Exam 2 Study Guide - Chapter 4 • Four levels of protein...

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Chapter 4 Four levels of protein structure: o Primary – sequence of amino acids in a polypeptide chain o Secondary – hydrogen bonds between amino acids forming a -helixes and b -sheets o Tertiary – completely folded single polypeptide chain o Quaternary – association of multiple polypeptide chains Weak non-covalent bonds and hydrophobic interactions facilitate protein folding o Van der Waals attractions – attractive forces between neutral atoms (electron cloud) o Electrostatic – attraction between negative/positive charged atoms o Hydrogen bonding o Hydrophobic interactions – hydrophobic sections associate together in the center of the protein away from the water Proteins can be denatured by a change in pH or temperature o Proteins unfold, causing a loss of function o Can cause disease such as Alzheimer’s (beta protein aggregation forms plaques) o Mad Cow Disease Chaperone proteins aid in protein folding by facilitating folding along the correct pathway o Can bind to parts of unfolded proteins or can create a closed container to isolate polypeptide for folding o GroEL/GroES complex Found in bacteria; belong to chaperonin family Example of a “container” that isolate polypeptide Has ATP binding site Hydrophobic stripe at opening a - helices o Backbones that contain hydrogen bonds (Every 4 th N) o Side chains point outward o 5.4 Å per turn o right/left handedness b -sheets o Strands are parallel/anti-parallel o Hydrogen bonds are between adjacent strands o 7 Å for one pleat o Side chains alternate sides o Not completely flat, slightly twisted. Intrinsically disordered regions o Region that lacks a definite structure o Functions include the binding, tethering domains within proteins, tethering interacting proteins Rational drug design -- using knowledge of biomolecular target (often the protein structure) to design a drug o Chronic mylogenous leukemia (CML) Chromosome 9 and 22 switch some genetic material and creates BCR-Abl (unregulated) o Gleevec – miracle drug but some patients immune because of random mutations
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BCR-Abl (unregulated) o Gleevec – miracle drug but some patients immune because of random mutations Works by inhibiting kinase Nilotinib – new drug developed using structure of Gleevec bound to to Abl kinase domain Lysozyme -- changes the shape of its substrate to stabilize the transition state o Hydrolase o Natural antibiotic o Substrate = polysaccharide chains Regulation of protein function o
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