BIOL 3510 1st Edition Lecture 3 Outline of Last Lecture I An Introduction to Proteins and Amino Acids II Bonds Covalent Polar Covalent Non covalent Forces Outline of Current Lecture I The Functions of Different Proteins II Enzymes and their actions a Lysozyme III Protein Regulation IV Antibodies and their uses Current Lecture Proteins II Proteins interact with other molecules Ligand anything bound by a protein Binding site area of a protein that interacts with a ligand selective binding is mediated by many non covalent bonds forces Proteins have diverse functions such as speed up the rate of chemical reactions enzymes provide support in and outside of cells like keratin and function in storage and transport like hemoglobin Enzyme protein that acts as a catalyst Enzymatic reactions The substrates ligand binds to an active site binding site Substrate is altered upon binding so that the desired reaction is favored 1 Holds substrates in alignment envourages reaction 2 Re arranges electrons stabilizes intermediates 3 Alters bond angles moves towards transition state These notes represent a detailed interpretation of the professor s lecture GradeBuddy is best used as a supplement to your own notes not as a substitute Example Lysozymes cleave polysaccharide chains found in bacterial cell walls Small molecules covalently attached to proteins increase protein functionality They are used for functions that amino acides cannot perform Fe binds oxygen in hemoglobin Metals near active sites make transient bonds with the substrate Regulation of protein function Amount of protein Location of protein Modification of protein activity by modifying the protein s shape 1 Feedback inhibition of allosteric proteins 2 Positive regulation of allosteric proteins 3 Protein phosphorylation 4 Other covalent modifications of proteins 5 Binding of GTP 6 Binding and hydrolysis of ATP Allosteric proteins undergo conformational changes upon ligand binding which alters their activity Feedback inhibition occurs when a product of a pathway inhibits an enzyme that acts earlier in the pathway Enzyme regulation can be positive or negative Protein phosphorylation can inhibit or stimulate protein function Kinase attaches phosphates to serine threonine or tyrosine side groups on a target protein Phosphatase Removges phosphates from a target protein Example cell cycle progression is controlled by phosphorylation Other covalent modifications also affect protein activity Binding GTP activates GTP binding proteins For example the elongation factor EF Tu undergoes a large conformational change after GTP hydrolysis Hydrolysis of bound ATP can provide directionality to a series of conformational changes like myosin walking along an actin microfilament A combination of different protein modifications and binding partners control protein complex assembly and function Antibodies are useful tools for studying proteins They recognize specific antigens can be used for immunoprecipitation and as molecular tags duing microscopy
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