Amino Acids

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The molecular structure of an amino acid is given. An amino acid has an alpha carbon to which an amino group, a carboxyl group, a hydrogen, and a side chain are attached. The side chain varies for different amino acids, and is designated as the R - group.
Amino acids have a central asymmetric carbon to which an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group) are attached.

Source: OpenStax Biology 2e

OpenStax Biology 2e

Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group.

Scientists use the name “amino acid” because these acids contain both amino group and carboxyl-acid-group in their basic structure. As we mentioned, there are 20 common amino acids present in proteins. Nine of these are essential amino acids in humans because the human body cannot produce them and we obtain them from our diet. For each amino acid, the R group (or side chain) is different.

– What are amino acids that are incorporated biosynthetically into proteins during translation?

Nullomers are codons that in theory code for an amino acid, however in nature there is a selective bias against using this codon in favor of another, for example, bacteria prefer to use CGA instead of AGA to code for arginine. This creates some sequences that do not appear in the genome. This characteristic can be taken advantage of and used to create new selective cancer-fighting drugs and to prevent cross-contamination of DNA samples from crime-scene investigations.

The molecular structures of the twenty amino acids commonly found in proteins are given. These are divided into five categories: nonpolar aliphatic, polar uncharged, positively charged, negatively charged, and aromatic. Nonpolar aliphatic amino acids include glycine, alanine, valine, leucine, methionine, isoleucine, and proline. Polar uncharged amino acids include serine, threonine, cysteine, asparagine, and glutamine. Positively charged amino acids include lysine, arginine, and histidine. Negatively charged amino acids include aspartate and glutamate. Aromatic amino acids include phenylalanine, tyrosine, and tryptophan.  For example, in the amino acid glycine, the R group is a single hydrogen; but in alanine the R group is upper C upper H subscript 3 baseline.
There are 20 common amino acids commonly found in proteins, each with a different R group (variant group) that determines its chemical nature.

Source: OpenStax Biology 2e

The chemical nature of the side chain determines the amino acid’s nature (that is, whether it is acidic, basic, polar, or nonpolar). For example, the amino acid glycine has a hydrogen atom as the R group. Amino acids such as valine, methionine, and alanine are nonpolar or hydrophobic in nature, while amino acids such as serine, threonine, and cysteine are polar and have hydrophilic side chains. The side chains of lysine and arginine are positively charged, and therefore these amino acids are also basic amino acids. Proline has an R group that is linked to the amino group, forming a ring-like structure. Proline is an exception to the amino acid’s standard structure since its amino group is not separate from the side chain.

– What is a chemical group that is attached to a core part of the molecule called the “main chain” or backbone?

A single upper case letter or a three-letter abbreviation represents amino acids. For example, the letter V or the three-letter symbol val represent valine. Just as some fatty acids are essential to a diet, some amino acids also are necessary. These essential amino acids in humans include isoleucine, leucine, and cysteine. Essential amino acids refer to those necessary to build proteins in the body, but not those that the body produces. Which amino acids are essential varies from organism to organism.

– What is a biosynthetic precursor to porphyrins used in red blood cells?

The sequence and the number of amino acids ultimately determine the protein’s shape, size, and function. A covalent bond, or peptide bond, attaches to each amino acid, which a dehydration reaction forms. One amino acid’s carboxyl group and the incoming amino acid’s amino group combine, releasing a water molecule. The resulting bond is the peptide bond.

– What are short chains of between two and fifty amino acids, linked by peptide bonds?

The formation of a peptide bond between two amino acids is shown. When the peptide bond forms, the carbon from the carbonyl group becomes attached to the nitrogen from the amino group. The upper O upper H from the carboxyl group and an upper H from the amino group form a molecule of water.
Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of one amino acid is linked to the incoming amino acid’s amino group. In the process, it releases a water molecule.

Source: OpenStax Biology 2e

The products that such linkages form are peptides. As more amino acids join to this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end the N terminal, or the amino terminal, and the other end has a free carboxyl group, also the C or carboxyl terminal. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, often have bound non-peptide prosthetic groups, have a distinct shape, and have a unique function. After protein synthesis (translation), most proteins are modified. These are known as post-translational modifications. They may undergo cleavage, phosphorylation, or may require adding other chemical groups. Only after these modifications is the protein completely functional.

– What is an α-amino acid that is used by almost all living beings in the biosynthesis of proteins?

Source:

Clark, M., Douglas, M., Choi, J. Biology 2e. Houston, Texas: OpenStax. Access for free at: https://openstax.org/details/books/biology-2e

https://en.wikipedia.org/wiki/Amino_acid

https://en.wikipedia.org/wiki/Side_chain

https://en.wikipedia.org/wiki/Peptide

https://en.wikipedia.org/wiki/Glutamic_acid

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