Auburn University, Biochemistry 5180: BCHEM 5180 Study Guide

Three energy barriers Form ES Convert substrate to product release product Rate limiting step Step with highest activation barrier Enzyme substrate binding models lock and key enzyme complimentary induced fit hy ...

Three energy barriers Form ES Convert substrate to product release product Rate limiting step Step with highest activation barrier Enzyme substrate binding models lock and key enzyme complimentary induced fit hypothesis Lock and key Favors ES complex Barrier between ES and EP Enzyme complimentary Substrate changes to fit enzyme Induced fit hypothesis Enzyme and substrate change after initial fit preferred model Types of enzyme catalyzed reactions General acid base catalysis covalent catalysis Metal ion catalysis electrostatic catalysis catalysis through transition state binding Covalent catalysis Forming covalent intermediate with enzyme Covalent Catalysis • Side chains of AAs provide nucleophilic centers for attack on electrophilic centers of substrates. • Form covalent intermediate which can be changed by water or a second substrate for desired product • Ping-pong kinetic mechanisms Glycogen Carbohydrate storage in animal liver Structural polysaccharides Aspartate Asp,D pKa: 3.63 Glutamate Glu,E pKa: 4.25 Serine Ser,S Threonine Thr,T Cysteine Cys,C pKa:8.18 Selenocysteine Sec,U pKa: 5.7 Asparagine Asn,N Glutamine Hyaluronate Proteoglycan Phospho-fructokinase Three steps for dissolving water Important interactions involving water (4) How do polar compounds interact with water? When crystalline substances dissolve in water their is an _ in entropy How is water involved in reaction with non-polar substances?How does water interact with amphipathic compounds? Two examples of water as a reactant Water's important interactions among biomolecules Effective Concentration Uncommon AA due to modification Uncommon AA due to different side group crystal structure:ribbon model of protein What does the ribbon model represent? What does the ribbon model represent? A separate amino acid chain of a protein, several identical or different chains can make up a protein. Combination of certain secondary structures like a helices and B sheets that can be found in several proteins, forming a protein family. Protein fold How does ammonium sulfate precipitation work? Describe how salting out works Size-Exclusion Chromatography Define hydrophobic chromotography. affinity chromatography: specific interactions What does the purification table describe? The ratio of enzyme activity relative to total protein is called absorbance spectroscopy What does absorbance spectroscopy identify? SDS-PAGE Isoelectric focusing Four steps of protein sequencing Trypsin What can amino acid sequencing tell us? What proteins are associated with the membrane through electrostatic interactions and H bonding with the hydrophilic domainsof integral proteins and the polar head groups of membrane lipids ? Membrane proteins How can peripheral proteins be removed from the membrane What are firmly associated with the membrane, removed only by agents that interfere with hydrophobic interactions, such as detergents, organic solvents, or denaturants. Covalently attached proteins can be removed from the membrane how? fibrous proteins BLOSUM scoring matrices How does BLOSUM scoring matrices work? What amino acids/sequences are most likely to be conserved? Evolutionary relationships Changes at C-terminus Addition of fatty acyl groups Changes in individual AAs Attachment of lipids to individual AAs Denaturation is a loss of _ and _ structure. The _ structure stays intact. What four things denature proteins? How do high temperatures denature a protein? Circular dichroism spectroscopy How is circular dichroism spectroscopy used? How do chaperons DnaJ and DnaK function in protein folding? Prevent folding of parts of the chain until the whole chain has been synthesized Role of ubiquitin in breakdown of cellular proteins What methods are available to detect the folding/unfolding of a protein/enzyme? The binding of a ligand is often coupled to a conformational change in the protein that makes the binding site more complementary to the ligand Why do we need proteins to transport oxygen? Why does oxygen bind to heme C and not a single Fe ion? Amino acids are not capable of binding to oxygen, so this capability is provided by In a multi-subunit protein, a conformational change in one subunit often affects the conformation of other subunits How do different pHs affect hemoglobin? Why are enzymes such good catalysts? What are the benefits of measuring the initial rate of a reaction V0? What does the steady state assumption, as applied to enzyme kinetics, imply? Inhibitors that bind covalently with or destroy a functional group that is essential for the enzymes activity Catalysis Mechanisms: Metal Ion Catalysis Sequential/Single Displacement Reaction leads to the formation of a Double displacement reactions proceed via the formation of _. Three steps of glycolytic pathway that differ from gluconeogenesis Why is gluconeogenesis catalyzed by different enzymes? Steps of glycolysis/gluconeogenesis that differ Main reactive oxygen species What role does the pentose phosphate pathway play in removal of reactive oxygen species? Structural role of sugar What about sugars makes it them good structural features of fibers? 1st 3 steps of enzyme hydrolase Hydrolysis of ATP:Resonance Hydrolysis of ATP:Ionization Hydrolysis of ATP:Standard Conditions Hydrolysis of ATP: Solvation What does the pentose phosphate pathway create How does the pentose phosphate only create NADPH or ribose? How does bifunctional enzyme phosphofructokinase-2/fructose- 2,6-bisphosphatase and product fructose-2,6-bisphosphate regulate glycolysis and gluconeogenesis What happens if a muscle preparation containing glycogen phosphorylase is treated with: phosphorylase kinase and ATP What happens if a muscle preparation containing glycogen phosphorylase is treated with: PP1 What happens if a muscle preparation containing glycogen phosphorylase is treated with: epinephrine How is glycolysis regulated by levels of ATP/AMP How is gluconeogenesis regulated by levels of ATP/AMP? What activates or inhibits phosphofructokinase How is NADH recycled under anaerobic conditions? How is NADh recycled in aerobic conditions?