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2.two: Structure & Part - Amino Acids

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• Professor (Biochemistry and Biophysics) at Oregon State University

Source: BiochemFFA_2_1.pdf. The entire textbook is bachelor for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy

All of the proteins on the face of the earth are made upwards of the same twenty amino acids. Linked together in long bondage called polypeptides, amino acids are the edifice blocks for the vast assortment of proteins found in all living cells.

"It is i of the more striking generalizations of biochemistry ...that the twenty amino acids and the four bases, are, with pocket-sized reservations, the same throughout Nature." - Francis Crick

All amino acids accept the aforementioned basic structure, which is shown in Figure 2.1. At the "center" of each amino acrid is a carbon called the α carbon and fastened to it are four groups - a hydrogen, an α- carboxyl grouping, an α-amine group, and an R-grouping, sometimes referred to as a side chain. The α carbon, carboxyl, and amino groups are common to all amino acids, so the R-group is the only unique feature in each amino acid. (A minor exception to this construction is that of proline, in which the end of the R-group is fastened to the α-amine.) With the exception of glycine, which has an R-group consisting of a hydrogen cantlet, all of the amino acids in proteins have iv unlike groups fastened to them and consequently can exist in ii mirror image forms, Fifty and D. With only very pocket-sized exceptions, every amino acid found in cells and in proteins is in the L configuration.

Effigy two.1 - General amino acid structure

There are 22 amino acids that are establish in proteins and of these, only xx are specified by the universal genetic code. The others, selenocysteine and pyrrolysine utilise tRNAs that are able to base of operations pair with stop codons in the mRNA during translation. When this happens, these unusual amino acids tin can be incorporated into proteins. Enzymes containing selenocysteine, for instance, include glutathione peroxidases, tetraiodothyronine 5' deiodinases, thioredoxin reductases, formate dehydrogenases, glycine reductases, and selenophosphate synthetase. Pyrrolysine-containing proteins are much rarer and are generally confined to archaea.

Essential and not-essential

Nutritionists dissever amino acids into two groups - essential amino acids (must exist in the diet because cells tin can't synthesize them) and non-essential amino acids (can exist fabricated by cells). This classification of amino acids has little to do with the structure of amino acids. Essential amino acids vary considerable from one organism to some other and even differ in humans, depending on whether they are adults or children. Table 2.1 shows essential and non-essential amino acids in humans.

Some amino acids that are normally nonessential, may demand to be obtained from the diet in sure cases. Individuals who do not synthesize sufficient amounts of arginine, cysteine, glutamine, proline, selenocysteine, serine, and tyrosine, due to affliction, for example, may need dietary supplements containing these amino acids.

Table 2.1 - Essential and not-essential amino acids

Not-protein amino acids

There are also α-amino acids institute in cells that are not incorporated into proteins. Common ones include ornithine and citrulline. Both of these compounds are intermediates in the urea bike. Ornithine is a metabolic forerunner of arginine and citrulline can be produced by the breakdown of arginine. The latter reaction produces nitric oxide, an important signaling molecule. Citrulline is the metabolic byproduct. Information technology is sometimes used as a dietary supplement to reduce musculus fatigue.

R-group chemical science

Table 2.2 - Amino acid categories (based on R-group backdrop)

We dissever the amino acids into categories based on the chemistry of their R-groups. If you compare groupings of amino acids in dissimilar textbooks, you volition see unlike names for the categories and (sometimes) the same amino acid being categorized differently past different authors. Indeed, we categorize tyrosine both every bit an aromatic amino acid and as a hydroxyl amino acid. Information technology is useful to allocate amino acids based on their R-groups, because it is these side chains that requite each amino acid its characteristic properties. Thus, amino acids with (chemically) similar side groups can be expected to part in similar means, for example, during poly peptide folding.

Non-polar amino acids

• Alanine (Ala/A) is one of the most abundant amino acids constitute in proteins, ranking second but to leucine in occurrence. A D-form of the amino acid is also found in bacterial jail cell walls. Alanine is non-essential, being readily synthesized from pyruvate. It is coded for by GCU, GCC, GCA, and GCG.
• Glycine (Gly/K) is the amino acid with the shortest side chain, having an R-group consistent only of a single hydrogen. As a event, glycine is the only amino acid that is not chiral. Its small side concatenation allows it to readily fit into both hydrophobic and hydrophilic environments.

Figure 2.2 - Amino acid side chain backdrop Wikipedia

• Glycine is specified in the genetic code past GGU, GGC, GGA, and GGG. It is nonessential to humans.
• Isoleucine (Ile/I) is an essential amino acid encoded by AUU, AUC, and AUA. Information technology has a hydrophobic side chain and is also chiral in its side chain.
• Leucine (Leu/Fifty) is a branched-concatenation amino acid that is hydrophobic and essential. Leucine is the only dietary amino acrid reported to straight stimulate protein synthesis in muscle, only caution is in society, every bit 1) at that place are conflicting studies and 2) leucine toxicity is unsafe, resulting in "the 4 D'south": diarrhea, dermatitis, dementia and death . Leucine is encoded by half-dozen codons: UUA,UUG, CUU, CUC, CUA, CUG.
• Methionine (Met/M) is an essential amino acid that is one of ii sulfurcontaining amino acids - cysteine is the other. Methionine is non-polar and encoded solely by the AUG codon. It is the "initiator" amino acid in protein synthesis, being the offset one incorporated into protein chains. In prokaryotic cells, the first methionine in a protein is formylated.

Figure 2.3 - Non-polar amino acids

• Proline (Pro/P) is the merely amino acid found in proteins with an R-grouping that joins with its own α-amino group, making a secondary amine and a ring. Proline is a non-essential amino acrid and is coded by CCU, CCC, CCA, and CCG. Information technology is the to the lowest degree flexible of the protein amino acids and thus gives conformational rigidity when present in a protein. Proline'south presence in a protein affects its secondary structure. It is a disrupter of α-helices and β-strands. Proline is ofttimes hydroxylated in collagen (the reaction requires Vitamin C - ascorbate) and this has the effect of increasing the protein'southward conformational stability. Proline hydroxylation of hypoxia-inducible factor (HIF) serves every bit a sensor of oxygen levels and targets HIF for devastation when oxygen is plentiful.
• Valine (Val/V) is an essential, non-polar amino acid synthesized in plants. Information technology is noteworthy in hemoglobin, for when it replaces glutamic acid at position number six, it causes hemoglobin to aggregate abnormally under low oxygen weather, resulting in sickle cell illness. Valine is coded in the genetic code by GUU, GUC, GUA, and GUG.

Carboxyl Amino Acids

• Aspartic acid (Asp/D) is a non-essential amino acid with a carboxyl grouping in its Rgroup. Information technology is readily produced by transamination of oxaloacetate. With a pKa of iii.9, aspartic acid'due south side chain is negatively charged at physiological pH. Aspartic acid is specified in the genetic lawmaking past the codons GAU and GAC.
• Glutamic acid (Glu/E), which is coded by GAA and GAG, is a non-essential amino acid readily made past transamination of α- ketoglutarate. It is a neurotransmitter and has an R-group with a carboxyl group that readily ionizes (pKa = 4.ane) at physiological pH.

Figure 2.4 - Carboxyl amino acids

Amine amino acids

• Arginine (Arg/R) is an amino acid that is, in some cases, essential, just non-essential in others. Premature infants cannot synthesize arginine. In addition, surgical trauma, sepsis, and burns increase demand for arginine. Near people, however, exercise non demand arginine supplements. Arginine's side chain contains a complex guanidinium grouping with a pKa of over 12, making it positively charged at cellular pH. It is coded for past six codons - CGU, CGC, CGA, CGG, AGA, and AGG.
• Histidine (His/H) is the only one of the proteinaceous amino acids to contain an imidazole functional grouping. Information technology is an essential amino acid in humans and other mammals. With a side chain pKa of 6, information technology can easily have its charge changed past a slight change in pH. Protonation of the ring results in 2 NH structures which can be drawn as two equally important resonant structures.

Figure 2.5 - Amine amino acids

• Lysine (Lys/Yard) is an essential amino acid encoded by AAA and AAG. It has an Rgroup that can readily ionize with a charge of +ane at physiological pH and tin can be posttranslationally modified to form acetyllysine, hydroxylysine, and methyllysine. It can also be ubiquitinated, sumoylated, neddylated, biotinylated, carboxylated, and pupylated, and. O-Glycosylation of hydroxylysine is used to flag proteins for export from the cell. Lysine is often added to animal feed because information technology is a limiting amino acid and is necessary for optimizing growth of pigs and chickens.

Aromatic amino acids

Figure 2.six - Aromatic amino acids

• Phenylalanine (Phe/ F) is a non-polar, essential amino acid coded by UUU and UUC. It is a metabolic precursor of tyrosine. Inability to metabolize phenylalanine arises from the genetic disorder known as phenylketonuria. Phenylalanine is a component of the aspartame artificial sweetener.
• Tryptophan (Trp/Due west) is an essential amino acid containing an indole functional grouping. Information technology is a metabolic precursor of serotonin, niacin, and (in plants) the auxin phytohormone. Though reputed to serve every bit a sleep assistance, there are no clear research results indicating this.
• Tyrosine (Tyr/Y) is a non-essential amino acrid coded by UAC and UAU. It is a target for phosphorylation in proteins past tyrosine protein kinases and plays a office in signaling processes. In dopaminergic cells of the brain, tyrosine hydroxylase converts tyrosine to l-dopa, an immediate forerunner of dopamine. Dopamine, in turn, is a precursor of norepinephrine and epinephrine. Tyrosine is also a precursor of thyroid hormones and melanin.

Hydroxyl amino acids

• Serine (Ser/S) is one of three amino acids having an R-grouping with a hydroxyl in it (threonine and tyrosine are the others). Information technology is coded by UCU, UCC, UCA, UGC, AGU, and AGC. Being able to hydrogen bond with water, it is classified equally a polar amino acid. It is non essential for humans. Serine is forerunner of many important cellular compounds, including purines, pyrimidines, sphingolipids, folate, and of the amino acids glycine, cysteine, and tryptophan. The hydroxyl group of serine in proteins is a target for phosphorylation past certain protein kinases. Serine is too a part of the catalytic triad of serine proteases.

Figure 2.7 - Hydroxyl amino acids

• Threonine (Thr/T) is a polar amino acid that is essential. It is one of iii amino acids bearing a hydroxyl grouping (serine and tyrosine are the others) and, equally such, is a target for phosphorylation in proteins. It is also a target for Oglycosylation of proteins. Threonine proteases use the hydroxyl group of the amino acrid in their catalysis and it is a precursor in one biosynthetic pathway for making glycine. In some applications, information technology is used as a pro-drug to increment brain glycine levels. Threonine is encoded in the genetic code by ACU, ACC, ACA, and ACG.

Tyrosine - come across Hither.

Figure 2.8 - Amino acid backdrop Wikipedia

Other amino acids

• Asparagine (Asn/N) is a non-essential amino acid coded by AAU and AAC. Its carboxyamide in the R-grouping gives it polarity. Asparagine is implicated in formation of acrylamide in foods cooked at loftier temperatures (deep frying) when it reacts with carbonyl groups. Asparagine can be made in the body from aspartate by an amidation reaction with an amine from glutamine. Breakdown of asparagine produces malate, which can exist oxidized in the citric acid wheel.
• Cysteine (Cys/C) is the only amino acrid with a sulfhydryl group in its side chain. It is nonessential for nigh humans, just may be essential in infants, the elderly and individuals who suffer from certain metabolic diseases. Cysteine's sulfhydryl group is readily oxidized to a disulfide when reacted with another one. In addition to being found in proteins, cysteine is also a component of the tripeptide, glutathione. Cysteine is specified by the codons UGU and UGC.

Figure ii.9 - Other amino acids

• Glutamine (Gln/Q) is an amino acid that is not normally essential in humans, simply may be in individuals undergoing intensive athletic training or with gastrointestinal disorders. It has a carboxyamide side chain which does not normally ionize under physiological pHs, just which gives polarity to the side chain. Glutamine is coded for by CAA and CAG and is readily made past amidation of glutamate. Glutamine is the well-nigh arable amino acid in circulating claret and is one of merely a few amino acids that can cross the blood-brain bulwark.
• Selenocysteine (Sec/U) is a component of selenoproteins found in all kingdoms of life. It is a component in several enzymes, including glutathione peroxidases and thioredoxin reductases. Selenocysteine is incorporated into proteins in an unusual scheme involving the cease codon UGA. Cells grown in the absence of selenium terminate protein synthesis at UGAs. Nonetheless, when selenium is present, certain mRNAs which incorporate a selenocysteine insertion sequence (SECIS), insert selenocysteine when UGA is encountered. The SECIS chemical element has characteristic nucleotide sequences and secondary construction base-pairing patterns. 20 five human proteins comprise selenocysteine.
• Pyrrolysine (Pyl/O) is a twenty second amino acrid, but is rarely found in proteins. Similar selenocysteine, it is not coded for in the genetic code and must be incorporated by unusual means. This occurs at UAG terminate codons. Pyrrolysine is found in methanogenic archaean organisms and at to the lowest degree one methane-producing bacterium. Pyrrolysine is a component of methane-producing enzymes.

Ionizing groups

pKa values for amino acid side chains are very dependent upon the chemical surroundings in which they are nowadays. For example, the R-group carboxyl found in aspartic acid has a pKa value of 3.9 when costless in solution, but can exist as high as fourteen when in certain environments within of proteins, though that is unusual and extreme. Each amino acid has at least i ionizable amine grouping (α- amine) and one ionizable carboxyl group (α- carboxyl). When these are spring in a peptide bond, they no longer ionize. Some, merely not all amino acids have R-groups that tin can ionize. The charge of a protein so arises from the charges of the α-amine group, the α- carboxyl group. and the sum of the charges of the ionized R-groups. Titration/ionization of aspartic acid is depicted in Effigy two.ten. Ionization (or deionization) within a protein's construction tin have significant effect on the overall conformation of the protein and, since structure is related to function, a major impact on the action of a protein.

Figure ii.10 - Titration bend for aspartic acid Image by Penelope Irving

Virtually proteins have relatively narrow ranges of optimal activity that typically correspond to the environments in which they are found (Effigy ii.11). Information technology is worth noting that formation of peptide bonds betwixt amino acids removes ionizable hydrogens from both the α- amine and α- carboxyl groups of amino acids. Thus, ionization/ deionization in a protein arises merely from i) the amino terminus; two) carboxyl terminus; iii) R-groups; or 4) other functional groups (such as sulfates or phosphates) added to amino acids post-translationally - see below.

Carnitine

Not all amino acids in a cell are found in proteins. The most common examples include ornithine (arginine metabolism), citrulline (urea cycle), and carnitine (Figure 2.12). When fatty acids destined for oxidation are moved into the mitochondrion for that purpose, they travel across the inner membrane attached to carnitine. Of the ii stereoisomeric forms, the Fifty class is the agile one. The molecule is synthesized in the liver from lysine and methionine.

Figure 2.12 - L-Carnitine

From exogenous sources, fatty acids must be activated upon entry into the cytoplasm past existence joined to coenzyme A. The CoA portion of the molecule is replaced by carnitine in the intermembrane space of the mitochondrion in a reaction catalyzed by carnitine acyltransferase I. The resulting acylcarnitine molecule is transferred across the inner mitochondrial membrane by the carnitineacylcarnitine translocase and then in the matrix of the mitochondrion, carnitine acyltransferase Two replaces the carnitine with coenzyme A (Figure 6.88).

Figure 2.11 - Enzyme action changes equally pH changes Image by Aleia Kim

Catabolism of amino acids

We categorize amino acids equally essential or non-essential based on whether or non an organism tin synthesize them. All of the amino acids, however, can be broken downwards by all organisms. They are, in fact, a source of energy for cells, especially during times of starvation or for people on diets containing very low amounts of carbohydrate. From a perspective of breakdown (catabolism), amino acids are categorized as glucogenic if they produce intermediates that can be made into glucose or ketogenic if their intermediates are made into acetyl-CoA. Figure 2.13 shows the metabolic fates of catabolism of each of the amino acids. Note that some amino acids are both glucogenic and ketogenic.

Effigy 2.13 - Catabolism of amino acids. Some have more than ane path. Image by Pehr Jacobson

Mail-translational modifications

Later on a protein is synthesized, amino acrid side chains inside information technology tin can be chemically modified, giving ascent to more than diverseness of structure and function (Figure ii.14). Mutual alterations include phosphorylation of hydroxyl groups of serine, threonine, or tyrosine. Lysine, proline, and histidine tin have hydroxyls added to amines in their R-groups. Other modifications to amino acids in proteins include addition of fat acids (myristic acid or palmitic acid), isoprenoid groups, acetyl groups, methyl groups, iodine, carboxyl groups, or sulfates. These tin can have the effects of ionization (addition of phosphates/sulfates), deionization (addition of acetyl grouping to the R-group amine of lysine), or have no effect on accuse at all. In addition, N-linked- and O-linkedglycoproteins have carbohydrates covalently attached to side bondage of asparagine and threonine or serine, respectively.

Some amino acids are precursors of important compounds in the body. Examples include epinephrine, thyroid hormones, Ldopa, and dopamine (all from tyrosine), serotonin (from tryptophan), and histamine (from histidine).

Figure 2.14 - Post-translationally modified amino acids. Modifications shown in green. Image by Penelope Irving

Figure 2.15 - Phosphorylated amino acids

Edifice Polypeptides

Although amino acids serve other functions in cells, their most important part is every bit constituents of proteins. Proteins, as we noted earlier, are polymers of amino acids.

Amino acids are linked to each other by peptide bonds, in which the carboxyl grouping of one amino acid is joined to the amino group of the next, with the loss of a molecule of water. Boosted amino acids are added in the same mode, past formation of peptide bonds between the free carboxyl on the end of the growing chain and the amino grouping of the next amino acid in the sequence. A chain made upwards of but a few amino acids linked together is called an oligopeptide (oligo=few) while a typical protein, which is made upwardly of many amino acids is chosen a polypeptide (poly=many). The stop of the peptide that has a free amino grouping is called the North-terminus (for NH2), while the end with the free carboxyl is termed the C-terminus (for carboxyl).

Figure 2.16 Formation of a peptide bond

As we've noted earlier, function is dependent on structure, and the string of amino acids must fold into a specific iii-D shape, or conformation, in order to brand a functional poly peptide. The folding of polypeptides into their functional forms is the topic of the next section.

Source: https://bio.libretexts.org/Bookshelves/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/02%3A_Structure_and_Function/202%3A_Structure__Function_-_Amino_Acids

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