enzymes Flashcards

1
Q

What are some examples of processes that would take a very long time in the absence of enzymes?

A

○ Extracting energy from glucose
○ Burning hydrocarbon fuels
○ Nitrogen fixation
○ Digesting food

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2
Q

What are the two ways a reaction can be accelerated?

A
  1. Adding heat: Increases the number of reactants with sufficient energy to overcome the activation energy barrier.
  2. Adding a catalyst: Decreases the activation energy barrier but does not react.
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3
Q

What are enzymes?

A

○ Mostly proteins.
○ Have primary, secondary, tertiary, and quaternary structures.
○ Typically globular proteins.
○ Their structure is determined by the same forces that govern protein structure (e.g., hydrogen bonds, Van der Waals interactions).

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4
Q

What are the key characteristics of enzymes as catalysts?

A

○ They accelerate reaction rates.
○ They are regenerated at the end of the reaction.
○ Can increase reaction rates by 106 to 1020 fold.
○ Highly specific for their substrates.
○ Do not produce side reactions.

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5
Q

What are some common features of enzyme nomenclature?

A

○ Enzyme names typically end in “-ase”.
○ The name often describes the process, substrate, product, or chemical reaction.

Ex: Citrate synthase, alcohol dehydrogenase, pyruvate decarboxylase.

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6
Q

How are enzymes regulated?

A

Enzymes are regulated through
* allosteric regulation
* competitive inhibiton
* reversible covalent modification
* gene expression and subcellular localization
* feedback inhibition
* Ionic signals
* substrate availability

Their structures are flexible & changing their shape can alter their function

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7
Q

What determines the speed of a thermodynamically favorable biochemical reaction?

A

the size of the activation energy barrier.

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8
Q

Do enzymes affect the free-energy change (ΔG) of a reaction?

A

No, they only affect the activation energy.

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9
Q

How do enzymes reduce the free energy of the transition state?

A

○ Removing substrates from aqueous solution (desolvation).
○ Proximity and orientation effects.
○ Taking part in the reaction mechanism.
○ Stabilizing the transition state.

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10
Q

What is the active site of an enzyme?

A
  • The region of the enzyme where catalysis occurs.
  • Usually a small portion of the protein.
  • Contains key amino acids involved in binding and catalysis.
  • Determines affinity, specificity, and rate of the reaction.
  • Complementary to the substrate or transition state.
  • Shape, hydrophobic interactions, hydrogen bonds, and ion pairs contribute to substrate binding.
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11
Q

Describe the lock and key model of enzyme-substrate binding.

A

This model suggests a rigid interaction where the enzyme’s active site is a perfect fit for the substrate, like a lock and key.

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12
Q

Describe the induced fit model of enzyme-substrate binding.

A

This model proposes that the active site changes shape as the substrate binds, leading to a more precise fit

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13
Q

What are the advantages of desolvation in enzyme catalysis?

A
  • Removal of the water shell accelerates reactions.
  • Enhances polar interactions (hydrogen bonds, ion pairs).
  • Prevents side reactions
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14
Q

How do proximity and orientation effects contribute to catalysis?

A

○ Chemical reactions require substrates to come together in the correct orientation.
○ Active sites bind substrates close to each other (proximity) and in the correct geometry (orientation).
○ This can enhance reaction rates by up to a thousandfold.

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15
Q

How can enzymes participate in reactions?

A

○ Some enzymes use functional groups in the active site to participate in reactions.
○ These groups may act as:
■ Acid/base catalysts
■ Covalent catalysts
■ Metal ion catalysts
○This can be achieved through amino acids or cofactors (or both).

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16
Q

What are cofactors?

A
  • Molecules or compounds that enhance the reactive potential of polypeptides.
  • They provide new reactive functional groups. Can be:
    ■ Metal ions (e.g., Fe, Zn, Cu, Na, Mg, K)
    ■ Coenzymes (organic molecules)
    ● Cosubstrates (e.g., NAD+)
    ● Prosthetic groups (e.g., FAD)
17
Q

What is the difference between an apoenzyme and a holoenzyme?

A
  • Holoenzyme: The functional enzyme with its prosthetic group attached.
  • Apoenzyme: The protein portion of an enzyme without its prosthetic group.
18
Q

How does transition state stabilization contribute to catalysis?

A

○ Binding the transition state lowers the activation energy (ΔG‡).
○ Enzyme active sites bind the transition state better than the substrate.
○ Transition state analogs are potent inhibitors because they bind with higher affinity than the substrate.

19
Q

What is V0 in enzyme kinetics?

A

Initial velocity, or the rate of product formation at the beginning of a reaction.

20
Q

What is Vmax in enzyme kinetics?

A

The maximum rate of product formation when the enzyme is saturated with substrate

21
Q

What is Km in enzyme kinetics?

A

The Michaelis constant.
○ Analogous to Kd in ligand binding.
○ Reflects the affinity of the enzyme for its substrate.
○ A smaller Km indicates higher affinity.
○ V0 = 50% Vmax when [substrate] = Km.

22
Q

What are some mechanisms for regulating enzyme activity that affect the intrinsic activity of the enzyme?

A

○ Competitive inhibition
○ Allostery
○ Reversible covalent modification
○ Ionic signals (e.g., Ca2+ ions)

23
Q

What are some mechanisms for regulating enzyme activity that do not affect the intrinsic activity of the enzyme?

A
  • Regulation of gene expression
  • Changes in subcellular localization
24
Q

How do competitive inhibitors work?

A

○ Bind reversibly to the active site.
○ Resemble the substrate or transition state but do not react.
○ Physically block the active site, preventing substrate binding.
○ Reduce the number of available active sites, leading to lower reaction rates.
○ Cause an apparent increase in Km.
○ Increasing substrate concentration can overcome competitive inhibition.
○ Vmax remains unchanged.

25
Q

Why are transition state analogs better competitive inhibitors than substrate analogs?

A

They bind to the enzyme with higher affinity, effectively blocking substrate binding

26
Q

What are allosteric enzymes?

A

○ Often oligomeric (multi-subunit) enzymes.
○ Exhibit cooperativity, similar to hemoglobin.
○ Show a sigmoidal relationship between substrate concentration and reaction velocity.
○ Have different states (T and R) with varying active site geometries.
○ Allosteric effectors can bind to sites other than the active site and affect the equilibrium between the T (low activity) and R (high activity) states.

Positive effectors stabilize the R state and increase enzyme activity
Negative effectors stabilize the T state, decreasing enzyme activity

27
Q

What is homoallostery?

A

The binding of a substrate molecule to one subunit of an allosteric enzyme, which affects the binding of substrate to other subunits.

28
Q

What is heteroallostery?

A

The binding of a molecule other than the substrate (an allosteric effector) to a site other than the active site, which modulates the enzyme’s catalytic activity.

29
Q

What are the two states of allosteric enzymes?

A

○ T state: Tense state, low activity
○ R state: Relaxed state, high activity

30
Q

How do allosteric activators and inhibitors affect enzyme activity?

A
  • Allosteric activators favor the R state (high activity).
  • Allosteric inhibitors favor the T state (low activity).
31
Q

What is reversible covalent modification?

A

○ Covalent modification of an amino acid residue that alters the 3° structure of a polypeptide, affecting enzyme activity.
○ Phosphorylation is the most common type, often occurring on Ser, Thr, or Tyr residues

32
Q

How does phosphorylation regulate enzyme activity?

A

○ Phosphorylation adds a phosphate group to an amino acid residue.
○ Increases the size, polarity, and negative charge of the residue.
○ Can either increase or decrease the activity of the target enzyme.

33
Q

What enzymes catalyze phosphorylation and dephosphorylation?

A

○ Protein kinases: Catalyze the phosphorylation of proteins using ATP.
○ Protein phosphatases: Catalyze the dephosphorylation of proteins by hydrolysis.

Both kinases and phosphatases are often regulated themselves

phosphorylation= adding a phosphate group
dephosphorylation = removal of a phospahet group