Enzymes Flashcards
What is an Enzyme
Enzymes are proteins that act as catalysts in biochemical reactions
Enzyme Structure
Proteins (can have primary, secondary, tertiary, or quaternary structure)
Typically globular proteins
The structure is determined by the same forces as any other protein
Specificity of Enzymes
Enzymes are highly specific because of the shape of their active site
How do Enzymes Work as Catalysts
Accelerate reaction rates
Regenerated at the end of the reaction
No side reactions
Enzyme Nomenclature
Typically end is -ase
The name often describes the process
How are Enzymes Regulated
The body distinguishes enzymes from non-biological catalysts
Enzyme structures are flexible
Changing the shape of an enzyme changes its function
The spontaneity of Biological Reactions
When the reaction is exergonic and “thermodynamically favourable”
Does not necessarily proceed at measurable rates though
What determines the speed of an uncatalyzed reaction?
It is determined by the size of the activation energy barrier
How does temperature increase the speed of an uncatalyzed reaction?
The energy of the molecules involved in the reaction increases and therefore more collisions happen
How do enzymes increase the speed of a reaction?
Enzymes reduce the free energy of the transition state
BUT they do not affect the free-energy change of the reaction
How do enzymes reduce the free energy of the transition state?
- Removing substrates from aqueous solution (desolvation)
- Proximity and orientation effects
- Taking part in the reaction mechanism
- Stabilizing the transition state
Active Sites
Region of the enzyme where catalysis occurs
Determines affinity, specificity, rate
Complementary to substrate/transition state
Key amino acids are found in the active site
Desolvation
Exclusion of water
Advantages:
1. removal of water shell accelerates reactions
2. enhance polar interactions
3. prevents side reactions
Induced fit
-some enzymes change shape when substate binds (excludes more water)
Complementarity in Substrate Binding
Lock and key model
design of the active site contributes to affinity and specificity
interactions between substrate and enzymes?
Proximity and Orientation
Chemical reactions only occur if substrates come together in the right orientation to react
Active sites bind substrates close to each other and in the correct geometry
Amino Acid Side Chains in Acid-Base Catalysis
Asp Glu His Lys Cys Tyr
Amino Acid Side Chains in Nucleophilic (covalent) Catalysis
Ser Tyr Cys Lys His
Cofactors
Molecules that may enhance the reactive potential of polypeptides by providing new reactive functional groups
Coenzymes (organic) vs metal ions
Induced Fit
The binding of a substrate to an enzyme causes the enzyme to change shape
Cosubstrate
an organic molecule that binds to the active sites of certain enzymes to assist in the catalysis of a reaction
will be released after a reaction
Prosthetic Group
enzyme partner molecules that bind tightly or covalently to the enzyme
a part of the enzyme
Holoenzyme
When a polypeptide is combined with the prosthetic group to form the functional tertiary structure
Apoenzyme
Without the prosthetic group
Transition State Stabilization
Enzyme active sites bind the transition state better than they bind the substrate
The more tightly an enzyme binds the transition state,= relative to the substrate the greater the catalytic activity of the enzyme
-inhibitor of enzymes because they bind to enzymes with higher affinity compared to the substrate
Processes by Which Enzymes can be Regulated
Affects the intrinsic activity of the enzyme -competitive inhibition allostery reversible covalent modification ionic signals
Doesn’t affect the intrinsic activity of the enzyme
- regulation of gene expression
- changes in subcellular localization
Competitive Inhibitors
substances that bind reversibly in the active site
resemble the substrate or transition state but do not react
physically block the active site but can be overcome by increasing the substrate concentration to outcompete the inhibitor
Allosteric Enzymes
enzyme activity can be cooperative
-sigmoidal relationship b/w substrate and reaction velocity
-reflects different states (T, R) for the active site
compounds besides the substrate may affect the equilibrium between T and R states - allosteric effectors
Why are transition state analogs better inhibitors than substrate analogs?
Because the transition state structure would bind more tightly to the active site than the actual substrate
Phosphorylation
the most common type of reversible covalent modification
-ser,the,try can be phosphorylated
-increases size, polarity and charge significantly
may increase or decrease activity of the target enzyme
