What are Proteins?

Proteins are the most pervasive biological macromolecules and are present in all cells. It’s also the most flexible organic molecule discovered in biological systems, and it is available in thousands of different variations in sizes, varying from small peptides to huge polymers. Peptide bonds hold the polymers of amino acids together covalently. Proteins are made up of the twenty naturally available amino acids. As a consequence, proteins are made up of amino acid polymers.

Properties of Proteins

Solubility in water.

• The relationship between proteins and water is intricate.
• One important aspect of the secondary structure of proteins is the interaction of peptide bonds with water via hydrogen bonds.
• Hydrogen bonds can also form between proteins (alpha and beta structures) and water. The protein-rich static ball is more soluble than the helical variants.
• While the hydrophobic chains and radicals in the tertiary structure prefer to engage with one another within the molecule, water induces the hydrophilic chains and radicals to align with the outside of the molecule (hydrophobic effect).

Renaturation as well as Denaturation

• Proteins can be denatured by substances, including heat and urea, that unroll polypeptide chains without causing the breakdown of peptide bonds.
• The denaturing agents disintegrate secondary and tertiary structures without changing the fundamental structure.
• Renaturation is when a denatured protein returns to its initial condition after the denaturing agent has been removed.

Some of the denaturing agents include:

Physical agents Three physical agents are pH, radiation, and heat.

Chemical agents  Detergents, organic solvents, and urea solutions are examples of chemicals that assist proteins in forming new hydrogen bonds.

Coagulation

• Coagulum, insoluble clumps, are produced as a result of heat-induced protein denature. Albumins and globulins are two examples of tiny fractions of proteins that can coagulate under heat.

Isoelectric Point

• The isoelectric point is the pH value where the ratio of positive to negative charges is equal, and the total charge on the amino acid is zero (pI).
• Proteins are isolated using the fact that at this stage when exposed to an electric field, neither the anode nor the cathode is moved by the proteins.

Molecular Weights of Proteins

• The average molecular weight of an amino acid is approximately 110 daltons.
• The approximative molecular weight of a protein is obtained by multiplying the total number of amino acids in that protein by 110 daltons.
• Since the content of amino acids varies among proteins, so do their molecular weights.
• The molecular weights of the proteins vary a lot, from as little as 12.40 Da (Cytochrome C) up to 450.000 Da (Ferritin horse).

Posttranslational modifications

• It happens after the ribosome has finished producing the protein.
• Phosphorylation modifies the charge and interactions between amino acid residues; glycosylation, ADP ribosylation, methylation, hydroxylation, and acetylation, which also changes the three-dimensional structure and the protein’s ability to perform its function.

Chemical Properties of Proteins

1. Biuret test

A violet color development after adding 2 ml of the test solution to an equivalent amount of 10% NaOH and one drop of 10% CuSO4 solution shows the existence of peptide linkage.

2. Ninhydrin test

The production of a violet hue after heating 1 ml of protein solution with 1 ml of Ninhydrin solution shows the existence of -amino acids.

Protein Structure

• A protein’s three-dimensional shape is defined by the linear arrangement of its amino acid residues in a polypeptide chain, and its structure determines its activity.
• Every protein includes the elements carbon, hydrogen, oxygen, nitrogen, and sulfur. Certain proteins might additionally possess phosphorus, iodine, and minute amounts of metal ions such as copper, zinc, and manganese.
• 20 distinct types of amino acids may be found in proteins. Either amino acid contains a unique side chain in addition to an amine group and an acid group at each end.
• All amino acids have a common backbone, but each amino acid has a unique side chain.
• Four layers of the organization may be identified in the structure of proteins:

1. Primary Structure

• The fundamental makeup of a protein is the arrangement of amino acids along the polypeptide chain.
• Peptide bonds are used to connect amino acids.
• The charges on a polypeptide chain are exclusively caused by the N-terminal amino group, the C-terminal carboxyl group, and the side chains on amino acid residues since dissociable protons are not present in peptide bonds.
• The secondary levels of protein molecule organization are determined by the main structure.

2. Secondary Structure

• The side chain atoms are not involved in any of the several local conformations that make up the secondary structure.
• Secondary structures are produced by a repeated pattern of hydrogen bond formation between backbone atoms.
• As a consequence of a pattern of hydrogen bond creation that repeats itself, the secondary structure is composed of helices, sheets, and other folding patterns.

The secondary structure of a protein could be :

• Alpha-helix
• Beta-helix

The α-helix is a right-handed coiled strand.

• In a -helix, the side-chain substituents of the amino acid groups stretch outward.
• Between the hydrogen of the N-H group of the peptide bond located four amino acids below it in the helix and the oxygen of the C=O of each peptide bond in the strand, hydrogen bonds occur.
• The amino acids’ side-chain substitutes fit next to the N-H groups.
• In a ß-sheet, there is inter-strand rather than intra-strand hydrogen bonding (intra-strand).
• Pairs of strands are arranged in a sheet shape and are laid side by side.
• The amino hydrogens of the neighboring strand form a hydrogen bond with the carbonyl oxygens of the first strand.
• The two strands can be parallel or anti-parallel based on whether the N-terminus to C-terminus strand directions are similar or opposing.
• The anti-parallel ß-sheet is more stable because the hydrogen bonds are more aligned.

3. Tertiary Structure

• The tertiary structure of a protein refers to its overall three-dimensional form.
• A protein’s three-dimensional structure is produced through non-covalent interactions between amino acid residues, such as hydrogen bonds, electrostatic interactions, and hydrophobic contacts.
• Disulfide covalent bonds can also exist.
• It is produced through interactions between residues of amino acids which may be situated far apart from one another in the polypeptide chain’s basic sequence.
• In contrast to hydrophilic residues, hydrophobic amino acid residues prefer to build up inside globular proteins, where they inhibit water, whereas hydrophilic amino acid residues are frequently found on the surface and interact with water.

4. Quaternary Structure

• One or more subunits work together to generate a functional protein by utilizing similar forces that keep the tertiary structure in place, which is referred to as the quaternary structure.
• It is the physical configuration of the protein’s many polypeptide chain components.

Protein classification

Depending on their chemical makeup, structure, shape, and solubility, proteins are categorized as shown below:

1. Simple Proteins: The building blocks of basic proteins are amino acid residues. Only upon hydrolysis do these proteins liberate their individual amino acids. It is further divided into:

Keratin, elastin, and collagen are fibrous proteins.

Albumin, globulin, glutelin, and histones make up the globular protein.

2. Conjugated proteins: Conjugated proteins are proteins that have an additional non-protein moiety. For instance, metalloprotein, phosphoprotein, lipoprotein, and nucleoprotein.
3. Derived proteins: Proteins that have been degraded from simple and conjugated proteins are known as derived proteins. They might be:

Primary-derived proteins include proteins, metaproteins, and coagulated proteins.

Proteoses, albunoses, peptones, and peptides are examples of secondary-derived proteins.

Functions of Proteins

• Proteins serve a plethora of purposes and are essential for both development and repair. They are the most significant by-products of the information pathways and have a huge variety of biological roles.
• Amino acid-based proteins play a variety of functions in the body (e.g., as enzymes, structural components, hormones, and antibodies).
• They serve as structural elements, similar to the collagen in bones and the keratin in hair and nails.
• The molecular tools through which genetic information is expressed are proteins.
• Through hemoglobin and certain enzymes found in red blood cells, they carry out their functions in the transportation of oxygen and carbon dioxide.
• Through the plasma proteins, they contribute to the homeostatic regulation of the volume of the blood in circulation and the interstitial fluids.
• Through the action of thrombin, fibrinogen, and other protein factors, they contribute to blood coagulation.
• The use of protein antibodies serves as the body’s defense against pathogens.
• They carry out hereditary transmission through the cell nucleus’ nucleoproteins.
• These storing proteins include ovary albumin and glutelin.
• The contractile protein necessary for muscle contraction is myosin and actin.

References

• Smith, C. M., Marks, A. D., Lieberman, M. A., Marks, D. B., & Marks, D. B. (2005). Marks’ basic medical biochemistry: A clinical approach. Philadelphia: Lippincott Williams & Wilkins.
• Rodwell, V. W., Botham, K. M., Kennelly, P. J., Weil, P. A., & Bender, D. A. (2015). Harper’s illustrated biochemistry (30th ed.). New York, N.Y.: McGraw-Hill Education LLC.
• John W. Pelley, Edward F. Goljan (2011). Biochemistry. Third edition. Philadelphia: USA.
• https://chemistry.tutorvista.com/biochemistry/proteins.html
• http://www.biologydiscussion.com/proteins/proteins-definition-importance-and-classification-biochemistry/41903
• https://www.particlesciences.com/news/technical-briefs/2009/protein-structure.html
• http://www.biologydiscussion.com/proteins/proteins-functions-structure-properties-and-classification/16912