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Protein

Proteins are biomolecules comprised of amino acid residues joined together by peptide bonds. Biomolecules are molecules produced by living organisms. As such, most of them are organic molecules. Proteins are one of the major biomolecules. The others are carbohydrates (especially, polysaccharides), lipids, and nucleic acids. Proteins can be distinguished from fats and carbohydrates by containing nitrogen. Other molecular components are carbon, hydrogen, oxygen, sulfur, and sometimes phosphorus. Proteins differ from each other through their amino acid composition and sequence, location, function, and spatial configuration. The amino acids in a protein are determined by the nucleotide sequence of the gene coding for them. The amino acid sequence often determines how the protein folds into a particular 3D configuration. This, in turn, determines the activity and function of the protein. In biological systems, proteins have varying functions. Some of them are structural materials (e.g. keratin) whereas others act as enzymes. Other functions include transport (e.g. hemoglobin), immunity (e.g. antibodies), and regulation.

Protein definition

An example of a 3D structure of a protein. In this image, the protein is a myoglobin, a protein in red skeletal muscle.

In biology and biochemistry, a protein is a biomolecule or a macromolecule characterized by being comprised of chain(s) of amino acidss that are joined together by peptide bonds. In nutrition, a protein refers to a food rich in biomolecular proteins and provide about 4 kcal/gram food energy.

Etymology

The term protein came from French protéine, from Late Greek prōteios, of the first quality, from Greek prōtos, meaning “first”.

Protein vs. peptide

A peptide is a compound consisting of amino acids connected by a peptide bond, particularly between the carboxyl group of one amino acid the amine group of another amino acid. When a peptide is comprised of two amino acids, it is called a dipeptide. A polypeptide is a peptide comprised of several amino acid residues forming an unbranched linear chain. A protein is comprised of polypeptides that carry out a particular function. Peptides that are less than 20 to 30 amino acid residues are often not considered as protein but an oligopeptide (short polypeptides).

Structure

Proteins are composed of polymers of amino acid residues. The amino acids are joined together by peptide bonds. Each protein is a linear polymer built from different amino acids. The type and the sequence of amino acids in a protein are specified by the DNA in the cell that produces them. The genetic code typically specifies for 20 standard amino acids. However, some organisms, such as archaea, have a genetic code that specifies for more. This sequence of amino acids is essential since it determines the overall structure and function of a protein. Some proteins can form a complex together with another protein. Others form a complex with other biomolecules other than the peptide. Some of these non-peptide groups in a protein are referred to as cofactors or prosthetic groups.
There are four distinct types of a protein structure: (1) primary structure, (2) secondary structure, (3) tertiary structure, and (4) quaternary structure. The primary structure pertains to the sequence of amino acids in a chain. The secondary structure of a protein refers to the regularly repeating local structures that are stabilized by hydrogen bonds. Examples of a secondary structure are α-helix and β-sheet. The tertiary structure (sometimes called fold) pertains to the spatial relationship of the secondary structures from one to another. It is often stabilized by nonlocal interactions, e.g. by disulfide bonds, salt bridges, and the formation of a hydrophobic core. This structure of the protein is what determines the fundamental function of the protein. The quaternary structure refers to the protein complex, i.e. when several polypeptide chains (sometimes referred to as protein subunits) constitute it. The tertiary and quaternary structures are often called conformations. The protein may transition from one structure to another and the transition between tertiary and quaternary is referred to as conformational change. Conformational changes may be induced for example when a substrate binds to a protein (particularly, an enzyme) at its active site. A protein domain is a segment of a protein that folds into distinct structural units.

Types

A protein may be classified based on its form and main functions: it can be a globular protein like most enzymes, fibrous protein which are for structural role, such as collagen, keratin, etc.; and membrane proteins that serve as receptors or channels for polar or charged molecule to pass through the cell membrane.

Biosynthesis

Protein synthesis is the creation of proteins. In biological systems, it is carried out inside the cell. In prokaryotes, it occurs in the cytoplasm. In eukaryotes, it initially occurs in the nucleus to create a transcript (mRNA) of the coding region of the DNA. The transcript leaves the nucleus and reaches the ribosomes for translation into a protein molecule with a specific sequence of amino acids.

Protein synthesis (also called protein biosynthesis when done by a life form) is a process of creating protein molecules. In biological systems, it involves amino acid synthesis, transcription, and translation. In amino acid synthesis, there is a set of biochemical processes that produce amino acids from carbon sources like glucose. Not all amino acids are produced by the body; other amino acids are obtained from diet. Within the cells, proteins are generated involving transcription and translation processes. Transcription is the process by which mRNA template, encoding the sequence of the protein in the form of a trinucleotide code, is transcribed from DNA to provide a template for translation. Translation is the process in which amino acids are linked together in a specific order according to the rules specified by the genetic code. It occurs in the cytoplasm where the ribosomes are located. It consists of four phases: (1) activation (the amino acid is covalently bonded to the tRNA), (2) initiation (the small subunit of the ribosome binds to 5′ end of mRNA with the help of initiation factors), (3) elongation (the next aminoacyl-tRNA in line binds to the ribosome along with GTP and an elongation factor), and (4) termination (the A site of the ribosome faces a stop codon). Following protein synthesis are events, e.g. proteolysis, post-translational modification, and protein folding.
Proteins abound in any cell. Eschericia coli, for example, contains about 2 million proteins. A human cell may contain about 1 to 3 billion proteins.(1) The number, though, may vary based on the cell’s activity.

Degradation

The lifespan of proteins varies depending on its kind. Some proteins are degraded after few minutes of production; others remain for years. Misfolded proteins are degraded at once to prevent them from causing damage due to their instability and dysfunctional nature. The cell may degrade or recycle them through protein turnover. Proteins may be degraded in proteasomes, i.e. cytoplasmic complexes that digest worn-out or misfolded proteins tagged with ubiquitin. In eukaryotes, another site of protein degradation is the lysosome. Lysosomes contain proteases that digest endocytosed proteins.

Biological functions

Proteins have several functions. Some of them are a structural component (e.g. keratin in hair, actin and myosin in muscle, etc.). Many proteins are enzymes. They catalyze various biochemical reactions and therefore are essential to metabolism. Other vital roles of proteins in biological system are as follows: as transporters (e.g. hemoglobin), as antibodies, and as regulators of gene expression. Not all proteins are biosynthesized de novo. They may be acquired through diet. In fact, animals require a protein diet to obtain the essential amino acids that they cannot synthesize on their own. Thus, in this regard, dietary proteins serve as a food source.

Related terms

See also

  • Amino acid
  • Enzyme
  • Biomolecule
  • References and further reading

    1. Milo, R. (December 2013). “What is the total number of protein molecules per cell volume? A call to rethink some published values”. BioEssays. 35 (12): 1050–55. doi:10.1002/bies.201300066. PMC 3910158. PMID 24114984.
    2. Types of Proteins. (2016). Retrieved from Utah.edu website: https://learn.genetics.utah.edu/content/basics/proteintypes/
    3. What are Proteins? (2016). Retrieved from Utah.edu website: https://learn.genetics.utah.edu/content/basics/proteins/
    4. Protein. (2012, September 18). Retrieved from The Nutrition Source website: https://www.hsph.harvard.edu/nutritionsource/what-should-you-eat/protein/
    5. Proteins. (2013). Retrieved from Msu.edu website: https://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/proteins.htm

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