Chemistry
L vs D amino acids refer to the stereochemistry of amino acids, with L-amino acids being the predominant form in living organisms. The designation L or D refers to the spatial arrangement of atoms around the chiral carbon atom in the amino acid molecule. L-amino acids are found in proteins and are essential for life, while D-amino acids have more specialized roles.
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7 Key excerpts on "L vs D Amino Acids"
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Voet's Principles of BiochemistryDonald Voet, Judith G. Voet, Charlotte W. Pratt(Authors)
2018(Publication Date)
Wiley(Publisher)
• The pK values of the ionizable groups of amino acids may be altered when the amino acid is part of a polypeptide. 2 Stereochemistry • Amino acids are chiral molecules. Only L-amino acids occur in pro- teins (some bacterial peptides contain D-amino acids). 3 Amino Acid Derivatives • Amino acids may be covalently modified after they have been incor- porated into a polypeptide. • Individual amino acids and their derivatives have diverse physiologi- cal functions. NH CH SH CH O C CH 2 CH 2 CH 2 CH 2 NH O C 2 H 3 N + COO – COO – NH CH S CH O C CH 2 CH 2 CH 2 S CH 2 CH 2 NH O C H 3 N + COO – COO – NH CH CH O C CH 2 CH 2 CH 2 NH O C H 3 N + COO – COO – Glutathione (GSH) (-Glutamylcysteinylglycine) 2 1 O 2 H 2 O Glutathione disulfide (GSSG) REVIEW QUESTIONS 1 List some covalent modifications of amino acids in proteins. 2 Cover the labels in Figs. 4-14 and 4-15 and identify each parent amino acid and the type of chemical modification that has occurred. 3 Discuss important functions of amino acid derivatives. 95 KEY TERMS protein 80 α-amino acid 81 α carbon 81 R group 81 zwitterion 84 condensation reaction 84 peptide bond 84 dipeptide 84 tripeptide 84 oligopeptide 84 polypeptide 84 residue 84 N-terminus 84 C-terminus 84 pI 86 optical activity 88 polarimeter 88 chiral center 89 chirality 89 enantiomers 89 absolute configuration 89 Fischer convention 89 stereoisomers 89 levorotatory 89 dextrorotatory 89 Fischer projection 89 Cahn–Ingold–Prelog (RS) system 90 racemic mixture 90 peptidase 90 neurotransmitter 93 isopeptide bond 94 PROBLEMS EXERCISES 1. Identify the amino acids that differ from each other by a single methyl or methylene group. 2. The 20 standard amino acids are called α-amino acids. Certain β and γ amino acids are found in nature. Draw the structure of β-alanine (3-amino-n-propionate) and γ-aminobutyric acid. 3. Glutamate, a 5-carbon amino acid, is the precursor of three other amino acids that contain a 5-carbon chain.
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Principles of BiochemistryDonald Voet, Charlotte W. Pratt, Judith G. Voet(Authors)
2014(Publication Date)
Wiley(Publisher)
In order to obtain a product with net asymme- try, a chiral process must be employed. One of the most striking characteris- tics of life is its production of optically active molecules. Biosynthetic processes almost invariably produce pure stereoisomers. The fact that the amino acid residues of proteins all have the L configuration is just one example of this phenomenon. Furthermore, because most biological molecules are chiral, a given molecule—present in a single enantiomeric form—will bind to or react with only a single enantiomer of another compound. For example, a protein made of L-amino acid residues that reacts with a particular L-amino acid does not readily react with the D form of that amino acid. An otherwise identical synthetic protein made of D-amino acid residues, however, readily reacts only with the corresponding D-amino acid. D-Amino acid residues are components of some relatively short (20 residues) bacterial polypeptides. These polypeptides are perhaps most widely distributed as constituents of bacterial cell walls (Section 8-3B). The presence of the D-amino acids renders bacterial cell walls less susceptible to attack by the peptidases (enzymes that hydrolyze peptide bonds) that are produced by other organisms to digest bacteria. Likewise, D-amino acids are components of many bacterially produced peptide antibiotics. Most peptides containing D- amino acids are not synthesized by the standard protein synthetic machinery, in which messenger RNA is translated at the ribosome by transfer RNA mol- ecules with attached L-amino acids (Chapter 27). Instead, the D-amino acids are directly joined together by the action of specific bacterial enzymes. The importance of stereochemistry in living systems is also a concern of the pharmaceutical industry. Many drugs are chemically synthesized as racemic mixtures, although only one enantiomer has biological activity.
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BiochemistryDonald Voet, Judith G. Voet(Authors)
2011(Publication Date)
Wiley(Publisher)
For -amino acids, the arrangement of the amino, carboxyl, R, and H groups about the C atom is related to that of the hydroxyl, alde- hyde, CH 2 OH, and H groups, respectively, of glyceralde- hyde. In this way, L-glyceraldehyde and L--amino acids are said to have the same relative configurations (Fig. 4-13). Through the use of this method, the configurations of the -amino acids can be described without reference to their specific rotations. All a-amino acids derived from proteins have the L stereo- chemical configuration; that is, they all have the same rela- tive configuration about their C atoms. In 1949, it was demonstrated by a then new technique in X-ray crystallog- raphy that Fischer’s arbitrary choice was correct: The des- ignation of the relative configuration of chiral centers is the same as their absolute configuration. The absolute configu- ration of L--amino acid residues may be easily remem- bered through the use of the “CORN crib” mnemonic that is diagrammed in Fig. 4-14. a. Diastereomers Are Chemically and Physically Distinguishable A molecule may have multiple asymmetric centers. For such molecules, the terms stereoisomers and optical iso- mers refer to molecules with different configurations about at least one of their chiral centers, but that are otherwise identical. The term enantiomer still refers to a molecule that is the mirror image of the one under consideration, that is, different in all its chiral centers. Since each asym- metric center in a chiral molecule can have two possible configurations, a molecule with n chiral centers has 2 n dif- ferent possible stereoisomers and 2 n1 enantiomeric pairs. Threonine and isoleucine each have two chiral centers and hence 2 2 4 possible stereoisomers. The forms of threo- nine and isoleucine that are isolated from proteins, which are by convention called the L forms, are indicated in Table 4-1.
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Amino Acids, Peptides and ProteinsVolume 8
R C Sheppard(Author)
2007(Publication Date)
Royal Society of Chemistry(Publisher)
The subscript g may be omitted except where confusion with the use of the small capital letter prefixes in amino-acid nomenclature is possible. Note : the structures of a-amino acids to show configurational relationships may be drawn in several ways. In Fischer-style formulas, the carbon chain is written vertically with the carboxyl group at the top. With L-amino acids, the amino group is shown at the left, with D-amino acids at the right. Rules and Tentative Rules on Nomenclature 453 COOH CH3 CH3 L,-threonine D,-t hreonine Alternatively, heavy and dotted lines may be used to represent bonds projecting respectively in front of and behind the plane of the paper. 2AA-4. Optically Inactive a-Amino Acids 4.1. Use Of DL or -c_ The optically inactive mixture or racemic compound of the enantiomers is designated by the prefix DL (no comma) or by the plus and minus sign (k) in parentheses. Examples : DL-leucine, ( rt )-leucine. 4.2. Use of meso The prefix meso or its abbreviation rns in lower case italic letters is used to denote those a-amino acids and derivatives of a-amino acids that are optically inactive because of internal compensation. Examples : meso-lanthionine, ms-cystine. 2AA-5. Configuration at Chiral Centres Other than a-C J.I. Use of Sequence Rule In general, the Sequence Rule symbols are used to designate configuration, where known, at centres other than a-C. The configuration at a-C is customarily designated by D or L placed immediately before the trivial name. Examples : (3R)-~,-threonine, (3S)-~~-isoleucine, (4S)-4-hydroxy-~,-proline (see 5.3). However, those who prefer not to use two different systems to indicate con- figuration in the same name may convey the same information as in the following examples: (2S,3R)-threonine, (2S,3S)-isoleucine, (2S,4S)-hydroxyproline.
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Peptide-based BiomaterialsMustafa O. Guler(Author)
2020(Publication Date)
Royal Society of Chemistry(Publisher)
Although design principles are finally emerging, they are still far from being a delineation of a general framework because of the vast variety of chemical diversity encoded by amino acids, and the fact that self-assembly is typically the result of a cooperative behaviour that amplifies subtle differences at the molecular structure level. 6.2.3 α -Helices While d -amino acid residues are known to induce turn structures, sequences containing all- l -amino acids prefer an extended conformation. Indeed, substitution of an l -amino acid with the d -analogue in an assembling coiled-coil sequence was reported by DeGrado and collaborators to destabilise α-helices, increasing the free energy of helix formation, compared to the homochiral peptide. 79 In an elegant work, several conformational analyses (CD, NMR, liquid chromatography) were used to determine the helix-destabilising effect of the d -enantiomer of all 19 proteogenic chiral amino acids. Because of an induction into turn-like structures, all the d -amino acids decreased the helicity content, compared to the l -analogues. This effect was highly related to the types of amino acid side chains and their steric effects. In particular, β-branched amino acids and both l - and d -forms of proline showed the highest disrupting effect, while histidine and aspartic acid displayed the highest propensity to form α-helical structures. 80 A recent computational study, employing all-atom molecular dynamics in explicit water, has systematically studied the influence of mixed l - and d -amino acids on helix-folding polyalanine peptides. The authors reported that even a single insertion of a d -Ala completely disrupted the α-helix. An increase of the number of d -Ala residues in the chain altered the helical orientation towards the opposite chirality (see Figure 6.5). 81 Figure 6.5 Chiral inversion of the α-helix induced by d -amino acids. Reproduced from ref
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BiochemistryDonald Voet, Judith G. Voet(Authors)
2021(Publication Date)
Wiley(Publisher)
Chapter 3 Amino Acids
1 The Amino Acids of Proteins
A. General Properties
B. Peptide Bonds
C. Nomenclature of Amino Acids
D. Classification and Characteristics
2 Stereochemistry of Amino Acids
A. An Operational Classification
B. The Fischer Convention
C. The Cahn–Ingold–Prelog System
D. Chirality and Biochemistry
3 Chemical Properties of Amino Acids
A. Acid–Base Properties
B. Reactions of Amino Acids
4 “Nonstandard” Amino Acids
A. Amino Acid Derivatives in Proteins
B. Specialized Roles of Amino Acids
It is hardly surprising that much of the early biochemical research was concerned with the study of proteins. Proteins form the class of biological macromolecules that have the most well-defined physicochemical properties, and consequently they were generally easier to isolate and characterize than nucleic acids, polysaccharides, or lipids. Furthermore, proteins, particularly in the form of enzymes, have obvious biochemical functions. The central role that proteins play in biological processes has therefore been recognized since the earliest days of biochemistry. In contrast, the task of nucleic acids in the transmission and expression of genetic information was not realized until the late 1940s and their catalytic function only began to come to light in the 1980s, the role of lipids in biological membranes was not appreciated until the 1960s, and the biological functions of polysaccharides are still somewhat mysterious.
In this chapter we study the structures and properties of the monomeric units of proteins, the amino acids. It is from these substances that proteins are synthesized through processes that we discuss in Chapter 27 . Amino acids are also energy metabolites and, in animals, many of them are essential nutrients (Chapter 23
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Biochemistry, International AdaptationDonald Voet, Judith G. Voet(Authors)
2023(Publication Date)
Wiley(Publisher)
Figure 3-6 Structures of the α-amino acids alanine, glutamine, and phenylalanine. The amino acids are shown as ball-and-stick models embedded in their transparent space-filling models. The atoms are colored according to type with C green, H white, N blue, and O red. Alanine Phenylalanine Glutamine Figure 3-7 The reaction linking two cysteine residues by a disulfide bond. C C NH H O CH 2 SH Cysteine residue + C C NH H O CH 2 HS Cysteine residue [O] H 2 O C C NH H O CH 2 S C C NH H O CH 2 S Section 3-2 Stereochemistry of Amino Acids 65 Optically active molecules have an asymmetry such that they are not superimposable on their mirror image in the same way that a left hand is not superimposable on its mirror image, a right hand. This situation is characteristic of substances that contain tetrahedral carbon atoms that have four different substituents. The two such molecules depicted in Fig. 3-8 are not superimposable since they are mirror images. The central atoms in such atomic constel- lations are known as asymmetric centers or chiral centers and are said to have the property of chirality (Greek: cheir, hand). The C α atoms of all the amino acids, with the excep- tion of glycine, are asymmetric centers. Glycine, which has two H atoms substituent to its C α atom, is superimposable on its mirror image and is therefore not optically active. Molecules that are nonsuperimposable mirror images are known as enantiomers of one another. Enantiomeric molecules are physically and chemically indistinguishable by most techniques. Only when probed asymmetrically, for example, by plane-polarized light or by reactants that also contain chiral centers, can they be distinguished and/or dif- ferentially manipulated. There are three commonly used systems of nomen- clature whereby a particular stereoisomer of an optically active molecule can be classified.
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