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MCBG > 8.4.16 Lecture > Flashcards

8.4.16 Lecture Flashcards

1
Q

What are enzymes?

A

Proteins that catalyze thousands of chemical reactions.

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2
Q

How do enzymes facilitate reactions?

A

Enzymes facilitate reactions by increasing the reaction rate.

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3
Q

Is the enzyme regenerated after the reaction is complete?

A

Yes

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4
Q

What does thermodynamics predict?

A
  1. Whether a chemical reaction is feasible 2. Whether the reaction will occur spontaneously with the release of energy.
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5
Q

Delta G = ?

A

G(product) - G(reactant)

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6
Q

If G(reactant) > G(product), what happens?

A

Delta G is negative and the reaction proceeds spontaneously, releasing energy.

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7
Q

Do thermodynamics affect the speed of the reaction?

A

No

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8
Q

Draw a Gibbs free energy diagram.

A
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9
Q

How does an enzyme affect the free energy diagram?

A

The enzyme lowers the activation energy (the energy it takes to convert a substrate to a product through an intermediate transition state). It does NOT lower the overall free energy of the reaction.

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10
Q

What is the active site of an enzyme?

A

The active site of an enzyme is the specific region of the enzyme that binds the substrate and carries out the catalysis of the reaction.

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11
Q

What is carboxypeptidase A?

A

A GI enzyme synthesized in the pancreas and delivered to the small intestine lumen, where it degrades peptides by removing amino acids from the C-terminus one by one.

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12
Q

How does the substrate bind to carboxypeptidase A?

A

It fits into a hydrophobic pocket C-terminus-first. This enzyme prefers large hydrophobic amino acids. In addition, the C-terminus COO- hydrogen bonds with Arginine (+).

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13
Q

Carboxypeptidase A contains a ___ ion, held in place by 2 ___ and 1 ___ via coordinate covalent bonds. ___ is also bound to this ion and will be used to hydrolyze the peptide bond.

A

Zinc; His; Glu; Water

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14
Q

Draw the mechanism by which carboxypeptidase A cleaves the peptide bond.

A
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15
Q

What is the induced fit theory?

A

The induced fit theory states that the binding of the substrate can induce conformational changes on the enzyme.

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16
Q

Define oxidoreductases and give an example.

A

Oxidoreductases move an electron, hydrogen, or oxygen from one substrate to another.

Example: Alcohol dehydrogenase moves an OH to an aldehyde.

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17
Q

Define transferases and give an example.

A

Transferases move a chemical group from one molecule to another.

Example: Kinase that moves a phosphate from ATP to a protein

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18
Q

Define hydrolases and give an example.

A

Hydrolayses use water to make two products from a substrate.

Example: carboxypeptidase A

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19
Q

Definse lyases.

A

Lyases cleave C-C, C-N, or C-O bonds. Sometimes they make them (these are called synthases).

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20
Q

Define isomerases.

A

Isomerases move a group or double bond within a molecule.

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21
Q

Define ligases.

A

Ligases join atoms together using energy, usually from ATP (also called synthetases).

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22
Q

What is a coenzyme?

A

A coenzyme is a small, nonpolypeptide molecule tightly associated with an enzyme that participates in the reaction that the enzyme catalyzes, often by forming a covalent bond to the substrate.

23
Q

What is a cofactor?

A

A cofactor is an inorganic ion or coenzyme required for an enzyme’s activity.

24
Q

What is a cosubstrate?

A

A cosubstrate is a cofactor that is modified during the reaction and leaves the active site.

25
Q

What is a prosthetic group?

A

A prosthetic group is a tightly bound cofactor that is regenerated after the reaction.

26
Q

Draw the reaction equation for a single substrate reaction that forms one product and is irreversible.

A
27
Q

What are k1, k2, and k3?

A

Rate constants; they determine the equilibrium dissociation constant (how tightly the substrate binds).

28
Q

What does the equilibrium dissociation constant measure?

A

How tightly the substrate binds

29
Q

If k3 is relatively small compared to k1 and k2…

A

…it indicates that ES –> E+P is the rate determing step and is thus designated as kcat (catalytic rate constant).

30
Q

v = ?

A

v = d[P]/dt

31
Q

When studying the effect of [S] on v0, v0 is determined…

A

..before much of S is used up and before enough P was formed to force the reverse reaction.

32
Q

Draw the curve described by the Michaelis-Menten equation.

A
33
Q

What is the Michaelis-Menten Equation?

A
34
Q

What are the two variables in the Michaelis-Menten equation? What are the two constants?

A

Variables: [S], [E0]

Constants: Km, kcat

35
Q

vmax = ?

A

(kcat)([E0])

36
Q

Km = ?

A

(k2 + k3)/(k1)

37
Q

If Km = [S], v = ?

A

vmax/2

38
Q

v0 increases directly with ____.

A

[E0]

39
Q

Enzyme rates are determined by ___.

A

kcat

40
Q

What is kcat?

A

The turnover number, which gives the number of substrate molecules that one enzyme molecule can convert to product in one second.

kcat = vmax/[E0]

41
Q

Derive the equation that describes the Lineweaver-Burk plot.

A
42
Q

Draw the Lineweaver Burk plot.

A
43
Q

What are enzyme inhibitors?

A

Enyzme inhibitors are chemical compounds that decrease the activity of an enzyme.

44
Q

___% of prescribed drugs inhibit enzymes.

A

30

45
Q

Describe competitive inhibition.

A

A competitive inhibitor binds to all or part of the substrate binding site, preventing substrate from binding. The substrate and inhibitor compete for the site.

46
Q

Draw a graph demonstrating the effect of a competitive inhibitor on Km and vmax.

A
47
Q

Describe the effects a competitive inhibitor has on Km and vmax.

A

Km appears to be higher, as it takes more substrate to reach vmax/2. vmax is not effected, as enough S will outcompete the inhibitor.

48
Q

Draw the Lineweaver Burk plot as affected by a competitive inhibitor.

A
49
Q

Describe noncompetitive inhibition.

A

In noncompetitive inhibition, the inhibitor binds to an allosteric site (not the active site), changing the structure and distorting the active site to prevent catalysis -> kcat ~ 0.

50
Q

Draw a graph demonstrating the effect of a noncompetitive inhibitor on Km and vmax.

A
51
Q

Describe the effects a noncompetitive inhibitor has on Km and vmax.

A

Km does not change, as S still binds to the active site. vmax decreases.

52
Q

Draw the Lineweaver Burk plot as affected by noncompetitive inhibition.

A
53
Q

What are the Michaelis-Menten equations for competitive and noncompetitive inhibition?

A

MCBG (28 decks)

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