH(OH-CH2-CO-SCoA.
- Z: 3-ketoacyl-CoA, represented as R-CO-CH2-CO-SCoA.
From the list of reaction types given below, choose those which correspond to the stages catalyzed by E1 and E3.
a) formation of an ester of ribonucleoside phosphate and carbonic acid,
b) transfer of a phosphoric acid residue on a substrate due to cleavage of high energy bond of another substrate (kinase reaction),
c) hydrolysis of an ester bond,
d) formation of a thioester of carbonic acid,
e) oxidative decarboxylation,
f) cleavage of a carbon-carbon bond.
Model Answer
E1 catalyzes a) formation of an ester of ribonucleoside phosphate and carbonic acid, and d) formation of a thioester of carbonic acid.
E3 catalyzes f) cleavage of a carbon-carbon bond.
Thus, the reaction types are:
E1 – a), d);
E3 – f).
Draw the intermediate of the E1 catalyzed reaction considering the formula of phytanic acid as R−COOH, where R is a hydrocarbon residue.
Model Answer
The intermediate is an adenosine monophosphate (AMP) ester of phytanic acid (phytanoyl-AMP), represented structurally as R-C(=O-O-P(=O)(O-)-O-adenosine.
B is further metabolized in a number of consecutive cycles of β-oxidation. Data on oxidative destruction of pristanic acid are given in the table below.
[VISUAL]
Determine the empirical and molecular formulae of phytanic acid A without deciphering α-cycle and establishing structural formula of pristanic acid.
Model Answer
From the table, the total number of carbon atoms in pristanic acid B is calculated as: 4 * 3 (from propionyl-CoA) + 3 * 2 (from acetyl-CoA) + 1 (from formyl-CoA) = 19 carbon atoms.
Since α-oxidation of phytanic acid A to pristanic acid B involves the loss of one carbon atom as CO2 (catalyzed by E3), phytanic acid A must contain 19 + 1 = 20 carbon atoms.
As a saturated fatty acid with one carboxyl group, the molecular formula of phytanic acid A is C20H40O2.
The empirical formula (the simplest integer ratio) is C10H20O.
Draw structural formulae of A and B with stereochemical details. Take into account that all chiral centers in these fatty acids but that nearest to the carboxylic group exist in R-configuration only.
Model Answer
Phytanic acid A (3,7,11,15-tetramethylhexadecanoic acid) chiral centers except the nearest to carboxyl exist in R-configuration only, giving diastereomers with configurations: (3S, 7R, 11R) and (3R, 7R, 11R).
Pristanic acid B (2,6,10,14-tetramethylpentadecanoic acid) chiral centers except the nearest to carboxyl exist in R-configuration only, giving diastereomers with configurations: (2S, 6R, 10R) and (2R, 6R, 10R).
Explain why phytanic acid cannot be involved in β-oxidation.
Model Answer
Phytanic acid cannot undergo β-oxidation because of the presence of the methyl group at the β-position (C-3). This substituent prevents the formation of a β-ketoacyl derivative during the third reaction of the β-oxidation cycle (the β-carbon lacks a hydrogen atom and therefore cannot be oxidized to a carbonyl group).
Suggest the mechanism of pristanoyl CoA racemization.
Model Answer
Thioesterification of pristanic acid to pristanoyl CoA significantly increases the acidity of the hydrogen atom attached to the α-carbon (C-2). This allows base-catalyzed deprotonation to form a planar enol/enolate intermediate. Subsequent non-stereospecific protonation from either face of the enolate double bond regenerates the thioester with either R- or S-configuration, resulting in racemization.
Draw (with stereochemical details) those metabolites of pristanic acid oxidation which are AMCAR substrates.
Model Answer
AMCAR (α-methylacyl-CoA racemase) catalyzes the stereospecific R to S conversion of 2-methylacyl-CoA intermediates. The intermediates from the degradation of pristanic acid that serve as AMCAR substrates are Metabolite 2 (2-methyldecanoyl-CoA, formed after the 2nd cycle of β-oxidation) and Metabolite 4 (formed after the 4th cycle of β-oxidation), both having the R-configuration at C-2.
During α-oxidation of A in mammals, only one pair of diastereomers is formed in E2 catalyzed reaction.
Based on sterical considerations, suggest configuration (R or S) of chiral centers in diastereomers A2.
Model Answer
Hydroxylation at C-2 is stereospecific and occurs from the face opposite to the C-3 methyl group due to less steric hindrance, meaning C-2 stereocenter configuration depends on the configuration at C-3:
- For the (3R)-isomer, hydroxylation yields the (2S)-configuration, giving the (2S, 3R)-diastereomer.
- For the (3S)-isomer, hydroxylation yields the (2R)-configuration, giving the (2R, 3S)-diastereomer.
Thus, the configurations of the chiral centers in diastereomers A2 are: 11R, 7R, 3R, 2S and 11R, 7R, 3S, 2R.