ZieglerLec4-5-ProteinStructureFunction-ppt1

ZieglerLec4-5-ProteinStructureFunction-ppt1 - Lectures 4-5:...

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Lectures 4-5: Lectures 4-5: Protein Structure and Protein Structure and Function Function BIOCHEMISTRY 100 Winter 2009 M. Ziegler
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Weekly Homework 1 (1/14/09) Weekly Homework 1 (1/14/09) 1. (1 pt) side chain carries negative charge in conjugate base form? *b) C 2. (1 pt) most hydrophobic side chain? *d) L 3. (1 pt) side chain can be BOTH a hydrogen bond donor and a hydrogen bond acceptor in its predominant form at pH 7? *a) N 4. (1 pt) His imidazole, pKa of 6.0, pH 7.0, ratio of uncharged to charged imidazole? *d) 10:1 5. (1 pt) The peptide bond is a(n) *c) amide bond 6. (1 pt) The most common protein secondary structures (the alpha helix and beta conformation) are stabilized primarily by *d) hydrogen bonds
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Learning Objectives Learning Objectives 1. Terminology (explain or defne; understand use oF terms) : primary, secondary, tertiary, quarternary structure (of a protein), supersecondary structure, Fbrous vs. globular proteins, subunit, denaturation (and denaturant), ligand, prosthetic group, fractional saturation, cooperativity, binding site, allosteric (allosteric site, allosteric regulator, allosteric regulation) 2. List examples of categories of secondary structure that occur in proteins. 3. Describe the α -helix, including what groups serve as hydrogen bond donors and acceptors, chirality of most α -helices in proteins (right- or left- handedness), orientation of R groups relative to axis of the helix, the helix dipole (which end is δ +, which is δ –), and packing density of atoms (are there spaces in the structure, e.g., a “hole” down the center, or are the atoms closely packed together?) 4. Describe β -conformation, including which groups serve as hydrogen bond donors and acceptors, and orientation of R groups in a β pleated sheet. 5. Explain parallel and antiparallel β conformation. 6. What type of noncovalent interaction is most important in stabilizing the α - helix and β -conformations?
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Learning Objectives Learning Objectives , continued , continued 7. Explain what a β -turn is, where β -turns are often found in proteins, and what types of amino acid residues are often found in β -turns. 8. Be able to identify α -helices and β -strands (or sheets consisting of 2 or more β -strands) on a ribbon depiction of a protein structure. 9. Be able to recognize common supersecondary structures in ribbon diagram format: βαβ , αα , β meanders, and Greek key; and common tertiary folding patterns (some of which incorporate those supersecondary structures): ( βα ) 8 , i.e., “ αβ barrels”; β barrels; and the globin pattern of 8 α helices with no β structure. 10. Describe the structure of collagen (tertiary and quaternary), contrast it qualitatively with the α helix (no actual numbers needed for residues per turn, etc.), and explain why it ʼ s important for every 3rd residue to be G. 11.
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This note was uploaded on 02/25/2009 for the course BCH 100 taught by Professor Staff during the Spring '08 term at UC Riverside.

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ZieglerLec4-5-ProteinStructureFunction-ppt1 - Lectures 4-5:...

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