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Biochemistry I > Enzymes > Flashcards

Enzymes Flashcards

1
Q

The first class of enzymes is _______________, which catalyzes electron transfer reactions, and an example is alcohol dehydrogenase.

A

Oxidoreductase

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2
Q

The second class of enzymes is ______________, which catalyzes group transfer reactions, and DNA polymerase is an example of one.

A

Transferase

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3
Q

The third class of enzymes is ___________________, which catalyzes hydrolysis reactions, and examples include chymotrypsin and RNase A.

A

Hydrolyase

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4
Q

The fourth class of enzymes is ____________, which catalyzes cleavage reactions or eliminations, and carbonic anhydrase is an example.

A

Lyase

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5
Q

The fifth class of enzyme is ______________, which catalyzes the transfer of groups within a molecule to yield isomers, and phosphohexose isomerase is an example.

A

Isomerase

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6
Q

The sixth and last class of enzymes is _____, which catalyzes the formation of covalent bonds by condensation reactions and ATP, and aminoacyl-tRNA synthetase is an example.

A

Ligase

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7
Q

There are four mechanisms in which an enzyme can catalyze a reaction. What are they?

A
  1. Electrostatic catalysis
  2. Proximity and orientation effects
  3. General acid/base catalysis
  4. Covalent or nucleophilic catalysis
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8
Q

_______________ catalysis involves charged groups in an active site that help stabilize the transition-state; the active sites are generally hydrophobic and exclude water, thereby enabling the reaction to occur at a low dielectric constant, which increases the strength of charged interactions.

A

Electrostatic

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9
Q

In electrostatic catalysis, pKa values can ______________ from tabulated values.

A

Differ greatly

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10
Q

An example of electrostatic catalysis discussed in class is the deprotonation of aspartate. When in the presence of ___________, a positively charged amino acid, aspartate is ______________ (more or less) likely to deprotonate, thereby _____________ the pKa.

A

Lysine

More likely

Lowering

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11
Q

In proximity and orientation effects, the enzyme brings the catalytic groups together, holding the enzyme and substrate in ______________________ thereby freezing _______________ and _____________ motion of the substrate and catalytic groups.

A

Proper orientation

Translational

Rotational

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12
Q

Proximity and orientation effects is based upon __________________, the theory that a reaction can only proceed when molecules are in the proper orientation and energy level when they collide.

A

Collision theory

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13
Q

_______________________ refers to proton transfers mediated by _____ acids and bases.

A

General acid/base catalysis

Weak acids and bases

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14
Q

General __________ catalysis involves catalysis where protein transfers from an acid occur.

A

Acid

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15
Q

General _______ catalysis involves catalysis where proton abstraction from a base occurs.

A

Base

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16
Q

What enzyme did we use in class that functioned as general acid/base catalyst?

A

RNase A, which catalyzes the hydrolysis of RNA of its sugar-phosphate backbone

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17
Q

In the acid/base catalysis of RNase A, two essential ___________ residues are required in the active site: _______12 and ______119.

A

Histidine

His12

His119

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18
Q

(Re RNase A)

First, His___ functions as a base and abstracts a proton from the hydroxyl group from the ___ (carbon) of ribose. This enables the oxygen atom from the hydroxyl group to function as a better _______________, allowing for its attack of the electrophilic ________ atom in the sugar-phosphate backbone. An unstable intermediate forms, requiring that the oxygen in the ____________ group “kick back” to break the phosphodiester bond. To do so, His___ must function as an acid, making for a better leaving group.

A

His12

C2’

Nucleophile

Phosphate

O = P

His119

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19
Q

(Re RNase A)

Ultimately, this results in the loss of a nucleoside and formation of an unstable intermediate. To regenerate the enzyme, His___ now functions as a base, abstracting a proton from water. The resulting hydroxide ion makes for a better _______________ and attacks the electrophilic phosphate. Ultimately, an unstable penta-intermediate forms, oxygen “kicks back,” and expels the ___ (carbon) oxygen on the ribose. This requires that the oxygen abstract a proteon from His___, which now functions as a _________.

A

His119

Nucleophile

C2’

His12

Acid

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20
Q

Make sure you understand the mechanism of RNase A (a hydrolase).

A
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21
Q

From the list of amino acids, which could be used as general acid catalysts?

A

Glutamic acid (E)

Aspartic acid (D)

Histidine (H)

Arginine (R)

Lysine (K)

Serine (S)

Cysteine (C)

Tyrosine (Y)

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22
Q

Under what conditions might the amino acids listed as acids NOT act as general acid catalysts?

A

When they are deprotonated, so when pH > pKas

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23
Q

From the list of amino acids, which could be used as general base catalysts?

A

Glutamic acid (E)

Aspartic acid (D)

Histidine (H)

Arginine (R)

Lysine (K)

Serine (S)

Cysteine (C)

Tyrosine (Y)

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24
Q

Under what conditions might the amino acids listed above NOT function as general base catalysts?

A

When protonated; pH < pKa

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25
Q

From the list of amino acids, which might serve as nucleophiles and under what specific conditions?

A

Serine (S)

Cysteine (C)

Tyrosine (Y)

Lysine (K)

Histidine (H)

Arginine (R)

Glutamic acid (E)

Aspartic acid (D)

When they are deprotonated; pH > pKa

26
Q

___________________ catalysis involves the transient formation of a covalent bond between the enzyme and substrate.

A

Covalent or nucleophilic catalysis

27
Q

Be familiar with the general mechanism of covalent or nucleophilic catalysis.

A
  1. Nucleophilic attack by a group on the enzyme that forms a covalent bond between E and S
  2. Stabilization of transition state by amino acids in the active site of the enzyme
  3. Regeneration of enzyme
28
Q

A type of covalent/nucleophilic catalysis we discussed in class was _______________, another hydrolase.

A

Chymotrypsin

29
Q

Chymotrypsin is a ______ protease because its catalytic mechanism involves a _______ acting as a nucleophile. In addition, two other amino acids, histidine and __________, serve important roles.

A

Serine

Serine

Aspartic acid

30
Q

The catalytic triad of chymotrypsin, like all serine proteases, consists of Ser195, His57, and ____102.

A

Asp102

31
Q

The catalytic traid perfectly aligns, and then a ___________ pocket forms around the oxygen atom.

A

Hydrophobic

32
Q

Chyotrypsin cleaves on the C-terminal sites of aromatic amino acids: _________, ____________, and ___________.

A

W, F, and Y

33
Q

The oxyanion hole stabilizes the ___________________ over the substrate.

A

Transition state

34
Q

In the chymotrypsin catalysis, His___ functions as a general base, abstracting a proton from Ser___. Asp___ hydrogen bonds with His___, making it a better base. Ser195 acts as a nucleophile, attacking the carbonyl carbon to the _______ (left or right) of an aromatic R group. A tetrahedral intermediate forms, which is unstable; however, the oxyanion moves into the _________ hole, which stabilizes the charge and the transition state. Oxygen “kicks back,” and expels the amino end after His57 functions as an _____, donating its proton to enable the loss of a better leaving group. A product leaves, and the enzyme-substrate _____________ complex is formed. His57 abstracts a proton from ________, which then functions as a nucleophile, attacking the remaining carbonyl carbon. Again, a tetrahedral intermediate forms, and the oxyanion moves into the __________ hole, stabilizing the transition state. Oxygen kicks back and expels the enzyme as it abstracts a proton from His_____. This regenerates the enzyme and results in the second product.

A

His57

Ser195

Asp102

His57

Right

Oxyanion hole

Acid

Enzyme-substrate covalent complex

Water

Oxyanion hole

His57

35
Q

You must be familiar with the mechanism of covalent/nucleophilic catalysis of a serine protease (i.e., chymotyrpsin, trysin, which cleaves after R and K).

A

Ser195

His57

Asp102

(vs. in general acid/base catalysis RE: RNase A - His12 & His119)

36
Q

How was the mechanism of chymotrypsin elucidated?

A

Kinetic studies in which p-Nitrophenol was reacted with chymotrypsin

37
Q

What is the “fast” step in the chymotrypsin mechanism?

A

The first acylation where Ser195 nucleophilically attacks the substrate

38
Q

What is the “slow” step in the chymotrypsin mechanism?

A

The second deacylation step in which water cleaves the ES covalent complex, reforming Ser195 and forming the second product

39
Q

The enzymatic action of chymotrypsin involves two substrates and is thus called a _________ reaction. These reactions can occur by single displacements or double displacements. ___________ reactions occur by double displacement, and they are often described using Cleland notation.

A

Bisubstrate

Ping Pong reactions

40
Q

Trypsin and elastase are homologs of chymotrypsin. If each of these proteases cleave peptide bonds in the same way, what dictates the specificity of each?

A

Differences in the protease pockets

41
Q

Chymotrypsin binds substrates based on _____________ pocket. Trypsin binds substrates based on ____________ pocket.

A

Hydrophobic

Negatively charged

42
Q

Chymotrypsin works in the small intestine to aid in digestion of proteins. It is synthesized in the pancreas in the form of a zymogen. What is a zymogen?

A

An inactive protein

43
Q

Why is the formation of chymotrypsin as a zymogen important?

A
44
Q

The formation of zymogens is a method of ___________ enzyme activity.

A

Regulating

45
Q

_____________ proteins can also regulate enzyme activity.

A

Inhibitor

46
Q

An example of oxidoreductase is ______________.

A

Alcohol dehydrogenase

47
Q

REDOX reactions require enzymes with ___________. Many use nicotinamid adenine dinucleotide (NAD+). Alcohol dehydrogenase is one such enzyme. In the mechanism, electrons move in the form of the hydride ion (:H-).

Ethanol + NAD+ –> Acetylaldehyde + NADH + H+

A

Cofactors

48
Q

Ethanol + NAD+ –> Acetylaldehyde + NADH + H+

Ethanol is _____________. NAD+ is ___________. Therefore, NAD+ is the _______________ agent, and ethanol is the ______________ agent.

A

Oxidized

Reduced

Oxidizing agent

Reducing agent

49
Q

What is the important point about oxidoreductase mechanism?

A

Zn2+ stabilizes the negative charge on oxygen of substrate to facilitate the reaction

50
Q

When a metal ion is used to help in enzymatic mechanicms, the catalysis is called __________________ catalysis.

A

Metal-ion

51
Q

Be sure to understand the mechanism of alcohol dehydrogenase, an oxidoreductase

A
  1. Zn2+ sits in active site
  2. Base deprotonates ethanol (alcohol), and Zn2+ stabilizes negative charge
  3. Negative charge kicks back onto carbon, ultimately releasing a hydride ion (:H-), which is extremely reactive
  4. The hydride attacks the coenzyme’s aromatic ring system
  5. Another hydrogen is attacked to the coenzyme, here NAD+, with appropriate shifts in ring structure
52
Q

DNA polymerase is an enzyme _____________ that catalyzes a phosphoryl group transfer reaction as it synthesizes DNA. The enzyme requires two Mg2+ ions in the active site; therefore, it is an example of _____________ catalysis.

A

Transferase

Metal-ion catalysis

53
Q

The role of Mg2+ in DNA polymerase mechanism is to stabilize the negative charge on the phosphate groups and to stabilize the negative charge that results from _______________ attack of the C3’ __________ group.

A

Nucleophilic attack

Hydroxyl

54
Q

An example of a lysase is ________________. It is an enzyme that catalyzes te rapid conversion of Co2 and H20 to bicarbonate and a proton in aqueous solution. It is classified as a _____________ because it contains a tightly bound metal ion cofactor that is essential for the reaction.

A

Carbonic anhydrase

Metalloenzyme

55
Q

The metalloenzyme of carbonic anhydrase is ________.

A

Zn2+

56
Q

The role of Zn2+ in carbonic anhydrase is to facilitate the acidification of water so that a proton can leave, providing the source of ____________ needed for the reaction to occur.

A

Hydroxide

57
Q

CO2 + H20 –> HCO3- + H+

This reaction is catalyzed by…?

A

Carbonic anhydrase, a lysase

58
Q

Three invariant histidines are required in the metal-ion catalysis with carbonic anhydrase. Be familiar with the mechanism.

A
59
Q

An example of an isomerase we explored in class was phosphohexose isomerase, which catalyzes the reversible isomerization of glucose-6-phosphate, a aldehyde monosaccharide, to _______________________, a ketone monosaccharide.

G6P <—-> F6P

A

Fructose-6-phosphate

  1. A base deprotonates C2
  2. A double bond forms between C2 and C1
  3. Oxygen from the carbonyl of C1 abstracts a protein from an acid
  4. A base deprotonates the C2 hydroxyl group
  5. The double bond between C2 and C1 abstracts a proton from an acid
60
Q

An example of a ligase is aminoacyl-tRNA synthetase. It catalyzes the esterification of an amino acid to its corresponding tRNA. The amino acid is attached to the 3’ OH of the terminal amino acid via ester linkage.

Most organisms have an amino-acyl tRNA synthetase for each amino acid

  1. An enzyme-bound intermediate (aminoacyl-AMP) is formed
  2. The aminoacyl group is transferred to its specific tRNA
A
61
Q

The reaction catalyzed by aminoacyl-tRNA synthetase is

amino acid + tRNA + ATP –> amino-acyl-tRNA + PPi + Amp –> 2Pi

The formation of inorganic phosphate from pyrrophosphate is the driving force of the reaction

A
62
Q
A

Biochemistry I (8 decks)

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