Enzymes: Mechanisms Of Action and membrane function Flashcards
Enzymes
- catalyze reversible reactions
- the specificity of each reaction is established through the use of specific enzymes that catalyze each reaction.
- diverse mechanisms of catalysis have evolved to solve the unique problems of synthesis, degradation, transport, replication, motility, and communication
- study through kinetic analysis of their behaviors
Why are enzymes over inorganic catalysts?
- greater reaction specificity: avoids side products
- milder reaction conditions: (37C, pH 7)
- higher reaction rates: in a biologically useful timeframe
- ## Capacity for regulation: control biological pathways
Proteins (enzymes)
- oxireductase
- transferase
- hydroplane
- leases
- isomerases
- ligase
RNA enzymes (Ribozymes)
- ribosomes
- hammerhead, hepatitis delta virus RNA, group I intron ribozymes
Oxireductases
- transfer of electrons
Transferases
-group transfer reactions
Hydrolases
-hydrolysis reactions (transfer of functional groups to water)
Lyases
- cleavage of C-C, C-O, C-S, and C-N bonds by condensation reactions coupled to cleavage of ATP or similar cofactor
Isomerases
-transfer of groups within molecules to yield isomeric forms
Ligases
-Formation of C-C, C-S, C-O, and C-N bonds by condensation reactions coupled to cleavage of ATP or similar cofactor
Enzyme Nomenclature
- some are still known by traditional names : pepsin, kinase, trypsin
- a numeric system of nomenclature
- first digit denotes class name
- the second digit denotes subclass
- third digit denotes the acceptor atom
- fourth digit denotes the acceptor
Prosthetic group
- tightly and stably incorporated into a protein’s structure by covalent or no covalent forces
Cofactors
-bind in a transient, dissociable manner either to the enzyme or to a substrate such as ATP
Coenzymes
- serve as group transfer as group transfer agents and transport many substrates from one point within the cell to another
Apoenzyme
- enzyme without the factor
Holoenzyme
-complete enzyme with prosthetic group
Pyruvate dehydrogenase Complex
- Enzymes:
1) E1- pyruvate dehydrogenase
2) E2- dihydrolipoyl transacetylase
3) E3 - dihydrolipoyl dehydrogenase - Coenzymes
1) TPP - bound to E1
2) Lipoate-covalently linked to E2
3) Coenzyme A - substrate for E2
4) FAD - bound to E3
5) NAD - substrate for E3 - reduced by FADH2
FAD and FMN
- flavin nucleotides are tightly bound to flavoproteins
NAD+ and NADP+
- contains vitamins B3 niacin
- involved in redox reactions, carrying electrons from one reaction to another. The coenzyme is found in two forms. NAD+ is an oxidizing agent - accepts electrons from other molecules and becomes reduced.
- Niacin deficiency causes pellagra
Tetrahydrofolate
- carrier of one C group
- deficiency causes low birth weight infant and spina bifida
Models of Enzyme-Substrate Interaction
- enzyme catalyzed reactions, a strong interaction is formed between a substrate and a cleft or pocket on the enzyme’s surface that forms part of a region called the active site.
- Lock and Key
- Induced Fit
Lock and Key
The enzyme dihydrofolate reductase with its substrate NADP+ , NADP+ binds to a pocket that is complementary to it in shape and ionic properties
Induced fit
-conformational changes induced by binding of a substrate
Catalysis by Proximity
- effective molarity concentration and orientation of substrate molecules in the active site of enzymes will enhance the rate of reactions. Eg. Substrate channeling by multi-enzyme complexes
Acid-base Catalysis
- ionizable functional groups of amino acid side chains and prosthetic groups contribute to catalysis by acting as acids of bases
Catalysis by Strain
- enzymes bind their substrates in an favorable conformation to weaken the bond that will undergo cleavage. Eg. Stickies model
Covalent Catalysis
-formation of a covalent bond between the enzyme and one or more substrates to create a more reactive enzyme. Eg. Group transfer reactions
AA in General in Acid-Base catalysis
- many organic reactions are promoted by proton donors or proton acceptors
- the active sites of some enzymes contain amino acid functional groups that can participate in the catalytic process as proton donors or acceptors