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Why are enzyme considered the biological catalysts?
provide the necessary environment for chemical reactions to progress at a reasonable rate
T/F enzymes are used up during the process
FALSE
What is the difference between a catalyzed and uncatalyzed reaction?
activation energy is lower in a catalyzed reaction
What is the basic scheme of an enzyme catalyzed reaction?
A + B ↔ AB ↔ AC ↔ A + C, where A is the catalyzing enzyme, B is the substrate, and C is the product
Define: part of an enzyme that has restricted access and contains an active residue
active site
What would have a better active site, a globular or fibrous protein?
globular because it can have a hydrophobic inside region
Define: ES in terms of enzymes
enzyme-substrate complex
Define: EP in terms of enzymes
enzyme-product complex
Define: unstable state mid-way between S and P and occurs at a point at which decay of S or P states is equally probable
transition state
how can drugs take advantage of knowing the transition state structure?
enzymes can be inhibited by stable analogs of their transition states
What is the difference between reaction intermediates and transition state?
TS occupy hill tops and reaction intermediates occupy valleys in free energy charts
T/F transition states can be detected experimentally
False, it is not a chemical species with any significant stability
What are the two major functions of the enzyme active site
substrate binding and substrate catalysis
What is meant by substrate binding?
the specificity of an enzyme and the process by which substrate molecules bind to their substrate binding sites
What is meant by substrate catalysis?
process where cofactors and functional groups from the polypeptide participate in transforming the bound substrate into products
T/F transition state complex (TSA) is formed during substrate catalysis
TRUE
Define: one or more inorganic ions involved in substrate binding and catalysis
cofactor
Define: organic or metallorganic molecules that are carriers of specific functional groups
coenzymes
How is Zn involved in the active site of alcohol dehydrogenase
bound to residues (2 cys and 1 his), binds the substrate acetyldehyde at the proximity of NADH
What are the two types of coenzymes?
acitvation transfer (forming covalent bonds w/ substrate) oxidation-reduction (part of oxidoreductases)
T/F nearly 1/3 of all known enzymes requires the presence of metal ions for catalytic activity
TRUE
What metal ions are involved in catalysis
Fe++, Fe+++, Cu++, Zn++, Mn++ or Co++
what is the role of zinc in the catalysis of carbonic anhydrase
activation of water molecule
List four common cofactors
thiamine pyrophosphate, coenzyme A, pyridoxal phosphate, nicotinamide adenine dinucleotide
What is the difference between the lock and key model and the induced fit model
induced fit model says that substrate binding induces rearrangement in the active site favoring optimal binding
what is the relationship between the transition state and activation energy
activation energy must be met to form transition state (at same point on graph)
Define: energy derived by the bonding of noncovalent interactions of the substrate and enzyme
binding energy
what is the role of binding energy
bring substrate molecules closer together, excludes solvents, and aligns catalytic functional groups and fabors transition state formation
T/F binding energy lowers the activation energy
TRUE
What is the substrate specificity of chymotrypsin?
a protease, specific for cleavae of peptide bond mainly adjacent to aromatic residues
What are the important residues in the chymotrypsin active site?
Asp 102, His 57 and Ser 195
What is the first step in the catalysis by chymotrypsin?
His 57 acts as a base in abstracting the proton from Ser 195 making Ser 195 a nucleophile
What is the second stape in chymotrypsin catalysis?
Ser 195 (w/ O-) nucelophilic attacks the carbonyl carbon of the peptide to be broken, forming a transient negative
How is the transient negative formed by the nucleophilic attack stabilized?
interaction with an oxyanion hole
What is an oxyanion hole?
h-bonding of the negative O by gly 193 and ser 195 to form a tetrahedral intermediate
What is the third step in chymotrypsin catalysis?
His 57 acts as an acid by donating an H to the amino group of the peptide bond, forms acyl-enzyme
What is the fourth step in chymotrypsin catalysis?
the amine component is set free from the enzyme
What is the fifth step in chymotrypsin catalysis?
amine component is replaced by a water, His 57 acts as a base to abstract proton from incoming water, forming the acyl-enzyme
What is the sixth step in chymotrypsin catalysis?
reformation of oxyanion hole (tetrahedral intermediate) His 57 acts as a base
What is the seventh and eighth steps of chymotrypsin catalysis?
tetrahedral intermediate breaks down to form caroxylic acid product and the product is released
Why is chymotrypsin called a serine protease?
Cleaves peptide bonds using serine
What distinguishes a catalytic transition state from an intermediate on an energy diagram?
intermediates are valleys while transition states are peaks
What AA residues are needed for the binding of chymotrypsin?
phe, tyr, or trp
What AA residues are needed for catalysis within the chymotrypsin active site?
Asp 102, His 57 and Ser 195
What AA's are commonly encountered in the enzyme active site for enzyme catalysis?
almost all polar amino acids (ser, thr, cys, pro, asp, and glu
Which AA's are involved in covalent catalysis in an enzyme active site?
ser, cys, lys, and his
Which AA's can be involved in peptide bond hydrolysis besides serine?
threonine, cysteine, aspartate
List two examples of enzymes that contain residues of threonine, cysteine, or apartate in their active site?
Threonine proteases and cysteine proteases
Describe how an activatin-transfer coenzyme help the enzyme
covalently bond directly with the substrate
What kind of active group does thiamine pyrophosphate have?
reactive carbon atom
What kind of active group does pyridoxal phosphate have?
reactive aldehyde group
What kind of active group does coenzyme A have?
reactive thiol group
T/F oxidation-reduction coenzymes form covalent bonds with the substrate
False, has a unique functional group that accepts and donates electrons
What function does Zn++ have in carbonic anhydrase?
activation of water molecule
What are the 6 major classes of enzymatic reactions?
oxidoreductase, transferases, hydrolases, lyases, isomerases, ligases
What do oxidoreductases do?
catalyze ox-redox reactions by transferring electrons, H atoms, or O atoms (dehydrogenases, oxidases, and oxygenases)
What do transferases do?
transfer functional groups (amino transferases, kinases, glycosyl transferases)
T/F Transaminases (type of transferase) transfers an amino group from one amino acid to a keto acid
TRUE
What do kinases catalyze?
transfer of phosphoryl group
What do glycosyl transferases transfer?
glucose from UDP-glucose to a growing chain of glycogen
What do hydrolases do?
catalyze hydrolysis reactions to cleave bonds (ester, peptide, phosphate, thioester or glycosidic)
What cleaves a peptide bond?
peptidases like chymotrypsin
What do lyases do?
addition or nonhydrolytic removal of elements of water, ammonia, or carbon dioxide (often cleaves C-C, C-O or C-N bonds)
What differentiates lyases from hydrolases?
lyase break bonds by means other than hydrolysis or oxidation
What lyase removes an element of CO2 from alpha, beta keto acids or amino acids
decarboxylases
What removes H2O, reversibly converting fumarate to malate?
fumarase (type of dehydratase)
What do isomerases do?
transfer of groups within molecules to yield isomeric form
What is an example of an isomerase?
triose phosphate isomerase
What do ligases do?
synthetic reaction where two molecules are joined at the expense of a high-energy bond of ATP
What is an example of a ligase?
pyruvate carboxylase (forms oxaloacetate from bicarbonate and pyruvate)