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Biological Chemistry Ministry of Health of Ukraine Zaporizhzhya State Medical University Biochemistry & Laboratory Diagnostics Department Biological chemistry A manual for independent work at home and in class preparation for licensing examination “KROK 1” on module 1 “General regularities of metabolism. Metabolism of carbohydrates, lipids, amino acids and their regulation” for students of International Faculty (the second year of study) speciality: 7.120 10001 «General Medicine» Zaporizhzhya 2015 ББК 28.072я73 Б63 УДК 577.1(072)=111 Editors: Dr. Hab., professor Aleksandrova K.V. PhD, ass. professor Krisanova N.V. PhD, ass. professor Ivanchenko D.G. PhD, as. profesor Rudko N.P. PhD, assistant Levich S.V. This manual is recommended for II year students of International Faculty of specialty 7.12010001 "General medicine" studying biological chemistry, as additional material to prepare for practical training module 1 and licensing exam “KROK 1: General medical training”. Reviewers: • Head of Biological Chemistry Department of National University of Pharmacy, doctor of biological science, professor Zagayko A.L. • Professor of Chemistry Department of Zaporizhzhya National University, doctor of pharmaceutical science, professor Omelianchyk L.O. ББК 28.072я73 УДК 577.1(072)=111 © Aleksandrova K.V., Krisanova N.V., Ivanchenko D.G., Rudko N.P., Levich S.V., 2015 1 CONTENT Introduction…………………………………………………………………... 3 Classification, physicochemical properties and functions of simple proteins in humans. The methods for indication, separation and release of proteins from biological fluids. Created by Levich S.V..……....................................... 4 Conjugated proteins. The methods of allocation and quantitative determination of proteins in biological fluids. Created by Levich S.V..... 18 Enzymes: Structure and physicochemical properties. classification and nomenclature of enzymes. Created by Krisanova N.V.................................... 29 The mechanism of action and kinetic properties of enzymes. The regulation of enzymatic activity. Created by Krisanova N.V............................................ 46 Principles of enzyme activity determination. Genetic deficiency of enzymes. Medical enzymology. Created by Krisanova N.V………………… 60 Common regularities of metabolism. Anabolic and catabolic processes in humans. Krebs Cycle. Created by Krisanova N.V........................................... 74 General bases of bioenergetics. Created by Krisanova N.V............................ 87 Anaerobic oxidation of glucose – glycolysis. Synthesis of glucose – gluconeogenesis. Created by Rudko N.P......................................................... 104 Aerobic oxidation of monosaccharides. Created by Rudko N.P...................... 123 Metabolism of polysaccharides. The regulation and disorders of carbohydrate metabolism. Created by Rudko N.P........................................... 141 Lipoproteins of blood plasma. Metabolism of triacylglycerols and of glycerophospholipids. Created by Ivanchenko D.G......................................... 159 High fatty acids and ketone bodies metabolism. Created by Ivanchenko D.G. 185 Cholesterol metabolism. The regulation and disorders of lipids metabolism: obesity, atherosclerosis. Created by Ivanchenko D.G...................................... 212 Literature.......................................................................................................... 245 Answers to tests tasks………………………………………………………... 246 2 INTRODUCTION The manual "Biological chemistry. A manual for independent work at home and in class preparation for licensing examination “KROK 1” on module 1 “General regularities of metabolism. Metabolism of carbohydrates, lipids, amino acids and their regulation” for students of International Faculty (the second year of study) speciality: 7.120 10001 «General Medicine»contains a summary of the theory, which facilitates finding the right answer test tasks. Tests of this manual are similar in content and form to the test tasks, provided Testing Center of Ministry of Health of Ukraine. Each test task has only one either correct or more correct answer, that must be chosen among the available ones by a student. As a self-study students are invited to give rationale for the choice of the correct answer, identify key words for case described in a test task. The authors hope that this special form of student work with test tasks, with detailed explanation described in these tasks mostly clinical situations allow foreign English-speaking students to prepare properly and pass licensing exam "KROK 1: General medical training". 3 CLASSIFICATION, PHYSICOCHEMICAL PROPERTIES AND FUNCTIONS OF SIMPLE PROTEINS IN HUMANS. THE METHODS FOR INDICATION, SEPARATION AND RELEASE OF PROTEINS FROM BIOLOGICAL FLUIDS (Levich S.V.) INFORMATIONAL MATERIAL Simple proteins are complex nitrogen containing organic compounds (polymers) that are consisted of α-amino acid residues, connected by peptide bonds. AMINO ACIDS AND THEIR CLASSIFICATION Amino acids are biologically important organic compounds composed of amine (-NH2) and carboxylic (-COOH) functional groups, along with a side-chain specific to each amino acid. In biochemistry, amino acids having both the amine and the carboxylic acid groups attached to the first (alpha-) carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids with the general formula represented on the fig. 1. Amino acids can be related to a specific stereochemical lines (D- or L-) using D-Glyceraldehyde as a reference compound. H O R C C OH NH2 Figure 1. General structure of α-amino acids, where R is an organic substituent known as a "side-chain". This group of amino acids includes the 20 proteinogenic ("protein- building") amino acids, which combine into peptide chains ("polypeptides") to form the building-blocks of a vast array of proteins. There are many ways to classify amino acids. These molecules can be assorted into 7 groups on the basis of their structure and the general chemical characteristics of their side-chain radicals: 4 Amino Acids with Hydrophobic Side Chain – Aliphatic NH2 O CH3 NH2 O CH3 NH2 O H3C C C OH H3C C C C C OH H3C C C C C OH H H2 H H H H2 H Alanine, Ala Isoleucine, Ile Leucine, Leu CH3 NH2 O H3C C C C OH H H Valine, Val Amino Acids with Hydrophobic Side Chain - Aromatic NH2 O NH2 O C C C OH HO C C C OH H2 H H2 H Phenylalanine, Phe Tyrosine, Tyr NH2 O C CH C OH HN H2 Tryptophan, Trp Sulfur-containing Amino Acid with Hydrophobic Side Chain NH2 O H3C S C C C C OH H2 H2 H Methionine, Met Amino Acids with Polar Neutral Side Chains O NH2 O NH2 O O NH2 O H2N C C C C OH HS C C C OH H2N C C C C C OH H2 H H2 H H2 H2 H Asparagine, Asn Cysteine, Cys Glutamine, Gln NH2 O CH3 NH2 O HO C C C OH HO C C C OH H2 H H H Serine, Ser Threonine, Thr Amino Acids with Negatively Charged Side Chains - Acidic 5 O NH2 O O NH2 O HO C C C C OH HO C C C C C OH H2 H H2 H2 H Aspartic acid, Asp Glutamic acid, Glu Amino Acids with Positively Charged Side Chains - Basic NH NH2 O NH2 O H2N C N C C C C C OH H2N C C C C C C OH H H2 H2 H2 H H2 H2 H2 H2 H Arginine, Arg Lysine, Lys NH2 O N C CH C OH HN H2 Histidine, His Unique Amino Acids O O H2N C C OH C N H2 H OH Glycine, Gly Proline, Pro The other type of amino acids classification based on the abilityof organism to synthesized them de novo. By this classification, amino acid can be divided on essential, non-essential and conditional amino acid. Essential amino acids cannot be synthesized by the human organism. As a result, they must come from food (histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine). Nonessential amino acids are produced in human organism even if they don't come from food (alanine, asparagine, aspartic acid, glutamic acid and serine). Conditional amino acids are usually not essential, except in times of illness and stress (arginine, cysteine, glutamine, tyrosine, glycine, proline and serine). QUALITATIVE REACTIONS FOR PROTEINS AND AMINO ACIDS 1. Piotrovsky’s test or biuretic test. This reaction proves the peptide bond in 6 proteins and peptides (starting from tripeptides). The protein solution during the interaction with copper ions gets blue-violet colour in the alkaline environment. 2. Ninhydrin reaction. There is the formation of blue-violet product after the additional of ninhydrin to protein solution. This reaction is used to prove the presence of α-aminoacids residues. 3. Sakaguchi’s test. Arginine is oxidized with sodium hypobromite and reaction with α-naphthol gives red colouring. 4. Fole’s test. This test is used to prove the presence one amino acid residue, only, in the composition of proteins – cysteine. 5. Millon’s test. Tyrosine, reacting with Milon’s reagent, forms mercurial salt coloured red. 6. Adamkiewicz’s test. Tryptophan can react with glyoxylic acid in acid environment. Red-violet coloured condensation products are formed. 7. Reaction with formaldehyde. Tryptophan, condensing with formaldehyde, forms with mineral acids blue-violet coloured salts. 8. Pauli’s test. The test is used to prove the presence of histidine and tyrosine which react with diazobenzene-sulfonic acid, forming cherry-red coloured complex. CLASSIFICATION OF PROTEINS All proteins can be classified: I. According to their function 1. Catalytic (enzymes) – more than 3000 proteins are enzymes. 2. Nutritive (reserve) – casein, ovalbumin etc. 3. Transport – blood serum proteins, which are capable to transport different compounds and substances to corresponding target organs (hemoglobin, blood
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