Editing Biochemistry

{{Short description|Study of chemical processes in living organisms}}
{{redir2|Biological chemistry|Physiological chemistry|the journals|Biochemistry (journal){{!}}''Biochemistry'' (journal)|and|Biological Chemistry (journal){{!}}''Biological Chemistry'' (journal)}}
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'''Biochemistry''', or '''biological chemistry''', is the study of [[chemical process]]es within and relating to living [[organism]]s.<ref>{{cite web|url=http://www.acs.org/content/acs/en/careers/college-to-career/areas-of-chemistry/biological-biochemistry.html.html|title=Biological/Biochemistry|work=acs.org|access-date=2016-01-04|archive-date=2019-08-21|archive-url=https://web.archive.org/web/20190821192332/https://www.acs.org/content/acs/en/careers/college-to-career/areas-of-chemistry/biological-biochemistry.html.html|url-status=live}}</ref>  A sub-discipline of both [[chemistry]] and [[biology]], biochemistry may be divided into three fields: [[structural biology]], [[enzymology]], and [[metabolism]]. Over the last decades of the 20th century, biochemistry has become successful at explaining living processes through these three disciplines.  Almost all [[List of life sciences|areas of the life sciences]] are being uncovered and developed through biochemical methodology and research.<ref name="Voet_2005">[[#Voet|Voet]] (2005), p. 3.</ref>  Biochemistry focuses on understanding the chemical basis that allows [[biomolecule|biological molecules]] to give rise to the processes that occur within living [[Cell (biology)|cells]] and between cells,<ref name="Karp2009">[[#Karp|Karp]] (2009), p. 2.</ref> in turn relating greatly to the understanding of [[tissue (biology)|tissues]] and [[organ (anatomy)|organs]] as well as organism structure and function.<ref name="MillerSpoolman2012">[[#Miller|Miller]] (2012). p. 62.</ref> Biochemistry is closely related to [[molecular biology]], the study of the [[molecule|molecular]] mechanisms of biological phenomena.<ref name="fn_1">[[#Astbury|Astbury]] (1961), p. 1124.</ref>

Much of biochemistry deals with the structures, functions, and interactions of biological [[macromolecule]]s such as [[protein]]s, [[nucleic acid]]s, [[carbohydrate]]s, and [[lipid]]s. They provide the structure of cells and perform many of the functions associated with life.<ref name="Biology">[[#Eldra|Eldra]] (2007), p. 45.</ref> The chemistry of the cell also depends upon the reactions of small [[molecule]]s and [[ion]]s.  These can be [[inorganic]] (for example, [[water]] and [[metal]] ions) or [[Organic compound|organic]] (for example, the [[amino acid]]s, which are used to [[Protein biosynthesis|synthesize proteins]]).<ref name="Marks">[[#Marks|Marks]] (2012), Chapter 14.</ref> The mechanisms used by [[Cell energy|cells to harness energy]] from their environment via [[chemical reaction]]s are known as [[metabolism]]. The findings of biochemistry are applied primarily in [[medicine]], [[nutrition]], and [[agriculture]]. In medicine, [[biochemist]]s investigate the causes and [[Pharmaceutical drug|cures]] of [[disease]]s.<ref>[[#Finkel|Finkel]] (2009), pp. 1–4.</ref> Nutrition studies how to maintain health and wellness and also the effects of [[nutritional deficiencies]].<ref name="FFL2010">[[#UNICEF|UNICEF]] (2010), pp. 61, 75.</ref> In agriculture, biochemists investigate [[soil]] and [[fertilizer]]s with the goal of improving crop cultivation, crop storage, and [[pest control]]. In recent decades, biochemical principles and methods have been combined with problem-solving approaches from [[engineering]] to manipulate living systems in order to produce useful tools for research, industrial processes, and diagnosis and control of disease{{mdash}}the discipline of [[biotechnology]].

==History==
{{Main| History of biochemistry}}
[[File:Gerty Theresa Radnitz Cori (1896-1957) and Carl Ferdinand Cori - restoration1.jpg|thumb|upright|[[Gerty Cori]] and [[Carl Cori]] jointly won the [[Nobel Prize in Physiology or Medicine|Nobel Prize]] in 1947 for their discovery of the [[Cori cycle]] at RPMI.]]

At its most comprehensive definition, biochemistry can be seen as a study of the components and composition of living things and how they come together to become life. In this sense, the history of biochemistry may therefore go back as far as the [[Ancient Greece|ancient Greeks]].<ref name="history of science">[[#Helvoort|Helvoort]] (2000), p. 81.</ref> However, biochemistry as a specific [[scientific discipline]] began sometime in the 19th century, or a little earlier, depending on which aspect of biochemistry is being focused on. Some argued that the beginning of biochemistry may have been the discovery of the first [[enzyme]], [[diastase]] (now called [[amylase]]), in 1833 by [[Anselme Payen]],<ref>[[#Hunter|Hunter]] (2000), p. 75.</ref> while others considered [[Eduard Buchner]]'s first demonstration of a complex biochemical process [[Ethanol fermentation|alcoholic fermentation]] in cell-free extracts in 1897 to be the birth of biochemistry.<ref>[[#Hamblin|Hamblin]] (2005), p. 26.</ref><ref>[[#Hunter|Hunter]] (2000), pp. 96–98.</ref>  Some might also point as its beginning to the influential 1842 work by [[Justus von Liebig]], ''Animal chemistry, or, [[Organic chemistry]] in its applications to [[physiology]] and [[pathology]]'', which presented a chemical theory of metabolism,<ref name="history of science" /> or even earlier to the 18th century studies on [[fermentation]] and [[Cellular respiration|respiration]] by [[Antoine Lavoisier]].<ref>[[#Berg|Berg]] (1980), pp. 1–2.</ref><ref>[[#Holmes|Holmes]] (1987), p. xv.</ref> Many other pioneers in the field who helped to uncover the layers of complexity of biochemistry have been proclaimed founders of modern biochemistry. [[Hermann Emil Fischer|Emil Fischer]], who studied the chemistry of [[proteins]],<ref>[[#Feldman|Feldman]] (2001), p. 206.</ref> and [[Frederick Gowland Hopkins|F. Gowland Hopkins]], who studied [[enzymes]] and the dynamic nature of biochemistry, represent two examples of early biochemists.<ref>[[#Rayner|Rayner-Canham]] (2005), p. 136.</ref>

The term "biochemistry" was first used when Vinzenz Kletzinsky (1826–1882) had his "Compendium der Biochemie" printed in Vienna in 1858; it derived from a combination of [[biology]] and [[chemistry]]. In 1877, [[Felix Hoppe-Seyler]] used the term ({{Lang|de|biochemie}} in German) as a synonym for [[physiological chemistry]] in the foreword to the first issue of ''[[Zeitschrift für Physiologische Chemie]]'' (Journal of Physiological Chemistry) where he argued for the setting up of institutes dedicated to this field of study.<ref>[[#Ziesak|Ziesak]] (1999), p. 169.</ref><ref>[[#Kleinkauf|Kleinkauf]] (1988), p. 116.</ref> The German [[chemist]] [[Carl Neuberg]] however is often cited to have coined the word in 1903,<ref name="Ben-Menahem 2009">[[#Ben|Ben-Menahem]] (2009), p. 2982.</ref><ref>[[#Amsler|Amsler]] (1986), p. 55.</ref><ref>[[#Horton|Horton]] (2013), p. 36.</ref> while some credited it to [[Franz Hofmeister]].<ref>[[#Kleinkauf|Kleinkauf]] (1988), p. 43.</ref>

[[File:DNA orbit animated.gif|thumb|left|upright|DNA structure ({{PDB2|1D65}})<ref>[[#Edwards|Edwards]] (1992), pp. 1161–1173.</ref>]]
It was once generally believed that life and its materials had some essential property or substance (often referred to as the "[[vital principle]]") distinct from any found in non-living matter, and it was thought that only living beings could produce the molecules of life.<ref>[[#Fiske|Fiske]] (1890), pp. 419–20.</ref> In 1828, [[Friedrich Wöhler]] published a paper on his [[serendipitous]] [[urea]] [[Wöhler synthesis|synthesis]] from [[potassium cyanate]] and [[ammonium sulfate]]; some regarded that as a direct overthrow of vitalism and the establishment of [[organic chemistry]].<ref>{{Cite journal|last=Wöhler|first=F.|date=1828|title=Ueber künstliche Bildung des Harnstoffs|url=http://dx.doi.org/10.1002/andp.18280880206|journal=Annalen der Physik und Chemie|volume=88|issue=2|pages=253–256|doi=10.1002/andp.18280880206|bibcode=1828AnP....88..253W|issn=0003-3804|access-date=2021-05-04|archive-date=2023-10-28|archive-url=https://web.archive.org/web/20231028023623/https://onlinelibrary.wiley.com/doi/10.1002/andp.18280880206|url-status=live}}</ref><ref name="Kauffman 20012">[[#Kauffman|Kauffman]] (2001), pp. 121–133.</ref>  However, the Wöhler synthesis has sparked controversy as some reject the death of vitalism at his hands.<ref>{{Cite journal|last=Lipman|first=Timothy O.|date=August 1964|title=Wohler's preparation of urea and the fate of vitalism|url=http://dx.doi.org/10.1021/ed041p452|journal=Journal of Chemical Education|volume=41|issue=8|pages=452|doi=10.1021/ed041p452|bibcode=1964JChEd..41..452L|issn=0021-9584|access-date=2021-05-04|archive-date=2023-10-28|archive-url=https://web.archive.org/web/20231028023621/https://pubs.acs.org/doi/abs/10.1021/ed041p452|url-status=live|url-access=subscription}}</ref>  Since then, biochemistry has advanced, especially since the mid-20th century, with the development of new techniques such as [[chromatography]], [[X-ray diffraction]], [[dual polarisation interferometry]], [[protein nuclear magnetic resonance spectroscopy|NMR spectroscopy]], [[radioisotopic labeling]], [[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 [[Krebs cycle]] (citric acid cycle), and led to an understanding of biochemistry on a molecular level.{{cn|date=March 2024}}

Another significant historic event in biochemistry is the discovery of the [[gene]], and its role in the transfer of information in the cell. In the 1950s, [[James D. Watson]], [[Francis Crick]], [[Rosalind Franklin]] and [[Maurice Wilkins]] were instrumental in solving [[DNA structure]] and suggesting its relationship with the genetic transfer of information.<ref>[[#Tropp|Tropp]] (2012), pp. 19–20.</ref> In 1958, [[George Beadle]] and [[Edward Tatum]] received the [[Nobel Prize]] for work in fungi showing that [[one gene-one enzyme hypothesis|one gene produces one enzyme]].<ref name="Krebs 2012">[[#Krebs|Krebs]] (2012), p. 32.</ref> In 1988, [[Colin Pitchfork]] was the first person convicted of murder with [[DNA]] evidence, which led to the growth of [[forensic science]].<ref name="Butler 2009">[[#Butler|Butler]] (2009), p. 5.</ref> More recently, [[Andrew Z. Fire]] and [[Craig C. Mello]] received the [[Nobel Prize in Physiology or Medicine|2006 Nobel Prize]] for discovering the role of [[RNA interference]] (RNAi) in the silencing of [[gene expression]].<ref name="Sen 2007">[[#Chandan|Chandan]] (2007), pp. 193–194.</ref>

== Starting materials: the chemical elements of life ==
[[Image:201 Elements of the Human Body.02.svg|thumb|upright|The main elements that compose the human body shown from most abundant (by mass) to least abundant]]
{{main|Composition of the human body|Dietary mineral}}

Around two dozen [[chemical elements]] are essential to various kinds of [[life|biological life]]. Most rare elements on Earth are not needed by life (exceptions being  [[selenium]] and [[iodine]]),<ref>{{cite book |last1=Cox, Nelson, Lehninger |title=Lehninger Principles of Biochemistry |date=2008 |publisher=Macmillan}}</ref> while a few common ones ([[aluminium]] and [[titanium]]) are not used. Most organisms share element needs, but there are a few differences between [[plants]] and [[animals]]. For example, ocean algae use [[bromine]], but land plants and animals do not seem to need any. All animals require [[sodium]], but is not an essential element for plants. Plants need [[boron]] and [[silicon]], but animals may not (or may need ultra-small amounts).<ref>{{Cite journal |last1=Sheng |first1=Huachun |last2=Lei |first2=Yuyan |last3=Wei |first3=Jing |last4=Yang |first4=Zhengming |last5=Peng |first5=Lianxin |last6=Li |first6=Wenbing |last7=Liu |first7=Yuan |date=2024 |title=Analogy of silicon and boron in plant nutrition |journal=Frontiers in Plant Science |volume=15 |pages=1353706 |doi=10.3389/fpls.2024.1353706 |doi-access=free |issn=1664-462X |pmc=10877001 |pmid=38379945|bibcode=2024FrPS...1553706S }}</ref>

Just six elements—[[carbon]], [[hydrogen]], [[nitrogen]], [[oxygen]], [[calcium]] and [[phosphorus]]—make up almost 99% of the mass of living cells, including those in the human body (see [[composition of the human body]] for a complete list). In addition to the six major elements that compose most of the human body, humans require smaller amounts of possibly 18 more.<ref>[[#Nielsen|Nielsen]] (1999), pp. 283–303.</ref>

==Biomolecules==
{{main|Biomolecule}}
The 4 main classes of molecules in biochemistry (often called [[biomolecule]]s) are [[carbohydrate]]s, [[lipid]]s, [[protein]]s, and [[nucleic acid]]s.<ref name="slabaugh">[[#Slabaugh|Slabaugh]] (2007), pp. 3–6.</ref> Many biological molecules are [[polymer]]s: in this terminology, [[monomer]]s are relatively small macromolecules that are linked together to create large [[macromolecule]]s known as polymers. When monomers are linked together to synthesize a [[Biopolymer|biological polymer]], they undergo a process called [[Dehydration reaction|dehydration synthesis]]. Different macromolecules can assemble in larger complexes, often needed for [[biological activity]].

===Carbohydrates===
{{Main|Carbohydrate|Monosaccharide|Disaccharide|Polysaccharide}}
<div class='skin-invert-image'>{{multiple image
| align     = right
| direction = vertical
| header    = [[Carbohydrates]]
| image1    = Beta-D-Glucose.svg
| width1    = 220
| caption1 = Glucose, a [[monosaccharide]]
| image2   = Sucrose-inkscape.svg
| width2   = 220
| caption2 = A molecule of [[sucrose]] ([[glucose]] + [[fructose]]), a [[disaccharide]]
| image3   = Amylose 3Dprojection.svg
| width3   = 220
| caption3 =[[Amylose]],  a [[polysaccharide]] made up of several thousand [[glucose]] units
}}</div>
Two of the main functions of carbohydrates are energy storage and providing structure. One of the common [[sugar]]s known as [[glucose]] is a carbohydrate, but not all carbohydrates are sugars. There are more carbohydrates on Earth than any other known type of biomolecule; they are used to store energy and [[Deoxyribose|genetic information]], as well as play important roles in cell to [[Cell–cell interaction|cell interactions]] and [[Cell signaling|communications]].{{cn|date=April 2023}}

The simplest type of carbohydrate is a [[monosaccharide]], which among other properties contains [[carbon]], [[hydrogen]], and [[oxygen]], mostly in a ratio of 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]] (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) is one of the most important carbohydrates; others include [[fructose]] (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>), the sugar commonly associated with the [[sweet taste]] of [[fruit]]s,<ref name="Whiting1970">[[#Whiting|Whiting]] (1970), pp. 1–31.</ref>{{Efn|Fructose is not the only sugar found in fruits. Glucose and sucrose are also found in varying quantities in various fruits, and sometimes exceed the fructose present. For example, 32% of the edible portion of a [[date (fruit)|date]] is glucose, compared with 24% fructose and 8% sucrose. However, [[peach]]es contain more sucrose (6.66%) than they do fructose (0.93%) or glucose (1.47%).<ref name=Whiting1970p5>[[#Whiting|Whiting]], G.C. (1970), p. 5.</ref>}} and [[deoxyribose]] (C<sub>5</sub>H<sub>10</sub>O<sub>4</sub>), a component of [[DNA]].  A monosaccharide can switch between [[Open-chain compound|acyclic (open-chain) form]] and a [[cyclic compound|cyclic]] form. The open-chain form can be turned into a ring of carbon atoms bridged by an [[oxygen]] atom created from the [[carbonyl group]] of one end and the [[hydroxyl]] group of another. The cyclic molecule has a [[hemiacetal]] or [[hemiketal]] group, depending on whether the linear form was an [[aldose]] or a [[ketose]].<ref>[[#Voet|Voet]] (2005), pp. 358–359.</ref>

In these cyclic forms, the ring usually has '''5''' or '''6''' atoms. These forms are called [[furanose]]s and [[pyranose]]s, respectively—by analogy with [[furan]] and [[pyran]], the simplest compounds with the same carbon-oxygen ring (although they lack the carbon-carbon [[double bond]]s of these two molecules).  For example, the aldohexose [[glucose]] may form a hemiacetal linkage between the hydroxyl on carbon 1 and the oxygen on carbon 4, yielding a molecule with a 5-membered ring, called [[glucofuranose]].  The same reaction can take place between carbons 1 and 5 to form a molecule with a 6-membered ring, called [[glucopyranose]]. Cyclic forms with a 7-atom ring called [[heptoses]] are rare.{{cn|date=April 2023}}

Two monosaccharides can be joined by a [[Glycosidic bond|glycosidic]] or [[ester bond]] into a ''[[disaccharide]]'' through a [[dehydration reaction]] during which a molecule of water is released. The reverse reaction in which the glycosidic bond of a disaccharide is broken into two monosaccharides is termed ''[[hydrolysis]]''.  The best-known disaccharide is [[sucrose]] or ordinary [[sugar]], which consists of a [[glucose]] molecule and a [[fructose]] molecule joined. Another important disaccharide is [[lactose]] found in milk, consisting of a glucose molecule and a [[galactose]] molecule. Lactose may be hydrolysed by [[lactase]], and deficiency in this enzyme results in [[lactose intolerance]].

When a few (around three to six) monosaccharides are joined, it is called an ''[[oligosaccharide]]'' (''oligo-'' meaning "few"). These molecules tend to be used as markers and [[Cell signaling|signals]], as well as having some other uses.<ref name="Varki_1999">[[#Varki|Varki]] (1999), p. 17.</ref> Many monosaccharides joined form a [[polysaccharide]]. They can be joined in one long linear chain, or they may be [[Branching (polymer chemistry)|branched]]. Two of the most common polysaccharides are [[cellulose]] and [[glycogen]], both consisting of repeating glucose [[monomer]]s.  ''Cellulose'' is an important structural component of plant's [[cell wall]]s and ''[[glycogen]]'' is used as a form of energy storage in animals.

[[Sugar]] can be characterized by having [[Reducing sugar|reducing]] or non-reducing ends. A [[reducing end]] of a carbohydrate is a carbon atom that can be in equilibrium with the open-chain [[aldehyde]] ([[aldose]]) or keto form ([[ketose]]). If the joining of monomers takes place at such a carbon atom, the free [[hydroxy group]] of the [[pyranose]] or [[furanose]] form is exchanged with an OH-side-chain of another sugar, yielding a full [[acetal]]. This prevents opening of the chain to the aldehyde or keto form and renders the modified residue non-reducing. Lactose contains a reducing end at its glucose moiety, whereas the galactose moiety forms a full acetal with the C4-OH group of glucose. [[Saccharose]] does not have a reducing end because of full acetal formation between the aldehyde carbon of glucose (C1) and the keto carbon of fructose (C2).

===Lipids===
{{Main|Lipid|Glycerol|Fatty acid}}

[[File:Common lipid types.svg|class=skin-invert-image|thumb|Structures of some common lipids. At the top are [[cholesterol]] and [[oleic acid]].<ref>[[#Stryer|Stryer]] (2007), p. 328.</ref> The middle structure is a [[triglyceride]] composed of [[oleate|oleoyl]], [[stearic acid|stearoyl]], and [[palmitate|palmitoyl]] chains attached to a [[glycerol]] backbone. At the bottom is the common [[phospholipid]], [[phosphatidylcholine]].<ref>[[#Voet|Voet]] (2005), Ch. 12 Lipids and Membranes.</ref>]]

[[Lipid|'''Lipids''']] comprise 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 [[phospholipid]]s, [[sphingolipid]]s, [[glycolipid]]s, and [[terpenoid]]s (e.g., [[retinoid]]s and [[steroid]]s). Some lipids are linear, open-chain [[aliphatic]] molecules, while others have ring structures. Some are [[aromatic]] (with a cyclic [ring] and planar [flat] structure) while others are not. Some are flexible, while others are rigid.<ref>{{Citation |last1=Ahmed |first1=Saba |title=Biochemistry, Lipids |date=2023 |url=http://www.ncbi.nlm.nih.gov/books/NBK525952/ |work=StatPearls |access-date=2023-11-30 |place=Treasure Island (FL) |publisher=StatPearls Publishing |pmid=30247827 |last2=Shah |first2=Parini |last3=Ahmed |first3=Owais}}</ref>

Lipids are usually made from one molecule of [[glycerol]] combined with other molecules. In [[triglyceride]]s, the main group of bulk lipids, there is one molecule of glycerol and three [[fatty acid]]s. Fatty acids are considered the monomer in that case, and may be [[Saturated and unsaturated compounds|saturated]] (no [[double bond]]s in the carbon chain) or unsaturated (one or more double bonds in the carbon chain).{{cn|date=April 2023}}

Most lipids have some [[Polar molecule|polar]] character and are largely nonpolar. In general, 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). {{cn|date=March 2024}}

In the case of phospholipids, the polar groups are considerably larger and more polar, as described below.

Lipids are an integral part of our daily diet. Most [[oil]]s and [[milk product]]s that we use for cooking and eating like [[butter]], [[cheese]], [[ghee]] etc. are composed of [[fat]]s. [[Vegetable oil]]s are rich in various [[polyunsaturated fatty acid]]s (PUFA). Lipid-containing foods undergo digestion within the body and are broken into fatty acids and glycerol, the final degradation products of fats and lipids. Lipids, especially [[phospholipid]]s, are also used in various [[pharmaceutical product]]s, either as co-solubilizers (e.g. in parenteral infusions) or else as [[drug carrier]] components (e.g. in a [[liposome]] or [[transfersome]]).

===Proteins===
{{Main|Protein|Amino acid}}

[[File:AminoAcidball.svg|thumbnail|The general structure of an α-amino acid, with the [[amine|amino]] group on the left and the [[carboxyl]] group on the right]]

[[Protein]]s are very large molecules—macro-biopolymers—made from monomers called [[amino acid]]s. An amino acid consists of an alpha carbon atom attached to an [[amino]] group, –NH<sub>2</sub>, a [[carboxylic acid]] group, –COOH (although these exist as –NH<sub>3</sub><sup>+</sup> and –COO<sup>−</sup> under physiologic conditions), a simple [[hydrogen atom]], and a side chain commonly denoted as "–R". The side chain  "R" is different for each amino acid of which there are 20 [[proteinogenic amino acid|standard ones]].  It is this "R" group that makes each amino acid different, and the properties of the side chains greatly influence the overall [[Protein tertiary structure|three-dimensional conformation]] of a protein. Some amino acids have functions by themselves or in a modified form; for instance, [[glutamate]] functions as an important [[neurotransmitter]]. Amino acids can be joined via a [[peptide bond]]. In this [[Dehydration reaction|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 thirty) are called ''[[peptides]]'' or [[polypeptides]]. Longer stretches merit the title ''proteins''. As an example, the important blood [[blood plasma|serum]] protein [[human serum albumin|albumin]] contains 585 [[Protein structure|amino acid residues]].<ref name="Metzler 2001">[[#Metzler|Metzler]] (2001), p. 58.</ref>
[[File:Amino acids 1.png|thumb|left|Generic amino acids (1) in neutral form, (2) as they exist physiologically, and (3) joined as a dipeptide]]

[[File:1GZX Haemoglobin.png|thumb|A schematic of [[hemoglobin]]. The red and blue ribbons represent the protein [[globin]]; the green structures are the [[heme]] groups.]]
Proteins can have structural and/or functional 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. Antibodies are composed of heavy and light chains. Two heavy chains would be linked to two light chains through [[disulfide linkage]]s between their amino acids. Antibodies are specific through variation based on differences in the N-terminal domain.<ref>{{cite journal |doi=10.1016/j.tibs.2009.11.005 |pmid=20022755 |pmc=4716677 |title=How antibodies fold |journal=Trends in Biochemical Sciences |volume=35 |issue=4 |pages=189–198 |year=2010 |last1=Feige |first1=Matthias J. |last2=Hendershot |first2=Linda M. |last3=Buchner |first3=Johannes }}</ref>

The [[enzyme-linked immunosorbent assay]] (ELISA), which uses antibodies, is one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins, however, are the [[enzyme]]s. Virtually every reaction in a living cell requires an enzyme to lower the [[activation energy]] of the reaction. These molecules recognize specific reactant molecules called ''[[substrate (biochemistry)|substrates]]''; they then [[Catalysis|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.

The structure of proteins is traditionally described in a hierarchy of four levels. The [[primary structure]] of a protein 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 (morphology being the study of structure). Some combinations of amino acids will tend to curl up in a coil called an [[alpha helix|α-helix]] or into a sheet called a [[Beta sheet|β-sheet]]; some α-helixes 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 alpha 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.<ref>[[#Fromm|Fromm and Hargrove]] (2012), pp. 35–51.</ref>

[[File:Protein structure examples.png|thumb|Examples of protein structures from the [[Protein Data Bank]]]]
[[File:Structural coverage of the human cyclophilin family.png|thumb|Members of a protein family, as represented by the structures of the [[isomerase]] [[protein domain|domains]]]]
Ingested proteins are usually broken up into single amino acids or dipeptides in the [[small intestine]] and then absorbed. They can then be joined to form new proteins. Intermediate products of glycolysis, the citric acid cycle, and the [[pentose phosphate pathway]] can be used to form all twenty amino acids, and most bacteria and plants possess all the necessary enzymes to synthesize them. Humans and other mammals, however, can synthesize only half of them. They cannot synthesize [[isoleucine]], [[leucine]], [[lysine]], [[methionine]], [[phenylalanine]], [[threonine]], [[tryptophan]], and [[valine]]. Because they must be ingested, these are the [[essential amino acid]]s. 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 form a protein.

A similar process is used to break down proteins. It is first hydrolyzed into its component amino acids. Free [[ammonia]] (NH3), existing as the [[ammonium]] ion (NH4+) in blood, is toxic to life forms. A suitable method for excreting it must therefore exist. Different tactics have evolved in different animals, depending on the animals' needs. [[Unicellular]] organisms release the ammonia into the environment. Likewise, [[Osteichthyes|bony fish]] can release ammonia into the water where it is quickly diluted. In general, mammals convert ammonia into urea, via the [[urea cycle]].

In order to determine whether two proteins are related, or in other words to decide whether they are homologous or not, scientists use sequence-comparison methods. Methods like [[sequence alignment]]s and [[structural alignment]]s are powerful tools that help scientists identify [[Sequence homology|homologies]] between related molecules. The relevance of finding homologies among proteins goes beyond forming an evolutionary pattern of [[Protein family|protein families]]. By finding how similar two protein sequences are, we acquire knowledge about their structure and therefore their function.

===Nucleic acids===
{{Main|Nucleic acid|DNA|RNA|Nucleotide}}
[[File:0322 DNA Nucleotides.jpg|thumbnail|The structure of [[deoxyribonucleic acid]] (DNA); the picture shows the monomers being put together.]]

[[Nucleic acids]], so-called because of their prevalence in cellular [[cell nucleus|nuclei]], is the generic name of the family of [[biopolymer]]s. They are complex, high-molecular-weight biochemical macromolecules that can convey [[genetic information]] in all living cells and viruses.<ref name="Voet_2005"/> The monomers 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.<ref>[[#Saenger|Saenger]] (1984), p. 84.</ref>

[[File:Nucleotides 1.svg|class=skin-invert-image|thumb|Structural elements of common nucleic acid constituents. Because they contain at least one phosphate group, the compounds marked ''nucleoside monophosphate'', ''nucleoside diphosphate'' and ''nucleoside triphosphate'' are all nucleotides (not phosphate-lacking [[nucleoside]]s).]]

The most common nucleic acids are [[deoxyribonucleic acid]] (DNA) and [[ribonucleic acid]] (RNA). The [[phosphate group]] and the sugar of each nucleotide bond with each other to form the backbone of the nucleic acid, while the sequence of nitrogenous bases stores the information. The most common nitrogenous bases are [[adenine]], [[cytosine]], [[guanine]], [[thymine]], and [[uracil]]. The [[nitrogenous base]]s of each strand of a nucleic acid will form [[hydrogen bonds]] with certain other nitrogenous bases in a complementary strand of nucleic acid. Adenine binds with thymine and uracil, thymine binds only with adenine, and cytosine and guanine can bind only with one another. Adenine, thymine, and uracil contain two hydrogen bonds, while hydrogen bonds formed between cytosine and guanine are three.

Aside from the genetic material of the cell, nucleic acids often play a role as [[second messenger]]s, as well as forming the base molecule for [[adenosine triphosphate]] (ATP), the primary energy-carrier molecule found in all living organisms. Also, the nitrogenous bases possible in the two nucleic acids are different: adenine, cytosine, and guanine occur in both RNA and DNA, while thymine occurs only in DNA and uracil occurs in RNA.

==Metabolism==

===Carbohydrates as energy source===
{{Main|Carbohydrate metabolism|Carbon cycle}}
Glucose is an energy source in most life forms. For instance, polysaccharides are broken down into their monomers by [[enzyme]]s ([[glycogen phosphorylase]] removes glucose residues from glycogen, a polysaccharide). Disaccharides like lactose or sucrose are cleaved into their two component monosaccharides.<ref>{{cite web |title=Disaccharide |url=https://www.britannica.com/science/disaccharide |access-date=14 October 2023 |website=Encyclopedia Britannica |archive-date=19 October 2023 |archive-url=https://web.archive.org/web/20231019212527/https://www.britannica.com/science/disaccharide |url-status=live }}</ref>

====Glycolysis (anaerobic)====
{{Glycolysis summary}}
Glucose is mainly metabolized by a very important ten-step [[Metabolic pathway|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 of converting [[Nicotinamide adenine dinucleotide|NAD<sup>+</sup>]] (nicotinamide adenine dinucleotide: oxidized form) to NADH (nicotinamide adenine dinucleotide: reduced form). 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 (lactic acid)]] (e.g. in humans) or to [[ethanol]] plus carbon dioxide (e.g. in [[yeast]]). Other monosaccharides like galactose and fructose can be converted into intermediates of the glycolytic pathway.<ref>[[#Fromm|Fromm and Hargrove]] (2012), pp. 163–180.</ref>

====Aerobic====
In [[aerobic glycolysis|aerobic]] cells with sufficient [[oxygen]], as in most human cells, the pyruvate is further metabolized. It is irreversibly converted to [[acetyl-CoA]], giving off one carbon atom as the waste product [[carbon dioxide]], generating another reducing equivalent as [[NADH]]. The two molecules acetyl-CoA (from one molecule of glucose) then enter the [[citric acid cycle]], producing two molecules of ATP, six more NADH molecules and two reduced (ubi)quinones (via [[FADH2|FADH<sub>2</sub>]] as enzyme-bound cofactor), and releasing the remaining carbon atoms as carbon dioxide. The produced NADH and quinol molecules then feed into the enzyme complexes of the respiratory chain, an [[electron transport system]] transferring the electrons ultimately to oxygen and conserving the released energy in the form of a proton gradient over a membrane ([[inner mitochondrial membrane]] in eukaryotes). Thus, oxygen is reduced to water and the original electron acceptors NAD<sup>+</sup> and [[quinone]] are regenerated. This is why humans breathe in oxygen and breathe out carbon dioxide. The energy released from transferring the electrons from high-energy states in NADH and quinol is conserved first as proton gradient and converted to ATP via ATP synthase. This generates an additional ''28'' molecules of ATP (24 from the 8 NADH + 4 from the 2 quinols), totaling to 32 molecules of ATP conserved per degraded glucose (two from glycolysis + two from the citrate cycle).<ref>[[#Voet|Voet]] (2005), Ch. 17 Glycolysis.</ref> It is clear that using oxygen to completely oxidize glucose provides an organism with far more energy than any oxygen-independent metabolic feature, and this is thought to be the reason why complex life appeared only after Earth's atmosphere accumulated large amounts of oxygen.

====Gluconeogenesis====
{{Main|Gluconeogenesis}}
In [[vertebrate]]s, vigorously contracting [[skeletal muscle]]s (during weightlifting or sprinting, for example) do not receive enough oxygen to meet the energy demand, and so they shift to [[Fermentation (biochemistry)|anaerobic metabolism]], converting glucose to lactate.
The combination of glucose from noncarbohydrates origin, such as fat and proteins. This only happens when [[glycogen]] supplies in the liver are worn out. The pathway is a crucial reversal of [[glycolysis]] from pyruvate to glucose and can use many sources like amino acids, glycerol and [[Krebs Cycle]]. Large scale protein and fat [[catabolism]] usually occur when those suffer from starvation or certain endocrine disorders.<ref>{{Cite book| url=https://www.oxfordreference.com/view/10.1093/acref/9780198714378.001.0001/acref-9780198714378| isbn=9780198714378| title=A Dictionary of Biology| date=17 September 2015| publisher=Oxford University Press| access-date=29 April 2020| archive-date=10 July 2020| archive-url=https://web.archive.org/web/20200710005409/https://www.oxfordreference.com/view/10.1093/acref/9780198714378.001.0001/acref-9780198714378| url-status=live}}</ref> The [[liver]] regenerates 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. The combined pathways of glycolysis during exercise, lactate's crossing via the bloodstream to the liver, subsequent gluconeogenesis and release of glucose into the bloodstream is called the [[Cori cycle]].<ref>[[#Fromm|Fromm and Hargrove]] (2012), pp. 183–194.</ref>

==Relationship to other "molecular-scale" biological sciences==
{{Multiple issues|section=y|
{{Unreferenced section|date=August 2023}}
{{Original research|section|reason=Section defines relationships between disciplines without citing any sources from those disciplines.|date=August 2023}}
}}
[[File:Schematic relationship between biochemistry, genetics and molecular biology.svg|thumb|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 developed in the fields of [[genetics]], [[molecular biology]], and [[biophysics]]. There is not a defined line between these disciplines. Biochemistry studies the [[chemistry]] required for biological activity of molecules, molecular biology studies their biological activity, [[genetics]] studies their heredity, which happens to be carried by their [[genome]]. This is shown in the following schematic that depicts one possible view of the relationships between the fields:
* '''''Biochemistry''''' is the study of the chemical substances and vital processes occurring in live [[organism]]s. [[Biochemist]]s focus heavily on the role, function, and structure of [[biomolecule]]s. The study of the chemistry behind biological processes and the synthesis of biologically active molecules are applications of biochemistry. Biochemistry studies life at the atomic and molecular level.
* '''''Genetics''''' is the study of the effect of genetic differences in organisms. This can often be inferred by the absence of a normal component (e.g. one [[gene]]). The study of "[[mutant]]s" – organisms that 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 "[[Gene knockout|knockout]]" studies.
* '''''Molecular biology''''' is the study of molecular underpinnings of the biological phenomena, focusing on molecular synthesis, modification, mechanisms and interactions. The [[central dogma of molecular biology]], where genetic material is transcribed into RNA and then translated into [[protein]], despite being oversimplified, still provides a good starting point for understanding the field. This concept has been revised 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 capsid]]s that can deliver [[gene therapy]] or [[Pharmaceutical drug|drug molecules]]).

==See also==
{{Main|Outline of biochemistry}}

=== Lists ===
{{div col|colwidth=22em}}
* [[List of important publications in chemistry#Biochemistry|Important publications in biochemistry (chemistry)]]
* [[List of biochemistry topics]]
* [[List of biochemists]]
* [[List of biomolecules]]
{{div col end}}

=== See also ===
{{div col|colwidth=22em}}
* [[Astrobiology]]
* [[Biochemistry (journal)]]
* [[Biological Chemistry (journal)]]
* [[Biophysics]]
* [[Chemical ecology]]
* [[Computational biomodeling]]
* [[Dedicated bio-based chemical]]
* [[Enzyme Commission number|EC number]]
* [[Hypothetical types of biochemistry]]
* [[International Union of Biochemistry and Molecular Biology]]
* [[Metabolome]]
* [[Metabolomics]]
* [[Molecular biology]]
* [[Molecular medicine]]
* [[Plant biochemistry]]
* [[Proteolysis]]
* [[Small molecule]]
* [[Structural biology]]
* [[TCA cycle]]
{{div col end}}

==Notes==
{{Notelist}}

==References==
{{Reflist}}

=== Cited literature ===
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* {{cite book |ref=Stryer |vauthors=Stryer L, Berg JM, Tymoczko JL |title=Biochemistry |publisher=W.H. Freeman |location=San Francisco |edition=6th |year=2007 |isbn=978-0-7167-8724-2 |url=https://archive.org/details/biochemistry0006berg |url-access=registration }}
* {{cite book |ref=Tropp |author=Tropp, Burton E. |title=Molecular Biology |edition=4th |year=2012 |publisher=Jones & Bartlett Learning |isbn=978-1-4496-0091-4 |url=https://books.google.com/books?id=CCQYtlufUIAC |access-date=2020-06-05 |archive-date=2023-10-28 |archive-url=https://web.archive.org/web/20231028024617/https://books.google.com/books?id=CCQYtlufUIAC |url-status=live }}
* {{cite book |ref=UNICEF |author=UNICEF |title=Facts for life |date=2010 |publisher=United Nations Children's Fund |location=New York |isbn=978-92-806-4466-1 |edition=4th |url=http://www.unicef.org/nutrition/files/Facts_for_Life_EN_010810.pdf |archive-url=https://ghostarchive.org/archive/20221009/http://www.unicef.org/nutrition/files/Facts_for_Life_EN_010810.pdf |archive-date=2022-10-09 |url-status=live }}
* {{cite journal |ref=Ulveling |doi=10.1016/j.biochi.2010.11.004 |pmid=21111023 |title=When one is better than two: RNA with dual functions |journal=Biochimie |volume=93 |issue=4 |pages=633–644 |year=2011 |last1=Ulveling |first1=Damien |last2=Francastel |first2=Claire |last3=Hubé |first3=Florent |s2cid=22165949 |url=https://hal-univ-diderot.archives-ouvertes.fr/hal-02127323/file/Ulveling%20Review%20revised.pdf |archive-url=https://ghostarchive.org/archive/20221009/https://hal-univ-diderot.archives-ouvertes.fr/hal-02127323/file/Ulveling%20Review%20revised.pdf |archive-date=2022-10-09 |url-status=live }}
* {{cite book | ref=Varki | vauthors=Varki A, Cummings R, Esko J, Jessica F, Hart G, Marth J | title=Essentials of glycobiology | publisher=Cold Spring Harbor Laboratory Press | year=1999 | isbn=978-0-87969-560-6 | url=https://books.google.com/books?id=lH72FFWIIpgC | access-date=2020-06-05 | archive-date=2023-10-28 | archive-url=https://web.archive.org/web/20231028024617/https://books.google.com/books?id=lH72FFWIIpgC | url-status=live }}
* {{cite book |ref=Voet |author1=Voet, D |author2=Voet, JG |year=2005 |title=Biochemistry |edition=3rd |publisher=John Wiley & Sons Inc. |location=Hoboken, NJ |url=http://www.chem.upenn.edu/chem/research/faculty.php?browse=V |isbn=978-0-471-19350-0 |url-status=dead |archive-url=https://web.archive.org/web/20070911065858/http://www.chem.upenn.edu/chem/research/faculty.php?browse=V |archive-date=September 11, 2007 }}
* {{Cite book |ref=Whiting |author=Whiting, G.C |year=1970 |chapter=Sugars |editor=A.C. Hulme |title=The Biochemistry of Fruits and their Products |volume=1 |place=London & New York |publisher=Academic Press |chapter-url=https://books.google.com/books?id=KYDwAAAAMAAJ |isbn=978-0-12-361201-4 |url-access=registration |url=https://archive.org/details/biochemistryoffr0000hulm }}
* {{cite book |ref=Ziesak |author1=Ziesak, Anne-Katrin |author2=Cram Hans-Robert |url=https://books.google.com/books?id=ulN4rKWA8c4C&pg=PA169 |title=Walter de Gruyter Publishers, 1749–1999 |publisher=Walter de Gruyter & Co |year=1999 |isbn=978-3-11-016741-2 |access-date=2015-07-27 |archive-date=2023-10-28 |archive-url=https://web.archive.org/web/20231028024618/https://books.google.com/books?id=ulN4rKWA8c4C&pg=PA169 |url-status=live }}
* {{cite news |last1=Ashcroft |first1=Steve |title=Professor Sir Philip Randle; Researcher into metabolism: [1st Edition] |newspaper=Independent |id={{ProQuest|311080685}} }}
{{refend}}

== Further reading ==
{{refbegin|30em}}
* Fruton, Joseph S.  ''[[iarchive:proteinsenzymesg0000frut|Proteins, Enzymes, Genes: The Interplay of Chemistry and Biology]]''.  Yale University Press: New Haven, 1999.  {{ISBN|0-300-07608-8}}
* Keith Roberts, Martin Raff, Bruce Alberts, Peter Walter, Julian Lewis and Alexander Johnson, ''Molecular Biology of the Cell''
** 4th Edition, Routledge, March, 2002, hardcover, 1616 pp. {{ISBN|0-8153-3218-1}}
** 3rd Edition, Garland, 1994, {{ISBN|0-8153-1620-8}}
** 2nd Edition, Garland, 1989, {{ISBN|0-8240-3695-6}}
* Kohler, Robert.  ''From Medical Chemistry to Biochemistry: The Making of a Biomedical Discipline''. Cambridge University Press, 1982.
* {{cite journal |doi=10.1371/journal.pone.0190046 |pmid=29267345 |pmc=5739466 |title=Wikipedia as a gateway to biomedical research: The relative distribution and use of citations in the English Wikipedia |journal=PLOS ONE |volume=12 |issue=12 |pages=e0190046 |year=2017 |last1=Maggio |first1=Lauren A. |last2=Willinsky |first2=John M. |last3=Steinberg |first3=Ryan M. |last4=Mietchen |first4=Daniel |last5=Wass |first5=Joseph L. |last6=Dong |first6=Ting |bibcode=2017PLoSO..1290046M |doi-access=free }}
{{refend}}

== External links ==
{{Library resources box}}
{{wikibooks}}
{{commons category|Biochemistry}}
{{WVD}}
* {{cite web |url= http://www.biochemistry.org/ |title = Biochemical Society}}
* [http://biochemweb.fenteany.com/ The Virtual Library of Biochemistry, Molecular Biology and Cell Biology]
* [https://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.systemsX.ch/ SystemsX.ch – The Swiss Initiative in Systems Biology]
* [http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy Full text of Biochemistry] by Kevin and Indira, an introductory biochemistry textbook.

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