Lecture 18 Enzymes I Flashcards
Enzyme
A protein (or protein-based molecule) that speeds up a chemical reaction in a living organism.
Enzyme acts as
A catalyst for specific chemical reactions, converting a specific set of reactions (substrates) into specific products
Catalysis
Increasing the speed of chemical reactions
Ex. O2 + iron = rust (takes centuries)
Add H2O and takes days
Enzymes and the energy of activation
Enzymes lower the energy of activation by forming an enzyme-substrate complex by allowing products of the enzyme reaction to be formed and released much faster
ES
Enzyme-substrate complex
Intermediate
Sir Archibald Edward Garrod
-inborn errors of metabolism
alkaptonuria - relation between disease and fundamental errors in biochemical reactions
-enzymes must be a link
Enzyme Specificity
3D structure of enzyme protein contributes to specificity of reaction
-lock and key
Active Site
Substrate binds, undergoes chemical alteration
Enzyme substrate complex
Lock and key VS. Induced fit
Evidence of an enzyme substrate complex
With a constant concentration of enzyme and increasing concentration of substrate, reaction rates increased to maximum
-Indirect evidence of ES complex
The limit in reaction rate is due to
Substrate occupying all the available catalytic sites
Maximal Velocity
Substrate is saturated all the enzymes
Evidence of an enzyme substrate complex
-X-ray crystallography
Ex. cytochrome P450 bound to its substrate camphor
Active Site
3D cleft or crevice formed from the residues of various protein regions and occupies small total volume
–shape dictates specificity
Specificity of binding depends on the precisely defined arrangement of atoms in the active site
Active site microenvironment
Active site contains a unique microenvironment, usually void of water and controls the proper shape, pH and polarity for substrate binding and chemical reactivity
Trypsin cleaves after
Arginine
1st Law of Thermodynamics
Conservation of energy
-in biochemical reactions - E is transferred from one form to another
Transition State
Intermediate structure that is not the substrate and not yet the product
- unstable and highest free energy
- double cross denotes the transition state
Gibbs Free Energy of Activation
The difference in free energy of the transition state and the substrate
Enzymes function to lower the activation energy
Delta G =
Free energy of substrate-free energy of product
Enzymes and reactions
Enzymes accelerate reactions by facilitating the formation of the transition state/lower activation energy
Cofactors
Small molecules that contribute to the chemical reaction of the enzyme
- many different roles in catalysis
- enzymes that use the same cofactor share similar mechanisms of catalysis
- Apoenzyme
- Haloenzyme
Apoenzyme
Enzyme without its cofactor
Haloenzyme
Cofactor bound and catalytically active
Metal Cofactors
Positively charged
Stable coordination of active site groups
Contribute to chemical reactivity
Ex. Zinc activates H2O to form OH- nucleophile
Coenzymes
Small organic molecules often derived from vitamins (bigger than ions)
When bound tightly called a prosthetic group
Prosthetic Group
When coenzymes are bound tightly
2 Types of Cofactors
1 Metals
2 Coenzymes
Scurvy
Cofactor deficiency
Vitamin C
Ariboflavinosis
Cofactor deficiency
Riboblavin (B2) required for FAD synthesis
NAD+ binding site of dehydrogenases
Binds the active site in a well-defined arrangement for substrate activation
6 Major Classes of Enzymes
- Oxidoreductases
- Transferases
- Hydrolases
- Lyases
- Isomerases
- Ligases
Oxidoreductases
Enzyme class
Oxidation - reduction
Ex. Lactate dehydrogenase
Transferases
Enzyme class
Group transfer
Ex. Nucleoside monophosphate kinase (NMP kinase)
Hydrolases
Enzyme class Hydrolysis reactions (transfer of functional groups to water) Ex. Chymotrypsin
Lyases
Enzyme class Addition or removal of groups to form double bonds Ex. Fumarase
Isomerases
Enzyme class Isomerization (intramolecular group transfer) Ex. Triose phosphate isomerase
Ligases
Enzyme class
Ligation of two substrates at the expense of ATP hydrolysis
Ex. Aminoacyl-tRNA synthetase
Oxidoreductases
Enzyme that catalyzes the transfer of electrons from one molecule to another
- Reductant
- Oxidant
Reductant
Hydrogen or electron donor
Oxidant
Hydrogen or electron acceptor
ADH
Alcohol dehydrogenases
Alcohol dehydrogenases
Converts alcohols to aldyhydes or ketones with the reduction of NAD+ (cofactor) to NADH
- Alcohol = oxidized
- NAD+ = reduced
Opposite of alcohol dehydrogenase
Fermentation
Transferases
Enzyme that catalyzes the transfer of a functional group from one molecule to another
- donor molecules required
- –Source of methyl groups or phosphates (ATP) as examples
Kinase Receptors
Phosphorylate proteins and themselves
-usually at tyrosine (TKRs), serine and threonine residues
Hyrolases
Enzyme that catalyzes the hydrolysis of covalent bonds
- cleave covalent bonds using water in the process
- transfer function groups to water
Disaccharidases
Hydrolases
- Cleave double sugars to single sugars
- Defects in lactase = lactose intolerance
Lyases
Enzyme that catalyzes the addition or removal of groups to form double bonds
Aldolase
Lyases
-catalyzes second step of glycolysis
Isomerases
Enzyme that catalyzes isomerization
- intramolecular group transfer
- product is an isomer of the substrate
- *bonds are just moved around
Triose phosphate isomerase
Isomerases example
-Intramolecular oxidation-reduction reaction
Ligases
Enzyme that catalyzes the covalent linkage of two substrates
- usually at the expense of ATP hydrolysis
- *glue things together, uses ATP
DNA Ligase
Forms two covalent phophodiester bonds between 3’ hydroxy ends of one nucleotide with the 5’ phosphate end of another
*uses ATP
