Instruct: Given a question, retrieve relevant passages that can help answer the question.
Query: Are there amino acids in oranges?
For Canadian markets, orange juice must be the fruit juice obtained from clean, sound, and mature oranges.[29] The juice must also contain a minimum of 1.20 milliequivalents of free amino acids per 100 millilitres, contain a minimum of 115 milligrams of potassium per 10 milliliters, and possess a minimum absorbance value for total polyphenolics of 0.380.[30] Sweeteners such as sugar, invert sugar, dextrose or glucose solids may be added. The orange juice must have a Brix reading of at least 9.7, excluding the sweetening ingredients, and contain between 0.5 and 1.8 percent of acid by weight calculated as anhydrous citric acid.[29] Added orange essences, orange oils and orange pulp adjusted in accordance with good manufacturing practice is permitted. Orange juice is also permitted to contain sugar, invert sugar, dextrose in dry form, glucose solids, a Class II preservative, amylase, cellulase and pectinase.[29]
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.
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]
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).
Proteins are very large molecules—macro-biopolymers—made from monomers called amino acids. An amino acid consists of a carbon atom attached to an amino group, –NH, a carboxylic acid group, –COOH (although these exist as –NH and –COO 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 standard ones. It is this "R" group that made each amino acid different, and the properties of the side-chains greatly influence the overall 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 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 serum protein albumin contains 585 amino acid residues.
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.
A protein is first phosphorylated using P-labeled ATP, usually via an "in vitro" kinase assay. Most of the amino acids 
in the protein are then hydrolyzed, usually by the use of a strong acid such as hydrochloric acid. These amino acids are then separated using 2-dimensional thin layer chromatography, along with amino acid standards for the three amino acids that are phosphorylated in eukaryotes: serine, threonine, and tyrosine. These amino acid standards can be visualized on the TLC substrate by exposure to ninhydrin, which colors the amino acids a visible purple when heated at ~100 °C. The radioactive amino acids can be detected via autoradiography, and an overlay of the two images will show which amino acids are phosphorylated.
The "Buchnera" genome has retained genes required for the biosynthesis of essential amino acids but has not retained genes responsible for the degradation of amino acids. The "A. pisum" genome on the other hand, contains 66 amino acid biosynthesis genes and 93 amino acid degradation genes. Both "A. pisum" and "Buchnera" contribute to the metabolic pathways of amino acid biosynthesis. This metabolic complementarity is illustrated by the use of asparagine, a nonessential amino acid in phloem sap, as a major precursor in the production essential and nonessential amino acids necessary for the growth and survival of "A. pisum" and "Buchnera".
Amino acid synthesis is the set of biochemical processes (metabolic pathways) by which the various amino acids are produced from other compounds. The substrates for these processes are various compounds in the organism's diet or growth media. Not all organisms are able to synthesize all amino acids. Humans are an excellent example of this, since humans can only synthesize 11 of the 20 standard amino acids (a.k.a. non-essential amino acid), and in time of accelerated growth, histidine, can be considered an essential amino acid.
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.
A dipeptide is an organic compound derived from two amino acids. The amino acids can be the same or different. When different, two isomers of the dipeptide are possible, depending on the sequence. Similar descriptions apply to tripeptide (three amino acid residues, two peptide bonds), tetrapeptide, and so on; longer chains are called oligopeptide, polypeptide, protein.
Dipeptides are produced by coupling amino acids. The amino group on one amino acid is rendered non-nucleophilic (P in eq) and the carboxylic acid group in the second amino acid is deactivated as its methyl ester. The two modified amino acids are then combined in the presence of a coupling agent, which facilitates formation of the amide bond:
Subsequent to this coupling reaction, the amine protecting group P and the ester are converted to the free amine and carboxylic acid, respectively.
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]
Transamination, a chemical reaction that transfers an amino group to a ketoacid to form new amino acids. This pathway is responsible for the deamination of most amino acids. This is one of the major degradation pathways which convert essential amino acids to nonessential amino acids (amino acids that can be synthesized de novo by the organism).
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.
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.
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.
Amino acid racemization analysis consists of sample preparation, isolation of the amino acid wanted, and measure of its D:L ratio. Sample preparation entails the identification, raw extraction, and separation of proteins into their constituent amino acids, typically by grinding followed by acid hydrolysis. The amino acid derivative hydrolysis product can be combined with a chiral specific fluorescent, separated by chromatography or electrophoresis, and the particular amino acid D:L ratio determined by fluorescence. Alternatively, the particular amino acid can be separated by chromatography or electrophoresis, combined with a metal cation, and the D:L ratio determined by mass spectrometry. Chromatographic and electrophoretic separation of proteins and amino acids is dependent upon molecular size, which generally corresponds to molecular weight, and to a lesser extent upon shape and charge.
Studies with mouse HES7 have demonstrated that the gene contains 4 exons. There are three known human HES7 variants due to alterative splicing. The gene product is a transcription factor protein. The Helix-loop-helix domain is located at the N-terminal end of the protein. Both the human and the mouse protein have been shown to contain 225 amino acids and feature an orange domain as well as a conserved sequence of four amino acids at the C-terminal end. The four amino acids are Tryptophan-Arginine-Proline-Tryptophan. This conserved sequence of four amino acids binds Groucho/TLE family members. Groucho/TLE are transcriptional corepressors. Hairy-related proteins can direct these transcriptional corepressors to target genes. Orange domains are motifs of ~35 amino acids that are found on the C-terminal side of basic helix-loop-helix domains in some transcription factors in eukaryotic organisms. Proteins with Orange domains are divided into four subfamilies, three in which all proteins contain a basic helix-loop-helix domain. The subfamilies that contain Orange domains and basic helix-loop-helix domains are Hairy, Enhancer of Split, and Hey. Transcription factors with Orange domains bind DNA and regulate biological processes such as cell differentiation and embryonic patterning.
Like other insects of the order Hemiptera, "A.pisum" utilizes an endosymbiotic bacterium to overcome the nutritional deficiencies of phloem sap. "A. pisum" feeds on phloem sap of host plants including "Medicago sativa" (alfalfa), "Pisum sativa" (pea), "Trifolium pretense" (red clover), and "Vicia faba" (broad bean). The phloem saps of these plants are nutritionally rich in carbohydrates but poor in terms of nitrogen. The ratio of essential amino acids to nonessential amino acids in these phloem saps ranges from 1:4-1:20. This ratio of essential to nonessential amino acids is severely disproportional compared to the 1:1 ratio present in animal tissues and necessary for survival. Animals, including "A. pisum", can produce nonessential amino acids "de novo" but cannot synthesize nine essential amino acids that must be obtained through their diets: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. In addition to these nine essential amino acids, "A. pisum" is unable to synthesize arginine due to missing urea cycle genes. The endosymbiotic relationship with "Buchnera" allows "A. pisum" to overcome this lack of essential amino acids in the phloem sap 
When provided with nonessential amino acids, "Buchnera" converts nonessential amino acids into essential amino acids to be returned to "A. pisum". This nutritional provisioning has been examined genomically (metabolic complementary, discussed below) and experimentally. Isolated bacteriocytes containing "Buchnera" have been shown to actively take up 14C labeled glutamine (a nonessential amino acid) where it is then converted into glutamic acid. This glutamic acid is then taken up by the individual "Buchnera" cells and used to synthesize the essential amino acids isoleucine, leucine, phenylalanine, and valine as well as nonessential amino acids that can be returned to "A. pisum." Mutual nutrient provisioning is likely the main reason for the persistence of this symbiosis.
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.
Amino acids must first pass out of organelles and cells into blood circulation via amino acid transporters, since the amine and carboxylic acid groups are typically ionized. Degradation of an amino acid, occurring in the liver and kidneys, often involves deamination by moving its amino group to alpha-ketoglutarate, forming glutamate. This process involves transaminases, often the same as those used in amination during synthesis. In many vertebrates, the amino group is then removed through the urea cycle and is excreted in the form of urea. However, amino acid degradation can produce uric acid or ammonia instead. For example, serine dehydratase converts serine to pyruvate and ammonia.[84] After removal of one or more amino groups, the remainder of the molecule can sometimes be used to synthesize new amino acids, or it can be used for energy by entering glycolysis or the citric acid cycle, as detailed in image at right.
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]
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.
D-amino acid oxidase (DAAO; also OXDA, DAMOX) is an enzyme with the function on a molecular level to oxidize D-amino acids to the corresponding imino acids, producing ammonia and hydrogen peroxide. This results in a number of physiological effects in various systems, most notably the brain. The enzyme is most active toward neutral D-amino acids, and not active toward acidic D-amino acids. One of its most important targets in mammals is D-Serine in the central nervous system. By targeting this and other D-amino acids in vertebrates, DAAO is important in detoxification. The role in microorganisms is slightly different, breaking down D-amino acids to generate energy.
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.