The essential amino acids in humans are: histidine , leucine , isoleucine , lysine , methionine , valine , phenylalanine , tyrosine and tryptophan [3]. These amino acids have to be supplied to the body via digested proteins that are then absorbed in the intestine and transported in the blood to where they are needed [4].
The digestion of cellular proteins is also an important source for amino acids. Non-essential amino acids can be synthesised from compounds already existing in the body such as how serine is synthesised from glycine [5].
Amino acids have been abbreviated into a 3 letter code as well as a 1 letter code. For example, glycine has the 3 letter code 'Gly' and is assigned the letter 'G' see single letter amino acid codes. The table below lists the 20 Amino acids, their single letter code, three letter code, their charges, and side chain polarity :. All amino acids have a carboxyl terminus called the C-terminus and an amino terminus called the N-terminus , but they differ in their residual groups.
Amino acids are bonded together by a covalent linkage called a peptide bond [6]. The core amino acid structure is:. Where R is the side chain unique to each different amino acid. Large amino acids form the rigid region of the polypeptide backbone while the small amino acids form the flexible regions of the polypeptide allowing the protein to fold into its three-dimensional shape. On the peptide backbone there is flexible rotation around the peptide bond and there is a rigid planar peptide which is caused by a partial double bond.
This is what allows the polypeptides primary sequence to fold to an alpha helix which is one strand coiled. A beta strand is two strands coiled to an antiparallel helix. The core of the polypeptide is made up of the hydrophobic amino acids like phenyalanine , tyrosine , and tryptophan [8].
These three amino acids are also aromatic and are the largest amino acids. The other hydrophobic amino acids, but are not aromatic, are: proline, valine, isoleucine, leucine and methionine.
Amino acids are referred to as chiral due to the alpha carbon being connected to four different groups. You need to actively tackle each amino acid individually. The amino acid gets its name from its two primary functional groups.
The amino acid has a central chiral carbon called the alpha carbon black. Attached to the central carbon you have a hydrogen atom gray , an amino or NH2 group green , and a carboxylic acid COOH group purple.
Finally we have the R group red , which is a variable side chain. There are 20 different amino acids distinguished by their unique side chains. They range from a simple hydrogen atom glycine to a complex 2-ring resonating aromatic system tryptophan. Since the carboxyl group is acidic and the amino group basic, the two will exist as a zwitterion in their conjugated charged forms in physiological pH.
More on zwitterion and amino acid charges in my next article link to follow. One final concept before we break down the individual amino acids, and that is the 3-dimensional protein structure. In a biological system structure determines function , so understanding amino acid characteristics is key to understanding structure and ultimately protein function.
Primary Structure of a 3-D Protein The first and more important determination factor of protein structure is the sequence of amino acids. If the polypeptide chain is attached in a different order, you get a very different overall structure.
Secondary Structure of a 3-D Protein The secondary structure comes from backbone hydrogen bonding interactions. The peptide bond turns every former carboxyl and amino group into an amide functional group. The secondary structure of alpha helix and beta pleated sheets come from hydrogen bonding between the partially negative oxygen on the carbonyl and the partially positive hydrogen on the nitrogen.
THIS is where knowledge and understanding of amino acid side chains are critical. Many students confuse this with secondary structure, which is only backbone interactions. Quaternary Structure of a 3-D Multi-Polypeptide Protein Quaternary structure refers to the variable group interactions between different polypeptides to form a single larger protein.
Quaternary structures are not found in every protein. If the protein contains just a single amino acid strand, then the highest level of folding is its tertiary structure. However, if the protein is made up of multiple polypeptide subunits, then the quaternary structure is what holds the different polypeptides together. This means you ignore any potential polarity on both the carboxyl and amino groups and ONLY look at the side chains.
Hydrophobic, as the name implies is hydro — water , phobic — fearing. Hydrophobic amino acids have little or no polarity in their side chains. The lack of polarity means they have no way to interact with highly polar water molecules, making them water fearing. However, if all you see are Cs and Hs you should automatically recognize a water-fearing amino acid.
But glycine only has a hydrogen at its side chain position. Since hydrogen is non-polar, glycine is a hydrophobic amino acid. The Hydrogen side-chain makes glycine the smallest amino acid. Alanine is a simple amino acid which has just a methyl or CH3 group as its side chain. Since you see nothing but carbon and hydrogen, Alanine is a non-polar hydrophobic amino acid. Valine is another simple amino acid with just an isopropyl variable group.
Just like alanine, we see nothing but carbon and hydrogen, making valine a non-polar hydrophobic amino acid. You can recognize leucine as having the same variable group as valine but with an extra CH2 group. Or you can simply recognize its isobutyl side chain. Isoleucine, as the name implies, is an isomer of leucine. The difference is the placement of the CH3 for a sec-butyl rather than a isobutyl side chain.
Just like its isomer, isoleucine is nonpolar and hydrophobic. Methionine is the first potentially tricky amino acid. Since the difference in electronegativity is less than 0. Pay attention to the structure of phenylalanine. It has a single carbon group with an attached benzene ring. Phenyl is the name for a benzene substituent, and this molecule has a benzene phenyl attached to the structure of alanine.
Since phenylalanine has nothing but Cs and Hs in its aromatic side chain, it is nonpolar and hydrophobic. This is a tricky one. Notice the N-H in this side chain. Connect and share knowledge within a single location that is structured and easy to search.
Glycine has a dipole moment, so why is it considered a nonpolar amino acid when discussing its occurrence in proteins? The first part of your question illustrates a common confusion of beginners between the physiochemical properties of free amino acids in solution , and the properties of that part of an amino acid that remains after it has participated in a condensation reaction to form part of a polypeptide.
They are different. The backbone of a protein has partial charges on the oxygen and nitrogen atoms of the peptide bond, as shown below. This is because it has a partial double-bonded character. Berg et al.
Section 3. Yes, glycine does have a dipole moment Since the structure of glycine is:. Thus glycine, though polar, is considered non-polar in protein structures. Glycine has no side chains. In a neutral solution; not forming a peptide bond, glycine has the following the following structure.
Once it forms a peptide bond with another aminoacids aa , it becomes in the following form:. As you can see, it doesn't have any charges on it since the amino group and the carboxylic acid group formed bonds with another 2 amino acids. Sign up to join this community. The best answers are voted up and rise to the top. Since glycine has such a small side chain, it can fit into many places where no other amino acid can. For example, only glycine can be the internal amino acid of a collagen helix.
Glycine is very evolutionarily stable at certain positions of some proteins for example, in cytochrome c, myoglobin, and hemoglobin , because mutations that change it to an amino acid with a larger side chain could break the protein's structure.
Most proteins contain only small quantities of glycine. A notable exception is collagen, which is about one-third glycine. In a team of astronomers from the University of Illinois, led by Lewis Snyder, claimed that they had found the glycine molecules in space.
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