Editing Biochemistry (section)

==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
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| 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.