BMS100_2_Reaction types_v1 (1).pdf

What are enzymes, and why do we need them? Enzyme Classifications ◼ ◼ ◼ ◼ ◼ ◼ EC 1) Oxidoreductases EC 2) Transferases EC 3) Hydrolases EC 4) Lyases EC 5) Isomerases EC 6) Ligases Oxidoreductases ◼ Oxidoreductases catalyze redox reactions ◼ Redox = reduction/oxidation ◼ Why do we care about re...

What are enzymes, and why do we need them? Enzyme Classifications ◼ ◼ ◼ ◼ ◼ ◼ EC 1) Oxidoreductases EC 2) Transferases EC 3) Hydrolases EC 4) Lyases EC 5) Isomerases EC 6) Ligases Oxidoreductases ◼ Oxidoreductases catalyze redox reactions ◼ Redox = reduction/oxidation ◼ Why do we care about redox reactions? ◼ Occur in a lot of anabolic (?) and catabolic (?) processes What defines a redox reaction? ◼ How can you tell if a redox reaction has happened? ◼ LEO the lion says GER Loss of Electrons = Oxidation, Gain of E lectrons = Reduction Oxidoreductases Redox Example: CAC (?) ◼ ◼ Diagram Questions: _________ is oxidized to make ________ ◼ _________ is reduced to make ________ ◼ What are FAD/FADH2 ? ◼ H H H H H H Based on: https://commons.wikimedia.org/wiki/File:Cycle_de_Krebs_08.png Oxidoreductases ◼ Redox Example: CAC ◼ Diagram Questions: _________ is oxidized to make ________ ◼ _________ is reduced to make ________ ◼ What are NAD+/NADH? ◼ Malate Based on: https://commons.wikimedia.org/wiki/File:Krebs_cycle_8_ l-malate_to_oxaloacetate.svg Oxaloacetate Oxidoreductases ◼ Specific examples of oxidoreductases include: Dehydrogenases – remove H’s and donate them to a molecule other than oxygen ◼ Oxidases – remove H’s and donate them to oxygen ◼ Oxidoreductases ◼ What type of oxidoreductase is used in these rxns? H H H H H H Transferases ◼ Next enzyme class = Transferases ◼ Transferases synthesize molecules by catalyzing the transfer of a group from one molecule to another - Often use a mechanism called “nucleophilic substitution” What is a nucleophilic substitution? Nucleophilic Substitution Nucleophile: Atom with lone electron pair Leaving Group: Group that will be substituted for by “A” A: + B-X A-B + X: Electrophile: Electron deficient atom Does this look familiar? See reactions from last day… Practice https://commons.wikimedia.org/wiki/File:Figure_03_01_01.jpg What is the nucleophile, electrophile and leaving group in disaccharide formation? ◼ Review: What makes the electrophile “electron deficient”? ◼ Base Base Base Base Base Base Based on: https://upload.wikimedia.org/wikipedia/commons/9/95/DNA_synthesis_PL.png What is the nucleophile, electrophile and leaving group in DNA formation? ◼ Review: What makes the electrophile “electron deficient”? ◼ Based on: https://commons.wikimedia.org/wiki/File:220_Triglycerides-01.jpg ◼ Which arrow correctly identifies the nucleophile and electrophile in the formation of triglycerides? ◼ The nucleophile in peptide bond formation is different than in the previous examples – which atom is the nucleophile? Based on: https://freesvg.org/peptidformationball ◼ What is the leaving group in this reaction? What name could you give to this reaction based on this? ◼ At home review: Are any of the previous examples similar with respect to the leaving group? Transferases ◼ Specific transferases include: ◼ Kinases ◼ ◼ Transfer a phosphate group from ATP to another (nonwater) molecule Polymerases ◼ Transfers a monomer to a polymer, especially wrt DNA and RNA Transferases ◼ Specific transferases continued: ◼ “X” transferases ◼ Transfer “X” from one molecule to another ◼ “X” = name of group being transferred, with the ending changed to “yl” ◼ Example: if “X”= a peptide, then the enzyme is a peptidyl transferase Transferases ◼ Determine the type of transferase + ATP Do you know which important metabolic pathway this reaction belongs to? + ADP https://commons.wikimedia.org/wiki/File:Gl%C3%BCk%C3%B3z-6-foszfat%C3%A1z.png https://commons.wikimedia.org/wiki/File:ATP_chemical_structure.png ◼ Sometimes, enzymes names are not what you would expect ◼ Could be named for the reverse reaction http://www.natuurlijkerwijs.com/english/citroenzuurcyclus.htm FYI: This a reaction in the breakdown of glucose for energy (glycolysis) Based on: https://commons.wikimedia.org/wiki/File:Figure_07_02_02.jpg Transferases ◼ Note that many transfer reactions require the use of a “carrier” ◼ Added to the transfer molecule in place of a functional group ◼ Better leaving group than the functional group it replaces Transferases ◼ CoASH (?) is the “carrier” that replaces the OH on fatty acids during TG formation CoAS CoAS CoAS - A fatty acid attached to CoASH is called a “fatty acyl” - What type of transferase enzyme is used to make TG’s? 3 CoASH Transferases ◼ The transfer of monosaccharides also uses carriers 3 1 UDP 2 + UDP Based on: https://commons.wikimedia.org/wiki/File:Figure_03_01_01.jpg and https://commons.wikimedia.org/wiki/File:SPS_Mechanism.png - What type of biomolecule is UDP? - Why is UDP a better leaving group than OH? - What type of transferase enzyme is being used? Hydrolases ◼ Next enzyme class = hydrolases ◼ Hydrolases catalyze hydrolysis reactions ◼ Specific hydrolyases include: ◼ Phosphatases ◼ Hydrolyse monophosphate esters (ex AMP, but not ATP) to release a phosphate group AMP: adenosine monophosphate ATP: adenosine triphosphate https://commons.wikimedia.org/wiki/File:DA MP_chemical_structure.svg https://commons.wikimedia.org/wiki/File:ATP_chemical_s tructure.png Hydrolases ◼ Specific hydrolases continued: ◼ ATPases ◼ ◼ Hydrolyse ATP to release a phosphate group “X”-ases, where “X” refers to the molecule being broken apart ◼ Ex Peptidases hydrolyse peptides to release smaller fragments In each case, water is acting as a nucleophile to break apart a molecule, so the mechanism is nucleophilic substitution Hydrolases ◼ ◼ What molecule is acting as a nucleophile in each reaction? Relate this to the reaction name. What type of hydrolase enzyme is being used by each reaction? + + + https://commons.wikimedia.org/wiki/File:Glycolysis_pathway_2.png https://commons.wikimedia.org/wiki/File:H2O_Lewis_Structure_PNG.png + https://en.wikipedia.org/wiki/Adenosine_diphosphate Hydrolases What are the molecules involved? ◼ What type of reaction is depicted? ◼ What is the enzyme class? ◼ What is the specific enzyme? ◼ OH https://commons.wikimedia.org/wiki/File:Lipid_hydrolysis.JPG Hydrolases What are the molecules involved? ◼ What type of reaction is depicted? ◼ What is the enzyme class? ◼ What is the specific enzyme? ◼ https://commons.wikimedia.org/wiki/File:Amylase_hydrolysisl_1-4.png Hydrolases What are the molecules involved? ◼ What type of reaction is depicted? ◼ What is the enzyme class? ◼ What is the specific enzyme? ◼ Can you figure out what same physiological process uses these last 3 reactions? https://commons.wikimedia.org/wiki/File:Peptide_bond_cleavage.svg Lyases ◼ Next enzyme class = lyases ◼ Three types of reactions catalyzed by lyases include: ◼ 1) Addition ◼ ◼ Adds one molecule to another, commonly across a 2X (or 3X) carbon bond Type of lysase = hydratase ◼ What molecule is added? FYI: This a reaction in the breakdown of fatty acids for energy (beta oxidation) https://commons.wikimedia.org/wiki/File:Enoyl-CoA_hydratase_reaction_cis.svg Lyases ◼ 2) Elimination ◼ ◼ Removes atoms in a molecule to create a double bond Types of lyases: ◼ Dehydratases: What is removed? ◼ Decarboxylases: What is removed? FYI: This a reaction in the synthesis of fatty acids http://www.lookfordiagnosis.com/images.php?term=https://commons.wikimedia.org/ wiki/File:3-hydroxyacyl-ACP_dehydrase_reaction.svgEnoylCoa+Hydratase&lang=1&from=8 https://commons.wikimedia.org/wiki/File:L-DOPA-to-dopamine.svg FYI: Synthesis of dopamine Lyases ◼ 3) Condensation ◼ ◼ Joins two molecules, creating a new C-C bond Type of lyase = synthase Porphobilinogen Synthase 2 New CC bond FYI: This a reaction in the synthesis of heme https://commons.wikimedia.org/wiki/File:Heme-Synthesis-Chemical-Details-Mirror.svg ◼ Sometimes, enzymes names are not what you would expect ◼ Could be that a common name is more widely used than the EC name http://www.natuurlijkerwijs.com/english/citroenzuurcyclus.htm This reaction is part of the CAC +H2O Fumarate Malate ◼ What type of lyase enzyme do you think is being used? Do you know this enzyme by another name? https://commons.wikimedia.org/wiki/File:Tenofovir_ disoproxil_fumarate.svg https://commons.wikimedia.org/wiki/File:Malate_Dehydrogenase _Catalyzed_Reaction_of_L-Malate_to_Oxaloacetate.jpg Post learning ◼ At home terminology review - differentiate the following terms: Hydration, hydrolysis, hydratase, hydrolase ◼ Dehydration, dehydratase, dehydrogenase ◼ Isomerases ◼ Next enzyme class = isomerases Isomerization = rearrangement of group(s) within a molecule: No net addition or elimination of atoms ◼ Specific isomerases include: ◼ ◼ Mutases: ◼ ◼ Epimerases: ◼ ◼ Transfer functional groups intramolecularly Interconvert the groups around an asymmetric carbon (?) in a molecule that has more than one asymmetric carbon Racemases: ◼ Interconvert the groups around an asymmetric carbon in a molecule that only has one asymmetric carbon Isomerases ◼ Name the type of isomerase for each reaction http://www.sparknotes.com/biology/cellrespiration/glycolysis/section2.rhtml https://commons.wikimedia.org/wiki/File:Aspartate_racemase_general_reaction.png https://commons.wikimedia.org/wiki/File:3PG-2PG.PNG http://www.fasebj.org/content/25/2/497/F1.expansion.html https://en.wikipedia.org/wiki/File:Ribulose-phosphate_3-epimerase_reaction.jpg ◼ Note: a reaction can be an isomerization but not use an enzyme from the isomerase class ◼ Example: aconitate hydratase for isomerization of citrate to isocitrate in the CAC Citrate ◼ Isocitrate The name is based on the last part of the mechanism Citrate Aconitate Isocitrate http://www.humboldt.edu/~rap1/C431.F01/C431Notes/C431n12nov.htm https://commons.wikimedia.org/wiki/File:Citrate-isocitrate_%28reaction%29.png Ligases ◼ Next enzyme class = ligases Ligases catalyze various reactions that join 2 molecules with the use of ATP for energy ◼ Specific ligases include: ◼ ◼ “X”-ligases and “X”-synthetases (sometimes both!) ◼ ◼ “X” refers to the name of the molecules being joined, or to the molecule being created FYI: Although “synthases” used to only be considered types of enzymes that joined molecules without the use of ATP, the term “synthase” can now also be synonymously with “synthetase” Ligases ◼ Example: glutamate-cysteine ligase, aka γglutamylcysteine synthetase FYI: This is the first step in making glutathione, an important antioxidant in our bodies https://commons.wikimedia.org/wiki/File:Gsh_mitochondria.jpg Overview Enzyme Class Reaction Example Enzyme Name Example(s) Oxidoreductase Redox Dehydrogenase, Oxidase Hydrolase Hydrolysis (nucleophilic sub.) Phosphatase, ATPase, Peptidase, Lipase, etc Transferase Group transfer (nucleophilic sub.) Kinase, Polymerase, “X”transferase Lyase Condensation Synthase Lyase Decarboxylation/elimination Decarboxylase Lyase Dehydration/elimination Dehydratase Lyase Hydration/addition Hydratase Isomerase Isomerization Mutase, epimerase, racemase Ligase Joining molecules with use of ATP “X”-ligase, synthetase, synthase