Instruct: Given a question, retrieve relevant passages that can help answer the question.
Query: What is the longest amino acid?
Titin is the third most abundant protein in muscle (after myosin and actin), and an adult human contains approximately 0.5kg of titin.[8] With its length of ~27,000 to ~33,000 amino acids (depending on the splice isoform), titin is the largest known protein.[9] Furthermore, the gene for titin contains the largest number of exons (363) discovered in any single gene,[10] as well as the longest single exon (17,106 bp).
In this area of research, the 20 encoded proteinogenic amino acids are referred to as standard amino acids, or alternatively as natural or canonical amino acids, while the added amino acids are called non-standard amino acids (NSAAs), or unnatural amino acids (uAAs; term not used in papers dealing with natural non-proteinogenic amino acids, such as phosphoserine), or non-canonical amino acids.
The genetic code encodes 20 standard amino acids for incorporation into proteins during translation. However, there are two extra proteinogenic amino acids: selenocysteine and pyrrolysine. These non-standard amino acids do not have a dedicated codon, but are added in place of a stop codon when a specific sequence is present, UGA codon and SECIS element for selenocysteine, UAG PYLIS downstream sequence for pyrrolysine.
All other amino acids are termed "non-proteinogenic". 
There are various groups of amino acids:
These groups overlap, but are not identical. All 22 proteinogenic amino acids are biosynthesised by organisms and some, but not all, of them also are abiotic (found in prebiotic experiments and meteorites). Some natural amino acids, such as norleucine, are misincorporated translationally into proteins due to infidelity of the protein-synthesis process. Many amino acids, such as ornithine, are metabolic intermediates produced biosynthetically, but not incorporated translationally into proteins. Post-translational modification of amino-acid residues in proteins leads to the formation of many proteinaceous, but non-proteinogenic, amino acids. Other amino acids are solely found in abiotic mixes (e.g. α-methylnorvaline). Over 30 unnatural amino acids have been inserted translationally into protein in engineered systems, yet are not biosynthetic.
In addition to these counts, data on the mutability and the frequency of the amino acids was obtained. The mutability of an amino acid is the ratio of the number of mutations it is involved in and the number of times it occurs in an alignment. Mutability measures how likely an amino acid is to mutate acceptably. Asparagine, an amino acid with a small polar side chain, was found to be the most mutable of the amino acids. Cysteine and tryptophan were found to be the least mutable amino acids. The side chains for cysteine and tryptophan have less common structures: cysteine's side chain contains sulfur which participates in disulfide bonds with other cysteine molecules, and tryptophan's side chain is large and aromatic. Since there are several small polar amino acids, these extremes suggest that amino acids are more likely to acceptably mutate if their physical and chemical properties are more common among alternative amino acids.
Amino acid similarity matrices are more complicated, because there are 20 amino acids coded for by the genetic code, and so a larger number of possible substitutions. Therefore, the similarity matrix for amino acids contains 400 entries (although it is usually symmetric). The first approach scored all amino acid changes equally. A later refinement was to determine amino acid similarities based on how many base changes were required to change a codon to code for that amino acid. This model is better, but it doesn't take into account the selective pressure of amino acid changes. Better models took into account the chemical properties of amino acids.
"C7orf43" encodes 2 isoforms, the longest being C7orf43 isoform 1, which is 2585 base pairs long and has with 11 exons and 10 introns. C7orf43 isoform 1 encodes a protein that is 580 amino acids long and only has one polyadenylation site. C7orf43 isoform 2 is 2085 base pairs long and encodes a protein of 311 amino acids. Two additional isoforms has been reported on several occasions, encoding for proteins with 199 and 206 amino acids.
Ankycorbin has four different isoforms (A, B, C, and D) with most isoforms containing one or more splice variants that mainly differ in the 5' UTR. Isoform D is the longest known isoform at 983 amino acids in length, however isoform A (980 amino acids) is the most predominant form of the protein.
Amino acids contain both amino and carboxylic acid functional groups. (In biochemistry, the term amino acid is used when referring to those amino acids in which the amino and carboxylate functionalities are attached to the same carbon, plus proline which is not actually an amino acid).
If the amino group is removed from an amino acid, it leaves behind a carbon skeleton called an α-keto acid. Enzymes called transaminases 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.
If one of the essential amino acids is less than needed for an individual the utilization of other amino acids will be hindered and thus protein synthesis will be less than what it usually is, even in the presence of adequate total nitrogen intake.
When taken up into the human body from the diet, the 20 standard amino acids either are used to synthesize proteins and other biomolecules or are oxidized to urea and carbon dioxide as a source of energy.[64] The oxidation pathway starts with the removal of the amino group by a transaminase; the amino group is then fed into the urea cycle. The other product of transamidation is a keto acid that enters the citric acid cycle.[65] Glucogenic amino acids can also be converted into glucose, through gluconeogenesis.[66] Of the 20 standard amino acids, nine (His, Ile, Leu, Lys, Met, Phe, Thr, Trp and Val) are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food.[67][68][69] In addition, cysteine, taurine, tyrosine, and arginine are considered semiessential amino-acids in children (though taurine is not technically an amino acid), because the metabolic pathways that synthesize these amino acids are not fully developed.[70][71] The amounts required also depend on the age and health of the individual, so it is hard to make general statements about the dietary requirement for some amino acids. Dietary exposure to the non-standard amino acid BMAA has been linked to human neurodegenerative diseases, including ALS.[72][73]
Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants can synthesize all twenty, but mammals can only synthesize eleven nonessential amino acids, so nine essential amino acids must be obtained from food. Some simple parasites, such as the bacteria "Mycoplasma pneumoniae", lack all amino acid synthesis and take their amino acids directly from their hosts. All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and glutamine. Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then transaminated to form an amino acid.
The coding sequence for the C15orf39 mRNA is 4443 base pairs long. The C15orf39 gene produces seven mRNA transcripts, with the longest coding isoform being 1047 amino acids long, and the shortest being 27 amino acids which has a truncated 3' end.
The DEPDC1B gene possesses two novel proteoforms. The longest variation, coded by mRNA isoform 1, is the most commonly used. The protein is 529 amino acids in length. The second novel proteoform, DEPDC1B.2 is coded by 10 exons, missing the 10th exon from the longest variation. The protein is 467 amino acids in length. The missing 62 amino acids follow the RhoGAP domain, in a region predicted to be highly phosphorylated
Alpha-carbon (α-carbon) is also a term that applies to proteins and amino acids. It is the backbone carbon before the carbonyl carbon atom in the molecule. Therefore, reading along the backbone of a typical protein would give a sequence of –[N—Cα—carbonyl C]– etc. (when reading in the N to C direction). The α-carbon is where the different substituents attach to each different amino acid. That is, the groups hanging off the chain at the α-carbon are what give amino acids their diversity. These groups give the α-carbon its stereogenic properties for every amino acid except for glycine. Therefore, the α-carbon is a stereocenter for every amino acid except glycine. Glycine also does not have a β-carbon, while every other amino acid does.
Some non-proteinogenic amino acids are not found in proteins. Examples include 2-aminoisobutyric acid and the neurotransmitter gamma-aminobutyric acid. Non-proteinogenic amino acids often occur as intermediates in the metabolic pathways for standard amino acids– for example, ornithine and citrulline occur in the urea cycle, part of amino acid catabolism (see below).[58] A rare exception to the dominance of α-amino acids in biology is the β-amino acid beta alanine (3-aminopropanoic acid), which is used in plants and microorganisms in the synthesis of pantothenic acid (vitamin B5), a component of coenzyme A.[59]
The K48-linked polyubiquitination is a marker for proteasomal degradation that releases two- to 24-amino-acid-long peptides, which are quickly degraded to amino acids by various oligopeptidases and aminopeptidases present in the cytoplasm. Amino acids are imported into the LCV through various amino acid transporters such as the SLC1A5 (neutral amino acid transporter).
The amino acids are the primary carbon and energy source of "L. pneumophila", that have almost 12 classes of ABC transporters, amino-acid permeases, and many proteases, to exploit it. The imported amino acids are used by "L. pneumophila" to generate energy through the TCA cycle (Krebs cycle) and as sources of carbon and nitrogen.
The most abundant variant of CCDC130 is encoded by the second longest open reading frame (ORF), corresponding to a 396 amino acid protein with a molecular weight of 44.8 kDa and an isoelectric point of 8.252. The CCDC130 protein is rich in charged amino acids and deficient in uncharged, non-polar amino acids. Mobyle @ Pasteur predicted CCDC130 to be extremely hydrophilic due to the large numbers of charged and polar amino acids, with no site scoring above zero on the hydrophobicity graph and some sites reaching as low as -6 (F180). There is a region in the coiled coil domain (182-214) in which 14 of 18 amino acids are charged. SAPS analysis predicted that this protein would be unstable. Due to its high hydrophilicity, this protein definitely does not contain transmembrane segments.
Some amino acids are more likely to be replaced. One of the factors that influences this tendency is physicochemical distance. Example of a measure of amino acid can be Graur's Stability Index. The assumption of this measure is that the amino acid replacement rate and protein's evolution is dependent on the amino acid composition of protein. Stability index "S" of an amino acid is calculated based on physicochemical distances of this amino acid and its alternatives than can mutate through single nucleotide substitution and probabilities to replace into these amino acids. Based on Grantham's distance the most immutable amino acid is cysteine, and the most prone to undergo exchange is methionine. 
Evolution of proteins is slower than DNA since only nonsynonymous mutations in DNA can result in amino acid replacements. Most mutations are neutral to maintain protein function and structure. Therefore, the more similar amino acids are, the more probable that they will be replaced. Conservative replacements are more common than radical replacements, since they can result in less important phenotypic changes. On the other hand, beneficial mutations, enhancing protein functions are most likely to be radical replacements. Also, the physicochemical distances, which are based on amino acids properties, are negatively correlated with probability of amino acids substitutions. Smaller distance between amino acids indicates that they are more likely to undergo replacement.
Several methods exist to synthesize amino acids. One of the oldest methods begins with the bromination at the α-carbon of a carboxylic acid. Nucleophilic substitution with ammonia then converts the alkyl bromide to the amino acid.[112] In alternative fashion, the Strecker amino acid synthesis involves the treatment of an aldehyde with potassium cyanide and ammonia, this produces an α-amino nitrile as an intermediate. Hydrolysis of the nitrile in acid then yields an α-amino acid.[113] Using ammonia or ammonium salts in this reaction gives unsubstituted amino acids, whereas substituting primary and secondary amines will yield substituted amino acids.[114] Likewise, using ketones, instead of aldehydes, gives α,α-disubstituted amino acids.[115] The classical synthesis gives racemic mixtures of α-amino acids as products, but several alternative procedures using asymmetric auxiliaries[116] or asymmetric catalysts[117][118] have been developed.[119]
Unnatural amino acids incorporated into proteins include heavy atom containing amino acids to facilitate certain x-ray crystallographic studies; amino acids with novel steric/packing and electronic properties; photocrosslinking amino acids which can be used to probe protein-protein interactions in vitro or in vivo; keto, acetylene, azide, and boronate containing amino acids which can be used to selectively introduce a large number of biophysical probes, tags, and novel chemical functional groups into proteins "in vitro" or "in vivo"; redox active amino acids to probe and modulate electron transfer; photocaged and photoisomerizable amino acids to photoregulate biological processes; metal binding amino acids for catalysis and metal ion sensing; amino acids that contain fluorescent or infra-red active side chains to probe protein structure and dynamics; α-hydroxy acids and -amino acids as probes of backbone conformation and hydrogen bonding interactions; and sulfated amino acids and mimetics of phosphorylated amino acids as probes of posttranslational modifications.
Several non-proteinogenic amino acids are toxic due to their ability to mimic certain properties of proteinogenic amino acids, such as thialysine. Some non-proteinogenic amino acids are neurotoxic by mimicking amino acids used as neurotransmitters (i.e. not for protein biosynthesis), e.g. Quisqualic acid, canavanine or azetidine-2-carboxylic acid.
Cephalosporin C has an α-aminoadipic acid (homoglutamate) backbone that is amidated with a cephalosporin moiety. Penicillamine is a therapeutic amino acid, whose mode of action is unknown.
Naturally-occurring cyanotoxins can also include non-proteinogenic amino acids. Microcystin and nodularin, for example, are both derived from ADDA, a β-amino acid.
The human PAK3 gene, the longest group I family member, is 283-kb long. The PAK3 gene is composed of 22 exons of which 6 exons are for 5’-UTR and generates 13 alternative spliced transcripts. Among PAK3 transcripts, 11 transcripts are for coding proteins ranging from 181- to 580-amino acids long, while remaining two transcripts are non-coding RNAs. The murine PAK3 gene contains 10 transcripts, coding six proteins from 544 amino acids and 559 amino acids long, and four smaller polypeptides from 23 to 366 amino acids.
As both the amine and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids is what creates proteins. This condensation reaction yields the newly formed peptide bond and a molecule of water. In cells, this reaction does not occur directly; instead, the amino acid is first activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase.[120] This aminoacyl-tRNA is then a substrate for the ribosome, which catalyzes the attack of the amino group of the elongating protein chain on the ester bond.[121] As a result of this mechanism, all proteins made by ribosomes are synthesized starting at their N-terminus and moving toward their C-terminus.
The phrase "branched-chain amino acids" or BCAA refers to the amino acids having aliphatic side chains that are non-linear; these are leucine, isoleucine, and valine. Proline is the only proteinogenic amino acid whose side-group links to the α-amino group and, thus, is also the only proteinogenic amino acid containing a secondary amine at this position.[38] In chemical terms, proline is, therefore, an imino acid, since it lacks a primary amino group,[45] although it is still classed as an amino acid in the current biochemical nomenclature,[46] and may also be called an "N-alkylated alpha-amino acid".[47]