What Is Protein

| October 4, 2013
What Is Protein

To know what is protein could be of great importance in order to understand how the cells function. Proteins are one of the three most important classes of large biological molecules – nucleic acids, proteins and carbohydrates. Protein consists of one or more than one chain of amino acid residues. To understand what is protein, one must know what is their structure, how they are synthesized, which are their primarily functions and particularly how they participate in the metabolism processes. The protein structure defines the protein primary function and determines the uniqueness of each protein. The specificity of the protein structure is dictated by the nucleotide sequence of corresponding genes which defines the actual amino acid sequence and composition. The order of amino acids and their interaction  results in specific folding of the protein and determines a particular three-dimensional structure that defines its activity. Proteins have many different functions within living organisms on cellular, system and organism level – regulation of biological processes; molecular transport; catalyzing metabolic reactions; responding to stimuli and many others.

What Is Protein Bio-polymer?

The main building blocks of proteins are 20 L-α-amino acids. All proteins consist one or more polymer chains of amino acids. All amino acids which build proteins have the three common structural features:

  •  an α-carbon to which an amino group
  •  a carboxyl group,
  •  a variable side chain are bonded

The first two determine the building of a repeatable and identical bonds between the amino acids, called peptide bond. When it becomes part of a protein chain, a single amino acid is called an amino acid residue or just residue. The single residues are linked to each other with series of carbon, nitrogen, and oxygen atoms known as protein backbone. While the side chains of the standard amino acids are quite variable in chemical structures and properties, which determines the specifics of the physico-chemical properties of the amino acids residues. As proteins are linear biopolymers, their two ends could be easily distinguished – the protein end with a free carboxyl group is denoted as the carboxy- or C-terminus, while the other end with a free amino group is known as the amino- or N-terminus. The interaction of the amino acid side chains determines protein 3D-structure and its overall biochemical function.
The understand what is protein, polypeptide, or peptide one should capture the specifics of the term meaning and also to put in the particular context. The term protein is preferred in the cases when the complete biological molecule is in a stable conformation, while peptide is generally used when the molecule is a short amino acid oligomers (up to 20–30 residues) often without stable 3D-structure. The term polypeptide stays in between – a variable in length sequence of amino acids, which does not have a defined conformation.

Protein Structure

Most protein molecules form an unique 3D-structure, which in normal conditions is known as its native conformation. There are four levels of organization of the protein structure:
  • Primary structure - denotes the composition and the order of the amino acid in the protein sequence. Strictly from biochemical prospective the protein molecules could be classified as polyamides.
  • Secondary structure: formed by hydrogen bonds between spatially close to each other amino acid residues. The most common types are the alpha helix, beta sheet and u-turns. In most of the proteins the residues forming a secondary structure are residues of the same protein molecule, but in other rare cases (beta sheets of structural proteins) they could be residues from different polypeptide molecules.
  • Tertiary structure: defines the overall conformation of a single protein molecule. This is achieved with numerous spatial interactions between different secondary structures of the protein molecule stabilized by salt bridges, formation of a hydrophobic core, hydrogen bonds, disulfide bonds, and some times by post-translational modifications. The tertiary structure is what defines the basic protein function, as it determines specific regions with particular phisico-chemical and biochemical activity.
  • Quaternary structure: the overall protein structure is formed when several protein molecules (called protein subunits) form and function as a single protein complex.
In the normal conditions of the biological systems, proteins could not be considered as rigid molecules - they switch between several related structures (called conformations) while they perform their biological functions. The transitions between the different structures are known also as "conformational changes". The conformational changes could be caused by the binding of a substrate molecule, activator or inhibitor to an specific site of an enzyme, or when physical region of the protein molecule is involved in chemical catalysis. Based on the overall form of their native tertiary structures, proteins can be classified into three main types: globular, fibrous and membrane proteins. Most of the globular proteins are soluble and function as enzymes. Fibrous usually have structural functions - they can be a major component of connective tissue, such as collagen; or like keratin, which is a  component of nails and hair. Usually membrane proteins serve as receptors or trans-membrane channels for polar molecules to pass through the cellular membrane.

What Is Protein Synthesis

The process of protein synthesis assembles the polypeptide molecules from amino acids. The actual composition and order of the amino acids in the polypeptide chain is encoded in genes. The genetic code is based on nucleotide triple sets called codons as each codon codes for a specific an amino acid. For each amino acid, there is more than one codon, because nucleic acids have four different nucleotides, which make 64 possible codons. The information encoded in genes as part of the DNA are first transcribed by RNA polymerase and other enzymes into pre-messenger RNA (mRNA). Using various types of post-transcriptional modification, most of the organisms process the pre-mRNA to form the mature mRNA, which can then be used as a pattern for protein synthesis by the ribosomes. The process of protein synthesis from an mRNA is also known as translation.

What Is Protein Function

Proteins are among the main functional units within the cell, as they perform the functions encoded in genes. The complete set of proteins expressed in a particular cell or cell type is forms its proteome. The overall protein function has 3 main components:
  •  molecular function
  •  participation in biological process
  •  cellular localization
Speaking simple, the function of a protein is defined when it is known what is its molecular function, in which biological processes the protein applies this molecular function and in which particular cellular localization they perform this function. Some of the main protein functions are dependent of the their ability to bind with other molecules specifically. Proteins have one or more regions responsible for binding another molecule, called binding site or "pocket". Proteins can bind to proteins and other macromolecules as well as to small-molecules. In case when proteins bind specifically to other molecules of the same type, they oligomerize and form fibrils, which is quite common for the structural proteins. Based on the protein main functional characteristics and their participation in major biological processes, we can distinguish the following main protein types:
  • Enzymes are the most abundant and best-known type of proteins in the cell. They catalyze different biochemical reactions in the cell which are part of major biological processes. The enzyme molecules usually bind highly specific to their substrates and catalyze only one or, rarely, a few biochemical reactions.
  • Cell signaling and ligand binding - Many proteins participate in the process of cell signaling and signal transduction. Some proteins called as hormones, such as insulin, transmit signals from the cell in which they were synthesized to other distant cells, tissues and organs. There are some membrane proteins receptors which primary function is to bind an external to the cell signaling molecule and induce a response in the cell.
  • Antibodies are proteins, which in the adaptive immune response have the main function to bind foreign substances, called antigens, and initiate their destruction. Antibodies are secreted into the extracellular matrix or anchored in the B-cells cellular membranes (plasma cells).
  • Transport proteins bind specific small molecules and transfer them to other locations in the body. A classical example of a transport protein is haemoglobin, which transports oxygen from the lungs to other organs and tissues in all vertebrates. Transport proteins are required to have a high binding affinity when their ligand is abundant and to release the ligand when it is in low concentrations in the target location.
  • Trans-membrane proteins can also serve as ligand transport proteins that alter the permeability of the cell membrane to small molecules and ions. The membrane alone has a hydrophobic core through which polar or charged molecules cannot diffuse.
  • Learning what is protein and how it functions is an important basis to understand how the cells and the organism maintain the main biological processes.

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