The chemistry of Amino acids

Wikipedia

Introduction

In the following paragraphs, I will talk about the chemical makeup of amino acids. Despite the fact that this subject could appear to be a little bit or should I say completely scientific, it demands that you give it the time and attention it deserves in order to thoroughly appreciate it. I'm going to do all in my power to clarify things so that we can comprehend them better.

Proteins are made up of molecules called amino acids. When someone consumes a protein-containing food, their digestive system disassembles the protein into amino acids. The amino acids are then combined by the organism in a variety of ways to perform biological activities.

Because a healthy body is capable of producing the other 11 amino acids, these substances do not typically have to be taken in through the food in order for the body to function properly.

Amino acids perform a variety of bodily processes, including muscular growth, triggering bodily chemical processes, delivering nutrition, fending off disease, and more. Low levels of amino acids can affect many different aspects of health, including immunity, digestion, depression, fertility, mental alertness, and infant growth.

The symptoms of a deficit vary according to the diverse functions that each of the essential amino acids performs in the body.

Chemistry of Amino Acids

Peptides and proteins, with the exception of proline, include α-amino acids, which have both a carboxylic acid (α-COOH) and an amino group (α-NH2) as functional groups.
They are bonded to a tetrahedral carbon atom that is referred to as the -carbon.
The R groups, which are unique to each amino acid, serve to separate them from one another. Each R group is also linked to a -carbon atom, and glycine, which has a hydrogen in its R position, is the simplest of the amino acids. The R groups can differ in structure, size, and electric charge, and they are also responsible for the amino acids' varying degrees of solubility in water.

A three-letter shorthand and one-letter symbol are given to the 20 protein amino acids.
They serve as shortcuts for indicating the content and order of amino acids in proteins.
To distinguish the carbon atoms in proteins, there are two conventions.
Starting with the - carbon, further carbons in R groups are assigned the letters β, γ,δ, ε etc.
The carboxyl carbon of an amino acid would be C-1 and the -carbon would be α-cabon C-2 in this serial numbering system starting from carbon with the substituent having the element with the greatest atomic number.

This is a classification of the 20 most prevalent amino acids.
depending on R groupings;

1. Branched-chain amino acids with nonpolar side chains

• Among the Amino Acids, glycine possesses the sole non-chiral and simplest side chain, which contains a H atom.

• Alanine has a methyl group, whereas valine, leucine, and isoleucine have branched chains (isomeric butyl groups)

• The side chain of methionine is thiol ether.

2.Those amino acids that have side chains that are aromatic

• Tryptophan, phenylalanine, and tyrosine are amino acids that are moderately bulky and non-polar (hydrophobic).

• The phenyl moiety is present in phenylalanine.

• There is an indole ring on tryptophan.

• tyrosine that has phenol group attached to it

• Tryptophan, tyrosine, and, to a lesser extent, phenylalanine are all amino acids that absorb UV radiation. 280 nm is the wavelength at which the vast majority of proteins exhibit their characteristically great light absorption.

• A conformational constraint is provided by the pyrrolidine side group on proline, a cyclic -imino acid (secondary amino group).

3. R groups that are polar and do not have any charges

Both serine and threonine include hydroxylic R groups, although the sizes of these groups are different.

Several sized amide side chains can be found attached to asparagine and glutamine.

Cysteine possesses a thiol group that frequently forms a disulfide bond with another cysteine residue by oxidation of both of its respective thiol groups; the resulting dimeric molecule is termed cystine (this is important in stability of many proteins)

4. Side chain with a negative charge that is polar (acidic)

The amino acids with an acidic pH
When the pH is more than 3, aspartic acid and glutamic acid take on a negative charge.
In their ionized states, the terms aspartate and glutamate are used to refer to them.

5. R groups carrying a positive charge (Basic)

Positive charges are seen by the basic amino acids at healthy pH levels.

• The lysine molecule has a butylammonium side chain; this provides the molecule with a second main amino group at the ε-location on its aliphatic chain.
• Arginine possesses a guanidino ring
• Histidine possesses imidazolium moiety
• Histidine is the sole amino acid, with a pKa of about 6, that ionizes within the physiological pH range.
• With a pH of 6, its imidazole side group is only 50% charged, which means that at the basic end of physiological pH, histidine is neutral. As a consequence of this, the histidine side chain is implicated in the catalytic reaction of enzymes.

6.Depending on metabolism

Leucine, which is only ketogenic in nature
The amino acids lysine, isoleucine, phenylalanine, tyrosine, and tryptophan are both ketogenic and glucogenic.
Purely glucogenic (other 14 AAs)

• alanine, glycine, valine, proline, histidine, serine, glutamic acid, methionine, cysteine, arginine, asparagine, aspartic acid, glutamine, threonine

7.On the basis of the nutritional need

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Essential Amino acids

• Isoleucine, leucine, threonine, lysine, methionine, phenylalanine, tryptophan, and valine are the eight amino acids that make up the essential amino acid profile.

Their Carbon skeletons cannot be produced by humans, and a lack of them in the diet will prevent proper growth and prevent the body from functioning at its best.
Histidine and arginine are two partially or semi-essential amino acids.
Children that are growing need them in their diet, while adults do not need them.

Nonessential
The body can produce the amino acids alanine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, proline, serine, and tyrosine, which make up the carbon skeleton.
Every protein in the body has nnessential amino acids.

Conditional essential
There may be a need for supplementation if illness prevents the body from synthesizing unnecessary Amino acids.
Digestion issues could also call for non-essential amino acid supplements.
They include glutamine, arginine, glycine, cysteine, tyrosine, and proline.

Amino acids that have been derived

There are amino acids that are not included in the list of the 20 most common amino acids.

Amino Acids that are derived and can be detected in protein
Certain amino acids are changed into modified forms after the production of proteins, such as 4-hydroxyproline and 5-hydroxylysine, which may both be found in the fibrous protein collagen, which is present in connective tissues.
Myosin, which is a protein present in contractile muscles, contains 6-N-methyllysine. -Carboxyglutamic acid, which is crucial in blood clothing protein, prothrombin, and other proteins that bind Ca2+, also contains this amino acid (biological function)

Desmosin, which is generated from the amino acid lysine and may be found in elastin, is a more complicated protein.
Selenocysteine is an extremely uncommon protein that is included throughout the process of protein synthesis rather than being modified afterwards. Selenocysteine is generated from serine and includes selenium.

Derived amino acids (AAs) not found in proteins
Some are present in free form within the cells.
Ornithine, homocysteine, citrulline, and thyrosine are some of the amino acids.

Non-alpha amino acids — γ-amino butyric acid is produced from glutamic acid, while β-alanine is found in pantothenic acid and coenzyme A (the amino group in this instance is in the -position).

Isoelectric and ampholyte point

In amino acids, the carboxylic acid and amino groups are totally ionized when the pH is in the physiological range. Since its molecular structure comprises both acidic and basic groups, amino acid may behave either as an acid or a base. It is possible to refer this kind as amphoteric; such are referred to as ampholytes (polyampholytes contain more than one basic and acidic groups).

Zwitterions are another name for dipolar ions, which refer to molecules that include charged groups that have the opposite polarity. This state, characterized by a net charge of zero, takes place at a pH that is isoelectric.
Consequently, the pH of an amino acid is said to be isoelectric when it has zero net charge and does not move in an electric field (pI)

pI is either the pH that is exactly in the middle of the two pKa values that are found on each side of the isoelectric pH or the pH that is just the average of the two pKa values that are necessary for the creation of the zwitterion form.

In summary, to date, researchers have identified twenty-two different amino acids as the fundamental components of proteins. They include the twenty most frequent amino acids as well as selenocysteine and pyrrolysine. There are several roles that amino acids play in the body. Their principal purpose is to participate in the production of proteins in the role of the monomer unit.

They may also be employed as substrates in biosynthetic activities; a variety of hormones and neurotransmitters, including nucleotide bases, are produced from amino acids. Intermediates produced during glycolysis or the Krebs cycle can be used to create amino acids. The synthesis of essential amino acids, which are the ones that can only be obtained from food, requires additional processes. When certain amino acids are loaded onto their appropriate tRNAs, they must first go through the process of synthesis.

References

• C. (n.d.). Amino Acid: Benefits & Food Sources. Cleveland Clinic. https://my.clevelandclinic.org/health/articles/22243-amino-acids
• Essential amino acids: Definition, benefits, and foods. (n.d.). Essential Amino Acids: Definition, Benefits, and Foods. https://www.medicalnewstoday.com/articles/324229
• Amino Acids, Evolution | Learn Science at Scitable. (n.d.). Amino Acids, Evolution | Learn Science at Scitable. https://www.nature.com/scitable/topicpage/an-evolutionary-perspective-on-amino-acids-14568445/
• Amino acids: MedlinePlus Medical Encyclopedia. (n.d.). Amino Acids: MedlinePlus Medical Encyclopedia. https://medlineplus.gov/ency/article/002222.htm