Bio 100/Dalbey BIOMOLECULAR CHIRALITY 9/14/11

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1 Assigned Reading 4th ed. Three Dimensional Structure is Described by Configuaration and Conformation p. 16 Interactions Between Biomolecules are Stereospecific p. 20 Amino Acids Share Common Structural Features p. 76 The Amino Acid Residues in Proteins are L Stereoisomers p. 77 Assigned Problems: 1-8, 3-6 a, b Assigned Reading 5th ed. Three Dimensional Structure is Described by Configuaration and Conformation p. 15 Interactions Between Biomolecules are Stereospecific p. 18 Amino Acids Share Common Structural Features p. 72 The Amino Acid Residues in Proteins are L Stereoisomers p. 74 Assigned Problems: 1-8, 3-6 a, b The term chirality was introduced by Lord Kelvin to describe any system or structure that possesses a sufficiently low degree of symmetry such that it is distinct from its mirror image: "I call any geometrical figure, or group of points, chiral, and say that it has chirality, if its image in a plane mirror, ideally realized, cannot be brought to coincide with itself." An object is chiral if it cannot be superimposed on (made congruent with) its mirror image by simple rotations and translations. Chiral objects do not have a plane of mirror symmetry. For example, all helices are chiral, but planar spirals are achiral. Chirality is observed at all orders of physical magnitude, from subatomic interactions mediated by the weak force to human anatomy, perhaps in the cosmos as a whole! It plays a particularly important role in biological systems because many biological molecules are chiral. In biochemistry, the concept of molecular chirality is often discussed in terms of "asymmetric Carbon atoms". Biomolecules with 0 asymmetric carbons are always achiral. Biomolecules with one 1 asymmetric carbon atom are always chiral. Biomolecules with multiple asymmetric carbon atoms may or may not be chiral (see below). Therefore, the presence/absence of a plane of mirror symmetry in the molecule may be a more reliable test for molecular chirality than the presence or absence of asymmetric carbons. A chiral molecule with a single asymmetric carbon exists as 2 enantiomers that are mirror images of each other. Enantiomers are mirror image pairs of chiral molecules. Enantiomerism is a form of stereoisomerism. Stereoisomers are configurational isomers. 1 of 8

2 Enantiomers have identical physical and chemical properties except when they interact with a chiral influence (antor chiral molecule). Racemases are enzymes that invert the stereochemical configuration of an asymmetric carbon atom. For example, alanine racemase will convert either pure L-alanine or pure D-alanine to a racemic mixture of L- and D- alanine. L-alanine <-----> D-alanine The stereospecific step in the synthesis of many amino acids is the transamination of an alpha keto carboxylic acid. Chiral molecules display optical activity, i.e. rotation of polarized light in a polarimeter. This is the empirical basis for the common L, D designation of enantiomers. You are not responsible for the R, S system of absolute sterochemical configuration. Stereoisomers of Molecules with 2 asymmetric Carbons General Case: The substituent groups of the 2 asymmetric carbons are not all identical Example: Isoleucine 4 stereoisomers (2 pairs of enantiomers) See text Fig COO - C R O α-ketoacid amino donor H 2 N COO - C * H R L Amino Acid The 4 stereoisomers of Isoleucine 2 of 8

3 Special Case: The substituent groups of the 2 asymmetic carbons are identical. Example: Tartaric Acid 3 stereoisomers (1 pair of enantiomers and a diastereomer) Pasteur s Classic Study of Biomolecular Chirality Pasteur s studies of the chemical, optical and crystallographic properties of tartrates preceded by some years his studies of fermentations. They were conducted while he was yrs. of age. Indeed, he was drawn to study fermentation partly by an interest in the stereochemistry of tartrates and other chiral molecules. His initial approach was from the standpoint of basic structural chemistry, not biochemistry or microbiology. Previous work by Biot, Haüy, Hershel, et al. Quartz crystals are optically active and occur in RH and LH forms. Optical activity and form are correlated. Certain natural (organic) substances demonstrate optical activity as liquids or in solution (unlike quartz). These include many sugars and tartaric acid. Pastruer s choice of tartrates was based on the ease of obtaining crystals suitable for study, and on the availability of an extensive literature on their chemistry. There was no direct connection initially, to enology, or the alcoholic fermentation in general. Tartrate crystals isolated from wine vats were of two forms. 3 of 8

4 Paratartaric Acid : True Tartaric Acid : solutions are optically inactive solution levorotatory; infrequently observed. Pasteur traveled widely through the viticultural regions in Europe in search of the elusive true tartaric acid. He discovered that parataric acid is a racemic mixture of R- and L- isomers. This involved the famous manual resoultion of a racemic crystal mixture. He also found that paratartaric (racemic) acid is always present initially in wine, but the D- form is gradually eliminated by fungal metabolism, leaving only pure L-. He also succeeded in the artificial synthesis of paratartaric acid. Crystals of Pure D and L Tartaric Acid For some years he attempted, without success, various exotic schemes to artificially synthesize pure L- (or D-) tartaric acid. Pasteur more or less correctly correlated optical activity and crystal chirality with molecular chirality. He also noted that optically active pure substances were always of organic origin or have been separated from racemic mixtures by a chiral influence. Other methods to separate enantiomers include seeding by crystal of one enantiomer, chemical reaction with chiral reactant, selective degradation by microorganisms. For indeed I must confess that my researches have long been dominated by the thought that the constitution of compounds considered from the point of view of molecular symmetry or lack of symmetry plays a considerable role in the most intimate laws of organization of living organisms and intervenes in their most hidden physiologic characteristics. Amino acids are chiral (except Glycine). Therefore, enzymes can be stereospecific catalysts. This is also the biochemical basis for the stereospecificity of perception. 4 of 8

5 Bio 100/Dalbey BIOMOLECULAR CHIRALITY 9/14/11 Total Chemical Synthesis of a D-Enzyme: The Enantiomers of HIV-1 Protease Show Demonstration of Reciprocal Chiral Substrate Specificity Milton, R. C., et al (1992) Science 256, HIV-1 Protease is homodimer of a 99 residue monomer. D-enzyme cleaves polypeptide substrate only if composed D-amino acids D-enzyme is inhibited only by enantiomer of a chiral inhibitor. Achiral inhibitor inhibits both D- and L-enzyme Note that the Left-Handed alpha helix in the Lenzyme structure is a Right-Handed alpha helix in the D-enzyme structure See also Petsko, G. A. (1992) Science 256, If we synthesize a population of polypeptide chains with the same primary sequence of amino acids, using a mixture of D and L forms, then the polypetides would fold into an enormous number of different conformations with different biochemical activities. This is strongly suggestive of a biochemical necessity for isomeric purity in monomers. (i.e. enantiomeric cross-inhibition). Carbohydrates, and therefore nucleic acids, are generally chiral. The origin of biomolecular chirality is among the most profound and enduring mysteries surrounding the origin of life. Frozen Accident hypothesis Chirality in the Cosmos Chiral molecules in meteorites Circular polarization of particle-scattered UV emission from proto star clusters preferentially degrades one enantiomer. Parity Violation Parity violation involving the weak force introduces a cosmic bias that enhances stability of L-amino acids and D-sugars. Parity Violating Energy Difference (PVED) between enantiomenric peptides is number of amino acids X kcal/mole. 5 of 8

6 The influence of biomolecular chirality may be propagated to higher levels of structure where it is exhibited in striking and profound ways. Odor Perception Ex.: Spearmint vs. Caraway. This is fairly straightforward, insofar as odor is a chemical sense based directly on stereospecific binding to protein receptors. Visual Perception Ex.: b vs. d. Unlike odor perception, apparently involves learning and cognition. Anatomical Form Frequency-dependent selection of chiral forms of african chiclids. Situs Inversus in Humans Frequency of situs inversus = One of each Siamese twin pair is reversed. The earliest manifestation of L-R asymmetry that has so far been observed in mammalian development is asymmetric expression of several genes (lefty-1, lefty-2, nodal, Pitx2) at somitogenesis. These genes are preferentially expressed on the left side of the early embryo. Asymmetric ciliary beating in transient (7.5 da gestation) Henson's Node structure during gastrulation. Normal ciliary action creates leftward flow of extra-embryonic fluid. Nodal cells are monociliated. Knockout of KIF3B (kinesin motor protein used for microtubule-dependent ciliary action) causes loss of nodal cilia and in utero lethality, with embryos exhibiting a series of malformations including a randomization of left-right asymmetry. Thus, asymmetry of the mammalian body may be traceable to the asymmetry of tubulin protein monomers comprising the cilium of nodal cells. 6 of 8

7 Bio 100/Dalbey BIOMOLECULAR CHIRALITY 9/14/11 You are not responsible on the exam for the details of this nodal flow model. STUDY QUESTION Diaminopimelic Acid (DAPA) is an intermediate in the biosynthesis of one of the 20 standard amino acids. It is also an important structural component of bacterial cell walls. Which amino acid is made from DAPA? (Hint: DAPA is converted to this amino acid by a single chemical reaction step.) How many different stereoisomers of DAPA are possible? How many of the DAPA stereoisomers are optically active (i.e. rotate polarized light in a polarimeter?) 7 of 8

8 REFERENCES Stereochemistry and its Applications in Biochemistry Alworth, W. L. (1972) Wiley-Interscience QD/415/A43 8 of 8