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After getting an overview of all the various functional groups involved in organic chemistry during class 11, you get to study in detail about each functional group in class 12 organic chemistry. Amino Acids, a part of the Biomolecules chapter is one of the important topics when preparing for entrance examinations. Analysing the previous year papers, it is evident that every year at least one question is asked straight from this topic both in JEE mains and advanced. Here, I have discussed some of the important points from this topic that you need to focus on.

What Are Amino Acids?

As the name suggests, amino acids are compounds having two functional groups, an amino group (-NH2) and a carboxylic group (-COOH) attached to itself. They are derivative of carboxylic acids and the amino acid group which may be attached to the central carbon atom at alpha, beta or gamma position.

Classification of Amino Acids

Amino acids are classified in a number of ways depending on the properties. They are –

  1. Classification based on the type and chemistry of side chain structure –
  • Non-Polar
  • Polar
  • Polar and acidic
  • Polar and Basic

The first two groups are the main classification groups, the other two being sub-groups.

Non-Polar amino acids have an equal number of amino and carboxyl groups and are neutral. There is no net charge on the ‘R’ group and are hydrophobic. The amino acids in this group are alanine, valine, leucine, glycine, etc.

Amino acids having polar side chain structure (e.g. Glutamate having a polar carboxylate end at the side chain structure capable of forming H-bonds) fall into the category of polar.

Acidic amino acids contain a second carboxyl group, giving them an acidic nature.

Basic amino acids are amino having a basic group which may be an additional amino group, giving them their basic nature.

2. Classification based on their requirements in the human body –

  • Non-essential – Those amino acids which are synthesized in the body are non-essential amino acids. Example – Glycine, Alanine, Serine, etc.
  • Essential – These amino acids are not produced naturally by the human body and must be taken in our diet. Some of them are – Valine, Leucine, Lysine, etc.
  • Conditionally essential – These amino acids are considered essential to recover from certain circumstances such as viral fever, wound healing, etc.

Zwitterion

Due to the presence of both the acidic carboxyl group and basic amino group in the same molecule of an amino acid, in aqueous solution, they exist in a form known as Zwitterion. This ion is formed as a result of an internal acid-base reaction of an amino acid molecule which proceeds by the carboxyl group losing a proton and the amino group accepting the same proton leading to the formation of a dipolar ion.  Even though the Zwitterion is charged, since it contains both a positive and negative charge of equal amount, overall it is electrically neutral. They are also amphoteric I nature, depending on the pH of the solution, the amino acid can donate as well as can accept a proton.

Due to the formation of this dipolar zwitterion, amino acids in an aqueous state, show a lot of variation from the expected results.

Physical Properties

Melting point – Amino acids are crystalline solids and show a surprisingly high melting point. They tend to decompose before they melt, hence noting the exact melting point in most cases is difficult.  Decomposition and melting tend to be in the 200 – 300o C range. Given the small size of an these molecule, this range is very high on account of the formation of the zwitterion.

Due to the formation of dipolar molecules, they have a strong ionic attraction between an ion and its neighbour. These ionic attractions take more energy to break and so the amino acids have a high melting point.

Solubility – Amino acids are generally soluble in water and insoluble in non-polar organic solvents such as hydrocarbons.

Zwitterions again act as a deciding factor in determining the solubility of ions. In water, the ionic attractions between the ions in the solid amino acid are replaced by strong attractions between polar molecules and the zwitterions. The extent of solubility depends on the nature and size of the attached alkyl group.

The lack of solubility in non-polar organic solvents is due to the lack of attraction between the molecules and zwitterions. Without strong attractions between solvent and amino acid, there won’t be enough energy released to pull the ionic lattice apart.

Optical Activity – As evident from the general formula of an amino acid, the central carbon atom four different groups attached to itself. Apart from glycine in which hydrogen atom forms the alkyl group, all other amino acids show optical activity due to the presence of central chiral carbon atom. This is equally true if you consider the structure of a zwitterion instead of the simpler structure.

The lack of a plane of symmetry means that there exists two stereoisomers of an amino acid, one the superimposable mirror image of the other.

Chemical Properties

The presence of a functional group in any molecule makes that molecule participate actively in a chemical reaction. In the case of an amino acid, due to the presence of two functional groups, they show the following characteristics reaction –

  1. Reactions involving the participation of carboxyl group.
  2. Reactions involving the participation of an amino group.
  3. Reactions involving the participation of both carboxyl group and an amino group.

Standard Amino Acids

One of the most practical means to classify amino acids is based on the polarity (that means the distribution of electric charge) of the R group (e.g., side chain).

Simply put, amino acids are basically molecules that, from a chemical perspective, are distinguished by the presence of an amine group and a carboxylic group (acid). And that’s how it derives its name. Its main task is to work as monomers for the synthesis of peptides and proteins. Amongst all the amino acids in nature, there is a specific set of around 20 amino acids that can be called standard, and they are used as building blocks for most of the proteins produced by any living being. Here is a list of all standard amino acids:

  • glycine
  • alanine
  • proline
  • valine
  • leucine
  • isoleucine
  • methionine
  • phenylalanine
  • tyrosine
  • tryptophan
  • serine
  • threonine
  • cysteine
  • asparagine
  • glutamine
  • lysine
  • arginine
  • histidine
  • aspartate
  • glutamate

Nonstandard Amino Acids

Nonstandard amino acids can be described as amino acids that have been chemically modified after they have been incorporated into a protein (called a “posttranslational modification”). Remember that the amino acids that are present in living organisms are not found in proteins. In these modified amino acids, there is γ-carboxyglutamic acid, which is a calcium-binding amino acid residue that is present in the blood-clotting protein prothrombin. One of the most abundant proteins in vertebrates by mass is collagen. Noteworthy proportions of the amino acids in collagen are modified forms of proline and lysine: 4-hydroxyproline and 5-hydroxylysine.

Nevertheless, apart from the standard amino acids, there are a lot of them which are found in some proteins and are termed as non-standard amino acids. The entire thought of ​​using these non-standard amino acids is pretty easy to understand. When the composition is different from the standard amino acids, then there are different physicochemical properties.

There are numerous non-standard amino acids found in the extracellular matrix proteins. Since the extracellular matrix is a quite a complex structure with frequent interactions with many different molecules (extracellular and cellular molecules), it is essential that the proteins that make up the matrix may present a high versatility in the interactions that they establish. Therefore, there’s this need to especially include some amino acids that have different characteristics. Here are some examples of non-standard amino acids:

  • Cystine, isodesmosine and desmosine are amino acids found in extracellular matrix proteins such as elastin.
  • Hydroxylysine and hydroxyproline are seen in the richest protein of the extracellular matrix category – collagen.
  • Gamma-carboxyglutamate, present in osteocalcin, is also an extracellular matrix protein of bone. But it is also in the pro-thrombin, which is imperative for the coagulation cascade.
  • Phosphothreonine, phosphoserine and phosphotyrosine are present in many kinds of proteins. It is simply because protein phosphorylation is the most common post-translational modification, and always comprises amino acids with hydroxyl groups in their side chains.
  • N-acetillysine, which is essential to the structure of histones
  • Found in myosin, methyllyisine is a motor protein of our cytoskeleton, more particularly related to the actin filaments.

Reactions

Amino acids can go through numerous chemical reactions by means of their various chemical functionalities (carboxyls, amino, and R groups). However, the two main reactions (peptide bond and cysteine oxidation) are particularly important due to their effect on protein structure.

Amino acids can be connected via a condensation reaction wherein an −OH is lost from the carboxyl group of one amino acid along with a hydrogen from the amino group of a second. It then forms a molecule of water and creates two amino acids that are linked via an amide—known as a peptide bond. In short, amino acids that are connected by a series of peptide bonds form a peptide.

Now, let’s talk about cysteine oxidation. Note that the thiol (sulfur-containing) group of cysteine is highly reactive and the most frequent reaction of this group is a reversible oxidation that leads to the formation of a disulfide. So, the oxidation process of two molecules of cysteine gives birth to cystine, which is a molecule that contains a disulfide bond. When it comes to extracellular fluids (such as blood), the sulfhydryl groups of cysteine get rapidly oxidized and eventually form cystine. Did you know that cystine is one of the least soluble amino acids? Therefore, even the crystallization of the excreted cystine is a result of the formation of calculi—more commonly known as “stones”—in the kidney, ureter, or urinary bladder.

Formation of the Peptide Bond

The compounds obtained by the condensation reaction between two or more, same or different alpha-amino acids are called peptides and the new bond that is formed between the carboxyl group of one molecule and the amino group of another molecule is called peptide bond.

Depending on the number of active functional groups and the reaction conditions, there might be a formation of more than one peptide bond in a reaction. Hence, peptide molecules are classified according to the number of the amino acid molecule undergoing the condensation reaction.

The peptide bond formed by the condensation of two amino molecules is called dipeptide, three amino molecules are called tripeptide and so on.

Iso-Electric Point

Amino acid, in ionized form, when placed in an electric field, will migrate towards the electrode having opposite charge. However, this movement of ions depends on two factors – the pH of the solution and the charge on the ion. In acidic medium, cation moves toward the cathode, in a basic medium, anion moves towards the anode. Zwitterion, being electrically neutral because of no net charge, does not migrate towards any of the electrodes.

The pH at which the amino acids molecules show a zero tendency to migrate towards any of the electrodes and exists as a zwitterion, this point is known as the iso-electric point. At the iso-electric point amino acids have zero solubility.

Importance in Daily-Life Chemistry

Amino acids are the building blocks of proteins and twenty percent of the human body is made up of proteins, so it is fair to say that amino acids have an influence on our existence and play a key role in the function of organs, glands, transport and storage of nutrients and giving cell their structure.

They are also an essential component in the field of medical and are used for dietary supplements, anti-aging, to fight cholesterol, diabetes and other various other illness.

The above content covers up all the major points that you need to study well on this topic. However, this was just a brief overview and it’s your task now to explore further into each of these topics and strengthen your preparation for the exam. In case of any doubts and other queries, you can always get them solved here at Toppr Bytes.

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If you want us to add anything else to the topic, do leave it in the comments’ section. Till then Toppr wishes you all the very best! 

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