Explanation of Amino Acid Groups.

Amino acids differ when they have different R Groups attached to them. Learning the structures is important, but understanding why  these molecules are arranged and placed where they are is equally important when learning and explaining this topic.

These groupings can be divided into :

1) Non-polar, aliphatic R groups. 

Aliphatic R groups are nonpolar and hydrophobic. Hydrophobicity improves with increasing number of C atoms in the hydrocarbon chain. While these amino acids prefer to remain within protein molecules, alanine and glycine are ambivalent. This means that they can be inside or outside the protein molecule. Glycine has such a small side chain that it does not have much effect on the hydrophobic interactions.

2)Polar uncharged R groups.

There are eight amino acids with polar, uncharged side chains. Serine and threonine contain hydroxyl groups. Asparagine and glutamine contain amide groups. Histidine and tryptophan contain heterocyclic aromatic amine side chains. Cysteine has a sulfhydryl group. Tyrosine has a phenolic side chain. The sulfhydryl group of cysteine, phenolic hydroxyl group of tyrosine, and imidazole group of histidine all show some degree of pH-dependent ionization.

3) Aromatic R groups.

This group is identified by having an unsaturated ring containing double bonds in a conjugated form, especially containing a benzene ring. Examples of Aromatic R groups are :  Phenylalanine, Tyrosine and Tryptophan.

4)Positively charged R groups.

In a neutral solution, the R group of a basic amino acid may gain a proton and become positively charged.  Interaction between positive and negative R groups may form a salt bridge, which is an important stabilizing force in proteins.

5) Negatively charged R groups.

In a neutral solution, the R group of an acidic amino acid may lose a proton and become negatively charged.including aspartic acid (aspartate) and glutamatic acid (glutamate).  In a neutral solution, the R group of an acidic amino acid may lose a proton and become negatively charged.

6)Sulfydryl groups.

These R groups contain a sulfur atom (S).  The disulfide bond formed between two cysteine residues provides a strong force for stabilizing the globular structure.  

For the structures and additional information on Amino acid groups, refer to the Amino acid and proteins part 1 lecture linked below.

Why do we need the 20 essential amino acids?

We have been taught about the 20 essential amino acids, but do we know why they are essential to our bodies? Below is a list of their responsibilities and functions. Alanine: It is one of the most significant among the 20 common amino acids. It offers energy to your system. It releases into the blood stream during exercise time and induces carbohydrate-consuming effect to the health system. It promotes enhancement in the area of protein synthesis and nitrogen balance.Arginine: Synthesized normally in the body, arginine is known to be a semi-essential amino acid. Sometimes more is required than normal production. Deficiencies may include poor wound healing, weakness in muscles, hair loss, irritations in skin, and constipation.  Asparagine: It is needed to maintain homeostatic balance in the nervous system. Amino acid transformation and ammonia synthesis are largely dependent on asparagine. Aspartic Acid: Aspartic acid is one of two acidic amino acids belonging to the group of 20 common amino acids. It promotes enzyme activity, maintenance of solubility in the body, as well as homeostasis in ionic characters of proteins. Cysteine: It is present only at the rate of 2.8% into proteins but it provides the 3-dimensional stability of the protein molecule. It also plays a crucial role in the metabolic process of many important enzymes.  Glutamic Acid: It is responsible for transportation of glutamate and other amino acids to the blood barrier.  Glutamine: Glutamine is able to eliminate excess ammonia from the body system. It enhances immune system. Apart from that, glutamine possesses anti-anxiety property that permits the mind to be relaxed. Glycine: It helps in the transformation of harmful toxic substances within the body to a non-toxic form.  Histidine: Histidine is required for infant development. Histidine deficiency may result in eczema, a kind of skin disease. There are few genetic disorders that promote non-metabolic state for histidine. This results in speech disorders and mental retardations among infants and toddlers.  Isoleucine: This amino acid is particularly important for stimulating the brain in order to produce mental alertness. Leucine: It is particularly effective for producing other essential biochemical compounds in the body. These chemicals are important for producing bodily energy and mental alertness.  Lysine: Lysine is important for proper growth, and it plays an essential role in the production of carnitine, a nutrient responsible for converting fatty acids into energy and helping to lower cholesterol. Lysine appears to help the body absorb calcium, and it plays an important role in the formation of collagen. It functions against the  herpes virus in particular by providing body required nutritional supplements.  Methionine: It functions at initiating the translation of messenger RNA.Phenylalaine: This amino acid profoundly affects brain cells at biochemical level. Proline: It significantly affects human nutrition. It is believed to act as a source of nitrogen.  Serine: Serine is intimately related to various bodily functions such as fat metabolism, tissue growth, enhancement of immune system and many more. It is an essential ingredient of brain protein.  Threonine: It helps in the maintenance of protein balance and also in assisting collagen formation.  Tryptophan:  This is particularly needed in the body for the production of vitamin B3.  Tyrosine: This is crucial in building link between dopamine and norepinephrine. It also reduces fat by suppressing appetite.  Valine: It is effective in promoting tissue growth and maintaining nitrogen balance in the health system.

Identifying the polarity of amino acid bonds.

A bond is said to be polar when there is a large amount of electronegativity difference between the atoms in a bond. Partial negative charges are found on the most electronegative atoms and the others are deemed partially positive.

Here are a few tips to aid in identifying the polarity and charges of amino acids.

1) If the amino acid side chain is a hydrocarbon, the amino acid is non-polar. There are 2 exceptions to this: Proline and Tryptophan. These exceptions however can easily be seen due to their steric hindrance.

2) If the amino acid chain has an atom that possesses electronegativity or polarity, but no charge, then the amino acid is polar uncharged.

3) If the amino acid has a charge on the side chain, it is polar.

Below is a table of standard amino acid abbreviations and their side chain properties.