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MCAT Biochem > Enzymes > Flashcards

Enzymes Flashcards

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1
Q

Enzymes are catalysts that can and can’t do what

A

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

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2
Q

Oxidoreductases

A

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

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3
Q

Transferases

A

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

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4
Q

Hydrolase

A

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

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5
Q

Lyase

A

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)

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6
Q

Isomerase

A

Catalyze reactions between stereoisomers as well as constitutional isomers

Some can be classified as oxidoreductases, transferases, lyases

Catalyze the rearrangement of bond within molecules

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7
Q

Ligases

A

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

Nucleic acid synthesis and repair

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8
Q

What is the impact of enzymes on activation energy?

A

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

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9
Q

endergonic vs exergonic

A

Delta G > 0
Delta G < 0

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10
Q

Why are reversible reaction catalyzed by enzymes nonexistent?

A

They are extremely energetically unfavorable

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11
Q

What stabilizes the special arrangement of the enzyme substrate complex

A

Hydrogen bonding
Ionic interactions
Transient covalent bonds

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12
Q

Explain the induced fit model

A

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

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13
Q

How are coenzymes and cofactors similar

A

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

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14
Q

Enzymes without their cofactors are called

A

Apoenzymes

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15
Q

Enzymes containing their cofactors are called

A

Holoenzymes

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16
Q

Cofactors are generally

A

Inorganic molecules or metal ions

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17
Q

Coenzymes are

A

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

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18
Q

Water soluble vitamins

A

B and C

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19
Q

Fat soluble vitamins

A

A D E K

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20
Q

B1 name

A

Thiamine

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21
Q

B2 name

A

Riboflavin

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22
Q

B3 name

A

Niacin

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23
Q

B5 name

A

Pantothenic acid

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24
Q

B6

A

Pyridoxal phosphate

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25
Q

B7

A

Biotin

26
Q

B9

A

Folic acid

27
Q

B12

A

Cyanocobalmin

28
Q

The Michaelis-Menten equation describes what?

A

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

29
Q

Michaelis-Menten equation

A

~
—K1~> —Kcat~>
E + S ES E + P
<~K-1-

30
Q

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

A

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

31
Q

When the reaction rate is equal to half Vmax

A

Km = [S]

32
Q

What is Km

A

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

33
Q

vmax

A

Max enzyme velocity
Measured in moles/second

34
Q

What is the relationship between Vmax and Kcat?

A

Vmax = [E]Kcat

35
Q

Kcat

A

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

36
Q

At very low substrate concentrations…

A

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

37
Q

Catalytic efficiency

A

Kcat/Km

38
Q

What is the Lineweaver Burk plot?

A

The double reciprocal graph of the Michaelis-Menten equation

39
Q

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

A

1/[S]

40
Q

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

A

1/v

41
Q

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

A

Negative reciprocal of X intercept

LB: X intercept is -1/Km

42
Q

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

A

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

43
Q

Tense versus relaxed states

A

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

44
Q

Hill’s coefficient>1

A

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

45
Q

Hill’s coefficient<1

A

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

46
Q

Hill’s coefficient=1

A

The enzyme does not exhibit cooperative binding

47
Q

How does temperature affect enzyme activity?

A

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

48
Q

How does pH affect enzyme activity?

A

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

49
Q

How does salinity affect enzyme activity?

A

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

50
Q

How are reversible inhibitors bonded?

A

Non-covalently

51
Q

Competitive inhibition

A

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

52
Q

Noncompetitive inhibition

A

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

53
Q

Mixed inhibition

A

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

54
Q

Uncompetitive inhibition

A

Lock the substrate in the enzyme

Bind to allosteric site

Lowers Km and Vmax

55
Q

Allosteric enzymes

A

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

56
Q

Covalently modified enzymes

A

The name holds the definition.

Phosphorylation, dephosphorylation, or glycosylation

57
Q

Zymogens

A

Zymogens contain a catalytic domain and regulatory domain

The regulatory domain must either be removed or altered to expose the active site

Trypsinogen

58
Q

the cDNA sequence is…

A

a DNA copy of the mRNA used to generate a protein

59
Q

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

A

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

60
Q

role of proline in secondary structure

A

rigid, causes turns in beta pleated sheets

61
Q

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

A

ideal temp generally lower w a catalyst than without

MCAT Biochem (12 decks)

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