Protein structure molecule

Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers – specifically polypeptides – formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer may also be called a residue indicating a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations driven by a number of non-covalent interactions such as hydrogen bonding, ionic interactions, Van der Waals forces, and hydrophobic packing. To understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. This is the topic of the scientific field of structural biology, which employs techniques such as X-ray crystallography, NMR spectroscopy, and dual polarisation interferometry to determine the structure of proteins.

Protein structures range in size from tens to several thousand amino acids. By physical size, proteins are classified as nanoparticles, between 1–100 nm. Very large aggregates can be formed from protein subunits. For example, many thousands of actin molecules assemble into a microfilament.

A protein generally undergo reversible structural changes in performing its biological function. The alternative structures of the same protein are referred to as different conformational isomers, or simply, conformations, and transitions between them are called conformational changes.

Primary structure

The primary structure of a protein refers to the sequence of amino acids in the polypeptide chain. The primary structure is held together by peptide bonds that are made during the process of protein biosynthesis. The two ends of the polypeptide chain are referred to as the carboxyl terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the free group on each extremity. Counting of residues always starts at the N-terminal end (NH₂-group), which is the end where the amino group is not involved in a peptide bond. The primary structure of a protein is determined by the gene corresponding to the protein. A specific sequence of nucleotides in DNA is transcribed into mRNA, which is read by the ribosome in a process called translation. The sequence of amino acids in insulin was discovered by Frederick Sanger, establishing that proteins have defining amino acid sequences. The sequence of a protein is unique to that protein, and defines the structure and function of the protein. The sequence of a protein can be determined by methods such as Edman degradation or tandem mass spectrometry. Often, however, it is read directly from the sequence of the gene using the genetic code. It is strictly recommended to use the words " amino acid residues" when discussing proteins because when a peptide bond is formed, a water molecule is lost, and therefore proteins are made up of amino acid residues. Post-translational modification such as phosphorylations and glycosyla-tions are usually also considered a part of the primary structure, and cannot be read from the gene. For example, insulin is composed of 51 amino acids in 2 chains. One chain has 31 amino acids, and the other has 20 amino acids.

Secondary structure

Secondary structure refers to highly regular local sub-structures on the actual polypeptide backbone chain. Two main types of secondary structure, the α -helixand the β -strand or β -sheets, were suggested in 1951 by Linus Pauling et al. These secondary structures are defined by patterns of hydrogen bonds between the main-chain peptide groups. They have a regular geometry, being constrained to specific values of the dihedral angles ψ and φ on the Ramachandran plot. Both the α -helix and the β -sheet represent a way of saturating all the hydrogen bond donors and acceptors in the peptide backbone. Some parts of the protein are ordered but do not form any regular structures. They should not be confused with random coil, an unfolded polypeptide chain lacking any fixed three-dimensional structure. Several sequential secondary structures may form a " supersecondary unit".

Tertiary structure

Tertiary structure refers to the three-dimensional structure of monomeric and multimeric protein molecules. The α -helixes and β -pleated-sheets are folded into a compact globular structure. The folding is driven by the non-specific hydrophobic interactions, the burial of hydrophobic residues from water, but the structure is stable only when the parts of a protein domain are locked into place by specific tertiary interactions, such as salt bridges, hydrogen bonds, and the tight packing of side chains and disulfide bonds. The disulfide bonds are extremely rare in cytosolic proteins, since the cytosol (intracellular fluid) is generally a reducingenvironment.

Quaternary structure

Quaternary structure is the three-dimensional structure consisting of the aggregation of two or more individual polypeptide chains (subunits) that operate as a single functional unit (multimer). The resulting multimer is stabilized by the same non-covalent interactions and disulfide bonds as in tertiary structure. There are many possible quaternary structure organisations. Complexes of two or more polypeptides (i.e. multiple subunits) are called multimers. Specifically it would be called a dimer if it contains two subunits, a trimer if it contains three subunits, a tetramer if it contains four subunits, and a pentamer if it contains five subunits. The subunits are frequently related to one another by symmetry operations, such as a 2-fold axis in a dimer. Multimers made up of identical subunits are referred to with a prefix of " homo-" (e.g. a homotetramer) and those made up of different subunits are referred to with a prefix of " hetero-", for example, a heterotetramer, such as the two alpha and two beta chains of hemoglobin.

C onclusion

Biochemistry, study of the chemical substances and processes that occur in plants, animals, and microorganisms and of the changes they undergo during development and life. It deals with the chemistry of life, and as such it draws on the techniques of analytical, organic, and physical chemistry, as well as those of physiologists concerned with the molecular basis of vital processes. All chemical changes within the organism-either the degradation of substances, generally to gain necessary energy, or the buildup of complex molecules necessary for life processes-are collectively termed metabolism. These chemical changes depend on the action of organic catalysts known as enzymes, and enzymes, in turn, depend for their existence on the genetic apparatus of the cell. It is not surprising, therefore, that biochemistry enters into the investigation of chemical changes in disease, drug action, and other aspects of medicine, as well as in nutrition, genetics, and agriculture.

The term biochemistry is synonymous with two somewhat older terms: physiological chemistry and biological chemistry. Those aspects of biochemistry that deal with the chemistry and function of very large molecules (e.g., proteins and nucleic acids) are often grouped under the term molecular biology. Biochemistry is a young science, having been known under that term only since about 1900. Its origins, however, can be traced much further back; its early history is part of the early history of both physiology and chemistry.

L iterature used

· Peet, Alisa (2012). Marks, Allan; Lieberman Michael A., eds. Marks' Basic Medical Biochemistry (Lieberman, Marks's Basic Medical Biochemistry) (4th ed.). ISBN 978-1-60831-572-7.

· Rayner-Canham, Marelene F.; Rayner-Canham, Marelene; Rayner-Canham, Geoffrey (2005). Women in Chemistry: Their Changing Roles from Alchemical Times to the Mid-Twentieth Century. Chemical Heritage Foundation. ISBN 978-0-941901-27-7.

· Rojas-Ruiz, Fernando A.; Vargas-Mé ndez, Leonor Y.; Kouznetsov, Vladimir V. (2011). " Challenges and Perspectives of Chemical Biology, a Successful Multidisciplinary Field of Natural Sciences". Molecules. 16 (3): 2672–2687. doi: 10.3390/molecules16032672. PMC 6259834. PMID 21441869.

· Saenger, Wolfram (1984). Principles of Nucleic Acid Structure. New York: Springer-Verlag. ISBN 978-0-387-90762-8.

· Slabaugh, Michael R.; Seager, Spencer L. (2013). Organic and Biochemistry for Today (6th ed.). Pacific Grove: Brooks Cole. ISBN 978-1-133-60514-0.

 

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