1.
Protein
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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, 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 rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds, 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 code specifies 20 standard amino acids, however. Sometimes proteins have non-peptide groups 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 period of time and are then degraded and recycled by the cells machinery through the process of protein turnover. A proteins lifespan is measured in terms of its half-life and covers a wide range and they can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly 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, 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, 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. Methods commonly used to study structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance. 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 structure as it contains an unusual ring to the N-end amine group. The amino acids in a chain are linked by peptide bonds. Once linked in the chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen. The peptide bond has two forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar
2.
Cell surface receptor
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Cell surface receptors are receptors that are embedded in the membranes of cells. They act in signaling by receiving extracellular molecules. They are specialized integral membrane proteins that allow communication between the cell and the extracellular space, in the process of signal transduction, ligand binding affects a cascading chemical change through the cell membrane. Transmembrane receptors are classified based on their tertiary structure. But, if the structure is yet undiscovered, then they can be classified based on experimentally verifiable membrane topology. The simplest polypeptide chains are found to cross the lipid bilayer once, while others, such as the G-protein coupled receptors, there are various kinds, such as glycoprotein and lipoprotein. Hundreds of different receptors are known and many more have yet to be studied, many membrane receptors include transmembrane proteins. Each cell membrane can have several kinds of receptor, in varying surface distribution. A specific receptor may also be distributed on different membrane surfaces, depending on the membrane sort. Since receptors usually cluster on the surface, the placement of every receptor on each membrane surface is heterogeneous. Two current models have been proposed to explain transmembrane receptors mechanism, dimerization, This dimerization model suggests that prior to ligand binding, receptors exist in a monomeric form. When contact occurs with a ligand, receptors bind together to form a dimer, prior to ligand binding, the extracellular protein loses flexibility while the intracellular portion gains it. Like any integral membrane protein, a receptor may be divided into three domains. The extracellular domain juts externally from the cell or organelle, if the polypeptide chain crosses the bilayer several times, the external domain comprises loops entwined through the membrane. By definition, a main function is to recognize and respond to a type of ligand. For example, a neurotransmitter, hormone, or atomic ions may bind to the extracellular domain as a ligand coupled to receptor. Klotho is an enzyme which effects a receptor to recognize the ligand, in the majority of receptors with known structures, transmembrane alpha helices constitute most of the transmembrane component. In certain receptors, such as the nicotinic receptor, the transmembrane domain forms a protein pore through the membrane
3.
DNA
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Deoxyribonucleic acid is a molecule that carries the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA and RNA are nucleic acids, alongside proteins, lipids and complex carbohydrates, most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are termed polynucleotides since they are composed of simpler units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases—cytosine, guanine, adenine, or thymine —a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two polynucleotide strands are bound together, according to base pairing rules, with hydrogen bonds to make double-stranded DNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison the total mass of the biosphere has been estimated to be as much as 4 trillion tons of carbon. The DNA backbone is resistant to cleavage, and both strands of the double-stranded structure store the same biological information and this information is replicated as and when the two strands separate. A large part of DNA is non-coding, meaning that these sections do not serve as patterns for protein sequences, the two strands of DNA run in opposite directions to each other and are thus antiparallel. Attached to each sugar is one of four types of nucleobases and it is the sequence of these four nucleobases along the backbone that encodes biological information. RNA strands are created using DNA strands as a template in a process called transcription, under the genetic code, these RNA strands are translated to specify the sequence of amino acids within proteins in a process called translation. Within eukaryotic cells DNA is organized into structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, eukaryotic organisms store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast prokaryotes store their DNA only in the cytoplasm, within the eukaryotic chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed, DNA was first isolated by Friedrich Miescher in 1869. DNA is used by researchers as a tool to explore physical laws and theories, such as the ergodic theorem. The unique material properties of DNA have made it an attractive molecule for material scientists and engineers interested in micro-, among notable advances in this field are DNA origami and DNA-based hybrid materials. DNA is a polymer made from repeating units called nucleotides
4.
Non-covalent interactions
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The chemical energy released in the formation of non-covalent interactions is typically on the order of 1-5 kcal/mol. Non-covalent interactions can be classified into different categories, such as electrostatic, π-effects, van der Waals forces, non-covalent interactions are critical in maintaining the three-dimensional structure of large molecules, such as proteins and nucleic acids. In addition, they are involved in many biological processes in which large molecules bind specifically but transiently to one another. These interactions also heavily influence drug design, crystallinity and design of materials, particularly for self-assembly, and, in general, for example, sodium fluoride involves the attraction of the positive charge on sodium with the negative charge on fluoride. These bonds are harder to break covalent bonds because there is a strong electrostatic interaction between oppositely charged ions. However, this interaction is easily broken upon addition to water. These interactions can also be seen in molecules with a charge on a particular atom. For example, the negative charge associated with ethoxide, the conjugate base of ethanol, is most commonly accompanied by the positive charge of an alkali metal salt such as the sodium cation. It is not a covalent bond, but instead is classified as a strong non-covalent interaction and it is responsible for why water is a liquid at room temperature and not a gas. In halogen bonding, a halogen atom acts as an electrophile, or electron-seeking species, the nucleophilic agent in these interactions tends to be highly electronegative, or may be anionic, bearing a negative formal charge. As compared to hydrogen bonding, the halogen atom takes the place of the positively charged hydrogen as the electrophile. Halogen bonding should not be confused with halogen-aromatic interactions, as the two are related but differ by definition, halogen-aromatic interactions involve an electron-rich aromatic π-cloud as a nucleophile, halogen bonding is restricted to monatomic nucleophiles. Van der Waals Forces are a subset of electrostatic interactions involving permanent or induced dipoles, dipole-dipole interactions are electrostatic interactions between permanent dipoles in molecules. These interactions tend to align the molecules to increase attraction, normally, dipoles are associated with electronegative atoms, including oxygen, nitrogen, sulfur, and fluorine. For example, acetone, the ingredient in some nail polish removers, has a net dipole associated with the carbonyl. They are not full charges because the electrons are shared through a covalent bond between the oxygen and carbon. If the electrons were no longer being shared, then the bond would be an electrostatic interaction. H δ + − Cl δ − ⋯ H δ + − Cl δ − Often molecules contain dipolar groups and this occurs if there is symmetry within the molecule that causes the dipoles to cancel each other out
5.
RNA
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Ribonucleic acid is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. RNA and DNA are nucleic acids, and, along with proteins and carbohydrates, like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA to convey information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome, some RNA molecules play an active role within cells by catalyzing biological reactions, controlling gene expression, or sensing and communicating responses to cellular signals. One of these processes is protein synthesis, a universal function where RNA molecules direct the assembly of proteins on ribosomes. This process uses transfer RNA molecules to deliver amino acids to the ribosome, analysis of these RNAs has revealed that they are highly structured. Unlike DNA, their structures do not consist of long double helices, in this fashion, RNAs can achieve chemical catalysis. For instance, determination of the structure of the enzyme that catalyzes peptide bond formation—revealed that its active site is composed entirely of RNA. Each nucleotide in RNA contains a sugar, with carbons numbered 1 through 5. A base is attached to the 1 position, in general, adenine, cytosine, guanine, adenine and guanine are purines, cytosine and uracil are pyrimidines. A phosphate group is attached to the 3 position of one ribose, the phosphate groups have a negative charge each, making RNA a charged molecule. The bases form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil, however, other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair. An important structural feature of RNA that distinguishes it from DNA is the presence of a group at the 2 position of the ribose sugar. The A-form geometry results in a deep and narrow major groove. RNA is transcribed with only four bases, but these bases, pseudouridine, in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and ribothymidine are found in various places. Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine, inosine plays a key role in the wobble hypothesis of the genetic code. The specific roles of many of these modifications in RNA are not fully understood, the functional form of single-stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule and this leads to several recognizable domains of secondary structure like hairpin loops, bulges, and internal loops
6.
Gene expression
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Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are proteins, but in non-protein coding genes such as transfer RNA or small nuclear RNA genes. The process of gene expression is used by all known life—eukaryotes, prokaryotes, several steps in the gene expression process may be modulated, including the transcription, RNA splicing, translation, and post-translational modification of a protein. Gene regulation gives the cell control over structure and function, and is the basis for differentiation, morphogenesis. In genetics, gene expression is the most fundamental level at which the genotype gives rise to the phenotype, the genetic code stored in DNA is interpreted by gene expression, and the properties of the expression give rise to the organisms phenotype. Such phenotypes are expressed by the synthesis of proteins that control the organisms shape. Regulation of gene expression is critical to an organisms development. A gene is a stretch of DNA that encodes information, genomic DNA consists of two antiparallel and reverse complementary strands, each having 5 and 3 ends. This RNA is complementary to the template 3 →5 DNA strand, therefore, the resulting 5 →3 RNA strand is identical to the coding DNA strand with the exception that thymines are replaced with uracils in the RNA. A coding DNA strand reading ATG is indirectly transcribed through the non-coding strand as AUG in RNA, in prokaryotes, transcription is carried out by a single type of RNA polymerase, which needs a DNA sequence called a Pribnow box as well as a sigma factor to start transcription. RNA polymerase I is responsible for transcription of ribosomal RNA genes, RNA polymerase II transcribes all protein-coding genes but also some non-coding RNAs. Pol II includes a C-terminal domain that is rich in serine residues, when these residues are phosphorylated, the CTD binds to various protein factors that promote transcript maturation and modification. RNA polymerase III transcribes 5S rRNA, transfer RNA genes, transcription ends when the polymerase encounters a sequence called the terminator. These include 5 capping, which is set of reactions that add 7-methylguanosine to the 5 end of pre-mRNA. The m7G cap is then bound by cap binding complex heterodimer, another modification is 3 cleavage and polyadenylation. They occur if polyadenylation signal sequence is present in pre-mRNA, which is usually between protein-coding sequence and terminator, the pre-mRNA is first cleaved and then a series of ~200 adenines are added to form poly tail, which protects the RNA from degradation. Poly tail is bound by multiple poly-binding proteins necessary for mRNA export, a very important modification of eukaryotic pre-mRNA is RNA splicing. The majority of eukaryotic pre-mRNAs consist of alternating segments called exons and introns, in certain cases, some introns or exons can be either removed or retained in mature mRNA
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