Biochem: Enzyme Types, Structure, and Function Flashcards
Hydrolase
Enzymes that catalyze the cleavage of a covalent bond using water.
Hydrolyzes chemical bonds (includes ATPases, proteases, and others)
an enzyme that catalyzes the hydrolysis of a particular substrate.
The natural function of most hydrolases is digestive to break down nutrients into smaller units for digestion.
Online: esterases including lipases, phosphatases ( cleave phosphate groups off molecules, Like ATP hydrolysis), glycosidases, peptidases, and nucleosidases. Esterases cleave ester bonds in lipids
Types of hydrolase include esterases, such as phosphatases, that act on ester bonds, and proteases or peptidases that act on amide bonds in peptides.
Isomerase
Rearranges bonds within a molecule to form an isomer
Ligase
Forms a chemical bond (DNA ligase)
Lyase
Lyases are enzymes that cleave bonds without the addition of water (non-hydrolytically)
Breaks chemical bonds by means other than oxidation and hydrolysis (pyruvate decarboxylase)
Compared to hydrolase -> Hydrolases are enzymes that catalyze the cleavage of, among other bond types, the phosphoric anhydride bonds found in GTP
ex. phosphatases, that act on ester bonds, see other examples with hydrolase
Kinase
Transfers a phosphate group to a molecule from a high energy carrier such as ATP (phosphofructokinase PFK)
Oxidoreductase
Oxidoreductase catalyze oxidation-reduction reactions
Runs redox reactions (includes oxidases, reductases, dehydrogenases, and others)
Polymerases
Polymerization (e.g. additon of nucleotides to the leading strand of DNA by DNA polymerase III)
Phosphatase
Removes phosphate group from a molecule
Phosphorylase
Transfers a phosphate group to a molecule from inorganic phosphate (e.g. glycogen phosphorylase)
Protease
proteolytic cleavage
Zymogen
Hydrolyzes peptide bonds (e.g. trypsin, chymotrypsin, pepsin, etc.). This is a hydrolysis reaction/ a type of hydrolase mentioned before
Protein cleaving enzyme/protein
Many enzymes and proteins are synthesized in inactive forms (zymogens) that are activated by cleavage by a protease
Enzymes have 2 roles
a) In one rxn test tube - enzyme is a catalyst with a kinetic role only
b) Many real life rxns in cell - enzyme controls outcomes by selectively promoting unfavorable reactions via reaction coupling (like using ATP bc hydrolysis of ATP so exergonic that is can cause an originally pos delta G to be neg delta G)
Enzymes stabilize the _____
ENZYMES STABILIZE THE TRANSITION STATE!
For example if a transition state intermediate possesses a transient negative charge, a positive charged amino acid would stabilize the neg charge in the intermediate or hydrogen of the NH2 group in glutamine or asparagine could hydrogen bond with the neg charge
D/L amino acids and D/L sugars
L amino acids (remember aLanine) and D sugars
What factors do enzymes not touch?
What happens if you swap out aa in active site neutral one for neg one?
Keq/ equalibrium constant
Feedforward stimulation (doesn’t seem like high yield)
Stimulation of an enzyme by its substrate or by a molecule used in synthesis of the substrate
Low Km means…
How to find Km:
…means not very much substrate needed to get the reaction rate to half maximum rate so enzyme has high affinity to substrate
Km = substrate concentration at which the reaction velocity is half its maximum
enyzmes can be active or _____
and can also be inactive or ______
Cooperativity: sigmoidal shape of graph
relaxed (everyone “turned on” open dating)
tense (everyone “turned off” not dating)
Competitive inhibitor bind to ____
Competitive inhibitors normally resemble the _____
What does it do to Vmax? Km?
bind to actives site and compete with substrate
Normally resemble the transition state that the active site normally stabilizes
Vmax same bc adding more substrate outcompetes the competitive inhibitor
Km increases
Noncompetitive inhibitor binds….
What does it do to Vmax? Km?
binds allosteric site
No matter how much substrate added, the inhibitor will not de displaced from its site of action so Vmax decreases
Km same bc substrate can still bind active site but doesn’t do anything
Binds to allosteric site (BUT doesn’t not change shape of active site, so substrate can still bind active site but transition state destabilized so rxn cannot occur)
Will changing enzyme concentration change Vmax?
Yes
Ex. increasing enzyme concentration will increase Vmax
Vmax depends on the enzyme concentration, so if you double the amount of enzyme you double Vmax. Km and kcat are constants so changing the enzyme concentration will not change their value
Uncompetitive inhibitor binds…
What does it do to Vmax? Km?
Does enzyme concentration affect Km?
bind to allosteric sites and bind the whole enzyme-substrate complex
IT’S GOING DOWN FOR REAL
Vmax decreases bc limits the amount of enzyme-substrate complex that can be converted to product
Decreases Km (bc apparent affinity higher bc clamps enzyme and substrate together so looks like they really want to be together)
Km is a constant for a given substrate acting on a given enzyme so enzyme number does not affect Km, unlike how it affects Vmax
Mixed-type inhibition binds…
What does it do to Vmax? Km?
Inhibitor can bind to either the unoccupied enzyme allosteric site or the enzyme-substrate complex
Binds at allosteric site of E alone and DOES change shape of active site (this is why seems like non competitive but since active site changes, Vmax decreases unlike for noncompet inhibitor) OR to ES complex
IT WILL HAVE A PREFERENCE FOR ONE
Vmax decreases
Km - it depends
Effect on Km: depends on which one it favors: when bind ES complex decrease Km (like a uncompetitive inhibitor)
But if change shape of active site this decrease affinity for substrate so increased Km
Line weaver plot
What does slope, y-intercept, x-intercept represent?
See paper diagrams to imagine what each inhibitor would look like
slope -> Km/Vmax
y-intercept -> 1/Vmax
x-intercept -> -1/Km
Dehydrogenase
is a type of oxidoreductase enzyme catalyzes the removal of a hydrogen from a molecule
Transferases
Transferases are a class of enzymes involved in the transfer of a functional group from a donor molecule to an acceptor molecule
Acyl transferases that catalyze the transfer of acyl groups
Hydrolases
Hydrolases are enzymes that catalyze the cleavage of, among other bond types, the phosphoric anhydride bonds found in GTP
(While Lyases are enzymes that cleave bonds without the addition of water (non-hydrolytically))
Esterification
What is one example of two reactants needed for this reaction?
Esterification -> is a reaction between alcohols and carboxylic acids that results in ester formation
Hydroxylation
hydroxylation describes a chemical process that introduces a hydroxyl group into an organic compound.
Literally pop on a hydroxyl group
Carboxylation
Carboxylation is a chemical reaction in which a carboxylic acid group is produced by treating a substrate with carbon dioxide.
Decarboxylation is the opposite (this is not redox), loss of CO2
Protease vs peptidase
Protease refers to an enzyme that breaks down proteins and peptides, while peptidase refers to an enzyme that breaks down peptides into amino acids.
