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Biochemistry > Lesson 7: Enzyme Mechanism > Flashcards

Lesson 7: Enzyme Mechanism Flashcards

1
Q

Types of Catalytic Strategies

A

Covalent Catalysis
Nucleophilic Catalysis
Electrophilic Catalysis
Specific Acid-Base
General Acid-Base
Metal Ion Catalysis

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2
Q

Covalent Catalysis

A

-Forms a transient covalent bond.
-Can cleave bonds between the substrate.
-Retrieve catalyst via hydrolysis

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3
Q

Nucleophilic Catalysis

A

-Nucleophilic centers (Nu-) on the enzyme attack electrophilic targets on substrate

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4
Q

Electrophilic Catalysis

A

-Involve coenzymes that form electrophiles (El+)

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5
Q

Specific acid-base

A

-Involves H+ or OH-
-Not dependent on buffer concentration

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6
Q

General acid-base

A

-H+ or OH- is formed in the transition state by another molecule

-Use acidic polar amino acids

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7
Q

General Acid Catalysis Mechanism

A
  1. Carbonyl bond attacks the H from the enzyme
  2. To maintain two bonds in O of carbonyl, one bond transfers to the C-H bond
  3. CH3 becomes C=CH2 as other H gets removed.
  4. Acid reacts with water to retrieve the enzyme.
  5. Product+Enzyme+OH-
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8
Q

General Basic Catalysis Mechanism

A
  1. Base gets the H from CH3
  2. H bond connecting to CH2 moves to the latter, forming C=CH2
  3. One bond from the carbonyl group gets transferred to oxygen, becoming O-.
  4. O- is stabilized by H+.
  5. Product+Base+H+
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9
Q

Metal ion catalysis

A

-Use of metals as redox cofactors
-Stabilize formation of negative (-) charge
-Act as a nucleophile at neutral pH

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10
Q

Metalloenzymes

A

Metal ion tightly bound

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11
Q

Metal-activated enzymes

A

Metal ion loosely bound

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12
Q

Lysozyme

A

-Cleaves peptidoglycan layer of the cell wall of bacteria

-Hydrolyzes glycosidic bond between N-acetylmuramic acid (NAM or MurNAc) and N-acetylglucosamine (NAG or GlcNAc)

-Mechanism involves two successive SN2 reactions

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13
Q

Gram-negative peptidoglycan layer

A

Has an outer wall covering the thin peptidoglycan layer

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14
Q

Gram Positive Peptidoglycan Layer

A

No outer layer, peptidoglycan layer is exposed and easier to access when staining

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15
Q

Binding Site

A

-Accomodate 6 sugar residues
-Cleavage occurs between D and E sites
-Sugar (NAM) is distorted at D site
-Alternate between NAM and NAG

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16
Q

Catalytic Residues for Lysozyme

A

-Asp52(D52): Nucleophile (undergoes Nu covalent catalysis)

-Glu35(E35): General Acid-Base

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17
Q

Chymotrypsin

A

Cuts C-side of Phe, Trp, Tyr, and Leu

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18
Q

Proteases

A

Proteins that hydrolyze peptide bonds

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19
Q

Serine Protease

A

Use Ser as the nucleophile

20
Q

Oxyanion hole

A

-Very reactive
-Tetrahedal intermediate

21
Q

Nucleophile

A

Ser195

22
Q

Catalytic Triad

A

Ser195- Nucleophile
Asp102- Orients H57
His57- General Acid-Base Catalyst

23
Q

S1 pocket (hydrophobic pocket)

A

-For specificity
Cuts nuetral nonpolar amino acids

24
Q

Burst Kinetic Study of Chymotrypsin

A
  1. Acylation
    -Faster because there’s a lot of enzymes that can cleave the bond
  2. Deacylation
    -Slower because it waits for the presence of water to go back to its original form.
25
Q

Chymotrypsin Mechanism

A
  1. Nucleophilic attack of Ser195 to peptide bond, undergoes covalent catalysis; forms a tetrahedal intermediate.
  2. Acylation, amine group separated from the carbonyl with catalyst attached to it. Amine group is stabilized by H from His57.
  3. Deacylation, OH- of water (other H comes from His57) acts as a nucleophile to form tetrahedal intermediate, breaking its bond with the enzyme.
  4. O- in the enzyme is stabilized using His57.
  5. Product formation and retrieval of enzyme success!
26
Q

Substrate level control

A

Rate depends on substrate availability
-No suubstrate, no enzyme activity

27
Q

Genetic Control

A

Determines the amount of gene present
-Gene is responsible for producing enzymes.

28
Q

Induced Enzymes

A

Enzymes produced by the gene to accomodate for the number of substrate (can be more or less enzymes)

29
Q

Feedback control/allosteric control

A

-Regulation at committed steps (irreversible reaction) of pathways
-Inhibition by one of its pathway’s product
-Mediated by allosteric enzymes wherein it binds in the alloseteric site since they are not complementary

30
Q

Covalent modification

A

Reversible covalent attachment of a chemical group

31
Q

Zymogems (proenzymes)

A

-Inactive precursors of enzymes
-Converted into their active forms via proteolytic enzymes
-Activation via irreversible modification

32
Q

Isoenzymes

A

Enzymes with slightly different subunits

33
Q

Allosteric Regulation Properties

A

-Sigmoidal Michealis-Menten Curve
-Cooperativity, has more than one subunit

34
Q

T-State

A

-Tense/taut
-low affinity state (substrate)

35
Q

R-state

A

-Relaxed
-High affinity state (substrate)

36
Q

Covalent Modification Various Types of Reactions

A

-Phosporylation
-Uridylation
-Methylation
-Adenylation
-ADP-ribosylation
-Disulfide bond formation

37
Q

Kinases

A

-Adds P group to OH-containing amino acids (such as Ser, Thr, Tyr)
-Transferase
-Phosporylated enzyme is not equal to active enzyme

38
Q

Phosphatases

A

-Removes P group
-Hydrolase (use water to cleave P group and enzyme)
-Dephosporylated enzyme is not equal to active enzyme

39
Q

Enteropeptidase

A

-Controls trypsin production

40
Q

Trypsin

A

-Cuts C-side of Arg and Lys (Basic)
-S1 Speicificity: Polar acidic (opposite charges)
-Activates trypisinogen to create more trypsin and other enzymes

41
Q

Proelatase active enzyme

A

Elatase

42
Q

Prolipase active enzyme

A

Lipase

43
Q

Chymotrypsinogen active enzyme

A

Chymotrypsin

44
Q

Procarboxypeptidase

A

Carboxypeptidase

45
Q
A

Biochemistry (6 decks)

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