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La '''biochimica''' studia le biomolecole e il loro [[metabolismo]].
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[[vi:Hóa sinh]]
[[zh:生物化學]]
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'''Biochemistry''' is the study of the [[chemistry]] of [[life]], a bridge between [[biology]] and chemistry that studies how complex [[chemical reaction]]s and chemical structures give rise to life. It is a hybrid branch of chemistry which specialises in the chemical processes and chemical transformations in living [[organism]]s. This article only discusses terrestrial biochemistry ([[carbon]]- and [[water]]-based), as all the life forms we know are on [[Earth]]. Since life forms alive today are believed to have descended from the same [[common descent|common ancestor]], they naturally have similar biochemistries, even for matters which would appear to be essentially arbitrary, such as the [[genetic code]] or [[chirality (chemistry)|handedness]] of various biomolecules. It is unknown whether alternate biochemistries are possible or practical.
Biochemistry is the study of the structure and function of [[cell (biology)|cellular components]], such as [[protein]]s, [[carbohydrate]]s, [[lipid]]s, [[nucleic acid]]s, and other [[biomolecule]]s. [[Chemical biology]] aims to answer many questions arising from biochemistry by using tools developed within [[chemical synthesis|synthetic chemistry]].
Although there are a vast number of different biomolecules, they tend to be composed of the same repeating subunits (called ''[[monomer]]s''), in different orders. Each class of biomolecules has a different set of subunits. Recently, biochemistry has focused more specifically on the chemistry of [[enzyme]]-[[catalysis|catalyzed]] reactions, and on the properties of proteins.
The biochemistry of [[cell metabolism]] and the [[endocrine system]] has been extensively described. Other areas of biochemistry include the [[genetic code]] ([[DNA]], [[RNA]]), [[protein synthesis]], [[cell membrane]] transport, and [[signal transduction]].
== Development of biochemistry ==
Originally, it was generally believed that life was not subject to the laws of science the way nonlife was. It was thought that only living beings could produce the molecules of life (from other, previously existing biomolecules). Then, in [[1828]], [[Friedrich Woehler|Friedrich Wöhler]] published a paper about the synthesis of [[urea]], proving that [[organic chemistry|organic]] compounds can be created artificially. The dawn of biochemistry may have been the discovery of the first enzyme, [[diastase]], in [[1833]] by [[Anselme Payen]]. Although the term “biochemistry” seems to have been first used in 1881, it is generally accepted that the formal coinage biochemistry occurred in [[1903]] by Carl Neuber, a German [[chemist]]. Since then, biochemistry has advanced, especially since the mid-[[20th century]], with the development of new techniques such as [[chromatography]], [[X-ray diffraction]], [[protein nuclear magnetic resonance spectroscopy|NMR spectroscopy]], [[radioisotopic labelling]], [[electron microscope|electron microscopy]] and [[molecular dynamics]] simulations. These techniques allowed for the discovery and detailed analysis of many molecules and [[metabolic pathway]]s of the [[cell (biology)|cell]], such as [[glycolysis]] and the [[citric acid cycle|Krebs cycle]] (citric acid cycle).
Today, the findings of biochemistry are used in many areas, from [[genetics]] to [[molecular biology]] and from [[agriculture]] to [[medicine]]. The first application of biochemistry was probably the making of [[bread]] using [[yeast]], about 5000 years ago.
==Carbohydrates==
{{main|Carbohydrate}}
[[Image:Saccharose.svg|thumb|[[Sucrose]]: ordinary table sugar and probably the most familiar carbohydrate.]]
The function of carbohydrates includes energy storage and providing structure. [[Sugar]]s are carbohydrates, although there are carbohydrates that are not sugars. There are more carbohydrates on Earth than any other type of biomolecule. The simplest type of carbohydrate is a [[monosaccharide]], which among other properties contains [[carbon]], [[hydrogen]], and [[oxygen]] in a ratio 1:2:1 (generalized formula C<sub>''n''</sub>H<sub>2''n''</sub>O<sub>''n''</sub>, where ''n'' is at least 3). [[Glucose]], one of the most important carbohydrates, is an example of a monosaccharide. So is [[fructose]], the sugar that gives [[fruit]]s their sweet taste.
Two monosaccharides can be joined together using [[dehydration synthesis]], in which a hydrogen atom is removed from the end of one molecule and a [[hydroxyl]] group (—OH) is removed from the other; the remaining residues are then attached at the sites from which the atoms were removed. The H—OH or H<sub>2</sub>O is then released as a molecule of [[water]], hence the term ''dehydration''. The new molecule, consisting of two monosaccharides, is called a ''[[disaccharide]]'' and is conjoined together by a glycosidic or ether bond. The reverse reaction can also occur, using a molecule of water to split up a disaccharide and break the glycosidic bond; this is termed ''[[hydrolysis]]''. The most well-known disaccharide is [[sucrose]], ordinary sugar (in scientific contexts, called ''table sugar'' or ''cane sugar'' to differentiate it from other sugars). Sucrose consists of a glucose molecule and a fructose molecule joined together. Another important disaccharide is [[lactose]], consisting of a glucose molecule and a [[galactose]] molecule. As most humans age, the production of [[lactase]], the enzyme that hydrolyzes lactose back into glucose and galactose, typically decreases. This results in [[lactase deficiency]], also called ''lactose intolerance''.
When a few (around three to six) monosaccharides are joined together, it is called an ''[[oligosaccharide]]'' (''oligo-'' meaning "few"). These molecules tend to be used as markers and signals, as well as having some other uses.
Many monosaccharides joined together make a [[polysaccharide]]. They can be joined together in one long linear chain, or they may be branched. Two of the most common polysaccharides are [[cellulose]] and [[glycogen]], both consisting of repeating [[glucose]] [[monomer]]s. Cellulose is made by [[plant]]s and is an important structural component of their [[cell wall]]s. [[Human]]s can neither manufacture nor digest it. Glycogen, on the other hand, is an [[animal]] carbohydrate; humans use it as a form of energy storage.
[[Image:Glycolysis10steps.gif|thumb|right|250px|A schematic of [[glucose]] undergoing [[glycolysis]] to produce [[pyruvate]].]]
Glucose is the major energy source in most life forms; a number of [[catabolism|catabolic]] pathways converge on glucose. For instance, polysaccharides are broken down into their monomers ([[glycogen phosphorylase]] removes glucose residues from glycogen). Disaccharides like [[lactose]] or [[sucrose]] are cleaved into their two component monosaccharides. Glucose is metabolized by a very important and ancient ten-step pathway called [[glycolysis]], the net result of which is to break down one molecule of glucose into two molecules of [[pyruvate]]; this also produces a net two molecules of [[Adenosine triphosphate|ATP]], the energy currency of cells, along with two reducing equivalents in the form of converting [[NAD]] to [[NADH]]. This does not require oxygen; if no oxygen is available (or the cell cannot use oxygen), the [[NAD]] is restored by converting the pyruvate to [[lactic acid|lactate]] (in humans, for instance) or to [[ethanol]] in [[yeast]]. Other monosaccharides like galactose and fructose can be converted into intermediates of the glycolytic pathway. In [[aerobic]] cells with sufficient oxygen, like most human cells, the pyruvate can be further metabolized. It is irreversibly converted to [[acetyl-CoA]], giving off one carbon atom as the waste product [[carbon dioxide]], generating another molecule of ATP, and generating another reducing equivalent as [[NADH]]. The two molecules acetyl-CoA (from one molecule of glucose) then enter the [[citric acid cycle]], producing two more molecules of ATP, six more [[NADH]] molecules and two of a related molecule [[FADH2|FADH<sub>2</sub>]], and releasing the remaining carbon atoms as carbon dioxide. The reduced NADH and FADH<sub>2</sub> then enter the [[electron transport system]], where the electrons are transferred to a molecule of [[oxygen]], producing water, and the original NAD<sup>+</sup> and FAD are regenerated. This is why humans breath in oxygen and breath out carbon dioxide. The energy in transferring the electrons from high-energy states in NADH and FADH<sub>2</sub> is used to generate an additional ''28'' molecules of ATP (only two had been produced in glycolysis), for a total of 32 molecules of ATP. It is clear that using oxygen to completely oxidize glucose provides an organism with far greater energy, and it is why complex life appeared only after Earth's atmosphere accumulated large amounts of oxygen.
In [[vertebrate]]s, vigorously contracting [[skeletal muscle]] (during weightlifting or sprinting, for example) does not receive enough oxygen to meet the energy demand, and so it shifts to [[anaerobic metabolism]], converting glucose to lactate (lactic acid). The [[liver]] can regenerate the glucose, using a process called [[gluconeogenesis]]. This process is not quite the opposite of glycolysis, and actually requires three times the amount of energy gained from glycolysis (six molecules of ATP are used, compared to the two gained in glycolysis). Analogous to the above reactions, the glucose produced can then undergo glycolysis in tissues that need energy, be stored as glycogen (or starch in plants), or be converted to other monosaccharides or joined into di- or oligosaccharides.
==Proteins==
{{main|Protein}}
[[Image:Hemoglobin.jpg|thumb|right|150px|A schematic of [[hemoglobin]]. The ribbon parts represent the protein [[globin]]; the four green parts are the [[heme]] groups.]]
Like carbohydrates, some proteins perform largely structural roles. For instance, movements of the proteins [[actin]] and [[myosin]] ultimately are responsible for the contraction of skeletal muscle. One property many proteins have is that they specifically bind to a certain molecule or class of molecules—they may be ''extremely'' selective in what they bind. [[Antibody|Antibodies]] are an example of proteins that attach to one specific type of molecule. In fact, the [[enzyme-linked immunosorbent assay]] (ELISA), which uses antibodies, is currently one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins, however, are the [[enzyme]]s. These amazing molecules recognize specific reactant molecules called ''[[substrate (biochemistry)|substrate]]s''; they then [[catalyze]] the reaction between them. By lowering the [[activation energy]], the enzyme speeds up that reaction by a rate of 10<sup>11</sup> or more: a reaction that would normally take over 3,000 years to complete spontaneously might take less than a second with an enzyme. The enzyme itself is not used up in the process, and is free to catalyze the same reaction with a new set of substrates. Using various modifiers, the activity of the enzyme can be regulated, enabling control of the biochemistry of the cell as a whole.
In essence, proteins are chains of [[amino acid]]s. An amino acid consists of a carbon atom bound to four groups. One is an [[amino]] group, —NH<sub>2</sub>, and one is a [[carboxylic acid]] group, —COOH (although these exist as —NH<sub>3</sub><sup>+</sup> and —COO<sup>−</sup> under physiologic conditions). The third is a simple [[hydrogen]] atom. The fourth is commonly denoted "—R" and is different for each amino acid. There are twenty standard amino acids. Some of these have functions by themselves or in a modified form; for instance, [[glutamate]] functions as an important [[neurotransmitter]].
[[Image:Amino acids 1.png|thumb|right|350px|Generic amino acids (1) in neutral form, (2) as they exist physiologically, and (3) joined together as a [[dipeptide]].]]
Amino acids can be joined together via a [[peptide bond]]. In this dehydration synthesis, a water molecule is removed and the peptide bond connects the nitrogen of one amino acid's amino group to the carbon of the other's carboxylic acid group. The resulting molecule is called a ''[[dipeptide]]'', and short stretches of amino acids (usually, fewer than around thirty) are called ''[[peptide]]s'' or polypeptides. Longer stretches merit the title ''proteins''. As an example, the imporant blood [[serum]] protein [[albumin]] contains 585 amino acid residues.
The structure of proteins is traditionally described in a hierarchy of four levels. The [[primary structure]] of a protein simply consists of its linear sequence of amino acids; for instance, "alanine-glycine-tryptophan-serine-glutamate-asparagine-glycine-lysine-...". [[Secondary structure]] is concerned with local morphology. Some combinations of amino acids will tend to curl up in a coil called an [[alpha helix|α-helix]]; some of these can be seen in the hemoglobin schematic above. [[Tertiary structure]] is the entire three-dimensional shape of the protein. This shape is determined by the sequence of amino acids. In fact, a single change can change the entire structure. The β chain of hemoglobin contains 146 amino acid residues; substitution of the [[glutamate]] residue at position 6 with a [[valine]] residue changes the behavior of hemoglobin so much that it results in [[sickle-cell disease]]. Finally [[quaternary structure]] is concerned with the structure of a protein with multiple peptide subunits, like hemoglobin with its four subunits. Not all proteins have more than one subunit.
Ingested proteins are usually broken up into single amino acids or dipeptides in the [[small intestine]], and then absorbed. They can then be joined together to make new proteins. Intermediate products of glycolysis, the citric acid cycle, and the [[pentose phosphate pathway]] can be used to make all twenty amino acids, and most bacteria and plants possess all the necessary enzymes to synthesize them. Humans and other mammals, however, can only synthesize half of them. They cannot synthesize [[isoleucine]], [[leucine]], [[lysine]], [[methionine]], [[phenylalanine]], [[threonine]], [[tryptophan]], and [[valine]]. These are the [[essential amino acid]]s, since it is essential to ingest them. Mammals do possess the enzymes to synthesize [[alanine]], [[asparagine]], [[aspartate]], [[cysteine]], [[glutamate]], [[glutamine]], [[glycine]], [[proline]], [[serine]], and [[tyrosine]], the nonessential amino acids. While they can synthesize [[arginine]] and [[histidine]], they cannot produce it in sufficient amounts for young, growing animals, and so these are often considered essential amino acids.
If the amino group is removed from an amino acid, it leaves behind a carbon skeleton called an α-[[keto acid]]. Enzymes called [[transaminase]]s can easily transfer the amino group from one amino acid (making it an α-keto acid) to another α-keto acid (making it an amino acid). This is important in the biosynthesis of amino acids, as for many of the pathways, intermediates from other biochemical pathways are converted to the α-keto acid skeleton, and then an amino group is added, often via [[transamination]]. The amino acids may then be linked together to make a protein.
A similar process is used to break down proteins. It is first hydrolyzed into its component amino acids. Free [[ammonia]] (NH<sub>3</sub>, existing as the [[ammonium]] ion NH<sub>4</sub><sup>+</sup>) in blood) is toxic to life forms. A suitable method for excreting it must therefore exist. Different strategies have evolved in different animals, depending on the animals' needs. [[Unicellular]] organisms, of course, simply release the ammonia into the environment. Similarly, [[osteichthyes|bony fish]] can release the ammonia into the water where it is quickly diluted. In general, mammals convert the ammonia into [[urea]], via the [[urea cycle]].
==Lipids==
{{main|Lipid}}
The term lipid comprises a diverse range of [[molecules]] and to some extent is a catchall for relatively water-insoluble or [[nonpolar]] compounds of biological origin, including [[wax]]es, [[fatty acid]]s, fatty-acid derived phospholipids, sphingolipids, glycolipids and terpenoids, such as retinoids and [[steroids]]. Some lipids are linear [[aliphatic]] molecules, while others have ring structures. Some are [[aromatic]], while others are not. Some are flexible, while others are rigid.
Most lipids have some [[polar molecule|polar]] character in addition to being largely nonpolar. Generally, the bulk of their structure is nonpolar or [[hydrophobic]] ("water-fearing"), meaning that it does not interact well with polar solvents like water. Another part of their structure is polar or [[hydrophilic]] ("water-loving") and will tend to associate with polar solvents like water. This makes them [[amphiphilic]] molecules (having both hydrophobic and hydrophilic portions). In the case of [[cholesterol]], the polar group is a mere -OH ([[hydroxyl]] or alcohol). In the case of phospholipids, the polar groups are considerably larger and more polar, as described below.
==Nucleic acids==
{{main|Nucleic acid}}
A nucleic acid is a complex, high-molecular-weight [[biochemistry|biochemical]] [[macromolecule]] composed of [[nucleotide]] chains that convey [[genetic information]]. The most common nucleic acids are deoxyribonucleic acid ([[DNA]]) and ribonucleic acid ([[RNA]]). Nucleic acids are found in all living cells and viruses.
Nucleic acid, so called because of its prevalence in cellular [[cell nucleus|nuclei]], is the generic name of family of [[biopolymer]]s. The [[monomer]]s are called [[nucleotide]]s, and each consists of three components: a nitrogenous [[heterocyclic]] [[base (chemistry)|base]] (either a [[purine]] or a [[pyrimidine]]), a [[pentose]] [[sugar]], and a [[phosphate]] group. Different nucleic acid types differ in the specific sugar found in their chain (e.g. DNA or deoxyribonucleic acid contains 2-[[deoxyribose]]s). Also, the nitrogenous bases possible in the two nucleic acids are different: [[adenine]], [[cytosine]], and [[guanine]] are possible in both RNA and DNA, while [[thymine]] is possible only in DNA and [[uracil]] is possible only in RNA.
==Relationship to other "molecular-scale" biological sciences==
[[Image:Schematic relationship between biochemistry, genetics and molecular biology.svg|thumb|250px|right|''Schematic relationship between biochemistry, genetics and molecular biology'']]
Researchers in biochemistry use specific techniques native to biochemistry, but increasingly combine these with techniques and ideas from [[genetics]], [[molecular biology]] and [[biophysics]]. There has never been a hard-line between these disciplines in terms of content and technique, but members of each discipline have in the past been very territorial; today the terms ''molecular biology'' and ''biochemistry'' are nearly interchangeable. The following figure is a schematic that depicts one possible view of the relationship between the fields:
*''Biochemistry'' is the study of the chemical substances and vital processes occurring in living [[organisms]].
*''Genetics'' is the study of the effect of genetic differences on organisms. Often this can be inferred by the absence of a normal component (e.g. one [[gene]]). The study of "[[mutant]]s" – organisms which lack one or more functional components with respect to the so-called "[[wild type]]" or normal [[phenotype]]. [[Genetic interactions]] ([[epistasis]]) can often confound simple interpretations of such "knock-out" studies.
*''Molecular biology'' is the study of molecular underpinnings of the process of replication, transcription and translation of the [[genetic material]]. The [[central dogma of molecular biology]] where genetic material is transcribed into RNA and then translated into protein, despite being an oversimplified picture of molecular biology, still provides a good starting point for understanding the field. This picture, however, is undergoing revision in light of emerging novel roles for [[RNA]].
*''Chemical Biology'' seeks to develop new tools based on [[small molecule]]s that allow minimal perturbation of biological systems while providing detailed information about their function. Further, chemical biology employs biological systems to create non-natural hybrids between biomolecules and synthetic devices (for example emptied viral capsids that can deliver gene therapy or drug molecules).
== Further reading ==
*Graeme K. Hunter, ''Vital Forces. The discovery of the molecular basis of life'', London: Academic Press 2000
== See also==
* [[Alternative biochemistry]]
* [[List of basic biochemistry topics|Biochemistry key topics]]
* [[Biological psychiatry]]
* [[Chemical biology]]
* [[Chemical ecology]]
* [[Chemical imbalance theory]]
* [[Computational biomodeling]]
* [[List of publications in biology#Biochemistry|Important publications in biochemistry (biology)]]
* [[List of publications in chemistry#Biochemistry|Important publications in biochemistry (chemistry)]]
* [[List of biochemistry topics]]
* [[List of biochemists]]
* [[List of biomolecules]]
* [[List of geneticists & biochemists]]
* [[Molecular biology]]
== External links ==
{{wikibooks}}
{{Wikibookspar|Wikiversity|Biochemistry}}
*[http://www.biochemweb.org/ The Virtual Library of Biochemistry and Cell Biology]
*[http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=stryer.TOC&depth=2 Biochemistry, 5th ed.] Full text of Berg, Tymoczko, and Stryer, courtesy of [[National Center for Biotechnology Information|NCBI]].
*[http://www.biotecnologia.co.cr/ Costa Rican Biotechnology Society]
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