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 functio...

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 • Glicoproteins • Lipoproteins • Albumin • Globulin PROTEIN FUNCTIONS AMINO ACIDS - CLASSIFICATION Common amino acids • 20 α-amino acids • Coded in DNA • Appear in proteins Derived amino acids Non-protein amino acids • Enzymatic modification of a common amino acids after it has been incorporated into a protein • Free or combined states, but not in proteins • Specific functions 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 Nonpolar amino acids Core of the protein Hydrophobic Polar amino acids In the surface of the protein In contact with water Hydrophilic 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). Uncharged amino acids Charged Acidic Basic 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  • 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. Dehydration 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 mainchain 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 and describes the local spatial arrangement of ts main-chain atoms • Types of secondary structure α−hélix β-pleated sheet PROTEINS - STRUCTURAL LEVELS Secondary structure – α 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 – α 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 – β-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 – β-pleated sheet Antiparallel β sheet Polypeptide chain runs in the opposite direction More frequent Parallel β sheet Polypeptide chain runs in the same direction PROTEINS - STRUCTURAL LEVELS Secondary structure – β-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  Glicine 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 • • Denaturing agents  pH, heat, detergents, organic solvents and urea Denaturation leads to protein precipitation  protein aggregates  exposed hydrophobic surfaces associate. Native conformation: The biologically active conformation of a protein Denaturation: Partial or complete unfolding of the specific native conformation of a protein such that the function of the molecule is lost. Renaturation: The refolding of an unfolded (denatured) protein so as to restore its native structure and function.