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8"6 0+-#"2$3 Condensation of 2 amino acids forms the peptide bond, the amide linkage holding amino acid residues in peptide and protein polymers Properties of the peptide bond have major consequences in terms of the 3-dimensional structures of proteins The size and composition of polypeptides exhibit tremendous but not unlimited variety Protein sequence determines its folded structure and function Proteins: secondary structure – major types of secondary structure found in many proteins: ! helix, " conformation, " turns – surface loops: not really secondary structure because not regular, repetitive Secondary structures are mainly stabilized by hydrogen bonds.
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!"5&-,-9 :;<"#4="3 Defne polymorphisme oF proteins What does determine structure and Function oF proteins ? Defne the primary structure Describe the peptide bond: what type oF reaction leads to the peptide bond, which atoms are involved Know backbone, Carboxyl terminal end (C-ter), Aminol terminal end (N-ter) Draw a peptide bond – identiFy atoms that are in the peptide plane Why is the trans confguration Favored ? What are Ramachandran angles ? Be able to identiFy phi and psi on a drawing oF a peptide. Are all phi and psi combinations allowed ? Why ? Describe and indicate atoms involved in backbone hydrogen bonding
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!"5&-,-9 :;<"#4="3> #+-4-%"7 Defne secondary structure. List examples oF categories oF secondary structure that occur in proteins. Describe the ! -helix, including what groups serve as hydrogen bond donors and acceptors, chirality oF most ! -helices in proteins (right- or leFt-handedness), number oF residues per turn, orientation oF R groups relative to axis oF the helix, the helix dipole (which end is # +, which is # –), packing density oF atoms, eFFect oF R groups on the stability. Describe " -conFormation, including which groups serve as hydrogen bond donors and acceptors, and orientation oF R groups in a " pleated sheet. Explain parallel and antiparallel " conFormation.
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!"5&-,-9 :;<"#4="3> #+-4-%"7 Identify the most important noncovalent interactions stabilizing the ! -helix and " -conformations. Explain what a " -turn is, where " -turns are often found in proteins, and what types of amino acid residues are often found in " -turns. Be able to identify ! -helices and " -strands (or sheets consisting of 2 or more " -strands) on a ribbon depiction of a protein structure. Be able to identify ! -helices and " -sheets in a Ramachandran diagram
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http://www.rcsb.org/pdb/static.do?p=education_discussion/educational_resources/index.html
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This note was uploaded on 01/30/2010 for the course BIOC 460 taught by Professor Ziegler during the Spring '07 term at University of Arizona- Tucson.

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lec5 -...

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