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BMS1. Enzymes (PATEL) > Enzymes Part 1 > Flashcards

Enzymes Part 1 Flashcards

1
Q

The 6 classes of enzymes:

A
  1. oxidoreducatases
  2. transferases
  3. hydrolases
  4. lyases
  5. isomerases
  6. ligases
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2
Q

Oxidoreducatases catalyze:

A

ox-redox reactions

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3
Q

Transferases catalyze:

A

transfer of C-, N-, or P- containing groups

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4
Q

Hydrolases catalyze:

A

cleavage of bonds via the addition of water

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5
Q

Lyases catalyze:

A

cleavage of C–C, C–S, and certain C–N bonds,

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6
Q

Isomerases catalyze:

A

racemization of optical or geometric isomers

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7
Q

Ligases catalyze:

A

formation of bonds between carbon and O, S, N coupled to hydrolysis of high-energy phosphates

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8
Q

Enzymes are:

A
  • protein catalysts that increase the velocity of a chemical reaction, and are not consumed during the reaction
  • NOTE: some RNA can act as catalysts - these are called ribozymes
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9
Q

General Enzyme Properties:

A
  • proteins
  • catalysts (are regenerated)
  • highly specific
  • able to be regulated
  • Do not change overall free energy of reaction
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10
Q

The set of enzymes made in a cell determines …

A

which metabolic pathways occur in that cell.

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11
Q

A holoenzyme is:

A

an active enzyme bound with its nonprotein component

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12
Q

An apoenzyme is:

A

an enzyme not bound to its nonprotein component that is inactive

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13
Q

Cofactors:

A

a nonprotein component required by an enzyme to function that is a metal ion such as Zn2+ or Fe2+

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14
Q

Coenzymes:

A
  • a nonprotein component required by an enzyme to function that is a small organic molecule
  • mostly derived from vitamins
  • Can be:
    1. co-substrates (transiently bound; dissociate from enzyme during altered state)
    2. prosthetic groups (permanently bound)
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15
Q

Cosubstrate:

A
  • a coenzyme that is only transiently associated with an enzyme
  • dissociates from the enzyme during an altered state
  • non-covalently bound to enzyme
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16
Q

Prosthetic Group:

A
  • a coenzyme that is permanently associated with an enzyme and returned to its original form
  • covalently bound to enzyme
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17
Q

Can cofactors/coenzymes limit rate of reactions?

A

Yes:

  • if not enough is available, it will limit the amount of active anzymes
  • some cofactors/coenzymes need to be regenerated at the end of a reaction. Reaction rates can slow during regeneration.
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18
Q

Cofactors provide functionalities that are not found in…

A
  • the natural amino acids
  • cofactors = small metal ions

NOTE: cysteine is the only amino acid that can participate in ox/redox reactions.

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19
Q

Isozymes:

A
  • Have different primary structures or amino acid sequences, but catalyze the same chemical reaction and act upon the same substrate(s)
  • allow for fine tuning of metabolic need based on the specific tissue
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20
Q

Isozymes have different:

A
  • kcat and Km values and temperature and pH dependencies
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21
Q

Measurement of isozyme levels can aid in:

A
  • diagnosis of certain diseases/injuries
    • i.e. LDH H4 and MB creatinine kinase levels after myocardial infarction
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22
Q

Lock and Key Model:

A
  • predefined active site
  • states that enzymes and substrates must fit together like a lock and key in order for the reaction to occur/be catalyzed.
  • model has been replaced by induced fit model
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23
Q

An enzyme Active Site is:

A
  • a 3D cleft (pocket) formed by catalytic amino acids that come from different parts of the protein sequence
  • the catalytic amino acid side chains line the active site and participate in substrate binding and catalysis
24
Q

Catalytic amino acids:

A
  • line the active site of an enzyme
  • participate in substrate binding and catalysis
  • are not sequential in the amino acid sequence of an enzyme - come together to form the active site after protein folding occurs to form the tertiary structure.
25
Q

In comparison to the total enzyme structure, the active site occupies:

A
  • a small volume of the total enzyme
  • Amino acids not involved in the active site provide the scaffolding/stabilization of the active site
    • ensures stable conformation of the active site
26
Q

Mutations in the catalytic amino acids of the active site are often:

A
  • fatal
  • mutations in the non-catalytic amino acids often lead to disease, but are not immediately fatal. They cause changes to the active site conformation and, therefore, the overall enzyme function
27
Q

Binding at the active site is:

A
  • reversible
  • both substrate and product can bind to the active site
28
Q

Substrate and active site amino acids interact:

A
  • non-covalently through:
  1. hydrogen bonds
  2. hydrophobic interactions
  3. ionic bonds
  4. dipole-dipole bonds
  • all of these weak interactions add up to allow tight enzyme-substrate binding
29
Q

The stronger the enzyme-substrate interaction, the:

A
  • longer the substrate stays in the active site of the enzyme
  • this can affect the reaction rate, as product may not easily dissociate/eject from the active site
30
Q

Character of the active site:

A
  • nonpolar
    • this enhances the substrate binding by increasing electrostatic interactions
31
Q

The noncovalent interactions of the active site work:

A
  • cooperatively
  • i.e. the reaction will not occur unless all possible noncovalent interactions are met
    • explains why glucokinase only binds glucose and not galactose
32
Q

Lock and key model is inadequate in explaining:

A
  • enzyme specificity
  • lock and key model does not explain why water does not interact with certain enzymes
33
Q

Induced Fit Model:

A
  • flexible active site
  • only a specific substrate binds to the enzyme active site and induces a conformational change in the enzyme.
  • This stabilizes the active conformation of the enzyme (strong binding/affinity and fast rate)
34
Q

In the induced fit model, a specific substrate activates the enzyme through:

A
  • inducing a conformational change in the enzyme that:
    • orients catalytic groups on enzyme
    • tighter transition state binding (more stabilized transition state)
    • excluding H2O (if not a reactant)
35
Q

Enzymes can increase rates of reaction:

A

106 to 1017 fold

36
Q

Reaction rates are inversely proportional to:

A

the activation energy of the reaction

37
Q

Enzymes create a new reaction pathway with a lower activation energy through:

A
  • specific binding to the transition state structure
  • this stabilizes the transition state structure, lowering its energy, which allows more substrate to reach its energy level.
38
Q

Enzymes accelerate rates of reactions by:

A
  • stabilizing the transition state, which lowers the energy of the transition state and makes it more feasible for substrate to reach it.
39
Q

Enzyme active sites have tighter binding for _____ rather than ______.

A
  • tighter binding for the transition state rather than the substrate.
40
Q

All the catalytic amino acid binding ability is utilized at the time of:

A
  • transition state formation (maximum stabilization).
  • Only a few of the catalytic amino acids bind to the substrate.
41
Q

Enzymes do not change the ____ of a reaction.

A
  • thermodynamics/free energy/equilibrium
  • enzymes only increase the rate of reaction and decrease the time in which equilibrium is reached
42
Q

The three things that affect enzyme reaction velocity:

A
  1. substrate concentration
  2. pH
  3. temperature
43
Q

Enzyme rate of reaction and substrate concentration:

A
  • rate increases with increasing [S] until Vmax is reached.
  • Vmax = point where all enzyme active sites are saturated with substrate.
44
Q

Enzyme rate of reaction and temperature:

A
  • initial increases in temperature increase the rate of reaction by causing more collisions between E and S
  • drastic temperature increases will denature the enzyme, and reaction rate will fall
  • mutations can decrease the thermal stability of the enzyme
45
Q

Enzyme rate of reaction and pH:

A
  • At extremes of pH, the enzyme is irreversibly denatured and activity is permanently lost
  • pH affects the ionization of enzyme functional groups involved in catalysis or substrate binding (side chains involved in the active site) and can alter the substrate’s ionization state.
46
Q

Keq =

A

[P]/[S]

tells us how much substrate and product will be present at the equilibrium of a reaction

47
Q

The two catalytic strategies all enzymes use:

A
  1. proximity
  2. transition state stabilization
48
Q

Catalytic Strategy: Proximity

A
  • substrates need to 1) collide and 2) orient in the right positions. Enzymes bring together the substrates in the proper orientation, allowing the reaction to occur.
49
Q

Catalytic Strategies of enzymes (5):

A
  1. Proximity (all enzymes employ this strategy)
  2. Transition state stabilization (all)
  3. Covalent catalysis or nucleophilic catalysis (some)
  4. General acid-base catalysis (most)
  5. Metal ion catalysis (many)
50
Q

A potent nucleophile at the active site of an enzyme is created via:

A

acid-base catalysis

51
Q

Catalytic triad in chymotrypsin protease:

A
  • serine, histidine, and aspartate
  • serine becomes a nucelophile, aided by histidine
  • if you mutate one amino acid in the catalytic triad, you affect reaction rate and enzyme activity
52
Q

Oxyanion hole:

A
  • a space in the enzyme active site ready to bind a negatively charged group
  • In chymotrypsin, the oxyanion hole stabilizes the tetrahedral intermediate. The active site has more interactions with the tetrahedral intermediate than does the substrate. Allows the reaction to move forward.
53
Q

General Base:

A

a catalytic amino acid that can extract a proton

54
Q

General Acid:

A

a catalytic amino acid that can accept a proton

55
Q

What is the favorite amino acid for general acid/base catalysis?

A
  • hisitidine
  • pKa near physiological pH, so can act as both an acid and a base

BMS1. Enzymes (PATEL) (3 decks)

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