A leucine zipper is a common three-dimensional structural motif in proteins. They were first described by Landschulz and collaborators in 1988 when they found that an enhancer binding protein had a characteristic 30-amino acid segment and the display of these amino acid sequences on an idealized alpha helix revealed a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns; the polypeptide segments containing these periodic arrays of leucine residues were proposed to exist in an alpha-helical conformation and the leucine side chains from one alpha helix interdigitate with those from the alpha helix of a second polypeptide, facilitating dimerization. Leucine zippers are a dimerization domain of the bZIP class of eukaryotic transcription factors; the bZIP domain is 60 to 80 amino acids in length with a conserved DNA binding basic region and a more diversified leucine zipper dimerization region. The leucine zipper is a common three-dimensional structural motif in proteins and it has that name because leucines occur every seven amino acids in the dimerization domain.
The localization of the leucines are critical for the DNA binding to the proteins. Leucine zippers are present in both eukaryotic and prokaryotic regulatory proteins, but are a feature of eukaryotes, they can be annotated as ZIPs, ZIP-like motifs have been found in proteins other than transcription factors and are thought to be one of the general protein modules for protein–protein interactions. The mechanism of transcriptional regulation by bZIP proteins has been studied in detail. Most bZIP proteins show high binding affinity for the ACGT motifs, which include CACGTG, GACGTC, TACGTA, AACGTT, a GCN4 motif, namely TGATCA. A small number of bZIP factors such as OsOBF1 can recognize palindromic sequences. However, the others, including LIP19, OsZIP-2a, OsZIP-2b, do not bind to DNA sequences. Instead, these bZIP proteins form heterodimers with other bZIPs to regulate transcriptional activities. Leucine zipper is created by the dimerization of two specific alpha helix monomers bound to DNA; the bZIP interacts with the DNA via basic, amine residues (see basic amino acids in of certain amino acids in the "basic" domain, such as lysines and arginines.
These basic residues interact in the major groove of the DNA, forming sequence-specific interactions. The leucine zipper is formed by amphipathic interaction between two ZIP domains; the ZIP domain is found in the alpha-helix of each monomer, contains leucines, or leucine-like amino acids. These amino acids are spaced out in each region's polypeptide sequence in such a way that when the sequence is coiled in a 3D alpha-helix, the leucine residues line up on the same side of the helix; this region of the alpha-helix- containing the leucines which line up- is called a ZIP domain, leucines from each ZIP domain can weakly interact with leucines from other ZIP domains, reversibly holding their alpha-helices together. When these alpha helices dimerize, the zipper is formed; the hydrophobic side of the helix forms a dimer with itself or another similar helix, burying the non-polar amino acids away from the solvent. The hydrophilic side of the helix interacts with the water in the solvent. Leucine zipper domains are considered a subtype of coiled coils, which are built by two or more alpha helices that are wound around each other to form a supercoil.
Coiled coils contain 3- and 4-residue repeats whose hydrophobicity pattern and residue composition is compatible with the structure of amphipathic alpha-helices. The alternating three- and four-residue sequence elements constitute heptad repeats in which the amino acids are designated from a’ to g’, whereas residues in positions a and d are hydrophobic and form a zigzag pattern of knobs and holes that interlock with a similar pattern on another strand to form a tight-fitting hydrophobic core. In the case of leucine zippers, leucines are predominant at the d position of the heptad repeat; these residues pack against each other every second turn of the alpha-helices, the hydrophobic region between two helices is completed by residues at the a positions, which are frequently hydrophobic. They are referred to as coiled coils. If, the case they are annotated in the “domain” subsection, which would be the bZIP domain. Leucine zipper regulatory proteins include c-fos and c-jun, important regulators of normal development, as well as myc family members including myc and mxd1.
If they are overproduced or mutated in a vital area, they may generate cancer. Leucine+zippers at the US National Library of Medicine Medical Subject Headings
A reverse transcriptase is an enzyme used to generate complementary DNA from an RNA template, a process termed reverse transcription. Reverse transcriptases are used by retroviruses to replicate their genomes, by retrotransposon mobile genetic elements to proliferate within the host genome, by eukaryotic cells to extend the telomeres at the ends of their linear chromosomes, by some non-retroviruses such as the hepatitis B virus, a member of the Hepadnaviridae, which are dsDNA-RT viruses. Retroviral RT has three sequential biochemical activities: RNA-dependent DNA polymerase activity, ribonuclease H, DNA-dependent DNA polymerase activity. Collectively, these activities enable the enzyme to convert single-stranded RNA into double-stranded cDNA. In retroviruses and retrotransposons, this cDNA can integrate into the host genome, from which new RNA copies can be made via host-cell transcription; the same sequence of reactions is used in the laboratory to convert RNA to DNA for use in molecular cloning, RNA sequencing, polymerase chain reaction, or genome analysis.
Reverse transcriptases were discovered by Howard Temin at the University of Wisconsin–Madison in RSV virions and independently isolated by David Baltimore in 1970 at MIT from two RNA tumour viruses: R-MLV and again RSV. For their achievements, both shared the 1975 Nobel Prize in Medicine. Well studied reverse transcriptases include: HIV-1 reverse transcriptase from human immunodeficiency virus type 1 has two subunits, which have respective molecular weights of 66 and 51 kDa. M-MLV reverse transcriptase from the Moloney murine leukemia virus is a single 75 kDa monomer. AMV reverse transcriptase from the avian myeloblastosis virus has two subunits, a 63 kDa subunit and a 95 kDa subunit. Telomerase reverse transcriptase; the enzymes are encoded and used by viruses that use reverse transcription as a step in the process of replication. Reverse-transcribing RNA viruses, such as retroviruses, use the enzyme to reverse-transcribe their RNA genomes into DNA, integrated into the host genome and replicated along with it.
Reverse-transcribing DNA viruses, such as the hepadnaviruses, can allow RNA to serve as a template in assembling and making DNA strands. HIV infects humans with the use of this enzyme. Without reverse transcriptase, the viral genome would not be able to incorporate into the host cell, resulting in failure to replicate. Reverse transcriptase creates double-stranded DNA from an RNA template. In virus species with reverse transcriptase lacking DNA-dependent DNA polymerase activity, creation of double-stranded DNA can be done by host-encoded DNA polymerase δ, mistaking the viral DNA-RNA for a primer and synthesizing a double-stranded DNA by similar mechanism as in primer removal, where the newly synthesized DNA displaces the original RNA template; the process of reverse transcription is error-prone, it is during this step that mutations may occur. Such mutations may cause drug resistance. Retroviruses referred to as class VI ssRNA-RT viruses, are RNA reverse-transcribing viruses with a DNA intermediate.
Their genomes consist of two molecules of positive-sense single-stranded RNA with a 5' cap and 3' polyadenylated tail. Examples of retroviruses include the human immunodeficiency virus and the human T-lymphotropic virus. Creation of double-stranded DNA occurs in the cytosol as a series of these steps: Lysyl tRNA acts as a primer and hybridizes to a complementary part of the virus RNA genome called the primer binding site or PBS. Reverse transcriptase adds DNA nucleotides onto the 3' end of the primer, synthesizing DNA complementary to the U5 and R region of the viral RNA. A domain on the reverse transcriptase enzyme called RNAse H degrades the U5 and R regions on the 5’ end of the RNA; the tRNA primer "jumps" to the 3’ end of the viral genome, the newly synthesised DNA strands hybridizes to the complementary R region on the RNA. The complementary DNA added in is further extended; the majority of viral RNA is degraded by RNAse H. Synthesis of the second DNA strand begins; the tRNA primer leaves and a "jump" happens.
The PBS from the second strand hybridizes with the complementary PBS on the first strand. Both strands are extended to form a complete double-stranded DNA copy of the original viral RNA genome, which can be incorporated into the host's genome by the enzyme integrase. Creation of double-stranded DNA involves strand transfer, in which there is a translocation of short DNA product from initial RNA-dependent DNA synthesis to acceptor template regions at the other end of the genome, which are reached and processed by the reverse transcriptase for its DNA-dependent DNA activity. Retroviral RNA is arranged in 5’ terminus to 3’ terminus; the site where the primer is annealed to viral RNA is called the primer-binding site. The RNA 5’end to the PBS site is called U5, the RNA 3’ end to the PBS is called the leader; the tRNA primer is unwound between 14 and 22 nucleotides and forms a base-paired duplex with the viral RNA at PBS. The fact that the PBS is located near the 5’ terminus of viral RNA is unusual because reverse transcriptase synthesize DNA from 3’ end of the primer in the 5’ to 3’ direction.
Therefore, the primer and reverse transcriptase must be relocated to 3’ end of viral RNA. In order to accomplish this reposition, multiple steps and various enzymes including DNA polymerase, ribonuclease H and polynucleotide unwinding are needed; the HIV reverse tr
Fibrin is a fibrous, non-globular protein involved in the clotting of blood. It is formed by the action of the protease thrombin on fibrinogen; the polymerized fibrin together with platelets forms a hemostatic clot over a wound site. When the lining of a blood vessel is broken, platelets are attracted forming a platelet plug; these platelets have thrombin receptors on their surfaces that bind serum thrombin molecules which in turn convert soluble fibrinogen in the serum into fibrin at the wound site. Fibrin forms long strands of tough insoluble protein. Factor XIII completes the cross-linking of fibrin so that it contracts; the cross-linked fibrin forms a mesh atop the platelet plug. Excessive generation of fibrin due to activation of the coagulation cascade leads to thrombosis, the blockage of a vessel by an agglutination of red blood cells, polymerized fibrin and other components. Ineffective generation or premature lysis of fibrin increases the likelihood of a hemorrhage. Dysfunction or disease of the liver can lead to a decrease in the production of fibrin's inactive precursor, fibrinogen, or to the production of abnormal fibrinogen molecules with reduced activity.
Hereditary abnormalities of fibrinogen are both quantitative and qualitative in nature and include afibrinogenaemia, hypofibrinogenaemia, dysfibrinogenaemia, hypodysfibrinogenaemia. Reduced, absent, or dysfunctional fibrin is to render patients as hemophiliacs. Fibrin from different animal sources is glycosylated with complex type biantennary asparagine linked glycans. Variety is found in the degree of core fucosylation and in the type of sialic acid and galactose linkage; the image at the left is a crystal structure of the double-d fragment from human fibrin with two bound ligands. The experimental method used to obtain the image was X-ray diffraction, it has a resolution of 2.30 Å. The structure is made up of single alpha helices shown in red and beta sheets shown in yellow; the two blue structures are the bound ligands. The chemical structures of the ligands are Ca2+ ion, alpha-D-mannose, D-glucosamine. D-dimer Fibrin glue Fibrin scaffold Fibrinolysis TGW1916.net, Defibrinated blood harvested from sheep Fibrin: Molecule of the Month, by David Goodsell, RCSB Protein Data Bank
International Standard Serial Number
An International Standard Serial Number is an eight-digit serial number used to uniquely identify a serial publication, such as a magazine. The ISSN is helpful in distinguishing between serials with the same title. ISSN are used in ordering, interlibrary loans, other practices in connection with serial literature; the ISSN system was first drafted as an International Organization for Standardization international standard in 1971 and published as ISO 3297 in 1975. ISO subcommittee TC 46/SC 9 is responsible for maintaining the standard; when a serial with the same content is published in more than one media type, a different ISSN is assigned to each media type. For example, many serials are published both in electronic media; the ISSN system refers to these types as electronic ISSN, respectively. Conversely, as defined in ISO 3297:2007, every serial in the ISSN system is assigned a linking ISSN the same as the ISSN assigned to the serial in its first published medium, which links together all ISSNs assigned to the serial in every medium.
The format of the ISSN is an eight digit code, divided by a hyphen into two four-digit numbers. As an integer number, it can be represented by the first seven digits; the last code digit, which may be 0-9 or an X, is a check digit. Formally, the general form of the ISSN code can be expressed as follows: NNNN-NNNC where N is in the set, a digit character, C is in; the ISSN of the journal Hearing Research, for example, is 0378-5955, where the final 5 is the check digit, C=5. To calculate the check digit, the following algorithm may be used: Calculate the sum of the first seven digits of the ISSN multiplied by its position in the number, counting from the right—that is, 8, 7, 6, 5, 4, 3, 2, respectively: 0 ⋅ 8 + 3 ⋅ 7 + 7 ⋅ 6 + 8 ⋅ 5 + 5 ⋅ 4 + 9 ⋅ 3 + 5 ⋅ 2 = 0 + 21 + 42 + 40 + 20 + 27 + 10 = 160 The modulus 11 of this sum is calculated. For calculations, an upper case X in the check digit position indicates a check digit of 10. To confirm the check digit, calculate the sum of all eight digits of the ISSN multiplied by its position in the number, counting from the right.
The modulus 11 of the sum must be 0. There is an online ISSN checker. ISSN codes are assigned by a network of ISSN National Centres located at national libraries and coordinated by the ISSN International Centre based in Paris; the International Centre is an intergovernmental organization created in 1974 through an agreement between UNESCO and the French government. The International Centre maintains a database of all ISSNs assigned worldwide, the ISDS Register otherwise known as the ISSN Register. At the end of 2016, the ISSN Register contained records for 1,943,572 items. ISSN and ISBN codes are similar in concept. An ISBN might be assigned for particular issues of a serial, in addition to the ISSN code for the serial as a whole. An ISSN, unlike the ISBN code, is an anonymous identifier associated with a serial title, containing no information as to the publisher or its location. For this reason a new ISSN is assigned to a serial each time it undergoes a major title change. Since the ISSN applies to an entire serial a new identifier, the Serial Item and Contribution Identifier, was built on top of it to allow references to specific volumes, articles, or other identifiable components.
Separate ISSNs are needed for serials in different media. Thus, the print and electronic media versions of a serial need separate ISSNs. A CD-ROM version and a web version of a serial require different ISSNs since two different media are involved. However, the same ISSN can be used for different file formats of the same online serial; this "media-oriented identification" of serials made sense in the 1970s. In the 1990s and onward, with personal computers, better screens, the Web, it makes sense to consider only content, independent of media; this "content-oriented identification" of serials was a repressed demand during a decade, but no ISSN update or initiative occurred. A natural extension for ISSN, the unique-identification of the articles in the serials, was the main demand application. An alternative serials' contents model arrived with the indecs Content Model and its application, the digital object identifier, as ISSN-independent initiative, consolidated in the 2000s. Only in 2007, ISSN-L was defined in the
An antibody known as an immunoglobulin, is a large, Y-shaped protein produced by plasma cells, used by the immune system to neutralize pathogens such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of the pathogen, called an antigen, via the fragment antigen-binding variable region; each tip of the "Y" of an antibody contains a paratope, specific for one particular epitope on an antigen, allowing these two structures to bind together with precision. Using this binding mechanism, an antibody can tag a microbe or an infected cell for attack by other parts of the immune system, or can neutralize its target directly. Depending on the antigen, the binding may impede the biological process causing the disease or may activate macrophages to destroy the foreign substance; the ability of an antibody to communicate with the other components of the immune system is mediated via its Fc region, which contains a conserved glycosylation site involved in these interactions. The production of antibodies is the main function of the humoral immune system.
Antibodies are secreted by B cells of the adaptive immune system by differentiated B cells called plasma cells. Antibodies can occur in two physical forms, a soluble form, secreted from the cell to be free in the blood plasma, a membrane-bound form, attached to the surface of a B cell and is referred to as the B-cell receptor; the BCR is found only on the surface of B cells and facilitates the activation of these cells and their subsequent differentiation into either antibody factories called plasma cells or memory B cells that will survive in the body and remember that same antigen so the B cells can respond faster upon future exposure. In most cases, interaction of the B cell with a T helper cell is necessary to produce full activation of the B cell and, antibody generation following antigen binding. Soluble antibodies are released into the blood and tissue fluids, as well as many secretions to continue to survey for invading microorganisms. Antibodies are glycoproteins belonging to the immunoglobulin superfamily.
They constitute most of the gamma globulin fraction of the blood proteins. They are made of basic structural units—each with two large heavy chains and two small light chains. There are several different types of antibody heavy chains that define the five different types of crystallisable fragments that may be attached to the antigen-binding fragments; the five different types of Fc regions allow antibodies to be grouped into five isotypes. Each Fc region of a particular antibody isotype is able to bind to its specific Fc Receptor, thus allowing the antigen-antibody complex to mediate different roles depending on which FcR it binds; the ability of an antibody to bind to its corresponding FcR is further modulated by the structure of the glycan present at conserved sites within its Fc region. The ability of antibodies to bind to FcRs helps to direct the appropriate immune response for each different type of foreign object they encounter. For example, IgE is responsible for an allergic response consisting of mast cell degranulation and histamine release.
IgE's Fab paratope binds to allergic antigen, for example house dust mite particles, while its Fc region binds to Fc receptor ε. The allergen-IgE-FcRε interaction mediates allergic signal transduction to induce conditions such as asthma. Though the general structure of all antibodies is similar, a small region at the tip of the protein is variable, allowing millions of antibodies with different tip structures, or antigen-binding sites, to exist; this region is known as the hypervariable region. Each of these variants can bind to a different antigen; this enormous diversity of antibody paratopes on the antigen-binding fragments allows the immune system to recognize an wide variety of antigens. The large and diverse population of antibody paratope is generated by random recombination events of a set of gene segments that encode different antigen-binding sites, followed by random mutations in this area of the antibody gene, which create further diversity; this recombinational process that produces clonal antibody paratope diversity is called VJ or VJ recombination.
The antibody paratope is polygenic, made up of three genes, V, D, J. Each paratope locus is polymorphic, such that during antibody production, one allele of V, one of D, one of J is chosen; these gene segments are joined together using random genetic recombination to produce the paratope. The regions where the genes are randomly recombined together is the hyper variable region used to recognise different antigens on a clonal basis. Antibody genes re-organize in a process called class switching that changes the one type of heavy chain Fc fragment to another, creating a different isotype of the antibody that retains the antigen-specific variable region; this allows a single antibody to be used by different types of Fc receptors, expressed on different parts of the immune system. The first use of the term "antibody" occurred in a text by Paul Ehrlich; the term Antikörper appears in the conclusion of his article "Experimental Studies on Immunity", published in October 1891, which states that, "if two substances give rise to two different Antikörper they themselves must be different".
However, the term was not accepted and several other terms for antibody were proposed.
A kinesin is a protein belonging to a class of motor proteins found in eukaryotic cells. Kinesins move along microtubule filaments, are powered by the hydrolysis of adenosine triphosphate; the active movement of kinesins supports several cellular functions including mitosis and transport of cellular cargo, such as in axonal transport. Most kinesins walk towards the positive end of a microtubule, which, in most cells, entails transporting cargo such as protein and membrane components from the centre of the cell towards the periphery; this form of transport is known as anterograde transport. In contrast, dyneins are motor proteins that move toward the negative end of a microtubule in retrograde transport. Kinesins were discovered as MT-based anterograde intracellular transport motors; the founding member of this superfamily, kinesin-1, was isolated as a heterotetrameric fast axonal organelle transport motor consisting of 2 identical motor subunits and 2 "light chains" via microtubule affinity purification from neuronal cell extracts.
Subsequently, a different, heterotrimeric plus-end-directed MT-based motor named kinesin-2, consisting of 2 distinct KHC-related motor subunits and an accessory "KAP" subunit, was purified from echinoderm egg/embryo extracts and is best known for its role in transporting protein complexes along axonemes during cilium biogenesis. Molecular genetic and genomic approaches have led to the recognition that the kinesins form a diverse superfamily of motors that are responsible for multiple intracellular motility events in eukaryotic cells. For example, the genomes of mammals encode more than 40 kinesin proteins, organized into at least 14 families named kinesin-1 through kinesin-14. Members of the kinesin superfamily vary in shape but the prototypical kinesin-1 is a heterotetramer whose motor subunits form a protein dimer that binds two light chains; the heavy chain of kinesin-1 comprises a globular head at the amino terminal end connected via a short, flexible neck linker to the stalk – a long, central alpha-helical coiled coil domain – that ends in a carboxy terminal tail domain which associates with the light-chains.
The stalks of two KHCs intertwine to form a coiled coil. In most cases transported cargo binds to the kinesin light chains, at the TPR motif sequence of the KLC, but in some cases cargo binds to the C-terminal domains of the heavy chains; the head is the signature of kinesin and its amino acid sequence is well conserved among various kinesins. Each head has two separate binding sites: one for the microtubule and the other for ATP. ATP binding and hydrolysis as well as ADP release change the conformation of the microtubule-binding domains and the orientation of the neck linker with respect to the head. Several structural elements in the Head, including a central beta-sheet domain and the Switch I and II domains, have been implicated as mediating the interactions between the two binding sites and the neck domain. Kinesins are structurally related to G proteins, which hydrolyze GTP instead of ATP. Several structural elements are shared between the two families, notably the Switch I and Switch II domains.
In the cell, small molecules, such as gases and glucose, diffuse to. Large molecules synthesised in the cell body, intracellular components such as vesicles and organelles such as mitochondria are too large to be able to diffuse to their destinations. Motor proteins fulfill the role of transporting large cargo about the cell to their required destinations. Kinesins are motor proteins that transport such cargo by walking unidirectionally along microtubule tracks hydrolysing one molecule of adenosine triphosphate at each step, it was thought that ATP hydrolysis powered each step, the energy released propelling the head forwards to the next binding site. However, it has been proposed that the head diffuses forward and the force of binding to the microtubule is what pulls the cargo along. In addition viruses, HIV for example, exploit kinesins to allow virus particle shuttling after assembly. There is significant evidence. Motor proteins travel in a specific direction along a microtubule. Microtubules are polar.
It has been known that kinesin move cargo towards the positive end of a microtubule known as anterograde transport/orthograde transport. However, it has been discovered that in budding yeast cells kinesin Cin8 can move toward the negative end as well, or retrograde transport; this means, kinesin has the novel ability to switch directionality. Kinesin, so far, has only been shown to move toward the negative end when in a group, with motors sliding in the antiparallel direction in an attempt to separate microtubules; this dual directionality has been observed in identical conditions where free Cin8 molecules move towards the minus end, but cross-linking Cin8 move toward the plus ends of each cross-linked microtubule. One specific study tested the speed at which Cin8 motors moved, their results yielded a range of about 25-55nm/s, in the direction of the spindle poles. On an individual basis it has been found that through the use of ionic conditions Cin8 motors can become as fast as 380nm/s, a notable jump.
This tells us that Cin 8 can change directions on a microtubule, in turn led to the plus end movement of kinesin on a microtubule. It is suggested that this unique ability
Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, transporting molecules from one location to another. Proteins differ from one another in their sequence of amino acids, dictated by the nucleotide sequence of their genes, which 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 20–30 residues, are considered to be proteins and are 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, encoded in the genetic code.
In general, the genetic code specifies 20 standard amino acids. Shortly after or during synthesis, the residues in a protein are chemically modified by post-translational modification, which alters the physical and chemical properties, stability and the function of the proteins. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can work together to achieve a particular function, they associate to form stable protein complexes. Once formed, proteins only exist for a certain period and are degraded and recycled by the cell's machinery through the process of protein turnover. A protein's lifespan covers a wide range, they can exist for years with an average lifespan of 1 -- 2 days in mammalian cells. Abnormal or misfolded proteins are degraded more 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 every process within cells.
Many proteins are enzymes that are vital to metabolism. Proteins 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. Other proteins are important in cell signaling, immune responses, cell adhesion, 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 variety of techniques such as ultracentrifugation, precipitation and chromatography. Methods used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance and mass spectrometry. 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, 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 CO–NH amide moiety into a fixed conformation. The side chains of the standard amino acids, detailed in the list of standard amino acids, have a great variety of chemical structures and properties; 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, the linked series of carbon and oxygen atoms are known as the main chain or protein backbone; 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 coplanar. The other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone; 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 words protein and peptide are a little ambiguous and can overlap in meaning. Protein is used to refer to the complete biological molecule in a stable conformation, whereas peptide is reserved for a short amino acid oligomers lacking a stable three-dimensional structure. However, the boundary between the two is not well defined and lies near 20–30 residues. Polypeptide can refer to any single linear chain of amino acids regardless of length, but implies an absence of a defined conformation. Proteins can interact with many types of molecules, including with other proteins, with lipids, with carboyhydrates, with DNA, it has been estimated. 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 pro