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Molecules to Cells > Enzymes pt. 1 > Flashcards

Enzymes pt. 1 Flashcards

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Organic Chemistry 101 flashcards
1
Q

Enzymes are _____ specific for reactants (substrate)

A

highly

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2
Q

What is a holoenzyme?

A

An enzyme WITH a cofactor; active

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3
Q

What is an apoenzyme?

A

An enzyme WITHOUT a cofactor; inactive

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4
Q

What are inorganic cofactors?

A

Metal ions

e.g. Zn2+, Mg2+, K+, etc.

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5
Q

What are organic cofactors?

A

Aka coenzymes

Loosely bound, changed by reaction, derived from vitamins

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6
Q

What are the two types of organic cofactors aka conezymes?

A

Co-substrate

Prosthetic group

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7
Q

Describe co-substrates.

A

Loosely bound

Changed by reaction

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8
Q

Describe prosthetic groups

A

Tightly or covalently bound

Not changed by reaction

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9
Q

Can enzymes differ in their degree of specificity?

A

Yes

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10
Q

What is deltaG/ Gibbs free energy?

A

Energy of reactants - energy of products

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11
Q

Does deltaG give you any information about the rate of reaction?

A

No!

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12
Q

What does deltaG tell you?

A

If a reaction is spontaneous (G less than 0) or non-spontaneous (G greater than 0)

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13
Q

How do you calculate deltaG?

A

deltaG = deltaG’ + RT ln ([pdts]/[reactants])

or… [C]^c[D]^d / [A}^a[B]^b

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14
Q

What is deltaG’?

A

Standard free energy change

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15
Q

At equilibrium, deltaG = ?

A

zero

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16
Q

At equilibrium, deltaG = 0, thus deltaG’ = ______

A

deltaG’ = -RT ln Keq

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17
Q

When Keq is greater than 1, _______ are favored and deltaG is ______ than zero

A

products, less than zero

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18
Q

When Keq is less than 1, _______ are favored and deltaG is ______ than zero

A

reactants, greater than zero

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19
Q

How do coupling reactions work?

A

They change the concentrations to make deltaG negative

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20
Q

How do enzymes lower the Ea?

A

Stabilizing the transition state

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21
Q

What does the transition state theory say?

A

The substrate and the transition species are in equilibrium

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22
Q

Keq = ?

A

Keq = e^(-Ea/RT)

Note, Ea also is deltaG of transition state

23
Q

Relatively small changes in activation energy can lead to relatively ______ changes in overall reaction rate.

A

Large!

Because it is an exponent!

24
Q

Once the fraction goes lower than the equilibrium fraction, free energy becomes _____ .

A

Negative.

e.g. if [pdt]/[reactant] = 0.5 at equilibrium, a new ratio of 0.18 is LOWER and thus deltaG is NEGATIVE

25
Q

What are common associations/non-covalent interactions in the active site of an enzyme?

A

Hydrogen bonds, Van der Waals interactions

26
Q

What is the role of reversible non-covalent bonds in enzymes?

A

They can be used to release free energy (bind energy)

27
Q

What are the 2 enzyme-substrate binding models?

A
  1. Lock and key (highly specific and rigid)

2. Induced fit (enzyme changes shape and becomes complementary to substrate)

28
Q

How do you achieve maximum binding energy between enzymes and substrates?

A

Multiple short range interactions

29
Q

Which binding model is supported by data?

A

Induced fit

30
Q

How is free energy (binding energy) released?

A

By the formation of weak interactions from the induced fit of enzyme and substrate

31
Q

The correct substrate for an enzyme results in more interactions and an ______ in binding energy.

A

Increase

Hence why substrate specificity is good

32
Q

What are the steps of chymotrypsin deacylation?

A
  1. Acyl-enzyme-H2O complex
  2. Tetrahedral intermediate (stabilized by oxyanion hole hydrogen bonding)
  3. Free enzyme
33
Q

In addition to the use of binding energy, what other strategies do enzymes use to stabilize the transition state?

A
  1. Covalent catalysis (covalent bond forms between substrate and enzyme)
  2. Acid-base catalysis (molecule other than water becomes a proton donor/acceptor)
  3. Catalysis by approximation (reactants are aligned and held close)
  4. Metal ion catalysis (metal ion promotes formation of a nucleophile or an electrophile whichstabilizes the negative charge on a reaction intermediate, serving as a bridge
34
Q

What does chymotrypsin do and where does it operate?

A

A serine protease that cleaves peptide bonds by hydrolysis in the gut

35
Q

What bond does chymotrypsin cleave?

A

C-terminal side of aromatic (Trp, Tyr, Phe) and large hydrophobic AAs (met)

36
Q

Is chymotrypsin hydrolysis thermodynamically favorable? kinetically favorable?

A

Thermodynamically favorable but NOT kinetically favorable due to partial double bond character of the peptide bond

37
Q

What is the catalytic triad of chymotrypsin?

A

His - Ser - Asp

38
Q

What is the mechanism of chymotrypsin hydrolysis?

A

His accepts proton form Ser hydroxyl group (acid-base)

Ser generates nucleophile to attack carbonyl

Asp stabilizes His through H bonding and electrostatics

39
Q

What are the stages of chymotrypsin hydrolysis?

A

Stage 1: Acylation (acyl enzyme created)

Stage 2: Deacylation (regeneration of enzyme)

40
Q

What are the 3 steps of chymotrypsin acylation?

A
  1. Enzyme-substrate complex
  2. Tetrahedral intermediate
  3. Acyl-enzyme intermediate
41
Q

What are the steps of chymotrypsin deacylation?

A
  1. Acyl-enzyme-H2O complex

2. Tetrahedral intermediate (stabilized by oxyanion hole)

42
Q

How does chymotrypsin control substrate specificity?

A

Binding an amino acid side chain into a deep hydrophobic cavity

43
Q

In the acylation stage of peptide hydrolysis by chymotrypsin, His 57 accepts a proton from Ser 195. What type of catalysis does the His action represent?

A

General base catalysis (remember its from the perspective of histidine!)

44
Q

Elastase is a serine protease like chymotrypsin but cleaves on the C-terminal side of residues like Ala. How would you expect the specificity pocket of elastase to compare with chymotrypsin?

A

Hydrophobic but smaller (alanine is relatively quite small!)

45
Q

How do coupled reactions work?

A

Coupling of reactions shifts the concentration of products or reactants present and thus is able to change ΔG.

46
Q

What is the relationship between the slope of a Lineweaver-Burk plot and catalytic efficiency under Michaelis-Menten kinetic assumptions for an enzyme?

A

The slope of the Lineweaver-Burk plot is Km/Vm and catalytic efficiency is defined as k3/Km. These share the term Km, but are inversely related. Vm= k3[E]t, which means that Vm and k3 are directly proportional. This means that the overall relationship between catalytic efficiency and the slope Km/Vm is an inverse one. In practice this means that steeper (numerically larger) slopes represent lower catalytic efficiency.

47
Q

When evaluating the effectiveness of an enzyme that follows Michaelis-Menten kinetics, an effective enzyme would have:

A

A low Km, because this will increase the catalytic efficiency.

48
Q

An inhibitor decreases apparent Vm but shows no decrease in apparent Km. You correctly suspect this might be:

A

An irreversible inhibitor or a noncompetitive inhibitor.

49
Q

Would adding an uncompetitive inhibitor change the slope of a Lineweaver-Burk plot for an enzyme under Michaelis-Menten kinetics?

A

No

50
Q

What does covalent modification do?

A

Add or remove charged groups to cause changes in enzyme conformation.

51
Q

What does a positive effector do?

A

In allosteric control shifts equilibrium from T to R state favoring ligand binding

52
Q

What does a negative effector do?

A

In allosteric control shifts equilibrium from R to T state reducing ligand binding

53
Q

In hemoglobin(Hb) the binding of oxygen increases the affinity of Hb for oxygen. This is an example of:

A

Allosteric control, where oxygen is a positive effector changing Hb from the T state to the R state.

Molecules to Cells (34 decks)

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