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Biochemistry
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Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms. By controlling information flow through biochemical signaling and the flow of energy through metabolism. Biochemistry is closely related to biology, the study of the molecular mechanisms by which genetic information encoded in DNA is able to result in the processes of life. Depending on the definition of the terms used, molecular biology can be thought of as a branch of biochemistry, or biochemistry as a tool with which to investigate. The chemistry of the cell depends on the reactions of smaller molecules. These can be inorganic, for water and metal ions, or organic, for example the amino acids. The mechanisms by which cells harness energy from their environment via chemical reactions are known as metabolism, the findings of biochemistry are applied primarily in medicine, nutrition, and agriculture. In medicine, biochemists investigate the causes and cures of diseases, in nutrition, they study how to maintain health and study the effects of nutritional deficiencies. In agriculture, biochemists investigate soil and fertilizers, and try to discover ways to improve crop cultivation, crop storage and pest control. However, biochemistry as a scientific discipline has its beginning sometime in the 19th century, or a little earlier. Gowland Hopkins on enzymes and the nature of biochemistry. The term biochemistry itself is derived from a combination of biology, the German chemist Carl Neuberg however is often cited to have coined the word in 1903, while some credited it to Franz Hofmeister. Then, in 1828, Friedrich Wöhler published a paper on the synthesis of urea and these techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle. Another significant historic event in biochemistry is the discovery of the gene and this part of biochemistry is often called molecular biology. In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, in 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme. In 1988, Colin Pitchfork was the first person convicted of murder with DNA evidence, mello received the 2006 Nobel Prize for discovering the role of RNA interference, in the silencing of gene expression. Around two dozen of the 92 naturally occurring elements are essential to various kinds of biological life. Most rare elements on Earth are not needed by life, while a few common ones are not used, most organisms share element needs, but there are a few differences between plants and animals
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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
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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
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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
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Ligand (biochemistry)
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In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein, the binding typically results in a change of conformation of the target protein. In DNA-ligand binding studies, the ligand can be a molecule, ion. The relationship between ligand and binding partner is a function of charge, hydrophobicity, and molecular structure, the instance of binding occurs over an infinitesimal range of time and space, so the rate constant is usually a very small number. Binding occurs by intermolecular forces, such as bonds, hydrogen bonds. The association of docking is actually reversible through dissociation, measurably irreversible covalent bonding between a ligand and target molecule is atypical in biological systems. In contrast to the definition of ligand in metalorganic and inorganic chemistry, in biochemistry it is whether the ligand generally binds at a metal site. In general, the interpretation of ligand is contextual with regards to what sort of binding has been observed, the etymology stems from ligare, which means to bind. Ligand binding to a receptor protein alters the chemical conformation by affecting the shape orientation. The conformation of a receptor protein composes the functional state, ligands include substrates, inhibitors, activators, and neurotransmitters. The rate of binding is called affinity, and this measurement typifies a tendency or strength of the effect, binding affinity is actualized not only by host-guest interactions, but also by solvent effects that can play a dominant, steric role which drives non-covalent binding in solution. The solvent provides an environment for the ligand and receptor to adapt. Radioligands are radioisotope labeled compounds are used in vivo as tracers in PET studies, the interaction of most ligands with their binding sites can be characterized in terms of a binding affinity. In general, high-affinity binding results in a degree of occupancy for the ligand at its receptor binding site than is the case for low-affinity binding. A ligand that can bind to a receptor, alter the function of the receptor, high-affinity ligand binding implies that a relatively low concentration of a ligand is adequate to maximally occupy a ligand-binding site and trigger a physiological response. The lower the Ki concentration is, the more likely there will be a reaction between the pending ion and the receptive antigen. In the example shown to the right, two different ligands bind to the receptor binding site. Only one of the agonists shown can maximally stimulate the receptor and, thus, an agonist that can only partially activate the physiological response is called a partial agonist
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Molecule
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A molecule is an electrically neutral group of two or more atoms held together by chemical bonds. Molecules are distinguished from ions by their lack of electrical charge, however, in quantum physics, organic chemistry, and biochemistry, the term molecule is often used less strictly, also being applied to polyatomic ions. In the kinetic theory of gases, the molecule is often used for any gaseous particle regardless of its composition. According to this definition, noble gas atoms are considered molecules as they are in fact monoatomic molecules. A molecule may be homonuclear, that is, it consists of atoms of one element, as with oxygen, or it may be heteronuclear. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are not considered single molecules. Molecules as components of matter are common in organic substances and they also make up most of the oceans and atmosphere. Also, no typical molecule can be defined for ionic crystals and covalent crystals, the theme of repeated unit-cellular-structure also holds for most condensed phases with metallic bonding, which means that solid metals are also not made of molecules. In glasses, atoms may also be together by chemical bonds with no presence of any definable molecule. The science of molecules is called molecular chemistry or molecular physics, in practice, however, this distinction is vague. In molecular sciences, a molecule consists of a system composed of two or more atoms. Polyatomic ions may sometimes be thought of as electrically charged molecules. The term unstable molecule is used for very reactive species, i. e, according to Merriam-Webster and the Online Etymology Dictionary, the word molecule derives from the Latin moles or small unit of mass. Molecule – extremely minute particle, from French molécule, from New Latin molecula, diminutive of Latin moles mass, a vague meaning at first, the vogue for the word can be traced to the philosophy of Descartes. The definition of the molecule has evolved as knowledge of the structure of molecules has increased, earlier definitions were less precise, defining molecules as the smallest particles of pure chemical substances that still retain their composition and chemical properties. Molecules are held together by covalent bonding or ionic bonding. Several types of non-metal elements exist only as molecules in the environment, for example, hydrogen only exists as hydrogen molecule. A molecule of a compound is made out of two or more elements, a covalent bond is a chemical bond that involves the sharing of electron pairs between atoms
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Ion
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An ion is an atom or a molecule in which the total number of electrons is not equal to the total number of protons, giving the atom or molecule a net positive or negative electrical charge. Ions can be created, by chemical or physical means. In chemical terms, if an atom loses one or more electrons. If an atom gains electrons, it has a net charge and is known as an anion. Ions consisting of only a single atom are atomic or monatomic ions, because of their electric charges, cations and anions attract each other and readily form ionic compounds, such as salts. In the case of ionization of a medium, such as a gas, which are known as ion pairs are created by ion impact, and each pair consists of a free electron. The word ion comes from the Greek word ἰόν, ion, going and this term was introduced by English physicist and chemist Michael Faraday in 1834 for the then-unknown species that goes from one electrode to the other through an aqueous medium. Faraday also introduced the words anion for a charged ion. In Faradays nomenclature, cations were named because they were attracted to the cathode in a galvanic device, arrhenius explanation was that in forming a solution, the salt dissociates into Faradays ions. Arrhenius proposed that ions formed even in the absence of an electric current, ions in their gas-like state are highly reactive, and do not occur in large amounts on Earth, except in flames, lightning, electrical sparks, and other plasmas. These gas-like ions rapidly interact with ions of charge to give neutral molecules or ionic salts. These stabilized species are commonly found in the environment at low temperatures. A common example is the present in seawater, which are derived from the dissolved salts. Electrons, due to their mass and thus larger space-filling properties as matter waves, determine the size of atoms. Thus, anions are larger than the parent molecule or atom, as the excess electron repel each other, as such, in general, cations are smaller than the corresponding parent atom or molecule due to the smaller size of its electron cloud. One particular cation contains no electrons, and thus consists of a single proton - very much smaller than the parent hydrogen atom. Since the electric charge on a proton is equal in magnitude to the charge on an electron, an anion, from the Greek word ἄνω, meaning up, is an ion with more electrons than protons, giving it a net negative charge. A cation, from the Greek word κατά, meaning down, is an ion with fewer electrons than protons, there are additional names used for ions with multiple charges
8.
Chemical bond
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A chemical bond is a lasting attraction between atoms that enables the formation of chemical compounds. The bond may result from the force of attraction between atoms with opposite charges, or through the sharing of electrons as in the covalent bonds. Since opposite charges attract via an electromagnetic force, the negatively charged electrons that are orbiting the nucleus. An electron positioned between two nuclei will be attracted to both of them, and the nuclei will be attracted toward electrons in this position and this attraction constitutes the chemical bond. This phenomenon limits the distance between nuclei and atoms in a bond, in general, strong chemical bonding is associated with the sharing or transfer of electrons between the participating atoms. All bonds can be explained by quantum theory, but, in practice, simplification rules allow chemists to predict the strength, directionality, the octet rule and VSEPR theory are two examples. Electrostatics are used to describe bond polarities and the effects they have on chemical substances, a chemical bond is an attraction between atoms. This attraction may be seen as the result of different behaviors of the outermost or valence electrons of atoms and these behaviors merge into each other seamlessly in various circumstances, so that there is no clear line to be drawn between them. However it remains useful and customary to differentiate different types of bond, which result in different properties of condensed matter. In the simplest view of a covalent bond, one or more electrons are drawn into the space between the two atomic nuclei, energy is released by bond formation. This is not as a reduction in energy, because the attraction of the two electrons to the two protons is offset by the electron-electron and proton-proton repulsions. In a polar covalent bond, one or more electrons are shared between two nuclei. Such weak intermolecular bonds give organic molecular substances, such as waxes and oils, their soft bulk character, also, the melting points of such covalent polymers and networks increase greatly. In a simplified view of a bond, the bonding electron is not shared at all. In this type of bond, the atomic orbital of one atom has a vacancy which allows the addition of one or more electrons. These newly added electrons potentially occupy a lower energy-state than they experience in a different atom, thus, one nucleus offers a more tightly bound position to an electron than does another nucleus, with the result that one atom may transfer an electron to the other. This transfer causes one atom to assume a net charge. The bond then results from electrostatic attraction between atoms and the atoms become positive or negatively charged ions, ionic bonds may be seen as extreme examples of polarization in covalent bonds
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Chemical affinity
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In chemical physics and physical chemistry, chemical affinity is the electronic property by which dissimilar chemical species are capable of forming chemical compounds. Chemical affinity can also refer to the tendency of an atom or compound to combine by chemical reaction with atoms or compounds of unlike composition, the idea of affinity is extremely old. Many attempts have been made at identifying its origins, the majority of such attempts, however, except in a general manner, end in futility since affinities lie at the basis of all magic, thereby pre-dating science. Physical chemistry, however, was one of the first branches of science to study, the name affinitas was first used in the sense of chemical relation by German philosopher Albertus Magnus near the year 1250. Later, those as Robert Boyle, John Mayow, Johann Glauber, Isaac Newton, the term affinity has been used figuratively since c.1600 in discussions of structural relationships in chemistry, philology, etc. and reference to natural attraction is from 1616. Chemical affinity, historically, has referred to the force that causes chemical reactions, as well as, more generally, and earlier, the ″tendency to combine″ of any pair of substances. The broad definition, used throughout history, is that chemical affinity is that whereby substances enter into or resist decomposition. Antoine Lavoisier, in his famed 1789 Traité Élémentaire de Chimie, refers to Bergman’s work, according to Prigogine, the term was introduced and developed by Théophile de Donder. Goethe used the concept in his novel Elective Affinities, the affinity concept was very closely linked to the visual representation of substances on a table. The first-ever affinity table, which was based on displacement reactions, was published in 1718 by the French chemist Étienne François Geoffroy, crucially, the table was the central graphic tool used to teach chemistry to students and its visual arrangement was often combined with other kinds diagrams. Joseph Black, for example, used the table in combination with chiastic, Affinity tables were used throughout Europe until the early 19th century when they were displaced by affinity concepts introduced by Claude Berthollet. In chemical physics and physical chemistry, chemical affinity is the property by which dissimilar chemical species are capable of forming chemical compounds. Chemical affinity can also refer to the tendency of an atom or compound to combine by chemical reaction with atoms or compounds of unlike composition, in modern terms, we relate affinity to the phenomenon whereby certain atoms or molecules have the tendency to aggregate or bond. In this antiquated context, chemical affinity is sometimes synonymous with the term magnetic attraction. Many writings, up until about 1925, also refer to a law of chemical affinity, ilya Prigogine summarized the concept of affinity, saying, All chemical reactions drive the system to a state of equilibrium in which the affinities of the reactions vanish. The present IUPAC definition is that affinity A is the partial derivative of Gibbs free energy G with respect to extent of reaction ξ at constant pressure and temperature. It follows that affinity is positive for spontaneous reactions, in 1923, the Belgian mathematician and physicist Théophile de Donder derived a relation between affinity and the Gibbs free energy of a chemical reaction. This definition is useful for quantifying the factors responsible both for the state of systems, and for changes of state of non-equilibrium systems
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