Editing Biochemistry (section)

===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.