Amino Acids and Proteins PDF

Amino acids, proteins Máté Mackei Proteins have specific 3D structure related to their specific functions  Alpha-L-amino acids All peptides, polypeptides and proteins in mammalian, bird and reptile species are polymers of alpha-L-amino acids. There are 20 alpha-amino aci...

Amino acids, proteins Máté Mackei Proteins have specific 3D structure related to their specific functions  Alpha-L-amino acids All peptides, polypeptides and proteins in mammalian, bird and reptile species are polymers of alpha-L-amino acids. There are 20 alpha-amino acids (see later) that are relevant to the make-up proteins. Several other amino acids are found in the body free or in combined states. These non-protein associated amino acids perform specialized functions (such as: ornithine, citrulline, gamma-amino butyrate, beta-alanine, OH- proline, OH-lysine, etc., see later)  Alpha amino acids The alpha-amino acids in peptides and proteins (excluding proline) consist of a carboxylic (-COOH) and an amino (- NH2) functional group attached to the same carbon atom. This carbon is the alpha-carbon. ‫מובחנות‬ ‫מבדילות‬ Distinct R-groups, that distinguish one amino acid from another, also are attached to the alpha-carbon except glycine, where the R-group is hydrogen The fourth substitution on the alpha-carbon of amino acids is hydrogen. shorter Optical properties of the amino acids A carbon atom with 4 distinct constituents is said to be chiral (asymmetric). The one amino acid not exhibiting chirality is glycine since its '"R-group" is a hydrogen atom. All of the amino acids in proteins exhibit the same absolute steric configuration (based on the arbitrary): proteinogenic L-amino acids are related to the L (levorotatory)-glyceraldehyde. D-amino acids are never found in proteins, although they exist in nature. D-amino acids are often found in polypetide antibiotics, microbes, plants, insects. D-AA-oxidase The general structure of an alpha-L-amino acid Optical properties of the amino acids Stereoisomers= mirror images of amino acids: L-isomers in the mammalian proteins All objects have mirror images. Like many biomolecules, amino acids exist in mirror-image forms (stereoisomers) that are not superimposable. Only the L-isomers of amino acids commonly occur in nature. (The Mirror of Venus (1898), Sir Edward Burne-Jones/Mueseu Calouste Gulbenkian Lisbon/The Birdgeman Art ) Library endaincon  guanidino group ↓ pyrrolidine ring indol ring imidasol ring  Amino acids can be zwitterions amino carboxylic group group Depending on the pH the amino acids can be cations, anions, or zwitterions cation Isoelectric point anion The pH value at which the amino acid has no net charge (zwitterion) is the isoelectric point Structure of proteins  Structure of proteins Primary structure The sequence of amino acids that make up a polypeptide chain. 20 different amino acids are found in proteins. The exact order of the amino acids in a specific protein is the primary sequence for that protein. Secondary structure Protein secondary structure refers to regular, repeated patterns of folding of the protein backbone. The two most common folding patterns are the alpha helix and the beta sheet. Alpha helix: the polypeptide backbone coils around an imaginary helix axis in clockwise direction. Beta sheet: the polypeptide backbone is nearly fully extended. The R- groups (not shown) are alternately pointed above and then below the extended backbone. Condensation of 2 amino acids (peptide bond) Condensation of 2 amino acids (peptide bond)  Polypeptide chain (N- and C-terminus)  Peptide chain 2AA = dipeptide 10-50 AA = polypeptide 2-10AA = oligopeptide More than 50 AA = protein  Primary structure Val Thr Cys  Structure of proteins Primary structure The sequence of amino acids that make up a polypeptide chain. 20 different amino acids are found in proteins. The exact order of the amino acids in a specific protein is the primary sequence for that protein. Secondary structure Protein secondary structure refers to regular, repeated patterns of folding of the protein backbone. The two most common folding patterns are the alpha helix and the beta sheet. Alpha helix: the polypeptide backbone coils around an imaginary helix axis in clockwise direction. Beta sheet: the polypeptide backbone is nearly fully extended. The R- groups (not shown) are alternately pointed above and then below the extended backbone.  Secondary structure The arrangement of a polypeptide into regularly repeating units (alpha-helix, beta structure = beta-pleated sheet, collagen helix), random coil or beta -turn configuration Intramolecular (intrachain / interchain) hydrogen bonds along the length of the chain  Secondary structure Intrachain H-bonds Interchain H-bonds  Alpha helix Intrachain Approximately H-bonds 3.6 amino acid /turn  Collagen helix Connective tissue of skin, bone, tendon Alpha-helix: alpha-keratin Beta-pleated sheet Chains are antiparallel parallel Interchain H-bonds Beta-pleated sheet: beta-keratin In birds and reptiles Beta keratin in feather, ‫נוצה‬ beak, scale ‫מקור‬ ‫קשקשת‬  Beta-pleated sheet: silk fibroin, cocoon, spider web Silk is a natural protein fibre containing about 70-75% of actual fibre fibroin secreted from two salivary glands in the head of the silkworm larva  Tertiary structure Regularly repeating units, irregular parts, orientation of side chains and stabilizing bonds. A tertiary structure of a protein refers to the protein's three-dimensional (spatial) structure by complete folding of the sheets and helices of a secondary structure held in position by apolar (inside) and polar (outside) bonds between the side chains.  Tertiary structure Triose Phosphate Glycolate Oxidase Isomerase  Chain conformation of proteins Each protein has at least one three-dimensional conformation in which it is stable and active under biological conditions of temperature and pH; this is the native conformation. In other words, function of proteins arises from chain- conformation, which is the three-dimensional arrangement (secondary and tertiary structure together) of atoms in a structure. Amino acid sequences (primary structure) are also important because they specify the conformation of proteins. Protein folding is the process by which a protein structure ‫מקבל‬ assumes its functional shape, active, native conformation ‫ שזה הצורה של‬.‫קיבל צורה מיוחדת כדי להיות פעיל ונמצא בנטיב כונפורמישיון‬ ‫המבנה השני והשלישי שלו יחדיוצרים את המ בנה שהוא צריך כדי להיות פעיל‬ ‫בתנאים מוסיימים של חומצה וטמפט‬ Protein folding ↓ P ro t e i n  Denaturation of proteins When proteins are heated, or exposed to acids or bases, or high salt concentrations, the variety of weak bonds stabilizing chain- conformation and quaternary structure can be disrupted so that the protein unfolds. Unfolding = denaturation resulting in loss of function. ‫כשהחלבון לא נעטף זה נקרא כך‬ Denaturation is sometimes reversible ; an unfolded protein can be restored to correct folding and regain biological activity. This is called renaturation. Denaturation can also occur irreversibly (as when egg white protein, albumin,is denatured by boiling to congeal as egg white). Renaturation is then no longer possible. Denaturation of proteins: at isoelectric point is easier, denaturated proteins can be hydrolysed easier  Denaturating agents ‫ בונד‬h‫שובר את ה‬ Heat coagulates almost every protein The increased motion within the molecule breaks the hydrophobic interactions and hydrogen bonds. Examples: Fried eggs Denaturation of proteins after skin burn. Ultraviolet radiation coagulates proteins Sterilization of instruments and clothing (Cold can also denature proteins) Acids and bases denature proteins by chainging the pH of the solution of the protein, and thus changing carboxyl groups to carboxylate ions, amino groups to ammonium ions, or vice versa. Ionic bonds in the protein are broken. ‫נשברים קשרים איונים‬  S Denaturating agents - Reducing-oxidizing agents convert disulfide bonds to free sulfhydryl groups. Oxidizing agents can convert sulfhydryl groups back to disulfide bonds, but the structure of the protein may be significantly different form the native protein. This is the basis of permanent waves. Hydrogen-bonding solvents denature proteins by disrupting the hydrogen bonds within the molecule. 70% ethanol is used as a disinfectant because it precipitates the protein present in bacteria and virus Heavy metal ions, such as Ag+, Hg2+, and Pb2+, denature proteins by reacting with sulfhydryl bonds to form stable metal-sulfur bonds or the carboxylate ions in the side chains of acidic amino acids. A 1% solution of silver nitrate, AgNO3, formerly was used to treat the eyes of newborns to kill the bacteria causing the infection. Salting out: removal of hydrate hull (ammonium sulphate, NaCl). Sodium duodecylsulphate, mercaptoethanol are used as denaturating agents at gel electrophoresis.  Quaternary structure of proteins Many proteins are formed from more than one polypeptide chain. The quaternary structure describes the way in which the different subunits are packed together to form the overall structure of the protein. For example, the human hemoglobin molecule shown below is made of four subunits. Subunits of proteins Quaternary structure of haemoglobin  Quaternary structure of insulin Insulin has a quaternary structure (6 subunits) if it is stored. This inactive hexamer will be activated: active monomer insulin molecules will be produced. A lot of enzymes have subunits and that’s why quaternary structure: lactate dehydrogenase, glutamate dehydrogenase Structure of proteins  Bonds in the protein molecules Primary structure Peptide bond (covalent)  between amino acids Secondary and tertiary structure (mainly between side chains) Disulfide bond (covalent)  between SH-containing side chains (Cys) Ionic bonds  between polar, charged side chains (acidic/basic amino acids: Arg, Lys, His, Glu, Asp) Dipol-dipol interactions  between polar, non-charged side chains (Ser, Thr, Asn, Gln etc.) Van der Waals dispersion force (hydrophobic) between (Leu, Val, Ile etc.) H-bonds  between CO and NH groups of peptide bonds Quaternary structure (between polypeptide subunits- chains) (dispersion, dipol, H-bond) Sometimes: disulfide bond (insulin)  Covalent bonds Peptide bond The peptide bond that connects two amino acids in a polymer, is formed between the α-amino group of one amino acid and the α-carboxyl group of another. This reaction, which is called condensation, liberates a water molecule. Because the carboxyl carbon and oxygen atoms are connected by a double bond, the peptide bond between carbon and nitrogen exhibits a partial double bond character. There is no freedom of rotation about the bond that connects the carbon and nitrogen atoms.  Covalent bonds Disulfide bond The disulfide bond is a covalent bond between two sulfur atoms. It results from the oxidation of the –SH (sulfhydryl) groups of two cysteine molecules, forming cystine. H2N-CH-(COOH)-CH2-SH + HS-CH2-CH-(COOH)-NH2 H2N-CH-(COOH)-CH2S–SCH2-CH-(COOH)-NH2 (cystine) The disulfide bond determines conformation of protein molecules and restricts the flexibility of the polypeptide chain. Interchain disulfide bonds occur to link cysteine in one polypeptide chain with cysteine in another polypeptide chain. Intrachain disulfide bonds also occur to form cyclic structures.  Non-covalent bonds van der Waals forces (dispersion force, hydrophobic) These exist between non-polar molecules or atoms. They are the weakest of all the intermolecular forces. On average the negative charge of the electrons in an atom or molecule is spread evenly. For brief periods of time the electrons are concentrated on one side of the atom or molecule more than the other. This gives the atom or molecule a temporary partial negative charge - a temporary dipole moment. This dipole moment will induce a temporary dipole in a neighboring atom by attracting/repelling its electron charge cloud. Van der Waals forces become significant in binding only when numerous atoms can simultaneously come close to numerous other atoms in the protein molecule.  Non-covalent bonds Dipole-Dipole interactions result when two polar molecules approach each other in space. When this occurs, the partially negative portion of one of the polar molecules is attracted to the partially positive portion of the second polar molecule.  Non-covalent bonds H bonding It results from the attractive force between a hydrogen atom covalently bonded to a very electronegative atom such as a N, O, or F atom and another very electronegative atom. In molecules containing N-H, O-H or F-H bonds, the large difference in electronegativity between the H atom and the N, O or F atom leads to a bond formation 1016 Because of the difference in electronegativity, the H atom bears a large partial positive charge and the N, O or F atom bears a large partial negative charge. A H atom in one molecule is electrostatically attracted to the N, O, or F atom in another molecule Hydrogen bonds + + + - + - -  Non-covalent bonds Ionic Bonds It can be formed at physiological pH between the negatively-charged carboxylate group and the positively-charged ammonium group or between the carboxyl group of an acidic amino acid (Glu, Asp) and the amino group of a basic amino acid (Lys, Arg, His), and help to pull portions of a chain together Different amino acids form different bonds in the protein molecules  Classification of proteins by shape and solubility ‫גלובולר וספריל‬ ‫כמו אלבומין וגלובלין‬ ‫מסיסים במים‬ ‫אנזימים והורמונים‬ Globular proteins have tightly folded peptide chains that are roughly spherical in shape. Albumins, such as ovalbumin in egg white, lactalbumin in milk, and serum albumin in the blood Globulins, such as gamma globulin in the blood Enzymes, hormones They are water soluble.  Classification of proteins by shape and solubility Fibrous proteins contain polypeptide chains arranged in extended, parallel layers, or sheet-like structures. Collagens in connective tissues (skin, bone, tendon, etc) ‫פיבורסוס שהם מתייחסים‬ ‫לקולגן עור עצם גידים וכו‬ Elastins in ligaments and arteries ‫ואלסטין רצועות ועורקים‬ ‫וקרתין שיער ציפורניים ופרסות‬ Keratins in hair, wool, nails, and hoofs ‫לא ממסים במים‬ They are water insoluble Protein structure in art: Julian Voss-Andreae's sculptures Heart of Steel Unraveling Collagen stainless steel stainless steel height 2 m height 3.40 m  Classification of proteins by shape and solubility „Other type”, intermediate proteins: long, rod-like structure + „globular parts” Myosins (muscle) Fibrinogen (blood clotting) ‫ארוכים כמו שרירים ופיברינוגן‬ ‫מסיסים במים‬ They are water soluble  Classification of proteins by composition Simple proteins contain only amino acids (or derivatives of amino acids) ‫רק חלבון‬ Conjugated proteins consist of a simple protein combined with a nonprotein compound ‫חלבון ועוד מולקולה שהיא לא חלבון‬ Conjugated proteins The prosthetic group is the nonprotein part of a conjugated protein: Glycoproteins have a carbohydrate, as the prosthetic group, membrane glycoproteins, sodium-potassium pump Nucleoproteins (found in ribosomes and some viruses) have nucleic acids as the prosthetic group. Phosphoproteins (such as casein in milk) contain phosphoric acid bound to the protein by ester groups Chromoproteins (such as haemoglobin, rhodopsine) have a colored prosthetic group Hemoproteins (such as haemoglobin and cytochrom C) Lipoproteins are proteins containing lipid molecules (such as cell membrane, plasma lipoproteins) Flavoproteins (FMN, FAD), riboflavin prosthetic group Metalloproteins (ferritin), metal (Fe3+) prosthetic group  Classification of proteins by function Contractile proteins are responsible for coordination of motion. They can stretch and contract and are found in muscle (actin, myosin) Transport proteins (such as haemoglobin and serum albumin, ion channels) circulate and carry other molecules Enzymes are biological catalysts. They are usually globular shaped and represent the largest variety of proteins Protein hormones, which regulate cell processes, are chemical messengers produced in endocrine glands. An example is insulin Protection proteins include antibodies and blood-clotting proteins Storage proteins store small molecules or ions (ovalbumin, casein, zein) Regulation proteins control the expression of genes (catabolite activator protein) Receptor proteins: hormone receptors Toxic proteins (snake venom, bacterial toxins) Thank you very much for your attention!