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Peptides to Proteins What are PROTEINS? Proteins are large, complex molecules that serve diverse functional and structural roles within cells. Proteins are the ACTION FORCE in the cell. Enzyme Defense Protease Antibody Fights Viruses Degrades Protein Proteins can be functionally classified. Motion Actin Transpor t Hemoglobin Contracts Muscle Fibers Carries O2 Regulation Insulin Controls Blood Glucose Support Keratin Forms Hair and Nails Proteins are chains of amino acids. O C OH N H H Short chains of amino acids are called peptides. Proteins are polypeptide molecules that contain many peptide subunits. N H H Amino acids have an amino group, carboxyl group, R group and hydrogen. R NH2 C H Amino Acid 1 COOH Each amino acid has unique chemical properties. Glycine Histidine Glutamine Glutamate Lysine Cysteine Aspartate Asparagine Arginine Isoleucine Methionine Serine Leucine Proline Alanine Threonine Tryptophan Phenylalanine Valine Tyrosine Peptide bonds form by dehydration synthesis R R NH2 C H Amino Acid 1 H N C O OH H C COOH H Amino Acid 2 H2O R R C COOH NH2 C H Amino Acid 1 H Amino Acid 2 Peptide bond A protein is a linear sequence of amino acids linked together by peptide bonds. The peptide bond is a covalent bond between the -amino group of one amino acid and the -carboxyl group of another. The peptide bond has partial double bond character and is nearly always in the trans configuration. The backbone conformation of a polypeptide is specified by the rotation angles about the Cα–N bond (phi, φ) and Cα–C bond (psi, ψ) of each of its amino acid residues. The sterically allowed values of φ and ψ are visualized in a Ramachandran plot. When two amino acids are joined by a peptide bond they form a dipeptide. Addition of further amino acids results in long chains called oligopeptides and polypeptides. Gene 3’ Nucleus Messenger Ribonucleic Acid (mRNA) Trp tRNA Ala tRNA Met Met Large Subunit Ribosome Met 5’ Amino Acidtransfer RNA tRNA Ala Empty tRNA Trp Empty tRNA A U G G C C U G G U A G Small Subunit Cytoplasm Ribonucleotides Codon 1 A U G = Methionine Codon 3 U G G = Tryptophan Codon 2 G C C Codon 4 U A G = Stop = Alanine A G C U is the synthesis of proteins in the cell. Primary There are 4 basic Secondary Tertiar y Quaternary L V M H G I Q Y P S E C K T F The primary structure is the sequence of amino acids. N R A P D Primary structure • The linear sequence of amino acids joined together by peptide bonds is termed as the primary structure of the protein. • The position of covalent disulfide bonds between cysteine residues is also included in the primary structure. The secondary structure is primarily composed of alpha helices and beta-pleated sheets. Folding Back and Coiling Alpha Helix Primary Structure Beta-Pleated Sheet Secondary structure • Secondary structure in a protein refers to the regular folding of regions of the polypeptide chain. • The two most common types of secondary structure are the -helix and the -pleated sheet. • The -helix is a cylindrical, rod-like helical arrangement of the amino acids in the polypeptide chain which is maintained by hydrogen bonds parallel to the helix axis. • In a -pleated sheet, hydrogen bonds form between adjacent sections of polypeptides that are either running in the same direction (parallel -pleated sheet) or in the opposite direction (antiparallel -pleated sheet). • Turns reverse the direction of the polypeptide chain and are often found connecting the ends of antiparallel pleated sheets. The tertiary structure is the protein’s 3D shape. Tertiary structure •Tertiary structure in a protein refers to the three-dimensional arrangement of all the amino acids in the polypeptide chain. •This biologically active, native conformation is maintained by multiple noncovalent bonds. The quaternary structure is the assembly of folded subunits. Quaternary structure • If a protein is made up of more than one polypeptide chain it is said to have quaternary structure. • This refers to the spatial arrangement of the polypeptide subunits and the nature of the interactions between them. Summary • Proteins are biological workhorses that carry out most of the functions within the cell. • Proteins are large biological molecules that serve diverse functional and structural roles within cells. • Proteins are synthesized during the translation process. Summary cont’d… • Proteins are composed of amino acids that are covalently linked by peptide bonds. • Proteins have four basic levels of structure. However, proteins must fold correctly in order to function properly. The four levels of structure in proteins. (a) Primary structure (amino acid sequence), (b) secondary structure (-helix), (c) tertiary structure, (d) quaternary structure