lec 24 - Genome DNA Polypeptide –(polymer of amino acids...

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Unformatted text preview: Genome - DNA Polypeptide – (polymer of amino acids) Protein structure Function Cell biology/Evolution/Disease Lecture 24: Protein structure - hierarchical structure Protein structure/function: overview Amino-acid sequence 3D structure Function Protein function depends on the aa sequence! Reminder: Amino acid C COO- + H 3 N H R amine acid link to next aa (NH 3 + ) link to next aa (COO- )-carbon Structure of a tripeptide C N C N C N C N C Directionality! N-terminus C-terminus Peptides, polypeptides, proteins Peptides = up to 20-30 aa Polypeptides > Peptides Proteins = “natural” polypeptides or complex of polypeptides with well-defined structure Size: daltons (1 dalton = 1 atomic mass unit) e.g. 10,000 Da or 10 kDa MW of 1 aa = on average ~110 Da Titin (3 MDa) Endomorphins: tetrapeptides Secondary structure No intramolecular noncovalent interaction -> “random coil” Noncovalent interactions (hydrogen bonds)-> stabilized structures:-helix-sheet or U-turns 60% of average polypetide chains Secondary + tertiary structure-helix-sheet Ras (= GTPase)-helix C= O N- H H-bond Periodicity! Many bonds -> stable All polar groups of backbone-> internal H-bonds->surface properties exclusively dependent on side chains Straight rods 8 Leu 7 6 5 4-helix 1 2 3 Ser His Ala Ile Leu Gly Asp- + hydrophobic rest of the protein hydrophilic exposed at the surface-helices can often be predicted due to periodicity of hydrophobic aa If an -helix is at the surface of a protein, one face will often display hydrophobic residues that will interact with other parts of the protein, while hydrophilic/charged residues will be exposed at the surface (interacting with water and maintaining the protein in solution). Typical periodicity for such helices is: i, i+3, i+4, i+7 In our example: residues i (1)= Leu, i+3 (4) = Ile, i+4 (5) = Ala, i+7 (8) = Leu 8 7 5 4 1 6 3 2 side view top view backbone (spiral) aa residues-sheet-strand (5-8 aa) NB: strands contributing to a sheet can belong to different polypetides turn-strands that are half buried in the protein core will tend to have hydrophobic residues at positions i, i+2, i+4, i+ 6 etc, and polar residues at positions i+1, i+3, i+5, etc. protein core H-bonds link two adjacent -strands Representations of tertiary structure Ras = small GTPase GDP Tertiary structure Polypetides packed in the smallest volume! Tertiary structure turn loop-helix-sheet Tertiary structure blue positive charges red negative charges General types of proteins Fibrous Globular Transmembrane Tertiary structure: motifs 4 O from hydrophilic residues + 1 O from backbone + 1 H 2 O-> chelate Ca 2+ Calcium-binding motif (found in > 100 Ca-binding proteins) Zn holds -helix and - strands together Found in DNA and RNA- binding proteins Why 7?...
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