D/L configuration for amino acids

D/L configuration for amino acids

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Why would this be "L-cysteine"? This is taken from the answer key for my biochem final.

From what I understand if the -NH3(+) is on the left then the alpha-amino acid is in the L-configuration.

Am I wrong, or is my prof wrong?

We can look at the list of amino acids on wikipedia for a start. And we can look at this L-alanine:

What makes your image confusing is that it's a Fischer Projection, and I hate those because you have to remember what way the stereochemistry goes. In Fischer Projections, vertical lines face away from you, while horizontal lines face towards you. So if we convert the L-alanine I provided to a Fischer Projection, first we have to rotate the alpha carbon to put the methyl side chain in line with the rest of the carbon backbone. Now we look at the alpha carbon with the NH2 and H looking at us to create the Fischer projection. Here, the amine is on the left, not the right. You drew the amine on the right, which would give you the opposite orientation. If your professor had the amine on the right, I think he was wrong.

Additionally, the D vs L nomenclature is confusing. I prefer the S vs R nomenclature because that's what I was taught for molecules in general. Most amino acids fall into the S configuration, but cysteine is an R, because the sulfur atom has higher priority. However, cysteine is still an L, and the amine would still appear on the left in the Fischer Projection. This is why biologists stick to D and L for amino acids.

Stereochemistry of Amino Acids RS to DL

Amino acids are biologically active molecules. 19 of the 20 common amino acids have a chiral alpha carbon, 2 amino acids (Leucine and Threonine) have a second chiral center in their side chain. This video shows you how to

  1. Find R/S for 3-D amino acids
  2. Find R/S and D/L for amino acid Fischer projections
  3. Trick to quickly convert R/S to D/L amino acids

(Watch on YouTube: Amino Acid Chirality. Click cc on the bottom right for video transcript)

Referenced in this video:

< — Watch Previous Video: Polar, Acidic and Basic Amino Acids
—> Watch Next Video: Zwitterion and Amino Acid Charge at Given pH value

Essential and non-essential

Nutritionists divide amino acids into two groups – essential amino acids and non-essential amino acids. Essential amino acids must be included in our diet because our cells can’t synthesize them. What is essential varies considerably from one organism to another and even differ in humans, depending on whether they are adults or children. Table 2.1 shows essential and non-essential amino acids in humans.

Some amino acids that are normally nonessential, may need to be obtained from the diet in certain cases. Individuals who do not synthesize sufficient amounts of arginine, cysteine, glutamine, proline, selenocysteine, serine, and tyrosine, due to illness, for example, may need dietary supplements containing these amino acids.

Table 2.1 – Essential and non-essential amino acids

Non-protein amino acids

There are also amino acids found in cells that are not incorporated into proteins. Common examples include ornithine and citrulline. Both of these compounds are intermediates in the urea cycle, an important metabolic pathway.

R-group chemistry

Table 2.2 – Amino acid categories (based on R-group properties)

Amino acids can be classified based on the chemistry of their R-groups. It is useful to classify amino acids in this way because it is these side chains that give each amino acid its characteristic properties. Thus, amino acids with (chemically) similar side groups can be expected to function in similar ways, for example, during protein folding. The specific category divisions may vary, but all systems are attempts to organize and understand the relationship between an amino acid’s structure and its properties or behavior as part of a larger system.

Detection of DBD-carbamoyl amino acids in amino acid sequence and D/L configuration determination of peptides with fluorogenic Edman reagent 7-[(N,N-dimethylamino)sulfonyl]-2,1,3-benzoxadiazol-4-yl isothiocyanate

A method for amino acid sequence and D/L configuration identification of peptides by using fluorogenic Edman reagent 7-[(N, N-dimethylamino)sulfonyl]-2,1,3-benzoxadiazol-4-yl isothiocyanate (DBD-NCS) has been developed. This method was based on the Edman degradation principle with some modifications. A peptide or protein was coupled with DBD-NCS under basic conditions and then cyclized/cleaved to produce DBD-thiazolinone (TZ) derivative by BF3, a Lewis acid, which could significantly suppress the amino acid racemization. The liberated DBD-TZ amino acid was hydrolyzed to DBD-thiocarbamoyl (TC) amino acid under a weakly acidic condition and then oxidized by NaNO2/H+ to DBD-carbamoyl (CA) amino acid which was a stable and had a strong fluorescence intensity. The individual DBD-CA amino acids were separated on a reversed-phase high-performance liquid chromatography (RP-HPLC) for amino acid sequencing and their enantiomers were resolved on a chiral stationary-phase HPLC for identifying their D/L configurations. Combination of the two HPLC systems, the amino acid sequence and D/L configuration of peptides could be determined. This method will be useful for searching D-amino-acid-containing peptides in animals.

Similarities Between L and D Amino Acids

  • L- and D-amino acids are two possible orientations of a particular amino acid in nature.
  • They are the mirror image of each other.
  • Also, they can be considered as the isomeric forms, stereoisomers or enantiomers.
  • However, the simplest amino acid, glycine, does not have stereoisomers.
  • Both contain a carboxylic acid group, an amine group, a carbon chain, and a hydrogen atom bound to the central carbon atom of the amino acid.
  • Further, this central carbon atom is called the alpha carbon or the chiral carbon.

Amino Acids with Hydrophobic Side Chain – Aliphatic

1 pKa is the negative of the logarithm of the dissociation constant for the -COOH group.
2 pKb is the negative of the logarithm of the dissociation constant for the -NH3 group.
3 pKx is the negative of the logarithm of the dissociation constant for any other group in the molecule.
4 pl is the pH at the isoelectric point.
Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.

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D,L Convention

The D,L convention, not to be confused with the d and l descriptors used to designate the direction of specific rotation of chiral compounds, is a convention used to distinguish between enantiomers of chiral monosaccharides and chiral alpha-amino acids, based on the molecule drawn as a Fischer projection in a specific orientation.

Application of D,L convention to monosaccharides:

One enantiomer of a chiral monosaccharide is labeled D and the other L. To determine whether a given enantiomer of a chiral monosaccharide is D or L, use the following procedure.

Step 1: Make sure the acyclic form of the molecule is drawn as a Fischer projection. If the monosaccharide is an aldose, the aldehyde group must be on top if it is a ketose, the carbonyl carbon must be the second carbon from the top.

Step 2: Number the carbon atoms starting at the top.

Step 3: Locate the carbon atom that bears the second highest number, which is known as the penultimate carbon. If the hydroxy group on the penultimate carbon is on the right of the carbon chain, assign the label D to the compound if it is on the left of the carbon chain, assign the label L.

To draw the enantiomer of a given chiral monosaccharide, simply draw its mirror image.

Application of D,L convention to alpha-amino acids:
One enantiomer of a chiral alpha-amino acid is labeled D and the other L. To determine whether a given enantiomer of a chiral alpha-amino acid is D or L, use the following procedure.

Step 1: Make sure that the molecule is drawn as the Fischer projection in which the carboxylic acid group is on top and the side chain on bottom.

Step 2: If the amine group is on the right of the carbon chain, assign the label D to the compound if it is on the left of the carbon chain, assign the label L.

To draw the enantiomer of a given chiral alpha-amino acid, simply draw its mirror image.

Amino Acids

Amino acids contain an amino (–NH2) and carboxyl (–COOH) functional groups. The amino acids in proteins are called alpha (α)-amino acids because the amino group is attached to the α-carbon. A carbon directly connected to carbonyl carbon is termed α-carbon.

Depending upon the relative position of the amino group with respect to the carboxyl group, the amino acids can be classified as α, β, ϒ, δ, and so on. Only α -amino acids are obtained by the hydrolysis of proteins. They may contain other functional groups also.

All α-amino acids have trivial names, which usually, reflect the property of that compound or its source. Glycine is so named since it has a sweet taste (in Greekglykos means sweet) and tyrosine was first obtained from cheese (in Greek, tyros means cheese.).

Amino acids are generally represented by a three-letter symbol. Sometimes one letter symbol is also used.

The amino acids, which can be synthesised in the body, are known as non-essential amino acids. On the other hand, those which cannot be synthesised in the body and must be obtained through diet, are known as essential amino acids(marked with an asterisk in Table). The deficiency of essential amino acids may cause diseases like Kwashiorkor in which water balance of the body is disturbed.

Characteristics of Amino Acids:

  • They are usually colourless, crystalline solids.
  • These are water-soluble, high melting solids and behave like salts rather than simple amines or carboxylic acids. This behaviour is due to the presence of both acidic (carboxyl group) and basic (amino group) groups in the same molecule.
  • In aqueous solution, the carboxyl group can lose a proton and amino group can accept a proton, giving rise to a dipolar ion known as a zwitterion. This is neutral but contains both positive and negative charges. In zwitterionic form, amino acids show amphoteric behaviour as they react both with acids and bases.
  • Except for glycine, all other naturally occurring α-amino-acids are optically active, since the α-carbon atom is asymmetric. These exist both in ‘D’ and ‘L’ forms. Most naturally occurring amino-acids have L-configuration. L-Aminoacids are represented by writing the –NH2 group on the left-hand side.

Classification of Amino Acids:

All amino acids (except proline) contain –H, -NH2, and –COOH bound to the α-carbon.They are differentiated by the side chains (called R-groups or alkyl groups) also bound to the α-carbon. Depending on the nature of alkyl group they are classified into four groups: nonpolar, polar acidic, polar basic, and polar-neutral amino acids.

They are known by common names and each is abbreviated using a three-letter code.

Amino Acids: Classification and Properties | Biochemistry

In this article we will discuss about the classification and properties of amino acids.

Classification of Amino Acids:

Amino acids may be classified in several different ways. Here the classification, based on the polarity of the side chains is discussed.

According to polarity of side chains, amino acids are of four types:

The struc­tures of the common amino acids, their three letter abbreviations and certain of their dis­tinctive features are given in the Table 8.10. There are more than 200 other amino acids that are present in nature (particularly in plant kingdom), but they do not appear in proteins. In proteins only twenty amino acids are present (Table 8.10).

Properties of Amino Acids:

A. Configuration:

All the amino acids, except glycine, are optically active and may exist in either the D-or L-enantiomeric from (Fig. 8.61). If we take the example of glyceraldehyde (Fig. 8.62), the amino group of the amino acid takes the place of the hydroxyl group.

It is interesting to note that the naturally occurring sugars belong to the D-series, whereas nearly all known plant and animal proteins are composed entirely of l-amino acids. Certain bacteria are known to possess some D-amino acids.

Streptococcus faecalis has a requirement for D-alanine several anti­biotics (actinomycin for one) contain varying amounts of D-leucine, D-phenyl-alanine, and D-valine. There are some amino acids which parti­cipate in various important biological func­tions but nevere became a part of protein molecules (Fig. 8.63).

B. Dipolar ion structure:

The amino acids are colourless, non­volatile, crystalline solids, melting with decomposition at temperatures above 200°C. They are soluble in water and insoluble in nonpolar organic solvents. The properties of the amino acids are more similar to those of inorganic salts than those of amines or organic acids.

The salt-like character of the amino acids is more readily accounted for if we assign a dipolar ion (also called inner salt or zwitterion) structure to amino acids in the solid state and in neutral solution. Since amino acids contain both acidic (-COOH) and basic (-NH2) groups within the same molecule, we may postulate an intermolecular neutralisa­tion reaction, leading to salt formation (Fig. 8.64):

Conductivity measurements confirm that at certain pH values, all amino acids exist in the neutral zwitterion form. When placed in an electric field, the dipolar ions migrate neither to the anode nor to the cathode, thus indicating a net charge of zero.

The pH at which an amino acid exists in solution as a zwitterion is called the isoelectric pH (that is, the pH at which the amino acid is electrically neutral and has no tendency to migrate toward either electrode). Each amino acid has its own characteristic iso­electric pH. Dipolar ions are amphoteric substances they are capable of donating or accepting pro­tons. Therefore, they may behave either as acids or as bases.

Watch the video: Amino Acid Stereochemistry R and S vs D and L Configuration (September 2022).


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