Biochem: Enzyme Types, Structure, and Function

Question 1

Hydrolase

Answer 1

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.

Question 2

Isomerase

Answer 2

Rearranges bonds within a molecule to form an isomer

Question 3

Ligase

Answer 3

Forms a chemical bond (DNA ligase)

Question 4

Lyase

Answer 4

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

Question 5

Kinase

Answer 5

Transfers a phosphate group to a molecule from a high energy carrier such as ATP (phosphofructokinase PFK)

Question 6

Oxidoreductase

Answer 6

Oxidoreductase catalyze oxidation-reduction reactions

Runs redox reactions (includes oxidases, reductases, dehydrogenases, and others)

Question 7

Polymerases

Answer 7

Polymerization (e.g. additon of nucleotides to the leading strand of DNA by DNA polymerase III)

Question 8

Phosphatase

Answer 8

Removes phosphate group from a molecule

Question 9

Phosphorylase

Answer 9

Transfers a phosphate group to a molecule from inorganic phosphate (e.g. glycogen phosphorylase)

Question 10

Protease
proteolytic cleavage
Zymogen

Answer 10

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

Question 11

Enzymes have 2 roles

Answer 11

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)

Question 12

Enzymes stabilize the _____

Answer 12

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

Question 13

D/L amino acids and D/L sugars

Answer 13

L amino acids (remember aLanine) and D sugars

Question 14

What factors do enzymes not touch?

What happens if you swap out aa in active site neutral one for neg one?

Answer 14

Keq/ equalibrium constant

Question 15

Feedforward stimulation (doesn’t seem like high yield)

Answer 15

Stimulation of an enzyme by its substrate or by a molecule used in synthesis of the substrate

Question 16

Low Km means…

How to find Km:

Answer 16

…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

Question 17

enyzmes can be active or _____

and can also be inactive or ______

Answer 17

Cooperativity: sigmoidal shape of graph
relaxed (everyone “turned on” open dating)
tense (everyone “turned off” not dating)

Question 18

Competitive inhibitor bind to ____
Competitive inhibitors normally resemble the _____
What does it do to Vmax? Km?

Answer 18

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

Question 19

Noncompetitive inhibitor binds….

What does it do to Vmax? Km?

Answer 19

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)

Question 20

Will changing enzyme concentration change Vmax?

Answer 20

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

Question 21

Uncompetitive inhibitor binds…
What does it do to Vmax? Km?

Does enzyme concentration affect Km?

Answer 21

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

Question 22

Mixed-type inhibition binds…

What does it do to Vmax? Km?

Answer 22

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

Question 23

Line weaver plot
What does slope, y-intercept, x-intercept represent?
See paper diagrams to imagine what each inhibitor would look like

Answer 23

slope -> Km/Vmax
y-intercept -> 1/Vmax
x-intercept -> -1/Km

Question 24

Dehydrogenase

Answer 24

is a type of oxidoreductase enzyme catalyzes the removal of a hydrogen from a molecule

Question 25

Transferases

Answer 25

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

Question 26

Hydrolases

Answer 26

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))

Question 27

Esterification

What is one example of two reactants needed for this reaction?

Answer 27

Esterification -> is a reaction between alcohols and carboxylic acids that results in ester formation

Question 28

Hydroxylation

Answer 28

hydroxylation describes a chemical process that introduces a hydroxyl group into an organic compound.

Literally pop on a hydroxyl group

Question 29

Carboxylation

Answer 29

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

Question 30

Protease vs peptidase

Answer 30

Protease refers to an enzyme that breaks down proteins and peptides, while peptidase refers to an enzyme that breaks down peptides into amino acids.