Enzymes

Question 1

Enzymes (as catalysts)

Answer 1

• Lower the activation energy
• Increase the rate of the reaction
• Do not alter the equilibrium constant
• Are not change or consumed in the reaction
• Are pH and temperature sensitive
• Do not affect the overall delta G of the reation
• Are specific for a particular reaction or class of reactions

Question 2

Oxidoreductases

Answer 2

• Catalyze oxidation-reduction reactions (transfer or electrons)
• Often have a cofactor that acts as an electron carrioer (NAD+ or NADP+)
• Reductant = electron donor
• Oxidant = electront acceptor
• “dehydrogenase” or “reductase”
• “oxidase”: Enzymes in which oxyge is the final electron acceptor

Question 3

Transferases

Answer 3

• Catalyze the movement of a functional group from one molecule to another
• Usually have “transferase” in name
• Kinases: Catalyze the transfer of a phosphate group, generally from ATP, to another molecule

Question 4

Hydrolases

Answer 4

• Catalyze the breaking of a compound into two molecules using the addition of water
• Many name for only their substrate (phosphatase = cleaves a phosphate group)
  
  • Peptidases, nucleases, and lipases

Question 5

Lyases

Answer 5

• Catalyze the cleavage of a single molecule into two products
• Do not require water as a substrate
• Can do reverse reaction: the synthesis of two molecules into a single molecule may also be catalyzed by a lyase, referred to as synthases

Question 6

Isomerases

Answer 6

• Catalyze the rearrangement of bonds within a molecule
• Some can also be classified as oxioreductases, transferases, or lyases
• Catalyze reaction between stereoisomers and constitutional isomers

Question 7

Ligases

Answer 7

• Catalyze the addition or synthesis reaction, generally between large similar molecules
• Often require ATP
• ***Synthesis of smaller molecule usually done by lyases (synthases)
• On test day = nucleic acid synthesis and repair

Question 8

Endergonic Reaction

Answer 8

Requires energy input

Delta G greater than zero

Question 9

Exergonic

Answer 9

Energy is given off

Delta G is less than zero

Question 10

Lock and Key Theory

Answer 10

• Less supported
• No alteration of the teritiary or quarternary structure is necessary upon binding the substrate

Question 11

Induced Fit Model

Answer 11

• Starts with a substrate and enzyme active site that don’t seem to fit together
• The shape of the enzyme becomes complementary only after the substrate begins binding to the enzyme
• Transition state is preferred

Question 12

Cofactors and coenzymes

Answer 12

• Non-protein molecules
• Usually carry charge through ionization, protonation, or deprotonation
• Usually kept at low concentration in cells, so they can be recruited only when needed
• Apoenzymes: Enzymes without their cofactors
• Holoenzymes: Enzymes containing their cofactor
• Prosthetic groups: Tightly bound cofactors or coenzymes that re necessaru for enzyme function
• Cofactors: Generally inorganic molecules or metal ions
  
  • Often ingested as dietary minerals
• Coenzymes: Small organic groups
  
  • Most are vitamins or derivatives of vitamins (NAD+, FAD, coenzyme A)
  • Water-soluble vitamins: B complex vitamins, C (abscorbic acid)
    
    • Must be replenished regularly because they are easily excrete
  • Fat-soluble vitamins: A, D, E, K

Question 13

v_max

Answer 13

• Maximum velocity
• The only way to increase v_max is by increasing the enzyme concentration
• Once v_max is reached, adding more substrate will not increase the rate of reaction

Question 14

Michaelis-Mentin Equation

Answer 14

• Relates the velocity of the enzyme to substrate concentration:
  
  • v = (v_max[S])/(K_m + [S])
• K_m = substrate concentration at which half of the enzyme’s active sites are full (1/2v_max)
• K_m is a measure of affinty of the enzyme for its substrate:
  
  • Lower K_m = higher affinity
  • Higher K_m = lower affinity
• K_m is intrinsic value and cannot be changed by changes in [S] or [E]
• Hyperbola shape:
  
  • When substrate concentration is less than K_m, changes in substrate concentration will greatly affect the reaction rate
  • When substrate concentration is greater than K_m, the reaction rate increases much more slowly as it approaches v_max
• Can be re-written using k_cat
  
  • _​v = (k_cat[E][S])/(K_m + [S])
• At very low substrate concentrations, where K_m >> [S]:
  
  • v = (k_cat/K_m)[E][S]

Question 15

k_cat

Answer 15

• Units (s^-1)
• Measures the number of substrate molecules “turned over” or converted to product, per enzyme per second
• v_max =

Question 16

Catalytic Efficiency

Answer 16

• Ratio of k_cat/K_m
• A large k_cat (high turnover) or a small K_m (high substrate affinity) will result in a higher catalytic efficiency, which indicates a more efficient enzyme

Question 17

Lineweaver-Burk Plots

Answer 17

• Double reciprocal graph of the Michaelis-Menten equation (1/v vs. 1/[S])
• x-intercept = -1/K_m
• y-intercept = 1/V_max
• Useful when determining the type of inhibition that an enzyme is experiencing

Question 18

Cooperativity

Answer 18

• Produce a graph
• Subunits and enzymes may exist in one of two states:
  
  • T: Low-affinity tense state
  • R: High-affinity relaxed state
• Binding of the substrate encourages the transition of other subunits from the T state to the R state
• Often regulatory enzymes in pathways
• Quantified by Hill’s coefficient

Question 19

Hill’s Coefficient

Answer 19

• Indicates the nature of binding by the molecule:
  
  • >1 = positively cooperative binding (after one ligand is bound, the affinity of the enzyme for further ligand(s) increases
  • <1 = negatively cooperative binding (after one ligand is bound, the affinity of the enzyme for further ligands decreases)
  • =1 = the enzyme does not exhibit cooperative binding

Question 20

Temperature Effect on Enzyme

Answer 20

• Enzyme-catalyzed reactions tend to double in velocity for every 10 degrees Celcius increase in temperature until the optimum temperate is reached
• After this, activity falls off sharply

Question 21

pH Effect on Enzymes

Answer 21

• pH affects the ionization of the active site and can lead to denaturation of the enzyme
• Human Blood:
  
  • Optimal = 7.4
  • Acidemia = < 7.35
  • EXCEPTION: Digestive tract enzymes operate around pH = 2; pancratic enzymes operate around pH=8.5
• *

Question 22

Types of Reversible Inhibition

Answer 22

Competitive

Non-competitive

Mixed

Uncompetitive

Question 23

Competitive Inhibition

Answer 23

• Simply involves occupancy of the active site
• Can be overcome by adding more substrate (higher substrate-to-inhibitor ratio)
• Does not alter the value of v_max because if enough substrate is added, it will outcompete the inhibtor and be able to run the reaction at maximum velocity
• Increases K_m value because substrate concentration has to be higher to reach half the maximum velocity in the presence of the inhibitor

Question 24

Noncompetitive Inhibition

Answer 24

• Noncompetitive inhibitors bind to an allosteric site instead of the active site, which induces a change in enzyme formation
  
  • Allosteric sites = non-catalytic
• Cannot be overcome by adding more substrate
• Noncompetitive inhibitors bind equally well the to the enzyme and the enzyme-substrate complex
• Decreases v_max because there is less enzyme available to react
• Does not alter the value of K_m because any copies of the enzyme that are still actuve maintain the same affinity for their substrate

Question 25

Mixed Inhibition

Answer 25

* When an inhibitor can bind to either the enzyme or the enzyme-substrate complex, but has **different affinity** for each * Bind at an **allosteric site** * Alters K_m depending on affinity preference: * **If inhibitor preferentially binds to the enzyme: K_m increases** * **If the inhibitor preferentially binds to the enzyme-substrate complex, K_m decreases** * **v_max decreases**

Question 26

Uncompetitive Inhibition

Answer 26

* Uncompetitive inhibitors only bind to the enzyme-substrate complex and essentially lock the substrate in the enzyme, preventing its release * Lower K_m value (increase affinity between enzyme and substrate) * Decrease V_max * Parallel lines on Lineweaver-Burk plot of curves for activity with and without an uncompetitive inhibitor are parallel _​

Question 27

Summary of Reversible Inhibitors and their Effect on K_m and V_max

Answer 27

Question 28

Irreversible Inhibition

Answer 28

The active site is made unavailable for a prolonged peiod of time or the enzyme is permanently altered. Prime drug mechanism

Question 29

Zymogen

Answer 29

* Danergous enzymes (if not tightly controlled) are often secreated as inactive zymogens * Zymogens contain **a catalytic (active) domain and regulatory domain**; the regulatory domain must be either removed or altered to expose the active site * **"ogen"**