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    Amino Acid Experiments

    Amino Acid Background Information

    Definition

    Amino acids are the building blocks of proteins. There are 20 standard amino acids that almost all proteins are made out of. Some amino acids are glycine, alanine, and tryptophan. In chemistry, an amino acid can refer to any molecule that contains both amine and carboxyl functional groups. In biochemistry, this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent.

    Basics

    Amino acids are molecules containing an amine group, a carboxylic acid group and a side chain that varies between different amino acids. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent. In the alpha amino acids, the amino and carboxylate groups are attached to the same carbon atom, which is called the α–carbon. The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. These side chains can vary in size from just a hydrogen atom in glycine, to a methyl group in alanine, through to a large heterocyclic group in tryptophan.

    Amino acids are critical to life, and their most important function is their variety of roles in metabolism. One particularly important function is as the building blocks of proteins, which are linear chains of amino acids. Every protein is chemically defined by this primary structure, its unique sequence of amino acid residues, which in turn define the three-dimensional structure of the protein. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked together in varying sequences to form a vast variety of proteins. Amino acids are also important in many other biological molecules, such as forming parts of coenzymes, as in S-adenosylmethionine, or as precursors for the biosynthesis of molecules such as heme. Due to this central role in biochemistry, amino acids are very important in nutrition. Amino acids are commonly used in food technology and industry. For example, monosodium glutamate is a common flavor enhancer that gives foods the taste called umami. They are also used in industry. Applications include the production of biodegradable plastics, drugs and chiral catalysts.

    History: The first few amino acids were discovered in the early 1800s. In 1806, the French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that proved to be asparagine, the first amino acid to be discovered. Another amino acid that was discovered in the early 19th century was cystine, in 1810, although its monomer, cysteine, was discovered much later, in 1884. Glycine and leucine were also discovered around this time, in 1820.

    Twenty-two amino acids are naturally incorporated into polypeptides and are called proteinogenic or standard amino acids.

    Aside from the twenty-two standard amino acids, there are a vast number of non-standard amino acids. These non-standard amino acids found in proteins are formed by post-translational modification, which is modification after translation in protein synthesis. These modifications are often essential for the function or regulation of a protein; for example, the carboxylation of glutamate allows for better binding of calcium cations, and the hydroxylation of proline is critical for maintaining connective tissues.

    Of the twenty-two standard amino acids, eight are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food. However, the situation is quite complicated since cysteine, taurine, tyrosine, histidine and arginine are semiessential amino acids in children, because the metabolic pathways that synthesize these amino acids are not fully developed. The amounts required also depend on the age and health of the individual, so it is hard to make general statements about the dietary requirement for some amino acids.

    Essential Nonessential
    Isoleucine Alanine
    Leucine Asparagine
    Lysine Aspartic Acid
    Methionine Cysteine*
    Phenylalanine Glutamic Acid
    Threonine Glutamine*
    Tryptophan Glycine*
    Valine Proline*
    Selenocysteine* Serine*
    Tyrosine*
    Arginine*
    Histidine*

    (*) Essential only in certain cases.

    Uses in technology: Amino acids are used for a variety of applications in industry but their main use is as additives to animal feed. This is necessary since many of the bulk components of these feeds, such as soybeans, either have low levels or lack some of the essential amino acids: lysine, methionine, threonine, and tryptophan are most important in the production of these feeds. The food industry is also a major consumer of amino acids, particularly glutamic acid, which is used as a flavor enhancer, and Aspartame (aspartyl-phenylalanine-1-methyl ester) as a low-calorie artificial sweetener. The remaining production of amino acids is used in the synthesis of drugs and cosmetics.

    Biodegradable plastics: Amino acids are under development as components of a range of biodegradable polymers. These materials have applications as environmentally-friendly packaging and in medicine in drug delivery and the construction of prosthetic implants. These polymers include polypeptides, polyamides, polyesters, polysulfides and polyurethanes with amino acids either forming part of their main chains or bonded as side chains. These modifications alter the physical properties and reactivities of the polymers. An interesting example of such materials is polyaspartate, a water-soluble biodegradable polymer that may have applications in disposable diapers and agriculture. Due to its solubility and ability to chelate metal ions, polyaspartate is also being used as a biodegradeable anti-scaling agent and a corrosion inhibitor. In addition, the aromatic amino acid tyrosine is being developed as a possible replacement for toxic phenols such as bisphenol A in the manufacture of polycarbonates.

    Chemical synthesis: Several methods exist to synthesize amino acids. One of the oldest methods, begins with the bromination at the α-carbon of a carboxyic acid. Nucleophilic substitution with ammonia then converts the alkyl bromide to the amino acid. Alternatively, the Strecker amino acid synthesis involves the treatment of an aldehyde with potassium cyanide and ammonia, this produces an α-amino nitrile as an intermediate. Hydrolysis of the nitrile in acid then yields a α-amino acid. Using ammonia or ammonium salts in this reaction gives unsubstituted amino acids, while substituting primary and secondary amines will yield substituted amino acids. Likewise, using ketones, instead of aldehydes, gives α,α-disubstituted amino acids. The classical synthesis gives racemic mixtures of α-amino acids as products, but several alternative procedures using asymmetric auxiliaries or asymmetric catalysts have been developed.

    Currently the most adopted method is an automated synthesis on a solid support (e.g. polystyrene beads), using protecting groups (e.g. Fmoc and t-Boc) and activating groups (e.g. DCC and DIC).

    Topics of Interest

    Amino acid dating is a dating technique used to estimate the age of a specimen in paleobiology, archaeology, forensic science, and other fields. This technique relates changes in amino acid molecules to the time elapsed since they were formed.

    A glucogenic amino acid is an amino acid that can be converted into glucose through gluconeogenesis. This is in contrast to the ketogenic amino acids, which are converted into ketone bodies.

    A degron is a specific sequence of amino acids in a protein that directs the starting place of degradation. A degron sequence can occur at either the N or C-terminal region, these are called N-Degrons or C-degrons respectively.

    Proteinogenic amino acids are those 22 amino acids that are found in proteins and that are coded for in the standard genetic code. Proteinogenic literally means protein building. Proteinogenic amino acids are assembled into a polypeptide (the subunit of a protein) through a process known as translation (the second stage of protein biosynthesis, part of the overall process of gene expression).

    The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences, called codons, and amino acids. A triplet codon in a nucleic acid sequence usually specifies a single amino acid (though in some cases the same codon triplet in different locations can code unambiguously for two different amino acids, the correct choice at each location being determined by context). Because the vast majority of genes are encoded with exactly the same code, this particular code is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact there are many variant codes. Thus the canonical genetic code is not universal. For example, in humans, protein synthesis in mitochondria relies on a genetic code that varies from the canonical code.

    Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.

    Proteins (also known as polypeptides) are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; however, in certain organisms the genetic code can include selenocysteine — and in certain archaea — pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Proteins can also work together to achieve a particular function, and they often associate to form stable complexes.

    Source: Wikipedia (All text is available under the terms of the GNU Free Documentation License and Creative Commons Attribution-ShareAlike License.)

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