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Biochemistry > Biochem Enzymes Lecture 1 > Flashcards

Biochem Enzymes Lecture 1 Flashcards

1
Q

These are proteins which catalyze biochemical reactions

A

Enzymes

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2
Q

The structure of enzymes are essential to their

A

Catalytic activity

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3
Q

Is the MW of enzymes variable?

A

Yes, vary from 12,000 to 1,000,000+

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4
Q

Some enzymes require and additional chemical component to function, called a

A

Cofactor

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5
Q

Cofactors tend to be one or more ___

They can also be a complex organic or metalloorganic molecule, called a

Or they can be both a

A

inorganic ions (Fe2+, Mg2+, Mn2+, Zn2+)

(coenzyme

Metal ion and a coenzyme

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6
Q

How are enzymes classified?

A

According the the type of reaction that they catalyze

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7
Q

Many enzymes ar enamed by addding _____ to the name describing their activity

A

“ase”

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8
Q

What does an enzyme do?

A

Provides an environment that speeds up a given reaction

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9
Q

This is the term describing a pocket on the enzymes where the enzymes-catalyzed reaction occurs

The surface of the above location is lined with _____ that help bind the substrate and catalyze its chemical transformation

A

Active Site

AA residues

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10
Q

This is the term describing the molecule that is bound in the active site and acted upon by the enzyme

A

Substrate

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11
Q

Does a reaction affect the equilibrium of a reaction? Yes or no?

A

No

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12
Q

What does an enzyme affect about a reaction?

A

The reaction rate

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13
Q

In a reaction diagram, the equilibrium between S and P reflects the difference in ____ of their ground states

A

Free energies

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14
Q

E + S → ES → EP → E + P

If the free energy of the ground state, P is lower than that of S, ΔG is _____ and the equilibrium favors ___ formation

A

Negative

P formation

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15
Q

Does a favorable equilibrium mean a fast conversion of products?

A

No.

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16
Q

The difference between energy levels of the ground state and the transition state is the ________ or ΔG‡

A

Activation energy

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17
Q

A higher activation energy means a faster/slower reaction?

A

Slower reactions

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18
Q

Catalysts increase reaction rates by lowering….

A

ΔG‡

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19
Q

This is the term describing the transient chemical species of a raection

A

Reaction Intermediates

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20
Q

This is the term describing the step in an enzymatic reaction with the highest activation energy, it determines the overall reaction rate

A

Rate-limiting step

21
Q

E + S → ES → EP → E + P

In the above reaction, the reaction rate is determined by the concentration of ___ and

What is the equation, then, for the rate of the reaction (V)?

What order is it?

What is the unit for the rate constant, k?

A

Reaction [S] and the rate constant, K

V=k[S]

First order

s^-1

22
Q

If a reaction is dependent upon two different compounds, S1 and S2, k is a _______ rate constant with units ____

What would the rate equation be then

A

Second Order

M-1s-1

V=k[S1][S2]

23
Q

What is the equation that describes how the rate constant and activation energy are related?

A

k=(kT/h)e ^-ΔG‡/RT

k=Boltzmann constant and h is Planck’s constant

24
Q

What helps to lower activation energies?

A

Weak, noncovalent interactions between substrate and enzyme

25
Q

What are the weak interaction between E and S in ES complexes?

A

H-bonds
Hydrophobic interactions
Ionic Interactions

Some of these weak interactions occur in the reaction transition state and stabilize the transition state

26
Q

The energy obtained from an enzyme substrate interaction is the _____

A

Binding energy, ΔG

27
Q

The binding energy is used by enzymes to to increase/lower the activation energies of reactions?

A

Lower the activation energies

28
Q

The binding energy can be used to lower substrate _______ or to cause a ___ change in the enzymes

A

Entropy

Conformational Change (induced fit)

29
Q

To successfully catalyze reactions, the enzye must be complementary the reaction ___ state

Weak interactions formed in the transition state make the major contribution to ____

A

Transition state

Catalysis

30
Q

Figure 6-5 describes how the free energy changes that occur depending upon how the enzyme interacts with the substrate

When the enzyme fits tightly to the substrate, is the substrate more or less difficult to move to the transition state?

What about when the enzyme fits well with the transition state?

A

More difficult because the substrate is stabilized

The substrate is destabilized and catalysis readily proceeds

31
Q

Fig 6-6 shows how the binding energy (ΔGB) lowers the activation energy.

The free energy released by the formation of weak interactions between E and S in the transition states partially offsets the __ energy for the reaction

A

Activation energy

32
Q

Binding energy also gives an enzyme its ______ for a particular substrate

A

Specificity

33
Q

Enzymes tend to be large. Why?

A

They provide functional groups located in specific positions to maximize multiple weak interactions in the transition state.

34
Q

The binding energy holds substrates in the proper orientation to react. This lowers the ____

A

entropy

35
Q

Enzyme-substrate interactions replace virtually all of the ______ bonds between the substrate and water

A

H-bonds

36
Q

Binding energy compensates kinetically or thermodynamically for the electron redistribution the substrate undergoes in order to react?

A

Thermodynamically

37
Q

Binding energy may be used to cause a conformation change in the enzyme itself when the substrate binds. This is called an ___

It changes the alignment of specific ___ groups

It also is important in the formation of additional ______ interactions in the transition state

A

Induced fit

Functional

Weak interactions

38
Q

Additional catalytic mechanisms involve transient ____ interactions with a substrate or group transfer to or from a substrate

A

Covalent

Different from the weak contributions found with the binding energy just discussed

39
Q

When there is no catalyst present, unstable, charged intermediates formed in many biochemical reactions tend to break down immediately to form reactants (and products will not be formed)

These charged intermediates can be stabilized by _____ to form a species that breaks down readily to products (instead of reactants)

A

Proton transfer

40
Q

This is acid-base catalysis that uses only the H+ or OH- ions present in water

This is acid-base catalysis of proton transfers facilitated by other classes of molecules

A

Specific Acid-Base catalysis

General Acid-Base Catalysis

41
Q

For nonenzymatic reactions in aqueous solutions, weak organic acids or bases can be proton _____ in addition to water

A

Donors

42
Q

In an enzyme’s active site, amino acid side chains can act as proton ____ and _____

Rate enhancements of ___ to ___ are observed

A

donors and acceptors

10^2 to 10^5

43
Q

________ are the most common biochemical reactions

A

Proton transfers

44
Q

This type of catalysis involves the formation of a transient covalent bond between an enzyme and substrate

In the uncatalyzed hydrolysis of an A-B bond

In the presence of a covalent catalyst (an enzyme with nucleophile X)

A

Covalent Catalysis

?

?

45
Q

Catalysis occurs when the newer pathway has a HIGHER/LOWER energy than the uncatalyzed reaction

Where do the nucleophiles come from?

A

Lower

AA side chains
Functional groups of some enzyme cofactors

46
Q

This type of catalysis is ionic interactions between an enzyme bound metal and a substrate

It can orient the ___ for reaction

Or stabilize the ____

A

Metal Ion Catalysis

Substrate

Transition state

47
Q

Metals are involved in ______ reactions

about 1/3 of all known enzymes require metal ions for activity

A

Oxidation/reduction

48
Q

In sum, most enzymes use a combination of catalytic strategies or one catalytic strategy?

What two processes does chemotrypsin use?

A

A combination

Covalent and general acid-base catalysis

Biochemistry (27 decks)

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