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Amino Acids

All metabolic activities of living bodies are regulated by Biomolecules. There are mainly four types of Biomolecules which take part in almost all the metabolic activities of living cells. These Biomolecules are carbohydrates, lipids, proteins and nucleic acid. These are polymeric forms of some monomer units. For example; proteins are composed of amino acids that are bonded to each other through peptide linkage.

Amino acids are organic molecules with two functional groups which are bonded to the same carbon atom of the molecule. One is an amino group (-NH2) and another is carboxylic group (-COOH). The carbon atom, at which both of the functional groups are bonded, is known as the alpha carbon atom and such amino acids are known as alpha amino acids. Only alpha amino acids involve in the polymerisation to form protein molecule. Beta and gamma amino acids cannot form protein molecules.

The amino group of one amino acid is involved in a condensation reaction with carboxyl group of another amino acid to form –CO-NH- linkage. This linkage is called as a peptide bond. Do you know both the functional groups of an amino acid molecule have different nature? One is acidic and another is alkaline in nature. Then what will be the nature of an amino acid molecule? Let’s discuss the properties of different amino acid molecules.

 

Amino Acid Definition

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Amino acids are generally referred as $\alpha$ amino acids. The general formula for amino acid is H2NCHRCOOH. Here 'R' is the functional group of the amino acids.

Amino Acid

Ball and stick model


The amino group is attached to the carbon atom immediately next to the carboxylate group that is $\alpha$ carbon, so, it is called $\alpha$ amino acids. Other amino acids also exist called beta and gamma amino acids, in which the amino group is attached to the carbon which is next to $\alpha$  carbon called $\alpha$ amino acid and the next is called $\alpha$ amino acid.

Ball and Stick Model

Classification of Amino Acids


Amino acids are classified into different ways based on polarity, structure, nutritional requirement, metabolic fate, etc.
Generally used classification is based on polarity. Amino acid polarity chart shows the polarity of amino acids.
Based on polarity, amino acids are classified into four groups as follows,
  1. Non-polar amino acids
  2. Polar amino acids with no charge
  3. Polar amino acids with positive charge
  4. Polar amino acids with negative charge

Classification based on polarity


Amino acid is classified based on those with non-polar R group, uncharged polar R group, charged polar R group. The non-polar side chain amino acids are called hydrophobic and the amino acid with uncharged polar side chain is called hydrophilic. It also contains the acid side chains and basic side chains.


Non Polar Amino Acids


Non Polar Amino Acids have equal number of amino and carboxyl groups and are neutral. These amino acids are hydrophobic and have no charge on the 'R' group. The amino acids in this group are alanine, valine, leucine, isoleucine, phenyl alanine, glycine, tryptophan, methionine and proline.

Non Polar Amino Acids

Polar Amino Acids with Positive Charge


Polar amino acids with positive charge have more amino groups as compared to carboxyl groups making it basic. The amino acids which have positive charge on the 'R' group are placed in this category. They are lysine, arginine and histidine.

Polar Amino Acids with Positive Charge

Polar Amino Acids with no Charge

These amino acids do not have any charge on the 'R' group. These amino acids participate in hydrogen bonding of protein structure. The amino acids in this group are - serine, threonine, tyrosine, cysteine, glutamine and aspargine.

Polar Amino Acids with no Charge

Polar Amino Acids with Negative Charge

Polar amino acids with negative charge have more carboxyl groups than amino groups making them acidic. The amino acids which have a negative charge on the 'R' group are placed in this category. They are called dicarboxylic mono-amino acids. They are aspartic acid and glutamic acid.

Polar Amino Acids with Negative Charge

Classification based on the availability of amino acids. The amino acids which cannot be synthesized in the body must be supplied to the body through diet are called essential amino acids. The amino acids which can be synthesized in the body are called non-essential amino acids.

Non-Essential Amino Acids

Functions of Amino Acid

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Amino acids can be found in most of the nutrients we eat. Amino acids are the building blocks of healthy protein. If the food consumed is rich in protein, our body digests the protein right down to individual amino acids and little links of amino acids are adequate to be taken over into the blood stream.

The main purposes of amino acids are to construct and rectify muscular tissue, but the uses go further than that. These things develop chemicals substance that grants our minds to function at its eminent potential.

Functions of Amino Acid


Structure of Amino Acid

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Amino acids are the building blocks of proteins. Each amino acid contains :
  1. Amino group (-NH2 group
  2. Carboxyl group (-COOH group)
  3. R group (side chain) which determines the type of an amino acid


Structure of Amino Acid

All three groups are attached to a single carbon atom called chiral carbon. There are 20 common amino acids characterised by different R groups. These 20 amino acids can be classified according to their mass, volume, acidity, polarity and hydrophobicity.
Out of the 20 amino acids in proteins, humans are able to synthesize only 11, called non-essential amino acids, the other 9 called essential amino acids, must be obtained in diet. The division between essential and nonessential amino acids is not clear cut however Tryosine for instance is sometimes considered non-essential because humans can produce it from phenylalanine, but phenylalanine itself is essential and must be obtained in the diet. Arginine can be synthesized by humans, but much of the arginine in proteins also comes from the diet.

Essential amino acids are not produced by the body. We can get them by eating complete protein foods or from a combination of incomplete vegetables. The nine essential amino acids include histidine, isoleucine, leucine, lysine, methionine, phenylalanine, tryptophan, and valine. The thirteen non-essential amino acids are alanine, arginine, aspartic acid, cysteine, cystine, glutamic acid, glutamine, glycine, hydroxyproline, proline, serine, and tyrosine.

Essential amino acids
Non-essential amino acids
Histidine Alanine
Isoleucine Arginine
Leucine Asparagine
Lysine Aspartic acid
Methionine Cysteine
Phenylalanine Glutamic acid
Threonine Glutamine
Tryptophan Glycine
Valine Proline
Serine
Tyrosine

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Standard Amino Acids

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The standard 20 amino acids differ only in the structure of the side chain or R group. They can be subdivided into smaller groupings on the basis of similarities in the properties of their side chains.

In addition to the 20 common amino acids there are non-standard amino acids. Two non-standard amino acids which appear in proteins and can be specified by genetic code are selenocysteine and pyrrolysine. There are also non-standard amino acids which do not appear in proteins.

Examples include lanthionine, 2-aminoisobutyric acid and dehydroalanine. They often occur as intermediates in the metabolic pathways for standard amino acids. Some non-standard amino acids are formed through modification to the R-groups of standard amino acids. One example is hydroxyproline which is made by a post translational modification of proline.

Properties of Amino Acids

The general properties of amino acids are listed below :
  • Solubility: Amino acids are soluble in water, acids, alkalies, but sparingly soluble in organic solvents.
  • Color: Amino acids are colorless, white solids.
  • State: Amino acids are solid crystalline compounds.
  • Melting points: Amino acids have high melting points.
  • Due to the presence of basic and acidic groups in the same molecule, they may be regarded as salts and hence, most of them either possess higher melting point or melt with decomposition.
  • Presence of asymmetric carbon
Amino Acids
  • Except for Glycine (the first member of amino acid series), all the amino acids contain at least one asymmetric carbon atom and hence, they are optically active and can exist in d and l-forms.
  • But it is very important to note that in nature they never exist in the racemic form.
  • In nature, they always occur in the optically active form.
  • All the naturally occurring amino acids are having L- configuration.
  • And this L-series of amino acids are biologically active compounds.
  • They exist in the form of internal salt, zwitter ion. (as we know aminoacids have acidic and basic functional groups in it)
Amino acids and carboxylic groups

Amino Acids and Carboxylic Groups

Decarboxylation of amino acids

Decarboxylation of Amino Acids

Deamination of amino acids

Deamination of Amino Acids

Ammonium salts from amino acids

Ammonium Salts from Amino Acids

Carboxylate salts from amino acids

Carboxylate Salts from Amino Acids

Isoelectric Point

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Zwitterions

Since in amino acids both carboxylic group(-COOH) and amino group(-NH3) exists, in aqueous solution the H+ ion is transformed from one end of the molecule to the other end to form zwitterions. It is considered as both electrically charged and electrically neutral also. Since it is having both the charges (positive and negative) the net charge of zwitterion is zero.

Zwitterions

Amino acid in zwitter ion form reacts with both acids and bases and it shows the amphoteric behavior. The point at which the zwitter ion has no net charge is called Iso-electric point. At this point the amino acid is considered as electrically neutral.

An important pH value relative to the various forms an amino acid can have in solution, is the pH at which it exists primarily in its zwitterion form, that is, its neutral form (no net charge). This pH value is known as the isoelectric point for the amino acids. An isoelectric point is the pH at which an amino acid exists primarily in its zwitter form. At the isoelectric point, almost all amino acid molecules in a solution (more than 99%) are present in their zwitterion form.

Every amino acid has a different isoelectric point. Fifteen of the 20 amino acids, those with non polar neutral side chain have isoelectric points in the range of 4.8-6.3. The three basic amino acids have higher isoelectric points, and the two acidic amino acids have lower ones. The list of isoelectric points for the 20 standard amino acids are given below.

Name
isoelectric point
alanine 6.01
arginine 10.76
asparagine 5.41
aspartic acid 2.77
Cysteine 5.07
glutamic acid 3.22
glutamine 5.65
glycine 5.97
histidine 7.59
isoleucine 6.02
leucine 5.98
lysine 9.74
methionine 5.74
phenylalanine 5.48
proline 6.48
serine 5.68
threonine 5.87
tryptophan 5.88
trrosine 5.66
valine 5.97

Expanded Genetic Code


Genetic code is the dictionary of nucleotide bases, which determines the sequence of amino acids in proteins. The genetic code (or) codons have triplet base sequences in m RNA, which act as code words for amino acids. The DNA sequence that code for a specific protein(or) polypeptide is called a gene. There are 4 different bases in m RNA - A, G, C and U. They produce 64 different triplets (43). Out of 64 codons 61 codons code for 20 amino acids. The 3 codons UAA, UAG and UGA do not code for amino acids and they are called non-sense codons. The codons AUG and GUG are called initiating codons.

However, there is only 20 amino acids, more than one codon can code for the same amino acid.

Example: CUU and CUC both code for leucine.
The genetic code has four noteworthy features
  1. The genetic code is universal as the same codons code for the same amino acid in all living organisms
  2. It is degenerate, i.e., more than one codons code for an amino acid.
  3. It is comma-less.
  4. The third base of the codon is less specific.
More topics in Amino Acids
Polar Amino Acids Peptide Bond
Arginine Asparagine
Aspartic Acid Cysteine
Glutamic Acid Glutamine
Glycine Histidine
Isoleucine Lysine
Methionine Phenylalanine
Proline Serine
Threonine Tryptophan
Tyrosine Valine
Leucine
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