102 handout 913 - MCB102 Handout 9/13 Levels of protein...

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MCB102 Handout 9/13 Levels of protein structure and the most significant interactions stabilizing them Primary -sequence of amino acid residues from N terminus to C terminus, covalent bonds Secondary -regular structure formed locally among nearby amino acids, noncovalent interactions (hydrogen bonding, van der Waals) Tertiary -three-dimensional structure of the entire protein, noncovalent interactions (hydrophobic, ionic interactions, hydrogen bonding) and covalent bonds (disulfide bonds) Quaternary -three-dimensional structure of protein complexes containing multiple amino acid chains (subunits), same interactions as tertiary Protein Folding Stepwise and cooperative -one part folding facilitates the folding of other parts Folded structure is stable by only a single hydrogen bond worth of free energy Proteins breathe -change structure locally without unfolding 1. Secondary structure forms locally 2. Hydrophobic collapse - nonpolar regions come together to minimize contact with water, molten globule - the compact state of a protein after the hydrophobic collapse, has secondary structure but not a fixed tertiary structure 3. Many intermediate structures are sampled until the most stable ( native ) tertiary structure is achieved, hydrogen bonding is optimized and ionic interactions ( salt bridges ) are formed between charged amino acids, mostly on the protein surface Chaperones -proteins that bind specifically to unfolded proteins (unfolding often caused by stresses such as heat) and use ATP to promote folding, DnaJ and DNAK in bacteria, hs proteins in eukaryotes Chaperonins -large protein complexes that contain a large cavity in which proteins fold, uses ATP Unfolded protein signal is unknown-exposed nonpolar regions? unpacked secondary structure? Isoelectric point -the pH at which a molecule (amino acid or peptide) has no net charge (positive and negative charges cancel out) WORKING WITH PROTEINS How to obtain proteins Chemical synthesis Only used for very small proteins (less than 100 amino acids) Synthesizes starting at the C terminus (truncated proteins will be missing N-terminal residues) 1. A chemical called Fmoc reacts with the amide nitrogen protecting it from subsequent reactions 2. The carboxyl oxygen then reacts with a chemical group on an insoluble bead (the support) 3. The Fmoc protecting group is removed from this first amino acid by adding base 4.
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