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BSCI330 Exam II ReviewProteins- Covalent modifications to proteinso 1. Phosphorylation Addition of a negatively charged phosphate group to the R-group of serine, threonine, tyrosine (b/c these all contain OH) Phosphate comes from ATP and forms the amino acid residue ADP Reaction is catalyzed by protein kinases (enzymes) Drives changes in protein structure and activity- Because each phosphate group adds two negative charges to the protein which participate in new ionic bonds with neighboring positively charged amino acid R groups or with ions in solution- Also because the added phosphate may create a new recognition sitethat allows other proteins to bind to the phosphorylated protein Removal of the phosphate group (dephosphorylation) is catalyzed by a second enzyme, a protein phosphatase - Phosphorylation of a protein by a protein kinase can either increase or decrease the protein’s activity, depending on the site of phosphorylation andthe structure of the proteino 2. Glycosylation Addition of sugars Carbohydrate chains can be O-linked to the OH group of serine or N-linked to the NH2 group of asparagineo 3. Addition of lipids or glycolipids Addition of phosopholipids and fatty acids to cysteine or N-terminal glycineresidues to form lipoproteins.  The fatty acid chain can insert into the hydrophobic core of membranes, anchoring a protein to the membrane.Enzymes- As a catalyst, an enzyme does not change ΔG for a reaction- Are only required in small amounts- Must be unchanged at the end of reaction, so that it can cycle back to bind more substrate 1BSCI330 Exam II Review- Catalyzes equally the forward and reverse reactions - Can increase the rate of a reaction by 108 to 1012 – fold. - Enzymes lower the EA for a reaction- Classificationo Oxy-reductases- catalyze the transfer of electronsfrom the electron donor to theelectron acceptoro Transferases - transfer functional groups from one molecule to anothero Hydrolases - catalyze hydrolysis of chemical bonds o Lyases - catalyze alteration or removal of a functional groupo Isomerases- convert a molecule from one isomer to anothero Ligases - catalyze joining of two molecules togethero Kinases – transfer phosphate groups- Substrate bindingo Enzymes weakly bind a substrate to reversibly form an enzyme substrate complex.. o This then can react on the enzyme to form a product (EP) o The product dissociates from the complex into enzyme and producto When enzyme and substrate are mixed in vitro, this reaction very rapidly reaches a steady state in which [ES] is stable and product is produced at a fixed rate. o The initial rate of product formation is therefore determined by the amount of ES formed. - Michaelis-Menten Kineticso As amount of substrate increases, the rate increaseso Km= “Michaelis Consttant” Generally lies within its substrate’s natural concentration range b/c synthesizing under-used enzymes takes energy 50% point Approx. equal to the dissociation constant for enzyme-substrate complex Inversely related to the protein affinity- Low Km  the enzyme has a high “affinity” for its substrate2BSCI330 Exam II Review- High Km  the enzyme has a low “affinity” for its substrateo Vmax= rate of product formation when the enzyme is saturated with substrateo- Enzyme Mechanismso Catalysis - the increase in the rate of a chemical reaction of two or more reactants due to the participation of an additional substance called a catalysto 1. Stabilizing the transition state Transition state- intermediate form contained within an enzyme-substrate complex between the product and reactant- Have higher energy than either the reactants or products before the reaction occurs- Enzymes stabilize transition states by lowering their energy (thus also lowering EA)o Binding a substrate into an enzyme’s active site often forces substrates into a new conformation which resembles the reaction’s transition stateo This induced fit distorts and strains bonds within the substrate and lowers the EAo 2. Changing substrate reactivity a. Formation of temporary covalent bonds- Formed between R-groups in enzyme’s active site and substrate- Will speed the reaction b. Acceptance or donation of electrons and/or protons between R-groups/cofactors and substrate functional groups- May weaken some bonds and strengthen others- Will speed the reaction c. Ionic interaction- Repulsion or attraction of charged R-groups with charged functionalgroups on the substrate- May weaken some bondsRate = Vmax .[S]/(Km +[S])The point at which the rate of production of substrate is most sensitive to substrate concentration (highest slope)Most sensitive to percent change3BSCI330 Exam II Review- Will speed the reaction- Prosthetic groups - non-protein molecules that aid catalysis. o In some cases these are covalently bound to the enzyme o E.g. Organo-metal compounds in which the metal can donate/accept electrons to/from the substrate o E.g. “Chromophores” - small organic molecules which absorb light- Cofactors and coenzymes – small organic molecules can function as aids in catalysis or binding of the substrate. o Many are produced from vitamins, which are needed to make other small molecules which are essential components for proteins- Multi-enzymeso Have more than one active site, connected by a “tunnel”o Allow for efficient transfer of products between active siteso Active site 1 produces ammoniadiffuses through the tunnel to active site 2o Combines w/ carboxy phosphate to form carbamate (highly unstable intermediate)o This then diffuses through the tunnel to active site 3 where it is phosphorylated by ATP to produce the final product, carbamoyl phosphate- Enzyme inhibitors o Reversible inhibitors (common in nature) Competitive- Reversibly bind to active site and compete with substrate. - Can be displaced by high substrate concentration- Increases Km  lower “affinity”- Do not reduce Vmax Non-competitive - Reversibly bind away from active site to cause change in enzyme structure that lowers catalytic efficiency- Lower Vmax- Do not increase or decrease Km - Do not affect substrate binding4BSCI330 Exam II Reviewo Allosteric Inhibition Non-competitive inhibition Seen in multi-subunit enzymes- Made of catalytic subunits and a regulatory subunit An allosteric inhibitor (small molecule) binds to a site on the regulatory subunit- Results in a change in the regulatory


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UMD BSCI 330 - Exam II Review

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