What is the structure of amino acids
Read more about Aspartate. The Journal of Biological Chemistry. At the current time, the most-adopted method is an automated synthesis on a solid support e.
So let me draw that for you here.
Amino Acids: Protein Building Blocks
First, you have your amino group, and up top you have your carboxylic acid. Here is your hydrogen atom, and at the bottom is the side chain, or R group. And just to orient you a bit, here in the center is the chiral carbon, the alpha carbon here. And then you have the four groups coming off of the chiral carbon. And the horizontal bonds here-- you can kind of picture those as coming out of the plane of the computer towards you. And then these vertical bonds here are coming out of the plane of the computer away from you.
And this particular configuration is called an L-amino acid. And conversely, you can have the mirror image of this, which I'll draw for you here. And this particular configuration is called a D-amino acid. And these two configurations are called enantiomers.
And enantiomers are mirror-image molecules that are not superimposable. So you can picture-- these are mirror images of each other, but if you were to take this D-amino acid and try to superimpose it on the L- you wouldn't be able to do that. You can kind of think of these two configurations like your left and right hand, and although your left and right hand are mirror images of each other, you can't superimpose them on one another.
And that's the relationship between an L- and a D-configuration for Fischer projections. And these two configurations look awfully similar and are really easy to mix up, and so the way that I like to keep them straight is if I look at where the amino group is-- let's take the L amino acid. If I look at where the amino group is, I can see that it is to the left of the projection, so L is for left amino group. Now, if I look at the D amino acid, I again look for the amino group, and I see that it's to the right of this configuration.
And so D, which actually means dextro, or right, in Latin, is for right amino group. That's kind of how I like to keep them straight.
So why is it important to distinguish between L- and D-amino acids? Well, the L- form of an amino acid is the only form that you will find within the human body, and so that's really important to remember-- that the L-configuration is the kind that you find within humans.
Now how about we review a little bit about everything that we learned? The alphabet is needed to construct words; words are needed to construct sentences; and sentences are needed to construct a paragraph. Similarly, a fully functional protein is assembled through four levels of hierarchy as illustrated below.
Image showing different levels of protein structure related to the alphabet and sentence analogy described in the text. Primary structure simply refers to the linear sequence of amino acids joined to each other through peptide bonds.
The sequence of amino acids determines the basic structure of the protein.
Image of primary protein structure. Unlike the rigid peptide bond, the bond linking the amino group to the alpha carbon atom and the bond linking the alpha carbon atom to the carbonyl carbon are single bonds—as shown in the image below. These two bonds are free to rotate about the amide bonds, allowing the amino acids in the polypeptide chain to take on a variety of orientations.
Image showing possible rotations and restricted rotations. The enhanced freedom of rotation with regards to these two bonds allows proteins to fold into a variety of shapes.
These folded secondary structures are stabilized by the formation of hydrogen bonds between the amino acids. This results in a strong hydrogen bond that has an optimum hydrogen to oxygen, H…. O, distance of 2. Image of an alpha helix. Sheets exist in two forms. You can see the two forms in the cartoons below. When several secondary structures come together, tertiary structures are formed. In tertiary structures, in addition to hydrogen bonding, amino acid side chains of the various secondary structures start interacting with each other in a number of ways.
These interactions include hydrophobic interactions, ionic interactions, and disulfide bonds as illustrated below. Image of tertiary protein structure.
When several tertiary structures come together, a quaternary protein structure is formed. For example, hemoglobin is a functional quaternary protein formed by the coming together of four tertiary structures, called globin proteins.
The same forces of interactions operate in a quaternary structure as operate in a tertiary structure. Forces that keep the different protein structures together.
In summary, the primary structure of a protein simply refers to the linear polypeptide with its amino acid sequence. The secondary structure is the folded version of the linear polypeptide stabilized by hydrogen bonding. The tertiary structure is formed by the coming together of several secondary structures that are held together by various types of interactions, and finally a quaternary structure is formed by the combination of several tertiary structures, again held together via different types of interactions.
This property is conceptually similar to the spatial relationship of the left hand to the right hand. One enantiomer is designated d and the other l. It is important to note that the amino acids found in proteins almost always possess only the l -configuration.
This reflects the fact that the enzymes responsible for protein synthesis have evolved to utilize only the l -enantiomers. Reflecting this near universality, the prefix l is usually omitted.
Some d -amino acids are found in microorganisms, particularly in the cell walls of bacteria and in several of the antibiotics. However, these are not synthesized in the ribosome. Compounds such as amino acids that can act as either an acid or a base are called amphoteric.
The pKa of a group is the pH value at which the concentration of the protonated group equals that of the unprotonated group. Thus, at physiological pH about 7—7. Any free amino acid and likewise any protein will, at some specific pH, exist in the form of a zwitterion. That is, all amino acids and all proteins, when subjected to changes in pH, pass through a state at which there is an equal number of positive and negative charges on the molecule.
The pH at which this occurs is known as the isoelectric point or isoelectric pH and is denoted as pI. When dissolved in waterall amino acids and all proteins are present predominantly in their isoelectric form.
Stated another way, there is a pH the isoelectric point at which the molecule has a net zero charge equal number of positive and negative chargesbut there is no pH at which the molecule has an absolute zero charge complete absence of positive and negative charges.
That is, amino acids and proteins are always in the form of ions; they always carry charged groups. This fact is vitally important in considering further the biochemistry of amino acids and proteins.
One of the most useful manners by which to classify the standard or common amino acids is based on the polarity that is, the distribution of electric charge of the R group e. Group I amino acids are glycinealaninevalineleucineisoleucineprolinephenylalaninemethionineand tryptophan. The R groups of these amino acids have either aliphatic or aromatic groups.
In aqueous solutions, globular proteins will fold into a three-dimensional shape to bury these hydrophobic side chains in the protein interior. The chemical structures of Group I amino acids are:. Isoleucine is an isomer of leucine, and it contains two chiral carbon atoms. Instead, its side chain forms a cyclic structure as the nitrogen atom of proline is linked to two carbon atoms.
Phenylalanine, as the name implies, consists of a phenyl group attached to alanine. Methionine is one of the two amino acids that possess a sulfur atom. Methionine plays a central role in protein biosynthesis translation as it is almost always the initiating amino acid.
Methionine also provides methyl groups for metabolism. Tryptophan contains an indole ring attached to the alanyl side chain. Group II amino acids are serinecysteinethreoninetyrosineasparagineand glutamine. The side chains in this group possess a spectrum of functional groups. However, most have at least one atom nitrogenoxygenor sulfur with electron pairs available for hydrogen bonding to water and other molecules.
The chemical structures of Group II amino acids are:. Tyrosine possesses a hydroxyl group in the aromatic ring, making it a phenol derivative. The hydroxyl groups in these three amino acids are subject to an important type of posttranslational modification: Like methionine, cysteine contains a sulfur atom. Asparagine, first isolated from asparagusand glutamine both contain amide R groups.Amino acid structure
The carbonyl group can function as a hydrogen bond acceptor, and the amino group NH 2 can function as a hydrogen bond donor. The two amino acids in this group are aspartic acid and glutamic acid. Each has a carboxylic acid on its side chain that gives it acidic proton -donating properties.
In the ionic forms, the amino acids are called aspartate and glutamate. The chemical structures of Group III amino acids are. Free glutamate and glutamine play a central role in amino acid metabolism. Glutamate is the most abundant excitatory neurotransmitter in the central nervous system. The three amino acids in this group are argininehistidineand lysine.
Each side chain is basic i. As mentioned above for aspartate and glutamate, the side chains of arginine and lysine also form ionic bonds.
Human nutrition in the developing world. Food and Nutrition Series — No. Food and Agriculture Organization of the United Nations. It lacks the NH 2 group because of the cyclization of the side chain and is known as an imino acid ; it falls under the category of special structured amino acids.
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