Soto Biochem 10/20, 10/22
Soto Biochem 10/20, 10/22 CHEM 351
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This 5 page Class Notes was uploaded by Kayli Antos on Saturday October 24, 2015. The Class Notes belongs to CHEM 351 at Towson University taught by Ana Soto in Summer 2015. Since its upload, it has received 24 views. For similar materials see Biochemistry in Chemistry at Towson University.
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Date Created: 10/24/15
Biochem Soto Fall 2015 z Enzymes 0 Chymotrypsin 0 0 A protease an enzyme that catalyzes the cleavage of peptide bonds which specifically breaks peptide bonds adjacent to aromatic amino acids It has two phases I Acylation phase the peptide bond is broken and a covalent bond is formed between the enzyme and the substrate I Deacylation phase the covalent bond is broken and the enzyme is free to interact with another peptide 0 Early Clues T o The Mechanism 0 0 Chymotrypsin is also a catalyst for the hydrolysis of small esters and amides Since these reactions are slower they re easier to observe and study We know that the acylation occurs rapidly and the overall enzyme reaction is slowed by the deacylation phase 0 Chymotrypsin Activity Depends On pH 0 0 The rate of catalysis with chymotrypsin vs pH is bell shaped The contributions of Kcat and 1KM to this shape come from the ionization state of His57 and Ile16 respectively The His is part of the catalytic triad and the Ile is the N terminus which makes an ion pair with Asp194 in order to stabilize the enzymes active conformation 0 Chymotrypsin Mechanism 0 0 When the substrate binds to the enzyme the side chain adjacent to the peptide bond that will be cleaved binds to a hydrophobic pocket There is a hydrogen bond network called the catalytic triad which consists of Ser195 His57 and Asp102 The Ser can be deprotonated due to its proximity to the His which accepts the proton His is able to act as a base due to its proximity to Asp When Ser is deprotonated it becomes a strong nucleophile and prevents the formation of an unstable positive charge on Ser The alkoxide ion in Ser can then attack the peptide carbonyl and form a short live tetrahedral intermediate This bonding creates a negative charge on the carbonyl oxygen which is stabilized by hydrogen bonds in the oxyanion hole 0 0 The negative charge on the carbonyl is unstable which causes the tetrahedral intermediate to collapse The double bond reforms to break the peptide bond The amino leaving group is protonated by His A water molecule gets deprotonated and becomes a strongly nucleophilic hydroxide ion This hydroxide ion attacks the carbonyl group generating a second tetrahedral intermediate which is again stabilized by hydrogen bonding in the oxyanion hole This second intermediate also collapses forming the carboxylate product As this second product diffuses from the active site the enzyme is regenerated 0 Hexokinase Mechanism 0 0 0 0 Hexokinase is a bisubstrate enzyme which catalyzes the reaction of glucose6phosphate from 3D Glucose The enzyme favors the glucose reaction over water by a factor of 106 Hexokinase takes a phosphate from ATP and adds it to glucose Induced fit when glucose binds it changes the conformation of the enzyme to have an affinity for the intermediate 0 Regulatory Enzymes 0 0 Groups of enzymes can work together in sequence to carry out a certain process Each of these pathways has at least one regulatory enzyme which is usually the first one The regulatory enzymes activates are modulated by I Allosteric enzymes are regulated by noncovalently binding to allosteric modulators or allosteric effectors I Others are regulated by reversible covalent modification I Others are activated or inhibited by binding to other regulatory proteins I Others are activated by proteolytic cleavage 0 Allosteric Enzymes 0 0 0 Conformational changes connect the more active and less active forms of the enzyme Typically larger and more complex than nonallosteric enzymes Usually have a sigmoid plot and do not follow MichaelisMenten kinetics 0 When an activator or substrate binds to the enzyme there is a transition from the T state to the R state 0 Phosphorylation 0 0 0 0 Phosphorylation attachment of phosphoryl groups catalyzed by lltinaes Dephosphorylation removal of phosphoryl groups catalyzed by phosphatases Phosphoryl groups are negatively charged and bulky and their introduction into the protein environment causes changes in it This can have great effects on the conformation of the protein Can occur at Tyr Ser Thr and His z Carbohydrates 0 The most abundant biomolecules 0 Arecan yield polyhydroxy aldehydes or lltetones Some have the empirical 0 0 0 0 formula CHZOn when n is equal to or greater than 3 There are three major classes Monosaccharides simple sugars Oligosaccharides short chains of monosaccharides Polysaccharides polymers containing more than 20 monosaccharides can be homopolysaccharides or heteropolysaccharides 0 Monosaccharides 0 Made of straight carbon chains One carbon is an aldehyde or a lltetone The other carbons will have a hydroxyl group Many of these carbons with hydroxyl groups are chiral centers They re water soluble crystalline solids that typically have a sweet taste All with the exception of dihydroxyacetone have at least one chiral carbon In a Fisher projection the horizontal bonds are projecting out of the page and the vertical bonds go into the page Many Stereoisomers I The longer the carbon chain of the sugar the more chiral centers and stereoisomers it will have The of stereoisomers 2Chiral Centers I Stereoisomers that only differ in one chiral center are called epimers Cyclic Structures I Alcohols can be added to carbonyls or lltetones to form hemiacetals and acetals or hemilltetals and lltetals I This attack from the alcohol can happen in two ways so the new chiral center that forms can be or or I These anomers can switch back and forth via a process called mutarotation 0 Haworth Perspectives I The groups on the right of the chain point down in a ring structure and the groups on the left point up I When the anomeric hydroxyl group is on the same side of the ring as carbon6 it s in 3 configuration 0 Configurations And Conformations I Five carbon rings are called furanoses and six carbon rings are called pyranoses I Pyranoses assume chair conformations I Anomer conformations can flip by mutarotation 0 Sugar Derivatives I There are sugars in which a hydroxyl group is replaced with another substituent 0 Monosaccharides Are ReducingAgents I Monosaccharides are able to be oxidized by mild oxidizing agents The carbonyl carbon is oxidized for a carboxylic group I This is only able to occur when the sugar is not in a ring form Disaccharides 0 When the hydroxyl group of one sugar reacts with the anomeric carbon of another an oglycosidic bond is formed 0 The product is still a reducing agent as long as only one of the sugars bound with its anomeric carbon 0 The free anomeric carbon is the reducing end When two sugars bind one water molecule is a byproduct gt9 When there is an anomeric carbon involved in the bond the bond must be named with either or or 3 depending on the conformation of the sugar 0 When rotating a ring to bind it to another flip it over to that the substituents on the top are not on the bottom 0 Glycosidic Bond I The name describes the compound with its nonreducing end on the left I To name the sugar The first monosaccharide its configuration and size The atom numbers bound together connected by an arrow The name of the second residue I The short hand notation is the abbreviated names of the sugars and in parenthesis the anomeric carbon configuration and the carbons involved in bonding
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