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Amino ACIDS PROTEINS

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Amino ACIDS PROTEINS Taras Shevchenko National University of Kyiv The Institute of Biology and Medicine METHODICAL POINTING from the course “Biological and bioorganic chemistry” (part 3. Amino acids and proteins) for the studens of a 1 course with English of educating Compiler – the candidate of biological sciences, the associate professor Synelnyk Tatyana Borysivna Readers: It is ratified to printing by meeting of scientific advice of The Institute of Biology and Medicine (“____”________________ 2018, protocol №____) Kyiv-2018 2 CONTENT 3.1. General information …………………………………………………….. 3 3.2. Nomenclature and classification of α-amino acids ……………. 4 3.3. Amphoteric and stereochemical properties of amino acids. Chiral carbon atom……………………………………………………………… 8 3.4. Isoelectric point of amino acid . Titration curves ……………… 9 3.4.1. The typical titration curve of amino acids with uncharged radical…………………………………………………………. 10 3.4.2. The titration curves of amino acids with charged radical ……………………………………………………………………….. 11 3.5. Chemical properties of amino acids and some methods for amino acids determination and separation…………………………….. 14 3.6. Peptide bond formation. Peptides. …………………………………. 15 3.7. Proteins. The levels of protein molecules organization ……… 16 3.7.1. Primary protein structure ……………………………………. 17 3.7.2. The secondary structure of proteins: types …………….. 18 3.7.3. Super secondary structure …………………………………… 22 3.7.4. Tertiary Structure of proteins ……………………………… 23 3.7.5. Domain structure of proteins ……………………………… 26 3.7.6. Quaternary Structure of proteins ………………………… 26 3.8. Methods of extraction and purification of proteins ………….. 28 3.8.1. Methods of extraction of proteins from cells or tissues in the dissolved state. ………………………………………………….. 28 3.8.2. Methods of separating a mixture of proteins 29 3.9. Physical and chemical properties of proteins 32 3.10. Protein classification …………………………………………………. 34 3.10.1. Simple proteins…………………………………………………. 37 3.10.2. Conjugated proteins…………………………………………… 40 3.11. Test questions …………………………………………………………… 45 3 3.1. General information Proteins are the biopolymers, the monomers of which are α-amino acids linked by peptide bonds. Functions of proteins: • structural ( collagen , elastin - proteins of connective tissue; keratin - nails and skin; glycoproteins - shells and cell walls); • catalytic (enzymes ); • regulatory ( protein hormones , inhibitors and activators of enzymes ); • receptors; • transport ( hemoglobin ; serum albumin ; transferrin ); • protective - immunoglobulins of the blood, plasma fibrinogen , interferon ; • contractile ( actin , myosin ); • nutritious ( casein milk , ovalbumin , wheat gliadin ); • energy (1 g of protein, when degraded to the end products, yields 17,6 kJ of energy). α-amino acids are derivatives of carboxylic acids, in which one hydrogen atom near the second (alpha) carbon atom is replaced by an amino group: In the proline, the amino group is included in the ring as α-imino group, so proline is more likely an α-imino acid than an α-amino acid: 20 amino acids are the part of the proteins. Others are called non- proteinogenic or non-standard amino acids. Non-standard amino acids that are found in proteins are formed by post-translational modification, which is modification after translation during protein synthesis. The examples of such amino acids are: - hydroxyproline (is formed from proline); - hydroxylysine (is formed from lysine); - ɣ-carboxyglutaminic acid (is formed from glutaminic acid); - selenocysteine (is formed from cysteine). These modifications are often essential for the function or regulation of a protein e.g; the carboxylation of glutamate allows for better binding of calcium cations, and the hydroxylation of proline is critical for maintaining connective tissues. 4 Other amino acids occur in the body, but are not found in proteins. They are: - citrulline, - ornithine - carnitine - homocysteine - taurine - GABA - iodinated amino acids (thyroid hormones T3 and T4). These nonstandard 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. α-amino acids differ one from other by their radical groups (R) . These radicals may contain hydrophilic or hydrophobic functional groups, can be positively or negatively charged and can have aliphatic or cyclic structures 3.2. Nomenclature and classification of α- amino acids Amino acids are named (Fig. 3.1): • by three letters (Ala, Trp) • by one letter: (A, W) - - + O COO NH2 Aspartic acid - + COO Arginine O NH3 (Asp, D) H2 N N H + (Arg, R) O NH3 - - COO Glutamic acid O - + (Glu, E) COO NH3 N Histidine NH + N 3 (His, H) H + H N COO- 3 Lysine + NH3 (Lys, K) Fig. 3.1. The examples of amino acids names 5 There are several classifications of amino acids: 1. Based on polarity , amino acids are classified into four groups as follows: • non-polar (hydrophobic) amino acids - Аlа, Val, Lei, Ile, Met, Pro, Phe, Trp, Gly; • polar (hydrophilic) amino acids with no charge - Ser, Thr, Cys, Tyr, Asn, Gln; • polar (hydrophilic) amino acids with positive charge – Lys, Arg, His - at the physiological pH are positively charged . They are basic amino acids • polar (hydrophilic) amino acids with negative charge - Аsp, Glu - at the physiological pH are negatively charged. They are acidic amino acids Polar and non-polar amino acids differ by occurrence of hydrophilic or hydrophobic functional groups in their radicals (R) (Fig. 3.2). Polar and nonpolar functional groups Polar functional groups in the amino acids radicals (R): amino acids ALWAYS belong to POLAR when they are present in the radical - OH Tyrosine Serine - SH Cysteine -COOH Glutaminic acid (-СОО -) -NH 2 Lysine + (-N H3) Non-polar functional groups in the amino acid radical (R): when they are present in the radical and in the absence of the polar substituents , the amino acids belong to the NON POLAR ones -CH 3 and fatty acid chains Alanine - cyclic structures Phenylalanine Fig. 3.2. Polar and non-polar functional groups in the amino acids radicals (R) Examples of polar and non polar amino acids are given on Fig. 3.3 and Fig. 3.4. 6 Non polar Polar amino acids amino acids Alanine Serine Valine Cysteine Isoleucine Threonine Phenylalanine Tyrosine (a quadrilateral is a radical of amino acids) Fig. 3.3. Examples of polar and non-polar amino acids ASPARAGINIC ACID - GLUTAMINIC ACID LYSINE ARGININE + HYSTIDINE (a quadrilateral is a radical of amino acids) Fig. 3.4. Examples of polar charged amino acids ( ‒COOH and ‒NH 2 groups in radicals of ‒ + these amino acids exist as ‒COO and ‒N H3 groups , respectively) 2. According to number of amino- and carboxylic groups (Fig. 3.5) : • monoamino monocarbonic acids (ex. Ser, Gli); • monoamino dicarbonic acids (acidic amino acids Glu, Asp) and their amides (Gln, Asn) • diamino monocarbonic acids (basic amino acids Lys, Arg); 7 • diamino dicarbonic acids (cystine – the amino acid derived from Cys). Amides of monoamino dicarbonic amino acids ASPARAGINE ASPARAGINIC ACID GLUTAMINE GLUTAMINIC ACID Monoamino dicarbonic LYSINE ARGININE CYSTINE diamino monocarbonic diamino dicarbonic (a quadrilateral is a radical of amino acids) , Fig. 3.5. Examples of monoamino dicarbonic, diamino monocarbonic, diamino dicarbonic amino acids and amides of monoamino dicarbonic amino acids 3. Based on the presence of cyclic structures: • cyclic ( aromatic – Phe, Tyr; heterocyclic – Trp, His, Pro) • acyclic . 4. Nutritional classification: • Essential amino acids: 8 amino acids that can’t be formed in the body and so, it is essential to be taken in diet. Their deficiency affects growth, health and protein synthesis - незамінні : (Val, Leu, Ile, Thr, Lys, Met, Phe, Trp); • Semiessential amino acids (conditional amino acids): These are formed in the body but not in sufficient amount for body requirements especially in children ) – His, Arg; • Non essential amino acids . Summary of essential and semiessential amino acids: Villa HM = Ten Th ousands Pound • V= valine i= isoleucine l= lysine l= leucine A = arginine* • H= histidine* M= methionine • T= tryptophan Th = threonine P= phenylalanine *= arginine and histidine are semiessential 8 5. Metabolic classification – according to metabolic or degradation products of amino acids they may be: • ketogenic amino acids which give ketone bodies . Lysine and leucine are the only pure ketogenic amino acids. • mixed ketogenic and glucogenic amino acids which give both ketonbodies and glucose . These are: isoleucine, phenyl alanine, tyrosine and tryptophan. • Glucogenic amino acids which give glucose . They include the rest of amino acids . These amino acids in their catabolism yield products that enter in glycogen and glucose formation. 3.3. Amphoteric and stereochemical properties of amino acids. Chiral carbon atom Amino acids have both basic and acidic groups and so can act as a base or acid (have an amphoteric properties ). is chiral : it (٭For all amino acids except for glycine , α-carbon atom (С bonds to four different groups (Fig. 3.6) : - a carboxyl group (1), - an amino group (2), - a R-group (different radicals) (3), - a hydrogen atom (4). ٭ Fig. 3.6. Existence of chiral carbon atom in amino acids molecules The presence of a chiral center determines the stereochemical properties of amino acids: • absolute configuration • optical activity According to absolute configuration amino acids are divided into amino acids of D- and L-series (by analogy with the absolute configuration of D- and L-glyceraldehyde) (Fig.
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