Amino Acids and Proteins PDF

Amino acids and Protiens Chiral and achiral molecules  Amino acids Configuration of amino acids  “R” Group attributes different properties to amino acids:  Charge on amino acids  Size of the amino acid  Polarity of amino acids Classification of Amino acids based on R-groups...

Amino acids and Protiens Chiral and achiral molecules  Amino acids Configuration of amino acids  “R” Group attributes different properties to amino acids:  Charge on amino acids  Size of the amino acid  Polarity of amino acids Classification of Amino acids based on R-groups 1. Non-Polar aliphatic amino acids 2. Aromatic amino acids 3. Polar Uncharged amino acids 4. Positively charged amino acids 4. Negatively charged amino acids  Uncommon amino acids Uncommon Amino Source and function Acids 4-hydroxyproline Found in plant cell wall proteins 5- hydroxylysine Found in plant cell wall proteins and collagen. 6-N -Methyllysine Present in myosine. γ- Found in blood clotting protein prothrombin. Carboxyglutamate Selenocysteine 1) Incorporated in protein during protein synthesis. 2) Contains Selenium instead of sulphure in cysteine. Pyrolysine 1) Found in Archeabacteria methyltransferase enzymes 2) Incorporated in protein during protein synthesis. Ornithine and 1) Not constituent of proteins. Citrulline 2) Act as intermediates in biosynthesis of argenine and in Urea cycle.  Amino acids are amphoteric in nature Exists as dipolar ion (zwittorion) when dissolved in water. Amino acid zwitterion can act either as acid or base Titration curve of amino acid gives following information: 1. Quantifies pKa values 2. Helps identifying buffering region. 3. Predicts the electric charge of an amino acid. pKa values of different amino acids Amino acid join through peptide bond to form peptides/Proteins Peptides and proteins have N and C- termini  Forces (interactions) stabilizing protein structure Disulphide linkages Hydrogen bonds Ionic interactions or Salt bridge van der Waals interactions Hydrophobic interactions Disulphide bond formation by Cysteine Oxidation Reduction  Hydrogen bonds H-bonding is an electrostatic interaction. Hydrogen bond is formed between H-atom (donor atom) bonded to a strong electronegative atom in a molecule and electronegative atom (acceptor atom) of another molecule. Acceptor atom Donor atom  Hydrogen bonds are directional. Hydrogen bonding is stronger when acceptor atom is at 180º anlge H-bonded atoms are at 180 angle with respect to  Van Der Waals interactions Vand Der Waals interactions are transient. When two uncharged atoms are brought very close together their surrounding electron clouds influence each other.  Transient dipole in one atom induces complimentary dipole in nearby atom. The distance required for Van Der Waals interaction depend upon the size of atoms and the electron cloud.  Ionic interactions/Salt bridges Oppositely charged molecules when in close proximity interact electrostatically. Carboxylate ion of an acidic residues e.g. aspartic acid or glutamic acid and an ammonium ion of the basic residue such as lysine, arginine or histidine.  Hydrophobic interactions Produced in non-polar molecules In protein forms between non-polar R groups of amino acids e.g. Valine, Leucine, Isoleucine, alanine, phenylalanine, tryptophan. Form within the core of the protein. Provide stability to the protein structure. Amino acid with higher hydropathy index tend to form hydrophobic interactions. Hydropathy index of different amino acids  Different levels of Protein structure Primary Secondary Tertiary Quaternary structure Structure Structure Stucture Amino α- Helix Polypeptide Assembled acid chain subunits residues  Primary Structure All covalent bonds which describe linkage of amino acid in a polypeptide chain. Primary structure of protein refers to amino acid sequence.  Protein Secondary Structure  Stable arrangement of amino acid residues producing repeating/recurring patterns.  Local conformation of part of a polypeptide. 1. αHelix Given by Linus Pauling and Robert Corey  Stability of α-helix Constrains affecting stability of α-helix (1) The bulkiness of adjacent R groups: the electrostatic repulsion (or attraction) between successive amino acid residues with charged R groups. (2) The interactions between R groups spaced three (or four) residues apart. (3) The occurrence of Pro and Gly residues. (4) The interaction between amino acid residues at the ends of the helical segment and the electric dipole inherent to the helix. Helix unstability:  Long chain of Glu residue does not form α-helix at pH 7.  Bulky amino acids e.g. threonine, Aspargine, serine and cystine when together do not form α-helix. Presence of Pro residue within amino acid sequence. Helix stability: Positively charged amino acid which are 3 residues away from negatively charged amino acid form ion pair. Hydrophobic amino acid residues located 3 residues apart interact through hydrophobic interaction  Presence of negatively charged amino acid near N-terminal and Vice versa.  2. β-Sheets  Polypeptide backbone extends in Zigzag manner called β-strand.  Strands can arrange side by side to form β-sheets.  Two types:  Anti- Parallel β-sheets  parallel β-sheets Ala and Gly residues are common in β-sheets  Tertiary structure of protein  Three dimensional folding of polypeptide chain  Quaternary structure of proteins  Arrangement of two or more polypeptides of a protein. Groups of proteins based on higher levels of protein structure 1) Fibrous proteins:  Long strand or sheet arrangement of polypeptide chain.  Examples: Keratin and Collagen 2) Globular proteins  Globular or spherical folding of polypeptide chain.  Examples: Hemoglobin and Myoglobin.  Fibrous proteins Properties: 1) Insoluble in water 2) Made up of repeating a particular secondary structure element. 3) Interior and exterior regions contain high concentration of hydrophobic amino acids.  α-Keratin  Belong to protein family called intermediate filament (IF) proteins.  Present in wool, nails, hooves, hair in mammals. Structure of α-Keratin:  Right handed α-helix.  Super-twisted coiled coil: supertwists left handed.  Each turn is 5.15 to 5.2 Å α -keratin is rich in the hydrophobic residues Ala, Val, Leu, Ile, Met, and Phe Secondary structure and properties of fibrous proteins  Collagen It is found in connective tissue viz, tendons, cartilage, the organic matrix of bone, and the cornea of the eye. Left-handed helix Three amino acids per turn. Supertwist of three polypeptide chains in right-handed manner. Proline, Glycine, 4-hydroxyproline And alanine. Repeating unit of tripeptides Gly-X-Y  Myoglobin  Structure:  Single polypeptide chain.  No. of amino acid residues – 153  Contains single Fe bound protoporphyrin or heme group.  70% residues are in α-helix.  Dense hydrophobic core.  Mol. Wt. – 16700.  Binds to oxygen in Muscle cells.  Hemoglobin  Present in red blood cells.  Transports oxygen to different organisms.  Structure:  It is tetrameric protein.  Four heme prosthetic group in each subunit.  Two types of polypeptide chains:  Two α-chains (141 amino acid residues)  Two β-Chains (146 amino acid residues)  α1 β1 dimer interacts with α2β2 dimer throught 30 residues.  Two conformations of hemoglobin T- State – low affinity for hemoglobin R-State – high affinity for hemoglobin  Binding of oxygen to hemoglobin is cooperative. T and R-states of Hemoglobin