Chaperonins assist protein folding. Three possible representations of the three-dimensional structure of the protein triose phosphate isomerase. Left : All-atom representation colored by using atom type. Middle: Simplified representation illustrating the backbone conformation, colored by secondary structure. Right : Solvent-accessible surface representation colored by residue type (acidic residues red, basic residues blue, polar residues green, nonpolar residues white). Main article: Protein structure further information: Protein structure prediction Most proteins fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native conformation. 20 Although many proteins can fold unassisted, simply through the chemical properties of their amino acids, others require the aid of molecular chaperones to fold into their native states. 21 biochemists often refer to four distinct aspects of a protein's structure: 22 Primary structure : the amino acid sequence.
5 The largest known proteins are the titins, a component of the muscle sarcomere, with a molecular mass of almost 3,000 kda and a total length of almost 27,000 amino resume acids. 16 Chemical synthesis main article: Peptide synthesis Short proteins can also be synthesized chemically by a family of methods known as peptide synthesis, which rely on organic synthesis techniques such as chemical ligation to produce peptides in high yield. 17 Chemical synthesis allows for the introduction of non-natural amino acids into polypeptide chains, such as attachment of fluorescent probes to amino acid side chains. 18 These methods are useful in laboratory biochemistry and cell biology, though generally not for commercial applications. Chemical synthesis is inefficient for polypeptides longer than about 300 amino acids, and the synthesized proteins may not readily assume their native tertiary structure. Most chemical synthesis methods proceed from C-terminus to n-terminus, opposite the biological reaction. 19 Structure The crystal structure of the chaperonin, a huge protein complex. A single protein subunit is highlighted.
The rate of protein synthesis is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second. 15 The process of synthesizing a protein from an mrna template is known as translation. The mrna is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer rna molecule, which carries the amino acid corresponding to the codon it recognizes. The enzyme aminoacyl trna synthetase "charges" the trna molecules with the correct amino acids. The growing polypeptide is often termed the nascent chain. Proteins are always biosynthesized from N-terminus to c-terminus. 14 The size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass, which is normally reported in units of daltons (synonymous with atomic mass units or the derivative unit kilodalton (kDa). The average size of a protein increases from Archaea to bacteria to eukaryote (283, 311, 438 residues and 31, 34, 49 kda respecitvely) due to a bigger number of protein domains constituting proteins in higher organisms. 13 For instance, yeast proteins are on average 466 amino acids long and 53 kda in mass.
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10 The concentration of individual protein copies ranges from a few molecules per cell up to 20 million. 11 Not all genes coding proteins are expressed in most cells and their number depends on, for example, cell type and external stimuli. For instance, of the 20,000 or so proteins encoded by the human genome, only 6,000 are detected in lymphoblastoid cells. 12 Moreover, the number of proteins the genome party encodes correlates well with the organism complexity. Eukaryotes, bacteria, archaea and viruses have on average 15145, 3200, 2358 and 42 proteins respectively coded in their genomes. 13 Synthesis biosynthesis A ribosome produces a protein using mrna as template main article: Protein biosynthesis Proteins are assembled from amino acids using information encoded in genes.
Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein. The genetic code is a set of three-nucleotide sets called codons and each three-nucleotide combination designates an amino acid, for example aug ( adenine - uracil - guanine ) is the code for methionine. Because dna contains four nucleotides, the total number of possible codons is 64; hence, there is some redundancy in the genetic code, with some amino acids specified by more than one codon. 14 Genes encoded in dna are first transcribed into pre- messenger rna (mRNA) by proteins such as rna polymerase. Most organisms then process the pre-mrna (also known as a primary transcript ) using various forms of Post-transcriptional modification to form the mature mrna, which is then used as a template for protein synthesis by the ribosome. In prokaryotes the mrna may either be used as soon as it is produced, or be bound by a ribosome after having moved away from the nucleoid. In contrast, eukaryotes make mrna in the cell nucleus and then translocate it across the nuclear membrane into the cytoplasm, where protein synthesis then takes place.
4 The end with a free amino group is known as the n-terminus or amino terminus, whereas the end of the protein with a free carboxyl group is known as the c-terminus or carboxy terminus (the sequence of the protein is written from N-terminus. The words protein, polypeptide, and peptide are a little ambiguous and can overlap in meaning. Protein is generally used to refer to the complete biological molecule in a stable conformation, whereas peptide is generally reserved for a short amino acid oligomers often lacking a stable three-dimensional structure. However, the boundary between the two is not well defined and usually lies near 2030 residues. 5 Polypeptide can refer to any single linear chain of amino acids, usually regardless of length, but often implies an absence of a defined conformation.
Interactions Proteins can interact with many types of molecules, including with other proteins, with lipids, with carboyhydrates, and with dna. 6 7 8 9 Abundance in cells It has been estimated that average-sized bacteria contain about 2 million proteins per cell (e.g. Coli and Staphylococcus aureus ). Smaller bacteria, such as Mycoplasma or spirochetes contain fewer molecules, on the order of 50,000 to 1 million. By contrast, eukaryotic cells are larger and thus contain much more protein. For instance, yeast cells have been estimated to contain about 50 million proteins and human cells on the order of 1 to 3 billion.
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Main articles: biochemistry, amino acid, and Peptide bond Most proteins consist of linear polymers built from series of up to 20 different l-α- amino acids. All proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, and a variable side chain are bonded. Only proline differs from this basic structure as it contains an unusual ring to the n-end amine group, which forces the conh amide moiety into a fixed conformation. 1 The side chains of the standard amino acids, detailed in the list trunk of standard amino acids, have a great variety of chemical structures and properties; it is the combined effect of all of the amino acid side chains in a protein that ultimately determines. 2 The amino acids in a polypeptide chain are linked by peptide bonds. Once linked in the protein chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen, and oxygen atoms are known as the main chain or protein backbone. 3 The peptide bond has two resonance forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar. The other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone.
Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized. Digestion breaks the proteins down for use in the metabolism. Proteins may be purified from other cellular components using a rna variety of techniques such as ultracentrifugation, precipitation, electrophoresis, and chromatography ; the advent of genetic engineering has made possible a number of methods to facilitate purification. Methods commonly used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, x-ray crystallography, nuclear magnetic resonance and mass spectrometry. Contents biochemistry Chemical structure of the peptide bond (bottom) and the three-dimensional structure of a peptide bond between an alanine and an adjacent amino acid (top/inset). The bond itself is made of the chon elements.
attached, which can be called prosthetic groups or cofactors. Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. Once formed, proteins only exist for a certain period and are then degraded and recycled by the cell's machinery through the process of protein turnover. A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 12 days in mammalian cells. Abnormal or misfolded proteins are degraded more rapidly either due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. Many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape.
Proteins perform a vast array of functions within organisms, including catalysing mattress metabolic reactions, dna replication, responding to stimuli, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific three-dimensional structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 2030 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; however, in certain organisms the genetic code can include selenocysteine and—in certain archaea — pyrrolysine.
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This article is about a class of molecules. For protein as a nutrient, see. For other uses, see, protein (disambiguation). A representation of the 3D structure of the protein myoglobin showing turquoise α-helices. This protein was the first to have its structure solved. Towards the right-center among the coils, a prosthetic group called a heme group (shown in gray) with a bound oxygen molecule (red). Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues.