Section3_Protein_structure_09

Section3_Protein_structure_09 - Protein Structure Ribosome...

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1 Protein Structure p53 Tumor Suppressor Antibody Rhinovirus Receptor and Antibodies Anthrax toxin HIV Reverse transcriptase HIV proteinase Ribosome Insulin Lysozyme B DNA EcoRI Potassium Channels David S. Goodsell http://www.scripps.edu/pub/goodsell/
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2 Protein Structure Proteins are polymers of amino acids. ie. Polyaminoacid or Polypeptides Peptide bond is the special name given to the amide bond that joins two amino acids: Peptide (amide) bond formed by condensation H 3 N + CH C R 1 O O - + H 3 N + CH C R 2 O O - H 2 O H 3 N + CH C R 1 O - O R 2 C CH N H O Protein Structure Proteins are linear molecules of amino acids joined by amide (peptide) bonds formed by ‘simple’ removal of H 2 O from: An example of a simple peptide is aspartame: 200 times sweeter than sucrose H 3 N + H 2 C COO - NH O CH 2 O O CH 3 O O - + H 3 N +
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3 Protein Structure Repeating backbone is non-ionizable , except the ends . Side-chains vary depending on amino acid. pK a , pI of side chains and termini are similar to free AA. Backbone { + H 3 N CH C O NH CH C NH O CH C O NH CH COO - CH 3 CH 2 OH CH 2 ) 4 NH 3 + CH 2 ) 2 COO - Side chains Amino-terminus Carboxy-terminus Internal "residues" Protein Structure When peptide bonds are formed, α -NH 3 + and α -COO - groups become covalently linked and can no longer ionize in solution. Charged groups of polypeptides are limited to the two ends (termini) and some of the R groups. Amino acid units in a peptide or protein are called residues. The amino acid sequence of peptides and proteins is always written with the N-terminal residue on the left and the C-terminal residue on the right: NH 3 + -AA 1 -AA 2 -AA 3 -AA 4 -AA 5 -AA 6 -COO
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4 Protein Structure • Polypeptide chains are very fexible , so the way they fold up to form a compact, 3D structure is an essential aspect of protein structure. • Folding of a protein is believed to be determined simply by its AA sequence. We cannot predict this yet, but we have many protein structures (determined by X- ray crystallography, or sometimes NMR) and the basic principles of protein folding are understood. • To describe the structure of a protein completely, four levels of structural information must be speci±ed. Protein Structure The four levels of protein structure: 1. Primary structure – linear sequence of amino acid residues. 2. Secondary structure – regular conformational patterns of contiguous portions of the polypeptide chain, stabilized by hydrogen bonds. 3. Tertiary structure – overall fold of the entire polypeptide chain to give a globular 3D structure. 4. Quaternary structure – The interaction of two or more globular polypeptides to form a multisubunit protein.
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5 Protein Structure 1. Primary structure – the sequence or order of amino acids in the protein is the primary structure. The Frst protein sequence was determined in the
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Section3_Protein_structure_09 - Protein Structure Ribosome...

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