Proteins and Amino Acid Structure, Classification, Functions, Sources and Examples of Proteins

Unlocking the Power of Proteins and Amino Acids| A Comprehensive Guide to Classification, Sources, and Examples of Proteins

  

Definition and Overview of Proteins

    The word protein is derived from the Greek word "proteios" meaning "holding the first place" or "of prime importance" and contains Carbon, Hydrogen, Nitrogen, and sometimes Sulphur.

    Definition of proteins

Proteins are highly complex nitrogenous colloidal substances made up of Amino acid (A.A) residues joined together by a peptide linkage.

    Important points/facts to know about proteins

• Proteins are macromolecules (also known as polymers), which are made up of Amino acids, whereas amino acids are the micro molecules (also known as monomers) of proteins.
• Amino acids are joined with each other through peptide Bonds or Peptide linkage.
• Proteins are present in all living organisms most abundantly.
• In comparison with salt or sugar molecule proteins are much larger than them.
• Proteins are nutritionally very important because they are directly involved in the chemical processes that are essential for life.
• Their importance can also be judged by knowing the fact that a single cell can contain thousands of proteins, each performing its own unique function.
• In the human body, proteins are synthesized according to the genetic code of genes (present in DNA) through the process of transcription and translation. 
• Protein is such a diverse group of biological molecules that it is not yet possible to explain all of the functions of a protein.
• Some enzymes and hormones (which are proteins in nature) occur in extremely small amounts, yet function very well. While on the other side, hairs, bones, and other organs and tissue with a low water content have a higher percentage of protein.

Amino acids (A.As) | The building blocks of proteins

    As we know that proteins are made up of Amino acids, so now we will discuss the structure of amino acids, the classification of amino acids, and the functions of some important amino acids in detail.

Structure of Amino Acid | Structure and Properties of Proteins

• Amino Acids are monomers, which by joining in one or more linear structures form a polymer known as proteins.
• They are called amino acids because they contain an amino group and an acidic group (called Carboxylic acid).
• Both of these groups i.e amino group & carboxylic acid group are attached with an alpha carbon atom, so more specifically they are known as Alpha amino acids.
• Amino acids also contain a site chain, known as the R-group, which determines the characteristics and functions of amino acids.
• R-group is needed for the identification of particular amino acids. For example, if the R-group is a hydrogen atom then the amino acid is named glycine, on the other side if it's a methyl group the amino acid is alanine.
• There are more than 300 amino acids have been described, particularly in plants, but only 20 amino acids have been found to be present in mammalian tissues and take part in protein synthesis.  
• Amino acids behave differently in different types of solutions, i.e

1.  Behavior of amino acids in acidic solution

    At a pH of less than 4, the COO group of amino acids combines with hydrogen ions (H+) and gets converted into an uncharged form (COOH).

2.  Behavior of amino acids in alkaline solution

At a pH above 9, the ammonium groups (NH3+) after losing their hydrogen ions get converted into amino groups (NH2).

3.  Behavior of amino acids at physiological pH 

    At the pH of 7.2 to 7.4, amino carry a positive charge i.e. become protonated and the carboxylic group carries a negative charge i.e. become deprotonated.

Polypeptides are peptide chains made up of more than 10 amino acids linked through peptide bonds. Proteins are sometimes referred to as polypeptides.           

What is a Peptide Bond, Peptide linkage, or Acid-Amide linkage?

    In a protein, two or more amino acids are joined together by the COOH group on one side and the NH2 group on the other side through a covalent bond forming an acid-amide linkage (CO-NH) known as a peptide Bond.

• A polypeptide chain is directional i.e. it has chemically two different ends i.e.         
• N-terminus: It has a free amino group and is located on the left side for every short polypeptide.
• C-terminus: It has a free Carboxyl group and is located on the right side for every short polypeptide.
• Being extremely stable, it is only cleaved by proteolytic enzymes.
• A molecule of water (H₂O) is eliminated in this process.

Types of Peptide bond on the basis of the number of Amino Acid residues| Oligopeptides and Polypeptides

    It is important to remember here that peptides mean amino acids, thus

1. Oligopeptides are the peptide chains made up of 2 to 10 amino acids linked through            peptide bonds, whereas

2. Polypeptides are peptide chains made up of more than 10 amino acids linked through peptide bonds. Proteins are sometimes referred to as polypeptides. 

Organization of protein structure

    The structure of the protein is organized at the following four different levels.

1. Primary structure 

    The number and order of amino acids in the street polypeptide chain is called the primary structure of proteins.

2. Secondary structure

    The folding of the polypeptide chains into a specific coiled structure held together by disulfide and hydrogen bonds is called the secondary structure of the proteins.

3. Tertiary structure

    The arrangement and inter-relationship of the coiled chains of proteins into specific layers or fibers is called the tertiary structure of the proteins.

4. Quaternary structure

  Several monomeric units, each with appropriate Primary, secondary, and tertiary structures may be combined together. The association of similar or dissimilar subunits is called the quaternary structure of proteins.

Classification of proteins

    Proteins can be classified in the following ways

1. Structural classification.

• The structure of a protein depends on the axial ratio of the proteins i.e. length divided by the width of the protein.
• If the ratio is less than 10 then the protein is globular protein. They are spherical or ovoid in shapes e.g. albumin and globulin.
• If the ratio is greater than 10 then the protein is a fibrous protein. They are thread-like in shape e.g. elastin and keratin.

2. Functional classification. 

    According to the performing functions,  proteins may also be classified into the following classes/groups

a. Structural proteins

   These proteins provide strength and stability to the body. For example, collagen, keratin, elastin, etc.

b. Regulatory proteins

   These proteins are hormones in nature and regulate the body's metabolic functions. For example, insulin, glucagon, growth hormones, etc.

c. Catalytic proteins

   These proteins are enzymes in nature,  which are the biological catalysts and catalyze or accelerate metabolic reactions.  For example,  amylase, protease, lipase, etc. 

d. Transport proteins

   These proteins perform the function of transporting different substances in our blood to tissues and cells. For example, Ferritin carries iron, and ceruloplasmin carries copper.

e. Contractile proteins

    These proteins cause muscle contraction. For example, actin and myosin.

f. Storage proteins

  These are the storage form of proteins that store nutritional substances. For example,  ovalbumin in egg white, gliadin in wheat, zein in maize, etc.

g. Genetic proteins

  These proteins, after combining with nucleic acids, synthesize DNA and RNA. For example, histones and protamine.

h. Defensive proteins

    These proteins provide a defense against infections. For example, immunoglobulin.  

3. Physico-chemical classification

    This type of classification of proteins is based on the physiochemical properties of proteins, such as glass transition temperature, melting point, isoelectric point, molecular weight, etc. Upon a physiochemical basis, proteins are further classified as simple proteins, compound proteins, and derived proteins. Their detail is given as

1. Simple proteins

   These are simple proteins in the sense that they yield only amino acids upon hydrolysis. Following are some examples of simple proteins.

A. Albumin

• It is a water-soluble protein that is synthesized only in our liver.
• It coagulates by heat.
• It is a carrier in its function i.e. it carries Ca++, bile salts, bilirubin, fatty acid, and steroids in our blood.
• It exerts oncotic pressure in the plasma.
• Thus its deficiency results in the loss of its carrier function as well as decreased oncotic pressure (which causes edema etc).

B. Globulin

• It is also a water-soluble protein that is synthesized only in our liver and spleen.
• Its beta-fraction has a carrier function e.g. transferrin.
• While it gamma-fraction has a defensive function e.g. gamma-globulins like immunoglobulin (Ig)/antibodies e.g. IgM, IgG, IgA, IgD, and IgE).
• Its deficiency can result in the loss of its carrier function as well as susceptibility to infection.

C. Globin

• It is the protein part of hemoglobin.
• Normal adult hemoglobin is composed of four globin chains i.e. two alpha chains, and two beta chains.
• Its deficiency in hemoglobin results in thalassemia.
• Mutation of the beta chains at Carbon#6 (where glutamic acid is replaced by valine) results in sickle cell anemia.   

D. Histone

• It combines with nucleic acids (DNA & RNA) to form nucleoproteins known as nucleohistones.
• Being rich in basic amino acids i.e. arginine, they act as basic proteins.  

E. Protamin

• It combines with nucleic acids (DNA & RNA) to form nucleoproteins known as nucleoproteins.
• Being rich in basic amino acids i.e. arginine, they act as basic proteins.
• They are present in spermatocytes (sperm cells).

F. Albuminoids (also known as scleroproteins)

• These fibrous proteins have great stability and form supporting structures.
• Albuminoids are of three types i.e. Keratin, Collagen, and Elastin. Their detail is given below

i. Keratin

• This hard protein is present in horns, hairs, nails, hooves, and feathers.
• It is mainly present in the outermost layer of our skin.
• Skin keratin is called pseudo-keratin because it is soft.

ii. Collagen

• This protein is present in our connective tissues and bones as a long, thin, partially crystalline substance.
• Nutritionally it is poor because it lacks tryptophan. 

iii. Elastin

• This protein is present in the elastic fiber of connective tissues ligaments, tendons, and blood vessels.
• It is also found in large amounts in the uterus during pregnancy.
• It is hydrolyzed by a pancreatic enzyme known as elastase.

2. Compound (Conjugated) proteins

• These proteins are compounds or conjugated proteins because besides amino acids they also yield non-proteinaceous substances known as a prosthetic group. These include the following types

            A.    Nucleoproteins

• These proteins contain histones and protamines + nucleic acid. For example, DNA and RNA.

            B.    Phosphoproteins

• They include proteins + phosphoric acid. For example, casein of milk, and vitellin of the egg yolk.

C.  Lipoproteins

These are proteins + lipids. For example, fatty acids, lecithins, and cephalins to form VLDL,  LDL and HDL.

D. Carbohydrate-containing proteins  

These are proteins + mucopolysaccharides. For example, hyaluronic acid, and chondroitin sulfate.

E.  Chromoproteins

These are proteins + pigments. For example, hemoglobin, cytochrome,  rhodopsin, etc.

F.  Metalloproteins

These are proteins + metals. For example, iron in hemoglobin, copper in ceruloplasmin, etc.

3. Derived proteins

These proteins are derived from simple or compound proteins by denaturation or hydrolysis.  They are further classified into the following two categories

A. Primary-derived proteins

These are obtained by the denaturation of proteins. For example, fibrin from fibrinogen and myosin from myosin.

B. Secondary-derived proteins

These are obtained by hydrolysis of simple proteins. For example, proteoses, peptones, and oligopeptides.

Functions | Importance of proteins

1.  Proteins are the important constituents of the Protoplasm of cells.

2.  Proteins carry heredity material from one generation to the next generation. For example, histones and protamines combined with a nucleic acid to form nucleoproteins.

3.  All enzymes that act as biological catalysts are also proteins.

4.  Some hormones are also proteins in nature. For example, insulin, glucagon, parathyroid hormones, etc.

5.  Proteins perform carrier functions. For example, hemoglobin carries Oxygen and Carbon dioxide, and albumin carries iron and bilirubin.

6. Proteins help in blood coagulation. For example, fibrinogen, and prothrombin.