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Flashcards in 8.4.16 Lecture Deck (53):
1

What are enzymes?

Proteins that catalyze thousands of chemical reactions.

2

How do enzymes facilitate reactions?

Enzymes facilitate reactions by increasing the reaction rate.

3

Is the enzyme regenerated after the reaction is complete?

Yes

4

What does thermodynamics predict?

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

5

Delta G = ?

G(product) - G(reactant)

6

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

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

7

Do thermodynamics affect the speed of the reaction?

No

8

Draw a Gibbs free energy diagram.

9

How does an enzyme affect the free energy diagram?

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. 

10

What is the active site of an enzyme?

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. 

11

What is carboxypeptidase 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. 

12

How does the substrate bind to carboxypeptidase 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 (+).

13

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.

Zinc; His; Glu; Water

14

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

15

What is the induced fit theory?

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

16

Define oxidoreductases and give an example.

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

 

Example: Alcohol dehydrogenase moves an OH to an aldehyde.

17

Define transferases and give an example.

Transferases move a chemical group from one molecule to another.

 

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

18

Define hydrolases and give an example.

Hydrolayses use water to make two products from a substrate.

 

Example: carboxypeptidase A

19

Definse lyases.

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

20

Define isomerases.

Isomerases move a group or double bond within a molecule.

21

Define ligases. 

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

22

What is a coenzyme?

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

What is a cofactor?

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

24

What is a cosubstrate?

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

25

What is a prosthetic group?

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

26

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

27

What are k1, k2, and k3?

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

28

What does the equilibrium dissociation constant measure?

How tightly the substrate binds

29

If k3 is relatively small compared to k1 and k2...

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

30

v = ?

v = d[P]/dt

31

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

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

32

Draw the curve described by the Michaelis-Menten equation.

33

What is the Michaelis-Menten Equation?

34

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

Variables: [S], [E0]

Constants: Km, kcat

35

vmax = ?

(kcat)([E0])

36

Km = ?

(k2 + k3)/(k1)

37

If Km = [S], v = ?

vmax/2

38

v0 increases directly with ____.

[E0]

39

Enzyme rates are determined by ___.

kcat

40

What is kcat?

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

Derive the equation that describes the Lineweaver-Burk plot.

42

Draw the Lineweaver Burk plot.

43

What are enzyme inhibitors?

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

44

___% of prescribed drugs inhibit enzymes.

30

45

Describe competitive inhibition.

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

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

47

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

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

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

49

Describe noncompetitive inhibition.

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

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

51

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

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

52

Draw the Lineweaver Burk plot as affected by noncompetitive inhibition.

53

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