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Chemistry and Functions of Proteins TVER STATE MEDICAL UNIVERSITY BIOCHEMISTRY DEPARTMENT CHEMISTRY AND FUNCTIONS OF PROTEINS ILLUSTRATED BIOCHEMISTRY Schemes, formulas, terms and algorithm of preparation The manual for making notes of lectures and preparation for classes Tver, 2018 AMINO ACIDS -amino acids -These are organic acids with at least a minimum of one of its hydrogen atoms in the carbon chains substituted by an amino group.( Show the radical, amino and carboxyl groups) NH2 R | C – H | COOH Proteinogenous and Nonproteinogenous Amino acids - Major proteinogenous (standard) amino acids. (Give the names of each amino acid) R R 1 H – 2 CH3 – 12 HO – CH2 – (CH3)2 CH – 3 CH3 – CH – (CH3)2 CH – CH2 – 4 13 | CH3 – CH2 – CH – OH 5 | CH 3 6 14 HS – CH2 – HOOC – CH2 – 15 CH3 – S – CH2 – CH2 – 7 HOOC – CH2 – CH2 – NH2 | – C – H - | COOH 8 16 NH2 – CO – CH2 – 9 NH2 – CO – CH2 – CH2 – 17 10 NH2 – (CH2)3 – CH2 – 18 NH2 – C – NH – (CH2)3 – CH2 – 11 || NH 19 20 СООН NH -Glycine -Arginine Alanine -Serine -Valine -Threonine Leucine -Cysteine Isoleucine -Methionine Aspartic acid -Phenylalanine Glutamic acid -Tyrosine Asparagine -Tryptophan Glutamine -Histidine Lysine -Proline •Rare proteinogenous (standard) amino acids. ( Derivatives of lysine, proline and tyrosine) NH2 | H2N – CH2 – CH – (CH2)2 – CH | | OH COOH •Nonproteinogenous amino acids. (Name and show them) NH2 NH2 | | H2N – (CH2)3 – CH HS – (CH2)2 – CH | | COOH COOH NH2 | NH2 – C – HN – (CH2)3 – CH || | O COOH Ornithine Homocysteine Citrulline 2 CLASSIFICATION OF PROTEINOGENOUS (STANDARD) AMINO ACIDS Amino acids are classified by: *The structure of the radical (show); - aliphatic amino acids -monoaminodicarboxylic amino acids -amides of amino acids -diaminomonocarboxylic amino acids -hydroxy amino acids -sulfur-containing amino acids -cyclic (aromatic and heterolytic) amino acids *the polarity of the radical (show); -Non-polar (hydrophobic –Ala, Val, Leu, Ile, Trp, Pro.) -Polar (hydrophilic). ·charged amino acids -negatively charged (Asp, Glu) -positively charged (Arg, Lys,His) -uncharged (Gly,Ser,Thr,Cys,Tyr). *the level of essentiality (biological classification); - Essential (VILL MTTPh)Val, Ile,Leu,Lys,Met,Thr, Trp, Phen) -Semi-essential (Arg,Tyr,His) - Nonessential (all the rest). *their acid-base properties; -acidic (Asp, Glu) -basic (Lys, Arg, His) -neutral (all the rest) PHYSICO-CHEMICAL PROPERTIES OF AMINO ACIDS •Ionization-(protonization and dissociation) of basic and acidic groups of amino acids in water. (Explain and open up the biological importance of this phenomenon). -Show the following: the acidic groups of the amino acids the basic groups of the amino acids the forms in which amino acids can exist( show the neutral, the transition and dipole states) 10 *The influence of pH on the ionization (charge) of an amino acid -show how the charges of amino acids in basic and acidic media are changed. -pH<7, the excess of hydrogen ions{H+}- acidic medium -pH>7, the excess of hydroxyl ions {OH-}-basic medium R H+ | OH- + – ? (+) H3N – CH – COO (+) ? рН 7 •The Isoelectric state and isoelectric pH point of amino acids. -Explain the meaning of the isoelectric pH of various amino acids. Prove various of the isoelectric points of the following amino acids. -neutral (alanine ) -acidic (aspartic acid) -basic (lysine ) - + COO NH3 | | CH CH2 3 (CH2)4 | | | + – H +N – CH – COO– + – H3 N – CH – COO 3 H3 N – СН – COO Asp Ala Lys + H+ ОH- 7 2,8 9,8 IEP IEP 11 •The amphoteric and buffer properties of amino acids -What is amphoterity? -Why do amino acids exhibit buffer properties? PROTEINS They are ; High –molecules Nitrogen containing Organic compounds (substances) Made up of amino acids joined in a chain with the help of peptide bonds and have a complex structural organization (Explain all these characteristics) -Elementary components of proteins (C50-54% , O21-23% , N15-17%, H6,5-7,3% , S0,5% ) -What are oligopeptides, polypeptides, proteins (up to 10 , 10-40 ,>40 amino acids) and their molecular masses ( the average molecular mass of one (1) amino acid is 110 a.u ) ? N.B a.u = atomic units - Biological functions of proteins (Give examples of proteins with different functions and give the characteristics of the actions of the proteins action in performing these functions) Function Example of protein Characteristics of the action Fermentative (Enzyme) Hormonal Receptive Transport Structural and Supportive Contractile Substrate - energetic Electro-osmotic Immunological Haemostatic Energo –transformative -There are about 50,000-100,000 different proteins functioning in the body of a human being. These different proteins perform the same number of different functions in the human organism. 12 - How can the different kinds of functions of proteins, their individual and immune properties be explained?(Sequence and the number of the 20 proteinogenous amino acids) .Explain your answer. STRUCTURAL LEVELS OF ORGANIZATION OF PROTEIN MOLECULES Primary ( Linear sequence of amino acids joined in a chain with the help of peptide bonds) R | H2N – CH – COOH R1 R2 R3 Rn Rextreme | | | | H2N – CH – CОOH + H2N – CH – CОOH + H2N – CH – CОOH + ….….… + H2N – CH – C – OH 1 – Н 2 О 2 – Н 2 О 3 – Н 2 О n R1 R2 R3 Rn O | | | | // H2N – CH – CО ––– NН – CH – CО ––– NН – CH – CО ………… NН – CH – C – OH A scheme of the primary structure of a protein R1 R2 R3 e.t.c. (n) times Rn …………………. (N С) -Show : -the peptide chain -the N- and C-terminals of polypeptide chain (ppc) 13 -the radicals of the amino acids Secondary structure of proteins. -It is a way of folding of the polypeptide chain (Primary structure ) into a regulate - spiral or a -structure ( kind of bond –Hydrogen bond) – О || – CO — NH– – C –– N – | Н + β-structure R4 -Explain the differences between the -spiral and the -spiral Tertiary structure of proteins -This is the folding of the -spiral (-helix) or the -structure in space (Globular, Fibrillar proteins, explain their structure) 14 -Show how the tertiary structure is stabilized by ionic, hydrogen, covalent (disulfide) bonds and hydrophobic interactions Quaternary structure -It is the joining the group of polypeptide chains with tertiary structures into a unit functional protein molecule. What are protomer (subunit), oligomer? What kinds of bonds stabilize the quaternary structure of a protein ? ( Show them on the above drawn diagram ) 15 Which molecules contain information about the primary, secondary , tertiary and quaternary structures of proteins and where are they located? Explain the importance of the primary and quaternary structures of proteins in the performance of their functional activities giving examples of ; - denaturation of proteins - sickle –cell anemia - different structures and functions of myoglobin and hemoglobin 16 PHYSICAL AND CHEMICAL PROPERTIES OF PROTEINS THE STRUCTURE, HYDRATE AND IONIC LAYERS OF PROTEIN MOLECULES. (0) OR The value of the charge depends on the amino acid composition and pH of the medium. Solubility of Proteins Show and explain how the number (quantity) of amino acids , the hydrate layer and the structure (conformation) affect the solubility of proteins -neutral proteins -acidic proteins. Isoelectric Point of proteins -using the diagram, show the value of the isoelectric point of the following proteins (pH<7, >7, =7) -basic proteins -Explain how changes in the pH medium can affect the charge of a protein molecule (<7, >7,=7) COO – 1) + NH3 – COO – 2) COO+ NH3 – COO 3) + NH3 + NH3 Acid medium pH 7 Basic medium [H+] [OH –] 17 - Using given diagrams explain: -the isoelectric state of a protein molecule -the isoelectric point (pI) of protein molecules. Amphoteric Properties of Proteins - Prove using the diagrams on pages 9 an 10 that, proteins are amphoteric polyelectrolytes. Which groups of atoms give a protein molecule acidic properties and which groups give basic properties? Buffer properties of proteins -What is a buffer? -Which groups of atoms exhibit buffer properties? -Explain the value of the buffer capacity of proteins. Colloid properties of proteins - What qualities of a protein molecule enable them to exhibit colloid properties? (molecular mass, size of the molecules, charge, hydrate layer).Explain your answer. -Name the colloid properties of protein solutions.(density, rate of diffusion, gel formation, optical properties, inability to penetrate trough semi-permeable membranes etc.). Osmotic properties of proteins (diffusion and osmosis) Semipermeable membr ane -Show on the diagram the osmotic (hydrostatic) pressure. -Explain what is meant by the acetic pressure of proteins. -Explain the importance of the oncotic pressure of proteins in the regulation of water in the organism (Water metabolism). 18 Salting-out and the denaturation of proteins -Using the diagram, explain how the following occur: -the increase in the solubility of proteins when minute (small) concentrations of the salts of alkaline or alkaline-earth metals are added to them in solution -the decrease in the solubility of proteins (salting-out) when high concentrations of the above mentioned salts are added to them -Factors that stimulate the above mentioned processes (choose the factors for denaturation and those for salting-out) -High temperatures -Vibration -Salts of alkaline and alkaline-earth metals -salts of heavy metals -Mineral and organic acids -Organic solvents -Ionized radiation -Explain the differences in the structure and function of protein molecules during denaturation and salting-out. CLASSIFICATION OF PROTEINS Proteins are classified by their: -electrochemical indications (acidic, basic
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