Amino Acids and Proteins PDF

AMINO ACIDS AND PROTEINS Lesson 3 AMINO ACIDS AND PROTEINS Characteristics, structure and classification of amino acids and proteins Peptide bond. Structural protein levels. GENERAL CHARACTERISTICS 50% of the body weight are proteins 3D structure of the protein is related with its...

AMINO ACIDS AND PROTEINS Lesson 3 AMINO ACIDS AND PROTEINS Characteristics, structure and classification of amino acids and proteins Peptide bond. Structural protein levels. GENERAL CHARACTERISTICS 50% of the body weight are proteins 3D structure of the protein is related with its function. Proteins are linear polymers formed from amino acids. Aa sequence depends on the genetic information encoded in DNA. GENERAL CHARACTERISTICS GENERAL CHARACTERISTICS GENERAL CHARACTERISTICS PROTEIN CLASSIFICATION In terms of In terms of structure shape Simple proteins Fibrous proteins Conjugated proteins Globular proteins Glycoproteins Albumin Lipoproteins Globulin PROTEIN FUNCTIONS AMINO ACIDS - CLASSIFICATION Common amino Derived amino Non-protein amino acids acids acids 20 α-amino acids Enzymatic Free or combined Coded in DNA modification of a states, but not in Appear in common amino proteins proteins acids after it has Specific functions been incorporated into a protein COMMON AMINO ACIDS STRUCTURE A carboxyl group and an amino group bonded to the same carbon atom (the α carbon) They differ from each other in their side chains (R groups) vary in structure, size, and electric charge Convention to identify the carbons in an amino acid: α carbon R group → β, γ, δ, ε (proceeding out from the α carbon) COMMON AMINO ACIDS CLASSIFICATION Five main classes based on the properties of their R groups1), particularly their polarity, or tendency to interact with water at biological pH (near pH 7.0). Nonpolar amino acids Core of the protein Hydrophobic Uncharged amino acids Polar amino acids Acidic Charged In the surface of the protein In contact with water Basic Hydrophilic COMMON AMINO ACIDS CLASSIFICATION COMMON AMINO ACIDS – CHEMICAL PROPERTIES STEREOCHEMISTRY The α carbon is bonded to four different groups : ✓ carboxyl group ✓ amino group ✓ R group (except for Glicine) ✓ hydrogen atom α-carbon → chiral center or asymmetric Asymmetric carbon Chiral center: An atom with substituents arranged so that the molecule is not superposable on its mirror image This means that aa exist as two mirror-image forms called the L isomer and the D isomer. Stereoisomers: Compounds that are non superposable mirror images of each other COMMON AMINO ACIDS – CHEMICAL PROPERTIES STEREOCHEMISTRY All amino acid residues in proteins are L stereoisomers Cells are able to specifically synthesize the L isomers of amino acids → the reactions they catalyze to be stereospecific COMMON AMINO ACIDS – CHEMICAL PROPERTIES AMPHOTERIC MOLECULES The amino and carboxyl groups of amino acids, along with the ionizable R groups of some amino acids, function as weak acids and bases zwitterion or dipolar ion Amphoteric: Capable of donating and accepting protons, thus able to serve as an acid or a base. COMMON AMINO ACIDS – CHEMICAL PROPERTIES AMPHOTERIC MOLECULES Acid-base titration involves the gradual addition or removal of protons Plateau regions→ Buffer solution zwitterion PEPTIDE BOND Two amino acid molecules can be covalently joined peptide bond Formed by removal of the elements of water → Dehydration Reverse reaction → Hydrolysis CHARACTERISTIC OF THE PEPTIDE BOND ✓ The peptide bond is a flat (planar) structure. ✓ It has great stability. ✓ It can participate in the formation of hydrogen bonds. Peptide: Two or more amino acids covalently joined by peptide bonds. PROTEINS Protein: A macromolecule composed of one or more polypeptide chains, each with a characteristic sequence of amino acids linked by peptide bonds. Peptide >50 aa The amino acid composition of a peptide chain has a profound effect on its physical and chemical properties ✓ Proteins rich in nonpolar aa → insoluble in water → structural role. ✓Proteins rich in polar amino acids → water-soluble. Protein structural levels PROTEINS - STRUCTURAL LEVELS Primary structure: A description of the covalent backbone of a polypeptide chain, including the sequence of amino acid residues Secondary structure: The local spatial arrangement of the main- chain atoms in a segment of polypeptide chain. Tertiary structure: The three-dimensional conformation of a polypeptide in its native, folded state. Quaternary structure: The three-dimensional structure of a multisubunit protein, particularly the manner in which the subunits fit together. PROTEINS - STRUCTURAL LEVELS Primary structure The sequence of amino acids that form part of the protein chain from the first amino acid to the last one. Importance of primary structure ✓Proteins with different functions always have different amino acid sequences ✓ A single change in the amino acid sequence can cause proteins with less activity or altered activity → Genetic diseases Peptides are named beginning with the amino-terminal residue, which by convention is placed at the left → aa 1 PROTEINS - STRUCTURAL LEVELS Secondary structure Segment of a polypeptide chain taht describes the local spatial arrangement of its main-chain atoms Types of secondary structure ✓−hélix ✓-pleated sheet PROTEINS - STRUCTURAL LEVELS Secondary structure –  helix Helical conformation of a polypeptide chain Backbone is tightly wound around an imaginary axis drawn longitudinally through the middle of the helix R groups of the amino acid residues extending outward Right-handed PROTEINS - STRUCTURAL LEVELS Secondary structure –  helix The structure is stabilized by a hydrogen bond These turns allow hydrogen bonding between residues spaced four apart The structure is stabilized by a hydrogen bond between the hydrogen atom attached to the electronegative nitrogen atom of a peptide linkage and the electronegative carbonyl oxygen atom of the fourth amino acid on the amino-terminal side of that peptide bond PROTEINS - STRUCTURAL LEVELS Secondary structure – -pleated sheet Extended conformation of polypeptide chains The backbone of the polypeptide chain is extended into a zigzag Arrangement of several strands side by side →Stabilized by hydrogen bonds The individual segments that form a β sheet are usually nearby on the polypeptide chain but can also be quite distant from each other in the linear sequence of the polypeptide PROTEINS - STRUCTURAL LEVELS Secondary structure – -pleated sheet Antiparallel β sheet Parallel β sheet Polypeptide chain runs in the opposite direction Polypeptide chain runs in the same direction More frequent PROTEINS - STRUCTURAL LEVELS Secondary structure – -pleated sheet β turns Amino acid residues are in turns or loops where the polypeptide chain reverses direction Connect the ends of two adjacent segments of an antiparallel β sheet 180° turn involving four amino acid residues → Glycine and proline Important in globular proteins → compacted PROTEINS - STRUCTURAL LEVELS Tertiary structure The overall three-dimensional arrangement of all atoms in a protein Biologically active conformation of a protein This structure reflects the overall shape of the molecule. Stabilized by interactions between side chain functional groups: ✓covalent disulfide bonds ✓hydrogen bonds ✓salt bridges ✓hydrophobic interactions PROTEINS - STRUCTURAL LEVELS Quaternary structure The three-dimensional structure of a multisubunit protein Two or more separate polypeptide chains, or subunits, which may be identical or different The smallest unit → monomer or subunit: Dimeric proteins Trimeric proteins Multimeric proteins DENATURATION Native conformation: The biologically active conformation of a protein Denaturing agents → pH, heat, detergents, organic solvents and urea Denaturation: Partial or complete unfolding of Denaturation leads to protein precipitation → the specific native conformation of a protein such that the function of the molecule is lost. protein aggregates → exposed hydrophobic surfaces associate. Renaturation: The refolding of an unfolded (denatured) protein so as to restore its native structure and function.