Proteins
Proteins Definition: Proteins are a class of complex nitrogenous organic compounds, composed of amino acid residues joined by peptide bonds.
Nomenclature: The term ‘protein1 has been derived from the Greek word, ‘proteos’, which means primary or of the first rank.
Proteins Source: Plants—different types of pulses, like lentils, peas, mung etc., seeds of soybean, gram, nuts, etc. Animals—fish, meat, eggs, milk, etc.
Proteins Structure: All protein molecules have a backbone made up of linear chains of polypeptides.
These polypeptides are made up of amino acids joined together by peptide bonds. These amino acids are called the building blocks of protein molecules.
Structural components: The elements that makeup proteins are carbon, hydrogen, oxygen and nitrogen. Sometimes, sulphur, phosphorus, iron and iodine are also present.
Structural unit—amino acid: The number of amino acids in a protein molecule may vary considerably. For example, the smallest protein is insulin, which is made up of 51 amino acid molecules.
” protein structure and function”
Examples of larger proteins are chymotrypsin (which contains 246 amino acid molecules) and haemoglobin (which contains 574 amino acid molecules). Amino acid has been discussed under a separate head.
Amino acid
Amino acid Definition: The structural unit of proteins, that is made up of carbon, hydrogen, oxygen and nitrogen are called amino acids.
Structure of amino acids: Chemically, amino acids are carboxylic acids containing at least one amino group.
In amino acids, the amino group (—NH2) is attached generally to the a-carbon atom (the carbon atom to which the functional group, in this case, the —COOH, is attached) of the molecule, hence they are called α-amino acids.
β or α -amino acid is the one where the amino group (—NH2) is attached to the other carbon rather than a -carbon and they are very uncommon in nature.
The following parts remain covalently attached to the a-carbon—
- A hydrogen molecule (H), a positively-charged, basic amino group (-NH2) A negatively-charged, acidic carboxyl group(-COOH),
- An alkyl group R may be H as in glycine, or methyl (—CH3) in the case of alanine or maybe some other group.
Types of amino acids: Amino acids can be classified based on the following—
According to nutritional importance: There are 20 different types of amino acids that can be combined to make a protein.
The sequence of amino acids determines each protein’s unique 3-dimensional structure and its specific function. Amino acids may be of two types—
- Essential and
- Non-essential.
Essential amino acids: These are the amino acids that are indispensable for the life and growth of an organism (usually referring to human) but is not produced in the body or produced in insufficient amounts.
primary structure of protein
They must be supplied through diet. The essential amino acids and their functions in the human body are listed below.
Non-essential amino adds: They are amino acids that are synthesised or derived from the essential amino acids within the body.
Hence, an organism does not have to depend solely on proteins in the diet as their sources. These have various important functions in the proper functioning and growth of an organism.
” protein structure primary secondary tertiary and quaternary”
According to the functional group, R: The following are the different types of amino acids based on the acidic or basic nature of the R group—
Acidic amino acids: These amino acids contain more than one —COOH group. Example Aspartic acid and glutamic acid.
Basic amino acids: These amino acids contain more than one —NH2 group. Example Lysine, Arginine.
Neutral amino acids: These amino acids contain one NH2 and one —COOH group. Example Glycine, Alanine.
According to electrical conductance: The following are the different types of amino acids on the basis of electrical conductance—
structure and function of proteins
Non-polar amino acids: They are insoluble in water and do not conduct electricity. Example glycine.
Polar uncharged amino acids: They have polar side chains. Example valine.
Polar-charged amino acids: They are soluble in water and have a positively or negatively charged group. Example lysine (positively charged), and glutamic acid (negatively charged).
According to the structure offside chain: The following chart shows the different types of amino acids on the basis of the structure of the side chain.
Aliphatic amino acids: These amino acids contain an aliphatic hydrocarbon chain. Examples are Glycine, alanine, valine, and isoleucine.
Aromatic amino acids: These amino acids contain aromatic side chains. Examples are Phenylalanine, tyrosine, and tryptophan.
Alcoholic amino acids: These amino acids contain hydroxyl groups in side chains. Examples are Serine and threonine.
Heterocyclic amino acids: These amino acids contain nitrogen in side chains. Example Histidine.
Sulphur-containing amino acids: These amino acids contain sulphur groups in side chains. Examples are Cysteine and methionine.
Pyrollidine ring-containing amino acid: These amino acids contain pyrollidine ring in side chains. Example Proline, hydroxyproline.
Structure Of Protein
Proteins are made up of polypeptide chains, where amino acids are joined together by peptide bonds.
There are generally four types of structures found in proteins—
Primary structure: Linear arrangement of amino acids linked by peptide bonds, in a peptide chain is called the primary structure of protein.
For example, insulin hormone is comprised of 51 amino acids in two chains, one of 21 and the other of 30 amino acids.
“structural organization of proteins “
Other than peptide bonds, intra and inter-chain disulphide bonds may also be present as covalent linkages between two amino acids, cysteine.
Secondary Structure: After Synthesis, polypeptide chains are folded or plated into different shapes, called their secondary structure. This folding or pleating leads to hydrogen bonding between the amino acids in the chain.
The hydrogen bonding exists between the oxygen atom of the carboxyl group of one amino acid with the hydrogen atom of the amino group of another amino acid. The hydrogen bonds, provide great stability to the shape of the protein.
Two common types of secondary structure are— Alpha (α) Helix and Beta (β) Pleated Sheets. (By Pauling and Corey)
α-helix: An α-helix structure is formed due to the twisting of the long polypeptide chains into a right-handed screw (helix).
Hydrogen bonds exist between the amino group of each amino acid molecule and the carboxyl group of an amino acid located at the adjacent turn of the helix.
The side chains of the amino acids are projected outwards in such a structure. Example Proteins present in hair, nails, feathers, beak etc., show this structure.
composition of proteins
β-pleated sheet: In some proteins, two or more polypeptides (in their primary structures) join each other laterally by hydrogen bonds and form a sheet-like structure, called a yS-pleated sheet.
In this case, the side chains of the amino acids reside one above the other.
For example, Fibroin protein in silk fibres shows this structure.
Tertiary structure: The tertiary structure is the final specific geometric shape that a protein assumes.
This may involve coiling or pleating, often with straight chains of amino acids in between.
Generally, this structure is visible in the case of globular proteins, such as histones, different enzymes, etc.
Tertiary structure is held together by four different bonds and interactions— disulphide bonds, ionic bonds, hydrogen bonds, van der Waals, hydrophobic and hydrophilic interactions. Examples myoglobin and many enzyme proteins.
Different bonds and interactions in the tertiary structure of a protein
- Disulphide bonds: Where two cysteine molecules are bound together, a strong double bond (S = S) is formed between the sulphur atoms within the cysteine monomers.
- Ionic bonds: If two oppositely charged ‘R1 groups (+ve and -ve) of two amino acids find themselves close to each other, an ionic bond forms between them.
- Hydrogen bonds: Bonds between the oxygen of the -C00H group and the hydrogen molecule of the -NH2 group.
- Hydrophobic and hydrophilic interactions: Some amino acids may be hydrophobic while others are hydrophilic. In a water-based environment, a globular protein will orient itself in such a way that its hydrophobic parts are towards its centre and its hydrophilic parts are towards its periphery.
- van der Waals interactions: It is the weakest intermolecular interaction between 2 or more atoms or molecules that are very close to each other on the polypeptide chain.
Quaternary structure: Some proteins are made up of multiple polypeptide chains of primary, secondary or tertiary structure, sometimes with an inorganic component.
These multiple polypeptides bind with each other through non-covalent interactions. For example, Haemoglobin exhibits a quaternary structure which is made up of two chains and two chains.
Properties of protein
Different properties of proteins are discussed below.
Properties of protein Nature: Usually colourless, crystalline solids in nature and polar molecules, usually soluble in water.
Properties of protein Stereoisomerism: All amino acids, except glycine, have at least one asymmetric carbon. Therefore they are chiral molecules and exhibit isomerism. They exist in either D or L isomeric form.
Absorption of light: The proteins in tissues and in protein crystals, strongly absorb ultraviolet (UV) light.
- Rather, it is the amino acids which make up the proteins that absorb the UV light.
- The amino acids tryptophan, tyrosine, and cysteine absorb light in the UV range.
- Therefore, different proteins can have different absorption coefficients and even the wavelength of maximum absorption may differ.
- This fact can be used to help identify different types of proteins by relatively fast and simple optical tests with the help of a spectrophotometer.
Amphoteric or ampholytic: Both amino and carboxyl groups present in an amino acid can react with acids and bases to form salts.
Such property is called amphoterism and the compounds are known as ampholytes or amphoteric compounds.
Isoelectric pH: The pH at which a protein is electrically neutral is called isoelectric pH. In this case, the carboxyl group can either lose a proton (H+) or the amino group can accept a proton.
Colloidal property: Due to their huge size the proteins exhibit many colloidal properties. E.g. slow diffusion rate, Tyndall effect, etc.
Zwitterion formation: If both carboxyl and amino groups of an amino acid are ionised, it forms a zwitterion or dipolar ion.
Denaturation and coagulation: The tertiary structure of proteins can be broken by heating or by using chemicals. On application of heat, the kinetic energy of protein molecules with a tertiary structure, increases.
This makes the structure vibrate more, and so the bonds that maintain their shape (which are mainly weak, non-covalent bonds) become more likely to break.
When a protein loses its shape in this way, it is said to be denatured. The proteins will not regain their original complex shape even after the temperature is lowered.
Hydration: Since the polar heads of the molecules are placed outward, they bind easily with water molecules.
The water molecules surrounding the protein molecule form a layer called hydration layer.
Solubility: Proteins are generally water soluble, some are soluble in salt solution or in weak acids or alkalies.
With the weight, and structure of the protein molecule as well as the pH of the medium, the solubility of the proteins changes.
Viscosity: Proteins show viscosity due to their large structures.
Precipitation: Magnesium sulphate, sodium sulphate etc., can precipitate proteins.
Putrefaction: In the presence of oxygen, proteins can give rise to products like NH3, C02, H20 and oxides of N.
Classification of proteins
Proteins are classified on the basis of different characteristics.
Classification based on structure: Proteins may be of three types—Simple, conjugate and derived proteins.
Simple proteins: These proteins yield only amino acids upon hydrolysis.
They are further divided into two types, according to their structure—
- Simple globular proteins and
- Simple fibrous proteins.
Simple globular proteins: The simple proteins that have globular or spherical shapes, fall under this category.
They are soluble in water, alcohol or alkaline medium.
They may be of the following types—
Albumins: These are water-soluble, for example, serum albumin of plasma, my albumin of muscle, ovalbumin of egg white, lactoalbumin of milk, etc.
Globulin: These are insoluble in water but soluble in salt solutions, for example, serum globulin of plasma, myoglobulin of muscle, ova globulin of egg yolk, etc.
Glutelins: These are plant proteins which are soluble in dilute acids and alkalies, for Example prize in of rice, glutenin of wheat, glutelin of corn, etc.
Prolamines: These are plant proteins found in seeds, soluble in 70-80% alcohol, for example, zein of corn, hordein of barley, gliadin of wheat, etc.
Sderoproteins or Albuminoids: These are found in the exoskeletal structures, for example, keratin of hair, horn, hooves, and nails, elastin and collagen of connective tissue—bones, cartilage, tendons, ligaments, etc.
Protamines: These are animal proteins, strongly basic and soluble in water, for example, salmon of salmon fish sperm and clupeid of herring fish sperm, etc.
Simple fibrous proteins: These simple proteins have long and thread-like structures. These are insoluble in cold water, and generally found only in animal cells. These are also known as selenoproteins. They are important for the formation of the structure of the body.
Examples:
- Keratin (constitutes hair, nails, horns etc.),
- Collagen (constitutes tendons, cartilage, etc.),
- Elastin (present in ligaments, blood vessels, cartilage, etc.),
- Fibrin is present in silk fibres.
Conjugated proteins: These yield simple globular proteins along with non-protein substances upon hydrolysis. Examples are nucleoprotein (histone + nucleic acid), metalloprotein, chromoprotein, etc.
Nucleoproteins: These are formed by the combination of two simple proteins, histone or protamine, with nucleic acids (DNA or RNA).
For example DNA + basic or histone deoxyribonucleoprotein (DNPs), RNA + acidic or non-histone protein= ribonucleoproteins (RNPs) of ribosomes.
Phosphoproteins: These are formed by the combination of simple protein with phosphoric acid. Example caseinogen of milk, ovovitellin of egg yolk, etc.
Metalloproteins: These are formed by the combination of simple proteins with metallic elements. For example, the enzyme carbonic anhydrase contains Zn ions, haemoglobin, and other enzyme proteins with metallic elements such as Co, Mn, Cu, Mg, etc.
Chromoproteins: These are coloured proteins, formed by the combination of simple proteins with at least one metallic protein. Examples are haemoglobin, haemocyanin, etc.
Glycoproteins or mucoproteins: Glycoproteins are formed by the combination of simple protein with carbohydrates. Example mucin of saliva, FSH, LH, etc.
When the hexosamine-rich mucopolysaccharide content in the proteins is more than 4%, they are known as mucoproteins.
Example haptoglobin. Components of plasma, combined with haemoglobin during haemolysis form a haptoglobinhaemoglobin compound which is removed from blood by the spleen.
Lipoproteins: They are formed by the combination of simple proteins with lipids. For example, lipoproteins are present in the cell membranes, the brain etc.
Derived proteins: These proteins are obtained as intermediate products during hydrolysis of simple or conjugated proteins. Example peptone, and proteases.
The derived proteins are mainly of two types—primary-derived proteins and secondary-derived proteins.
Primary derived proteins: These derived proteins are formed from other proteins, without the process of hydrolysis. These proteins do not vary in size from the original molecule. For example, egg albumin can be coagulated into a derived protein by high temperature, X-rays, UV-rays, etc.
The primary derived proteins are of the following types—
Protean: It is an insoluble substance, that is produced by the action of enzymes, water or dilute acids on proteins. Example fibrin produced from fibrinogen.
Metaproteins: It is insoluble in water but soluble in acid or alkalies. They are produced by further action of acid and alkali on proteins at 30-60°C. Example acid and alkali metaproteins.
Coagulated proteins: It is an insoluble substances produced by heat or alcohol. Example coagulated egg white, cooked meat, etc.
Secondary derived proteins: These derived proteins are produced from larger protein molecules as a result of hydrolysis of the peptide bonds.
Because of hydrolysis, these are smaller than the original proteins. For example, proteins are converted into peptones within the stomach.
The secondary derived proteins are of the following types—
Proteoses: These are water-soluble derived proteins, coagulable by heat, produced when acid hydrolysis proceeds beyond the level of metaproteins. Examples are albumose from albumin, globulose from globulin, etc.
Peptones: Proteose forms a precipitate with ammonium sulphate but peptone does not.
These are water soluble derived proteins, non-coagulable by heat, produced by enzyme catalysed reaction or acid hydrolysis as it proceeds beyond the level of proteoses.
Classification based on the presence of essential amino acids: Based on the presence of essential amino acids in their structure, proteins are classified into two types—
First-class or complete proteins: The proteins that contain essential amino acids, along with other non-essential amino acids, in proper quantities, are called first-class proteins. Example animal proteins.
Second-class or incomplete proteins: The proteins that contain essential amino acids in lesser quantities or may not contain any of the essential amino acids are called second-class proteins. Example plant proteins.
Classification on the basis of the number of polypeptide chains:
Based on the number of polypeptide chains, proteins are divided into two types—
Monomeric proteins: Proteins made of a single polypeptide chain are called monomeric proteins. Example monomeric G-protein.
Polymeric proteins: Proteins made of more than one polypeptide chain are called polymeric proteins.
- Example globin protein of haemoglobin.
- Biological importance of proteins
Proteins have enormous biological importance. These are—
Component of body structures: Proteins form the major building components of our body. Cell membranes and membranes of organelles are composed of lipids and proteins.
In order to give strength and protection to biological structures, various proteins serve as supporting filaments.
For example, tendons and cartilage are formed of collagen, ligaments contain elastin, etc.
Functional proteins: Enzymes, hormones, plasma proteins, pigments, etc., are important proteins which carry out different important cellular functions.
Source of energy: In the absence or shortage of carbohydrates and lipids, proteins act as a source of energy.
During fasting and disorders like diabetes, energy is utilised from the oxidation of proteins. The calorific value of proteins is 4.2kcal/g.
SDA of protein of thermoregulation: During protein metabolism about 30% extra heat is generated in our body as specific Dynamic Action and this heat is used to regulate our body temperature.
Growth, repair and protection: Proteins are essential for normal growth, protection and repair of damaged tissues and cells.
Cellular communication: Proteins help during cellular communication.
Immunity: Many proteins take part in defence mechanisms against pathogens. The immunoglobulins produced by lymphocytes of vertebrates, participate in the immunological functions.
Fibrinogen and thrombin are blood clotting proteins which repair damaged vascular systems. Various toxins and venoms produced by plants and animals have defensive functions.
Biological value of protein
The efficiency of a given protein, which supplies the nitrogen requirements to the animal body, is called the biological value of proteins. It actually depends on the dietary protein content which contains all essential amino acids.
Biological value of protein is determined by the formula—
\(\begin{aligned}& \text { Biological value } \\
& \text { of protein }
\end{aligned}=\frac{\mathrm{N}_2 \text { present in the food }}{\mathrm{N}_2 \text { absorbed in the body }} \times 100\)
Neural function: Proteins are also responsible for regulating certain functions of the nervous system.
Several proteins act as neurotransmitters which take part in the conduction of nerve impulses throughout the nervous system.
Encephalin, a pentapeptide, stimulates a type of nerve endings called nociceptors.
This leads to metabolic reactions within the body during severe chemical, mechanical or thermal stimulations.
Regulatory functions: Several functional proteins regulate the metabolism within the body. Proteins also regulate gene function.
Detoxification: There are several proteins which take part in detoxification, i.e., degradation and/or elimination of toxins, drugs, medicines or harmful chemicals. These proteins have antioxidative properties.
They help to maintain physiological balance in organisms.
Storage: Storage proteins serve as biological reserves of important metal ions and amino acids. Plants store such proteins in seeds. In animals, these proteins are found in egg whites and milk.
Contractile protein: Actin and myosin are filamentous proteins present in the skeletal muscles that help in contraction during movement and
locomotion.
Role in cellular functions: Spindle microtubules, cilia, and flagella are formed by polymerisation of protein tubulin dimers. Spindle microtubules take part in cell division.
Flagella and cilia help in the movement of bacteria, algae, etc. Microtubules form the tail of sperm in animals.