أحماض أمينية مركبة للپروتينات

الأحماض الأمينية المركبة للپروتينات تمثل جزء صغير من جميع الأحماض الأمينية.

الأحماض الأمينية المركبة للپروتينات Proteinogenic amino acids، هي الأحماض الأمينية التي أُدمجت حيوياً في الپروتينات أثناء الترجمة. في جميع أشكال الحياة المعروفة، يوجد 22 حمض أميني مكون للپروتين مشفر وراثياً، 20 في الشفرة الوراثية القياسية و2 إضافيين يمكن دمجهما عبر آليات ترجمة خاصة.[1]

In contrast, non-proteinogenic amino acids are amino acids that are either not incorporated into proteins (like GABA, L-DOPA, or triiodothyronine), misincorporated in place of a genetically encoded amino acid, or not produced directly and in isolation by standard cellular machinery (like hydroxyproline). The latter often results from post-translational modification of proteins. Some non-proteinogenic amino acids are incorporated into nonribosomal peptides which are synthesized by non-ribosomal peptide synthetases.

Both eukaryotes and prokaryotes can incorporate selenocysteine into their proteins via a nucleotide sequence known as a SECIS element, which directs the cell to translate a nearby UGA codon as selenocysteine (UGA is normally a stop codon). In some methanogenic prokaryotes, the UAG codon (normally a stop codon) can also be translated to pyrrolysine.[2]

In eukaryotes, there are only 21 proteinogenic amino acids, the 20 of the standard genetic code, plus selenocysteine. Humans can synthesize 12 of these from each other or from other molecules of intermediary metabolism. The other nine must be consumed (usually as their protein derivatives), and so they are called essential amino acids. The essential amino acids are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine (i.e. H, I, L, K, M, F, T, W, V).[3]

The proteinogenic amino acids have been found to be related to the set of amino acids that can be recognized by ribozyme autoaminoacylation systems.[4] Thus, non-proteinogenic amino acids would have been excluded by the contingent evolutionary success of nucleotide-based life forms. Other reasons have been offered to explain why certain specific non-proteinogenic amino acids are not generally incorporated into proteins; for example, ornithine and homoserine cyclize against the peptide backbone and fragment the protein with relatively short half-lives, while others are toxic because they can be mistakenly incorporated into proteins, such as the arginine analog canavanine.

The evolutionary selection of certain proteinogenic amino acids from the primordial soup has been suggested to be because of their better incorporation into a polypeptide chain as opposed to non-proteinogenic amino acids.[5]

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البُنىَ

The following illustrates the structures and abbreviations of the 21 amino acids that are directly encoded for protein synthesis by the genetic code of eukaryotes. The structures given below are standard chemical structures, not the typical zwitterion forms that exist in aqueous solutions.

Table of amino acids
Grouped table of 21 amino acids' structures, nomenclature, and their side groups' pKa values


الخصائص الكيميائية

Following is a table listing the one-letter symbols, the three-letter symbols, and the chemical properties of the side chains of the standard amino acids. The masses listed are based on weighted averages of the elemental isotopes at their natural abundances. Forming a peptide bond results in elimination of a molecule of water. Therefore, the protein's mass is equal to the mass of amino acids the protein is composed of minus 18.01524 Da per peptide bond.

الخصائص الكيميائية العامة

الحمض الأميني الاختصار الرمز الكتلة الذرية (دالتون) نقطة التعادل الكهربائي pI ثابت انحلال الهيدوكسيل
pK1 		ثابت انحلال الأمين
pK2
ألانين A Ala 89.09404 6.01 2.35 9.87
سيستين C Cys 121.15404 5.05 1.92 10.70
حمض الأسپارتيك D Asp 133.10384 2.85 1.99 9.90
حمض الگلوتاميك E Glu 147.13074 3.15 2.10 9.47
فنايل‌ألانين F Phe 165.19184 5.49 2.20 9.31
گليسين G Gly 75.06714 6.06 2.35 9.78
هيستيدين H His 155.15634 7.60 1.80 9.33
إيسولوسين I Ile 131.17464 6.05 2.32 9.76
ليسين K Lys 146.18934 9.60 2.16 9.06
لوسين L Leu 131.17464 6.01 2.33 9.74
مثيونين M Met 149.20784 5.74 2.13 9.28
أسپاراجين N Asn 132.11904 5.41 2.14 8.72
پيروليسين O Pyl 255.31
پرولين P Pro 115.13194 6.30 1.95 10.64
گلوتامين Q Gln 146.14594 5.65 2.17 9.13
أرجنين R Arg 174.20274 10.76 1.82 8.99
سيرين S Ser 105.09344 5.68 2.19 9.21
ثريونين T Thr 119.12034 5.60 2.09 9.10
سيلينوسيستين U Sec 168.053 5.47 1.91 10
ڤالين V Val 117.14784 6.00 2.39 9.74
تريپتوفان W Trp 204.22844 5.89 2.46 9.41
تيروسين Y Tyr 181.19124 5.64 2.20 9.21

خصائص السلسلة الجانبية

الحمض الأميني الاختصار الرمز السلسة الجانبية كاره
للماء 		pKa§ قطبية pH صغيرة دقيقة عطرية
أو أليفاتية 		van der Waals
volume (Å3)
ألانين A Ala -CH3 X - - - X X أليفاتية 67
سيستين C Cys -CH2SH X 8.55 - حمضية X X - 86
حمض الأسپارتيك D Asp -CH2COOH - 3.67 X حمضية X - - 91
حمض الگلوتاميك E Glu -CH2CH2COOH - 4.25 X حمضية - - - 109
فنايل‌ألانين F Phe -CH2C6H5 X - - - - - عطرية 135
گليسين G Gly -H X - - - X X - 48
هيستيدين H His -CH2-C3H3N2 - 6.54 X قاعدية ضعيفة - - عطرية 118
إيزوليوسين I Ile -CH(CH3)CH2CH3 X - - - - - أليفاتية 124
ليسين K Lys -(CH2)4NH2 - 10.40 X قاعدية - - - 135
ليوسين L Leu -CH2CH(CH3)2 X - - - - - أليفاتية 124
مثيونين M Met -CH2CH2SCH3 X - - - - - أليفاتية 124
أسپاراجين N Asn -CH2CONH2 - - X - X - - 96
پيروليسين O Pyl -(CH2)4NHCOC4H5NCH3 - N.D. X قاعدية ضعيفة - - -
پرولين P Pro -CH2CH2CH2- X - - - X - - 90
گولتامين Q Gln -CH2CH2CONH2 - - X - - - - 114
أرجينين R Arg -(CH2)3NH-C(NH)NH2 - 12.3 X قاعدية قوية - - - 148
سيرين S Ser -CH2OH - - X - X X - 73
ثريونين T Thr -CH(OH)CH3 - - X - X - - 93
سيلنوسيستين U Sec -CH2SeH - 5.43 - حمضية X X -
ڤالين V Val -CH(CH3)2 X - - - X - أليفاتية 105
تريپتوفان W Trp -CH2C8H6N - - X - - - عطرية 163
تيروسين Y Tyr -CH2-C6H4OH - 9.84 X حمضية ضعيفة - - عطرية 141

§: Values for Asp, Cys, Glu, His, Lys & Tyr were determined using the amino acid residue placed centrally in an alanine pentapeptide.[6] The value for Arg is from Pace et al. (2009).[7] The value for Sec is from Byun & Kang (2011).[8]

N.D.: The pKa value of Pyrrolysine has not been reported.

Note: The pKa value of an amino-acid residue in a small peptide is typically slightly different when it is inside a protein. Protein pKa calculations are sometimes used to calculate the change in the pKa value of an amino-acid residue in this situation.

التعبير الجيني والكيمياء الحيوية

الحمض الأميني الاختصار الرمز الشفرات التواجد

في پروتينات العتائق

(%)&

التوجد

في پروتينات الجراثيم

(%)&

التوجد

في پروتينات حقيقيات النوى

(%)&

التواجد
في الپروتينات البشرية
(%)& 		Essential‡ في البشر
ألانين A Ala GCU, GCC, GCA, GCG 8.2 10.06 7.63 7.01 لا
سيستين C Cys UGU, UGC 0.98 0.94 1.76 2.3 مشروط
حمض الأسپارتيك D Asp GAU, GAC 6.21 5.59 5.4 4.73 No
حمض الگلوتاميك E Glu GAA, GAG 7.69 6.15 6.42 7.09 مشروط
فنايل‌ألانين F Phe UUU, UUC 3.86 3.89 3.87 3.65 نعم
گليسين G Gly GGU, GGC, GGA, GGG 7.58 7.76 6.33 6.58 مشروط
هيستيدين H His CAU, CAC 1.77 2.06 2.44 2.63 نعم
إيسولوسين I Ile AUU, AUC, AUA 7.03 5.89 5.1 4.33 نعم
ليسين K Lys AAA, AAG 5.27 4.68 5.64 5.72 نعم
ليوسين L Leu UUA, UUG, CUU, CUC, CUA, CUG 9.31 10.09 9.29 9.97 نعم
مثيونين M Met AUG 2.35 2.38 2.25 2.13 نعم
أسپاراجين N Asn AAU, AAC 3.68 3.58 4.28 3.58 لا
پيروليسين O Pyl UAG* 0 0 0 0 لا
پرولين P Pro CCU, CCC, CCA, CCG 4.26 4.61 5.41 6.31 لا
گلوتامين Q Gln CAA, CAG 2.38 3.58 4.21 4.77 لا
أرجنين R Arg CGU, CGC, CGA, CGG, AGA, AGG 5.51 5.88 5.71 5.64 مشروط
سيرين S Ser UCU, UCC, UCA, UCG, AGU, AGC 6.17 5.85 8.34 8.33 لا
ثريونين T Thr ACU, ACC, ACA, ACG 5.44 5.52 5.56 5.36 نعم
Selenocysteine U Sec UGA** 0 0 0 >0 لا
ڤالين V Val GUU, GUC, GUA, GUG 7.8 7.27 6.2 5.96 نعم
تريپتوفان W Trp UGG 1.03 1.27 1.24 1.22 نعم
تيروسين Y Tyr UAU, UAC 3.35 2.94 2.87 2.66 مشروط
Stop codon† - Term UAA, UAG, UGA†† - -

* UAG is normally the amber stop codon, but in organisms containing the biological machinery encoded by the pylTSBCD cluster of genes the amino acid pyrrolysine will be incorporated.[9]
** UGA is normally the opal (or umber) stop codon, but encodes selenocysteine if a SECIS element is present.
† The stop codon is not an amino acid, but is included for completeness.
†† UAG and UGA do not always act as stop codons (see above).
‡ An essential amino acid cannot be synthesized in humans and must, therefore, be supplied in the diet. Conditionally essential amino acids are not normally required in the diet, but must be supplied exogenously to specific populations that do not synthesize it in adequate amounts.
& Occurrence of amino acids is based on 135 Archaea, 3775 Bacteria, 614 Eukaryota proteomes and human proteome (21 006 proteins) respectively.[10]


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مطيافية الكتلة

In mass spectrometry of peptides and proteins, knowledge of the masses of the residues is useful. The mass of the peptide or protein is the sum of the residue masses plus the mass of water (Monoisotopic mass = 18.01056 Da; average mass = 18.0153 Da). The residue masses are calculated from the tabulated chemical formulas and atomic weights.[11] In mass spectrometry, ions may also include one or more protons (Monoisotopic mass = 1.00728 Da; average mass* = 1.0074 Da). *Protons cannot have an average mass, this confusingly infers to Deuterons as a valid isotope, but they should be a different species (see Hydron (chemistry))

الحمض الأميني الاختصار الرمز الصيغة Mon. Mass§ (Da) متوسط الكتلة (Da)
ألانين A Ala C3H5NO 71.03711 71.0779
سيستين C Cys C3H5NOS 103.00919 103.1429
حمض الأسپارتيك D Asp C4H5NO3 115.02694 115.0874
حمض الگلوتاميك E Glu C5H7NO3 129.04259 129.1140
فنايل‌ألانين F Phe C9H9NO 147.06841 147.1739
گليسين G Gly C2H3NO 57.02146 57.0513
هيستيدين H His C6H7N3O 137.05891 137.1393
إيسولوسين I Ile C6H11NO 113.08406 113.1576
ليسين K Lys C6H12N2O 128.09496 128.1723
لوسين L Leu C6H11NO 113.08406 113.1576
مثيونين M Met C5H9NOS 131.04049 131.1961
أسپاراجين N Asn C4H6N2O2 114.04293 114.1026
پيروليسين O Pyl C12H19N3O2 237.14773 237.2982
پرولين P Pro C5H7NO 97.05276 97.1152
گلوتامين Q Gln C5H8N2O2 128.05858 128.1292
أرجنين R Arg C6H12N4O 156.10111 156.1857
سيرين S Ser C3H5NO2 87.03203 87.0773
ثريونين T Thr C4H7NO2 101.04768 101.1039
سيلينوسيستين U Sec C3H5NOSe 150.95364 150.0489
ڤالين V Val C5H9NO 99.06841 99.1311
تريپتوفان W Trp C11H10N2O 186.07931 186.2099
تيروسين Y Tyr C9H9NO2 163.06333 163.1733

§ Monoisotopic mass

قياس اتحادية العناصر وقيمة الأيض في الخلية

The table below lists the abundance of amino acids in E.coli cells and the metabolic cost (ATP) for synthesis of the amino acids. Negative numbers indicate the metabolic processes are energy favorable and do not cost net ATP of the cell.[12] The abundance of amino acids includes amino acids in free form and in polymerization form (proteins).

الحمض الأميني Abundance
(# of molecules (×108)
per E. coli cell) 		ATP cost in synthesis
under aerobic
condition 		ATP cost in synthesis
under anaerobic
condition
ألانين 2.9 -1 1
سيستين 0.52 11 15
حمض الأسپارتيك 1.4 0 2
حمض الگلوتاميك 1.5 -7 -1
فنايل‌ألانين 1.1 -6 2
گليسين 3.5 -2 2
هيستيدين 0.54 1 7
إيسولوسين 1.7 7 11
ليسين 2.0 5 9
لوسين 2.6 -9 1
مثيونين 0.88 21 23
أسپاراجين 1.4 3 5
پيروليسين 1.3 -2 4
گلوتامين 1.5 -6 0
أرجنين 1.7 5 13
سيرين 1.2 -2 2
ثريونين 1.5 6 8
تريپتوفان 0.33 -7 7
تيروسين 0.79 -8 2
ڤالين 2.4 -2 2

ملاحظات

الحمض الأميني الرمز ملاحظات
ألانين A Ala Very abundant and very versatile, it is more stiff than glycine, but small enough to pose only small steric limits for the protein conformation. It behaves fairly neutrally, and can be located in both hydrophilic regions on the protein outside and the hydrophobic areas inside.
أسپاراجين أو حمض الأسپاراتيك B Asx A placeholder when either amino acid may occupy a position
سيستين C Cys The sulfur atom bonds readily to heavy metal ions. Under oxidizing conditions, two cysteines can join together in a disulfide bond to form the amino acid cystine. When cystines are part of a protein, insulin for example, the tertiary structure is stabilized, which makes the protein more resistant to denaturation; therefore, disulfide bonds are common in proteins that have to function in harsh environments including digestive enzymes (e.g., pepsin and chymotrypsin) and structural proteins (e.g., keratin). Disulfides are also found in peptides too small to hold a stable shape on their own (e.g. insulin).
حمض الأسپارتيك D Asp Asp behaves similarly to glutamic acid, and carries a hydrophilic acidic group with strong negative charge. Usually, it is located on the outer surface of the protein, making it water-soluble. It binds to positively charged molecules and ions, and is often used in enzymes to fix the metal ion. When located inside of the protein, aspartate and glutamate are usually paired with arginine and lysine.
حمض الگلوتاميك E Glu Glu behaves similarly to aspartic acid, and has a longer, slightly more flexible side chain.
فنايل‌ألانين F Phe Essential for humans, phenylalanine, tyrosine, and tryptophan contain a large, rigid aromatic group on the side chain. These are the biggest amino acids. Like isoleucine, leucine, and valine, these are hydrophobic and tend to orient towards the interior of the folded protein molecule. Phenylalanine can be converted into tyrosine.
گليسين G Gly Because of the two hydrogen atoms at the α carbon, glycine is not optically active. It is the smallest amino acid, rotates easily, and adds flexibility to the protein chain. It is able to fit into the tightest spaces, e.g., the triple helix of collagen. As too much flexibility is usually not desired, as a structural component, it is less common than alanine.
هيستيدين H His His is essential for humans. In even slightly acidic conditions, protonation of the nitrogen occurs, changing the properties of histidine and the polypeptide as a whole. It is used by many proteins as a regulatory mechanism, changing the conformation and behavior of the polypeptide in acidic regions such as the late endosome or lysosome, enforcing conformation change in enzymes. However, only a few histidines are needed for this, so it is comparatively scarce.
إيسولوسين I Ile Ile is essential for humans. Isoleucine, leucine, and valine have large aliphatic hydrophobic side chains. Their molecules are rigid, and their mutual hydrophobic interactions are important for the correct folding of proteins, as these chains tend to be located inside of the protein molecule.
لوسين أوإيسولوسين J Xle A placeholder when either amino acid may occupy a position
ليسين K Lys Lys is essential for humans, and behaves similarly to arginine. It contains a long, flexible side chain with a positively charged end. The flexibility of the chain makes lysine and arginine suitable for binding to molecules with many negative charges on their surfaces. E.g., DNA-binding proteins have their active regions rich with arginine and lysine. The strong charge makes these two amino acids prone to be located on the outer hydrophilic surfaces of the proteins; when they are found inside, they are usually paired with a corresponding negatively charged amino acid, e.g., aspartate or glutamate.
لوسين L Leu Leu is essential for humans, and behaves similarly to isoleucine and valine.
مثيونين M Met Met is essential for humans. Always the first amino acid to be incorporated into a protein, it is sometimes removed after translation. Like cysteine, it contains sulfur, but with a methyl group instead of hydrogen. This methyl group can be activated, and is used in many reactions where a new carbon atom is being added to another molecule.
أسپاراجين N Asn Similar to aspartic acid, Asn contains an amide group where Asp has a carboxyl.
پيروليسين O Pyl Similar to lysine, but it has a pyrroline ring attached.
پرولين P Pro Pro contains an unusual ring to the N-end amine group, which forces the CO-NH amide sequence into a fixed conformation. It can disrupt protein folding structures like α helix or β sheet, forcing the desired kink in the protein chain. Common in collagen, it often undergoes a post-translational modification to hydroxyproline.
گلوتامين Q Gln Similar to glutamic acid, Gln contains an amide group where Glu has a carboxyl. Used in proteins and as a storage for ammonia, it is the most abundant amino acid in the body.
أرجنين R Arg Functionally similar to lysine.
سيرين S Ser Serine and threonine have a short group ended with a hydroxyl group. Its hydrogen is easy to remove, so serine and threonine often act as hydrogen donors in enzymes. Both are very hydrophilic, so the outer regions of soluble proteins tend to be rich with them.
ثريونين T Thr Essential for humans, Thr behaves similarly to serine.
سيلينوسيستين U Sec The selenium analog of cysteine, in which selenium replaces the sulfur atom.
ڤالين V Val Essential for humans, Val behaves similarly to isoleucine and leucine.
تريپتوفان W Trp Essential for humans, Trp behaves similarly to phenylalanine and tyrosine. It is a precursor of serotonin and is naturally fluorescent.
غير معروف X Xaa Placeholder when the amino acid is unknown or unimportant.
تيروسين Y Tyr Tyr behaves similarly to phenylalanine (precursor to tyrosine) and tryptophan, and is a precursor of melanin, epinephrine, and thyroid hormones. Naturally fluorescent, its fluorescence is usually quenched by energy transfer to tryptophans.
حمض الگلوتاميك أو گلوتامين Z Glx A placeholder when either amino acid may occupy a position

Catabolism

Amino acids can be classified according to the properties of their main products:[13]

  • Glucogenic, with the products having the ability to form glucose by gluconeogenesis
  • Ketogenic, with the products not having the ability to form glucose: These products may still be used for ketogenesis or lipid synthesis.
  • Amino acids catabolized into both glucogenic and ketogenic products


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انظر أيضاً


المصادر

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  6. ^ Thurlkill RL, Grimsley GR, Scholtz JM, Pace CN (May 2006). "pK values of the ionizable groups of proteins". Protein Science. 15 (5): 1214–8. doi:10.1110/ps.051840806. PMC 2242523. PMID 16597822.
  7. ^ Pace CN, Grimsley GR, Scholtz JM (May 2009). "Protein ionizable groups: pK values and their contribution to protein stability and solubility". The Journal of Biological Chemistry. 284 (20): 13285–9. doi:10.1074/jbc.R800080200. PMC 2679426. PMID 19164280.
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