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Biochemistry 2288A
Derek Mc Lachlin

topic pages introduction 1-6, 11-22, 26-35 1. central dogma 2. amino acids 72-73 3. protein structure 121-140 3. protein function 120, 138-143 5. enzyme catalysis 89-92, 99-103, 6. protein purification 140-143, 146-148, 152-153 164-167 for proteins - form and function are intrinsically linked name function example enzyme catalyzes chemical reactions protease structural provides mechanical support and structure to cells and tissues a-keratin transport carries small molecules or ions hemoglobin motor generates movement in cells and tissues myosin storage stores small molecules or ions ferritin signal carries signals from cell to cell insulin receptor detects signals and transmits them to the cell rhodopsin gene determines which sections of the genetic code will be regulator manifested; binds to DNA to switch genes on or off globular protein: polypeptide chains fold up into compact shape like an irregularly shaped ball - enzymes tend to be globular fibrous proteins: simply elongated 3D shape (for proteins that need to span a long distance) ex. a-keratin: extremely stable long-lived found in hair, nail, horn > coiled coil dimer - common outside the cell - part of the extracellular matrix that binds cells together to form tissues proteins are flexible > can undergo conformational changes - results in changes in the position of structural domains - can be caused by environmental changes, binding of different molecules, etc - crucial for the function of motor proteins, sensory proteins, etc proteins can come in a huge variety of shapes and electronic topography (arrangement of polarity on the protein) > due to variety of amino acid side chain properties and tertiary folding patterns > therefore allows for extreme specificity when binding to molecules - through multiple weak bonds (non-covalent) - a small area of the protein surface will be complementary to the structure of the molecule > the associated molecule is called the ligand - for enzymes it's called the substrate or active site > protein might recognize just 2 out of thousands of other molecules > proteins can have more than one binding site > therefore the binding of one ligand might cause conformational changes in protein structure, affecting the binding of another ligand allows proteins to act as catalysts, structural support, signal receptors, tiny motors > can be very tight or weak and short-lived Kd (dissociation constant)- affinity of an enzyme for its substrate  lower the Kd the stronger the affinity, tighter the binding  the more PL (protein ligand complex) is formed the lower the Kd  units: M o range: femtomolar (10^-15) – millimolar (10^-3) the protein-ligand complex  proteins form complexes with other proteins/ligands in order to perform a specific function within the cell  ex. Ribosomes: a complex of 50+ proteins and RNA some proteins are secreted by the cell to attach to the cell membrane or to be part of the extracellular matrix  proteins are directly exposed to the extracellular conditions so their polypeptide chains must be stabilized by covalent cross-linkages in order to keep their structure WHY? o tie together two amino acids in the same protein o connect two polypeptide chains in a multisubunit protein disulfide bonds: most common covalent cross-linkage bonds  form as protein is being exported from cell  catalyzed in the endoplasmic reticulum o enzyme links together SH bonds from adjacent cysteine side chains in the protein o acts as an ‘atomic staple’ that reinforces the favourable conformation  does not change protein structure/conformation  recall: disulfide bonds cannot form within the cell cytosol o high concentration of reducing agents reverts the bonds COLLAGEN collagen: most abundant fibrous protein in animal tissues (25%)  3 long polypeptide chains each containing glycine every 3rd position (commonly quite long ~1000 residues)  results in a triple helix with glycine at the core o bind to each other side by side and end on end - results in overlapping arrays o strong collagen fibrils that hold tissue together; forms sheets or fibers pol
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