Enzymes

Question 1

Enzymes are catalysts that can and can’t do what

Answer 1

They…

Lower the activation energy
Increase the rate of reaction
Do not alter the equilibrium constant
Are not changed or consumed in the reaction
Are pH and temperature, sensitive with optimal activity at specific pH ranges and temperatures
Do not affect the overall delta G of the reaction
Are specific for a particular reaction or class of reactions

Question 2

Oxidoreductases

Answer 2

Catalyze oxidation reduction reactions
Transfer of electrons between biological molecules
Often have a cofactor that acts as an electron carrier NAD+ NADP+
Electron donor is known as the reductant
Electron acceptor is known as the oxidant

Dehydrogenase
Reductase
Oxidase

Question 3

Transferases

Answer 3

Catalyze the movement of a functional group from one molecule to another

Most will be straightforwardly named, but remember that kinases are also a member of this class

Question 4

Hydrolase

Answer 4

Catalyze the breaking of a compound into two molecules, using the addition of water
Many named for substrate
Phosphatase
Peptidase
Nuclease
Lipase

Question 5

Lyase

Answer 5

Catalyze the cleavage of a single molecule into two products

Do not require water as a substrate, and do not act as oxidoreductase

The synthesis of two molecules into a single molecule may also be catalyzed by lyase (synthase)

Question 6

Isomerase

Answer 6

Catalyze reactions between stereoisomers as well as constitutional isomers

Some can be classified as oxidoreductases, transferases, lyases

Catalyze the rearrangement of bond within molecules

Question 7

Ligases

Answer 7

Catalyze addition or synthesis reactions generally between large similar molecules and often require ATP

Nucleic acid synthesis and repair

Question 8

What is the impact of enzymes on activation energy?

Answer 8

It lower the activation energy, but not the overall free energy of the reaction

They make it easier for the substrate to reach the transition state

Question 9

endergonic vs exergonic

Answer 9

Delta G > 0
Delta G < 0

Question 10

Why are reversible reaction catalyzed by enzymes nonexistent?

Answer 10

They are extremely energetically unfavorable

Question 11

What stabilizes the special arrangement of the enzyme substrate complex

Answer 11

Hydrogen bonding
Ionic interactions
Transient covalent bonds

Question 12

Explain the induced fit model

Answer 12

Unlike the lock and key theory, which suggests that the enzymes active site is already appropriately conformed for the substrate, and the substrate has induced a change in the shape of the enzyme, which requires energy, making the bonding of the two endergonic in nature

The release of the enzyme from the active site is exergonic

Question 13

How are coenzymes and cofactors similar

Answer 13

Small in size
Bind to active site of an enzyme, usually by carrying charge through ionization, protonation, or deprotontation
usually kept at low concentrations
Tightly bound cofactors or co-enzymes that are necessary for enzyme function are known as prosthetic groups

Question 14

Enzymes without their cofactors are called

Answer 14

Apoenzymes

Question 15

Enzymes containing their cofactors are called

Answer 15

Holoenzymes

Question 16

Cofactors are generally

Answer 16

Inorganic molecules or metal ions

Question 17

Coenzymes are

Answer 17

Small organic groups, the vast majority of which are vitamins or derivatives of vitamins

Question 18

Water soluble vitamins

Answer 18

B and C

Question 19

Fat soluble vitamins

Answer 19

A D E K

Question 20

B1 name

Answer 20

Thiamine

Question 21

B2 name

Answer 21

Riboflavin

Question 22

B3 name

Answer 22

Niacin

Question 23

B5 name

Answer 23

Pantothenic acid

Question 24

B6

Answer 24

Pyridoxal phosphate

Question 25

B7

Answer 25

Biotin

Question 26

B9

Answer 26

Folic acid

Question 27

B12

Answer 27

Cyanocobalmin

Question 28

The Michaelis-Menten equation describes what?

Answer 28

How the rate of the reaction depends on the concentration of both the enzyme and the substrate which forms the product

Question 29

Michaelis-Menten equation

Answer 29

~ —K1~> —Kcat~> E + S ES E + P <~K-1-

Question 30

Under a constant concentration of enzyme, write the equation describing the relationship between velocity and substrate concentration

Answer 30

v = (vmax[S])/(Km+[S])

Question 31

When the reaction rate is equal to half Vmax

Answer 31

Km = [S]

Question 32

What is Km

Answer 32

Substrate concentration at which half of the enzymes active site are full Under certain conditions, it is a measure of the affinity of the enzyme for its substrate An enzyme with a higher Km has the lower affinity for its substrate, because it requires a higher substrate concentration to be half saturated Constant value

Question 33

vmax

Answer 33

Max enzyme velocity Measured in moles/second

Question 34

What is the relationship between Vmax and Kcat?

Answer 34

Vmax = [E]Kcat

Question 35

Kcat

Answer 35

Measures the number of substrate molecules converted to product per enzyme molecule per second

Question 36

At very low substrate concentrations…

Answer 36

v = (Kcat/Km) x [E][S]

Question 37

Catalytic efficiency

Answer 37

Kcat/Km

Question 38

What is the Lineweaver Burk plot?

Answer 38

The double reciprocal graph of the Michaelis-Menten equation

Question 39

What does the X axis of the Lineweaver Burk plot represent?

Answer 39

1/[S]

Question 40

What does the Y axis of the Lineweaver Burk plot represent?

Answer 40

1/v

Question 41

How can one find the Km value in the Lineweaver Burk plot?

Answer 41

Negative reciprocal of X intercept LB: X intercept is -1/Km

Question 42

What does an S shaped sigmoidal Michaelis-Menten plot mean?

Answer 42

Cooperativity Cooperative enzymes have multiple subunits and multiple active sites Cooperative enzymes are also subject to activation and inhibition both completely and through allosteric sites

Question 43

Tense versus relaxed states

Answer 43

Low affinity versus high affinity Binding of the substrate encourages the transition of other subunits from T State to R state which increases the likelihood of substrate binding by these other subunits Loss of substrate can encourage the transition from the R state to the T state and promote dissociation of substrate from the remaining subunits

Question 44

Hill’s coefficient>1

Answer 44

Positively cooperative bonding is occurring such that after one ligand is bound the affinity of the enzyme for further ligands increases

Question 45

Hill’s coefficient<1

Answer 45

Negatively, cooperative binding is occurring such that after one ligand is bound the affinity of the enzyme for further ligands decreases

Question 46

Hill’s coefficient=1

Answer 46

The enzyme does not exhibit cooperative binding

Question 47

How does temperature affect enzyme activity?

Answer 47

Enzyme catalyzed reactions tend to double in velocity for every 10°C increase in temperature until the optimum temperature is reached For the human body this is 37°C After this the enzyme will denature at high temperatures Some enzymes that are overheated may regain their function if cooled

Question 48

How does pH affect enzyme activity?

Answer 48

pH affects the ionization of the active site Can lead to denaturation Enzymes that circulate function in human blood optimal pH is 7.4 A pH less than 7.35 is acidemia

Question 49

How does salinity affect enzyme activity?

Answer 49

Altering the concentration of salt can change enzyme activity in vitro Increasing levels of salt can disrupt, hydrogen and ionic bonds, causing a partial change in the conformation of the enzyme, and in some cases causing denaturation

Question 50

How are reversible inhibitors bonded?

Answer 50

Non-covalently

Question 51

Competitive inhibition

Answer 51

Occupancy of the active site Can be overcome by adding more substrate Adding a competitive inhibitor does not alter the value of Vmax Increase of Km

Question 52

Noncompetitive inhibition

Answer 52

Bind to an allosteric site instead of the active site Induces a change in enzyme conformation Adding more substrate won’t do shit Decrease vmax

Question 53

Mixed inhibition

Answer 53

Inhibitor can bind to either the enzyme or the enzyme substrate complex Has different affinity for each Do not bind at the active site, but an allosteric site If the inhibitor preferentially binds to the enzyme it increases the km value If the inhibitor binds to the enzyme substrate complex it lowers the km value Vmax is decreased regardless

Question 54

Uncompetitive inhibition

Answer 54

Lock the substrate in the enzyme Bind to allosteric site Lowers Km and Vmax

Question 55

Allosteric enzymes

Answer 55

Multiple binding sites Active site is present and at least one other site that can regulate the availability of the active site Michaelis-Menten plots of cooperative allosteric enzyme kinetics often have a sigmoidal curve

Question 56

Covalently modified enzymes

Answer 56

The name holds the definition. Phosphorylation, dephosphorylation, or glycosylation

Question 57

Zymogens

Answer 57

Zymogens contain a catalytic domain and regulatory domain The regulatory domain must either be removed or altered to expose the active site Trypsinogen

Question 58

the cDNA sequence is…

Answer 58

a DNA copy of the mRNA used to generate a protein

Question 59

to find the pI of an amino acid with a basic side chain…

Answer 59

we ignore pKa of carboxyl group, avg the side chain and the amino group

Question 60

role of proline in secondary structure

Answer 60

rigid, causes turns in beta pleated sheets

Question 61

How does the ideal temp for a rxn change with and without an enzyme catalyst?

Answer 61

ideal temp generally lower w a catalyst than without