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Malika Biochem MCAT > Chapter 2 > Flashcards

Chapter 2 Flashcards

1
Q

Enzymes

A

Are Biological catalysts that increase the rate of the reaction by lowering the activation energy because they bind more tightly to the transition state than to the reactants.

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2
Q

Characteristics of enzymes

A

-They are pH and temperature sensitive, they have an optimal temperature at which they operate
- They aren’t changed or consumed in a reaction; they appear in both the reactants and products
- they are required in small amounts
- They don’t alter the equilibrium constant
-They don’t affect the overall delta G of a reaction
- They are specific for particular reactions (enzyme specificity)

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3
Q

What is an oxidoreductase?

A

It is the enzyme responsible for catalyzing, oxidation, and reduction reactions. Usually these enzymes have cofactors attached to them such as NAD or NADP, which act as electron carriers.

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4
Q

What are transferases?

A

They are enzymes that catalyze the movement of a functional group from one molecule to another. An example is kinase which catalyzes the transfer of a phosphate group.

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5
Q

What are hydrolases?

A

They are enzymes that catalyze the breaking of a compound into two molecules using the addition of H2O. Examples include nucleases, lipases, peptidases

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6
Q

What are lyases?

A

Enzymes that catalyze the cleavage of a single molecule into two molecules but they don’t require the addition of H2O

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7
Q

Name a subgroup of lyase enzymes.

A

Synthases which catalyze the synthesis of two small molecules into a single molecule.

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8
Q

What are isomerases?

A

They are enzymes that catalyze the rearrangement of bonds within a molecule.
Ex: Phopshoglucoisomerase converts glucose-6-phosphate into fructose-6-phosphate (aldose to ketose)

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9
Q

What are ligases?

A

They are enzymes that catalyze the synthesis of large similar molecules and often require ATP.

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10
Q

Apoenzymes

A

Enzymes without their cofactors (think of a- prefix “without”)

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11
Q

Holoenzymes

A

Enzymes that do have their cofactors

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12
Q

Cofactors

A

Inorganic molecules or metal ions that bind to the enzyme active site or allosteric site and aid in catalysis

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13
Q

Coenzymes

A

Small organic groups bound to the enzyme; they are usually vitamins or derivatives of vitamins

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14
Q

Induced Fit Model of Enzyme Substrate Binding

A

Theory that suggests the substrate that binds to the enzyme induces a conformation change in the enzyme when binding, so that the shape of the active site becomes complementary only after the binding of the substrate

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15
Q

What kind of bonds aid in binding of the substrate to the enzyme active site?

A

Ionic binds, H bonds, and hydrophobic interactions

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16
Q

What is Vmax in enzyme kinetics?

A

It is the initial velocity of the reaction of the theoretical saturation point of the enzyme.

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17
Q

What is the Michaelis constant (Km)?

A

It is the substrate concentration when the velocity is 1/2 of Vmax. Basically, the substrate concentration at which half of the enzymes’ active sites are full.

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18
Q

Km (Michaelis constant) is used to compare the measure of the affinity of an enzyme for its substrate.
So if Km is high, is the affinity for the substrate high or low?

A

It is low. (Think of inverse relationship)

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19
Q

What are the necessary rules for plotting a MM graph?

A

-The total enzyme concentration is always much smaller than the substrate concentration
-Only the initial reaction rate of each [S] is plotted because [S] is depleted as the reaction moves forward

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20
Q

What are the units for Vmax?

A

Units of moles of enzyme per second

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21
Q

How do you increase Vmax?

A

You can only increase Vmax by increasing the enzyme concentration. They are directly proportional, so increasing [E] by 2, increases Vmax by 2, etc…

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22
Q

What is kcat?

A

the turnover rate = number of substrate molecules converted to product per enzyme molecule per second.

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23
Q

Equation to calculate Kcat

A

Vmax/[Total enzyme concentration]

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24
Q

True or false:
When total enzyme concen. is constant, kcat is directly proportional to Vmax.

A

TRUE
In this question, you can find the kcat on the graphs by comparing the Vmaxes, since total [E] is constant

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25
Q

State the Michaelis Menten Equation:

A

V = Vmax ([S] / ([S] + Km)

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26
Q

What is the equation to determine catalytic efficiency of an enzyme?

A

kcat/Km

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27
Q

What factors influence the activity and velocity of an enzyme?

A

Temperature, pH, and high salinity

28
Q

How does temperature influence enzyme activity?

A

An enzyme catalyzed reaction doubles in velocity for every 10°C increase until the optimum temperature is reached. At high temperatures enzymes will denature.

29
Q

How does pH influence enzyme activity?

A

Most enzymes in our body function at a specific optimal pH, depending on the region of the body. Changes in pH can lead to denaturation.

30
Q

How does salinity affect enzyme activity?

A

Altering the concentration of salt can change enzyme activity internally. It can disrupt hydrogen and ionic bonding, causing a partial confirmational change in the enzyme.

31
Q

What are the two types of feedback regulation?

A

…

32
Q

What is a zymogen?

A

It is an inactive form of an enzyme which contains a catalytic active domain and a regulatory domain. To make the enzyme active the regulatory domain must be either cleaved or altered.

33
Q

What is a feedforward system?

A

In this system to maintain homeostasis, and output of one stage of the control system is sent to a later stage of the process to affect later outcome of products.

34
Q

What is a positive feedback system?

A

A process in which the end products of an action cause more of that action to occur in a feedback loop. An example is during labor when the hormone oxytocin is released from the posterior pituitary gland which stimulates uterine contractions and these contractions cause even more intense contractions.

35
Q

Explain negative feedback.

A

In order to maintain homeostasis, once there is enough product, the product acts as an inhibitor to an earlier stage in the system, to decrease the amount of product produced.

36
Q

Name some examples of negative feedback in the human body

A
  1. After you consume a meal, your blood sugar level is elevated. This triggers, the release of insulin from the pancreas and insulin, then transports the glucose in the blood into the cells to be stored. Thus decreasing the level of blood sugar.
  2. The parathyroid gland, secretes parathyroid hormone which regulates the calcium blood level. If calcium in the blood decreases, the parathyroid gland senses this and secretes more parathyroid hormone. If there is too much calcium in the blood, the parathyroid gland decreases secretion of PTH.
37
Q

Can enzymes be regulated covalently?

A

Yes, enzymes can be regulated by phosphorylation which activates or dephosphorylation which deactivates the enzyme.

38
Q

Explain the process of allosteric regulation.

A

This is when an allosteric inhibitor or activator binds to an allosteric site of the enzyme, this is a distinct site from the active site, causing a confirmational change of the active site.
-This can either stimulate or inhibit the enzyme’s reactivity
- The confirmational change that is induced can happen on the same protein subunit, to which the allosteric inhibitor/activator binded to or it can happen in a different subunit of the protein complex

39
Q

What are cooperative enzymes?

A

Enzymes that have multiple subunits and multiple active sites. The active sites exist in either two states: low affinity tense state (T) or high affinity relaxed state (R).

40
Q

What is positive cooperative binding?

A

It is when a substrate binds to the first subunit active site, causing the other subunits to go from a T to R state, increasing their affinity for substrate (key part).

41
Q

What is negative cooperative binding?

A

It is when the first binding event of a substrate decreases the affinity of other subunits to binding additional substrates. These subunits stay in the low affinity tense state (T).

42
Q

What is the Hill’s coefficient used to measure?

A

The Hills coefficient measures cooperative binding of an enzyme.

43
Q

Hyperbolic dependence on substrate concentration is a sign of what cooperative binding?

A

Either no cooperative binding or negative cooperative binding

44
Q

Positive cooperative binding produces what kind of curve on a graph?

A

Sigmoidal curve

45
Q

What is competitive inhibition?

A

It is when a reversible inhibitor competes with a substrate to bind to the enzyme active site. This type of inhibition increases Km without affecting Vmax.

46
Q

What is noncompetitive inhibition?

A

It is when an inhibitor binds to an allosteric site on the enzyme, which causes a confirmational change in the enzyme, active site. This type of inhibition doesn’t affect Km, but it decreases Vmax.

47
Q

What is uncompetitive inhibition?

A

It is when an inhibitor binds to an allosteric site on the enzyme-substrate complex only after the substrate has already been bound. But instead of inducing a confirmational change, it locks the substrate in the enzyme active site preventing its release. This decreases both Km and Vmax.

48
Q

What kinds of bonds are salt bridges in tertiary protein folding?

A

Salt bridges are bonds formed between acidic and basic R groups

49
Q

What is the strongest type of protein folding interaction?

A

Disulfide bond, which occurs between two oxidized cysteine residues.

50
Q

What is the difference between a catalyst and an enzyme?

A

Catalysts: can be inorganic molecules or organic, don’t have specificity for substrate like enzymes
Enzymes : organic molecules, highly specific for substrates, all enzymes are a type of catalyst

51
Q

Out of the following which ones do enzymes affect: reaction rate, equilibrium, yield, percent yield, Keq, energy of activation

A

Enzymes affect reaction rate and energy of activation. They increase the rate and lower energy of activation.

52
Q

How does substrate concentration affect reaction rate?

A

At low substrate concentrations, initial reaction rate (V0) increases because the enzyme’s active sites aren’t full. As the substrate concentration increases, the reaction rate levels off (steady) because the enzymes’ active sites become full.

53
Q

How does enzyme concentration affect reaction rate (velocity)?

A

When the initial enzyme concentration is low, adding more enzyme will increase the reaction rate. However, the more enzymes are added, the reaction rate approaches saturation level because there are not enough substrate molecules for enzyme, active sites.

54
Q

Describe the Lineweaver Burk Plot graph for a competitive inhibitor in comparison to control.

A

Competitive inhibitor line will intercept with the control line at the y axis only.

55
Q

Describe the Lineweaver Burk Plot graph for a noncompetitive inhibitor in comparison to control.

A

The noncompetitive inhibitor line will intercept with the control line at the x axis only.

56
Q

Describe the Lineweaver Burk Plot graph for an uncompetitive inhibitor in comparison to control.

A

The uncompetitive inhibitor will run parallel to the control line.

57
Q

What is Kd used to measure?

A

Kd is a dissociation constant. It measures the tendency of a protein-ligand complex to separate from each other.
Small Kd = low tendency to separate
High Kd = high tendency to separate from each other

58
Q

True or false:
A prosthetic group has a high Kd.

A

False
A prosthetic group involves a tightly bound ligand which would mean it has a low Kd (dissocation constant).

59
Q

Of the following choices: catalytic turnover, catalytic efficiency, Vmax, Km
Which ones enzyme concentration affect?

A

Changes in enzyme concentration affects Vmax only.
Because Kcat = Vmax/total enzyme concentration, both sides of the ratio increase by same factor so Kcat remains the same ratio

60
Q

What is the difference between phosphatases and phosphorylases?

A

Phosphatases remove phosphate groups from molecules.
Phosphorylases break a bond by adding an inorganic phosphate group.

61
Q

What are thermophilic enzymes and how do they compare to regular enzymes?

A

-Thrive at temps above 40C
-Low catalytic rate at low temps
-Resistant to heat denaturation

62
Q

Interpreting Lineweaver Burke plot

A

Y intercept: going further up causes decrease in Vmax
X intercept: going away from origin (0) decreases Km

63
Q

What is the function of a mutase enzyme?

A

Moves a functional group within the same molecule
Ex: Phosphoglucomutase converts glucose-6-phosphate to glucose-1-phosphate

64
Q

Compare the different types of inhibition, in terms of how they affect Km and Vmax.

A

Competitive - increases Km, no effect on Vmax
Noncompetitive - no effect on Km, decreases Vmax
Uncompetitive - Km decreases, Vmax decreases by same proportion
Mixed/higher affinity to ES complex - Km decreases, Vmax decreases
Mixed/higher affinity to E ONLY - Km increases, Vmax decreases

65
Q

Name the different types of cooperative binding

A

Positive binding - Hills coefficient >1
No binding - hills coefficient = 1
Negative binding - hills coefficient < 1

Malika Biochem MCAT (11 decks)

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