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BMSC 200 > Module 6 > Flashcards

Module 6 Flashcards

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1
Q

Co factors

A

Inorganic ions like Mg2+ and Fe2+

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2
Q

Co enzymes

A

Complex molecules (Vitamins)

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3
Q

Prosthetic Groups

A

Co enzyme or Co factor that is tightly associates with the enzyme is called a prosthetic group
Different enzymes that use the same coenzymes usually perform similar types to reactions

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4
Q

Catalysts

A

Lower the amount of energy required for a reaction to proceed
Sped up attainment of equilibrium but do not change the equilibrium
Are uncharged by the reaction ; recycled to participate in another reaction

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5
Q

Speed

A

Enzymes are often much faster than chemical catalysts, some approaching catalytic perfection

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6
Q

Conditions

A

Many chemical catalysts require extremes of temperature, pressure and pH while enzymes function under physiological conditions

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7
Q

Specificity

A

Enzymes have a higher degree of specificity than most chemical catalysts

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8
Q

Regulation

A

unlike chemical catalysts many enzymes are responsiveness to the dynamic needs of the cell and organism

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9
Q

Circe effect

A

Enzyme rates of catalysis can approach the physical limit of rates of diffusion of molecules in solution
Some enzymes have rate determining steps that are roughly as fast as the binding of substrates to the enzymes
Some enzymes are able to catalyze reaction faster then predicted by diffusion control limits

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10
Q

Equilibrium and ES complex

A

E + S -> ES -> E+P

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11
Q

Substrate

A

Molecule acted upon by the enzyme

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12
Q

Product

A

The molecule produced by the enzyme

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13
Q

Active site

A

The portion of Enzyme responsible for binding the substrate to form the enzyme substrate complex
Active site is a 3D cleft formed from different parts of the polypeptide chain
Active site represents just a small part of the enzyme
Active sites are unique to microenviroments
Substrates are bound to enzymes by multiple weak interactions
Specificity of substrate binding depends on the precisely defined arrangement of atoms in the active site. Enzymes and their active sites cab be quite flexible. Substrate binding can cause induced fit or conformational change

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14
Q

delta g negative

A

Spontaneous. the exaction will proceed without the input of energy and the reaction releases energy (Exergonic)

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15
Q

delta g positive

A

An input of free energy is requires to drive such reactions (Endergonic)

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16
Q

Free Energy in Enzymes

A

Activation energy, Delta G between S and P determined the rate at which equilibrium is achieved
Enzymes provide an alternate, lower energy pathway between the substrate and the product lowering delta G

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17
Q

The relationship between rate of reaction and activation energy is

A

Inverse and Exponential

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18
Q

Difference in free energy between S and P

A

Determines the Equilibrium of the reaction

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19
Q

Enzymes rate enhancements and Equilibrium

A

Enzymes provide a lower energy pathway between the substrate and product decreasing the activation energy for the Transition state and increasing rate of reaction
Enzymes do not effect the difference in free energy between the substrate and product and therefore do not influence the equilibrium of reaction

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20
Q

What are the forces that lower the Activation energy

A

Binding effects
Chemical effects

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21
Q

Binding effects

A

Substrate binding
Transition state Stabilization

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22
Q

Chemical effects

A

Acid/base catalysis
Covalent Catalysis

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23
Q

Binding Effects

A

Binding of substrate in the active sites provides specificity and catalytic power
Catalytic mechanisms limited to binding properties can still increase reaction rates by over 10,000 fold

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24
Q

Substrate Binding

A

Reduces entropy (Decreased freedom of motion of two molecules in solution)
Alignment of reactive functional groups of the enzyme with the substrate
Desolation of the substrate (Removal of water molecules) to expose reactive groups
Distortion of substrates
Induced fit of the enzyme in response to Substrate binding

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25
Transition State Stabilization
An increased interaction of the enzyme and substrate occurs in the transition state The essence of catalysis is stabilization of the transition state The Enzyme distorts the substrate, forcing it toward transition state The Active site is complementary to the transition state in shape and chemical character
26
Transition state analogs (TSAs)
Stable compounds that resemble unstable transition states
27
Competitive inhibitors
Inhibitors are molecules that bind to the active site of an enzyme, they tend to resemble the substrate molecule TSAs can bind the active site of a target enzyme active site with high affinity preventing substrate binding
28
Chemical effects
After Substrate binding, the enzyme can act upon the substrate to promote formation of the product The active site often contains chemically reactive side chains
29
Side chains include
Polar ionizable such as Asp, Glucose, His, Cys, Tyr, Lys, Arg, Ser
30
Acid Base Catalysis
Reaction acceleration is achieved by catalytic transfer of a proton The side chains of some amino acids can act either as bases to acids pKa of a functional group is influenced by the chemical microenvironment Functional groups of amino acids cab have different pKas within the active site which make them more suitable for acid/base catalysis
31
What is often involved with Acid / base Catalysis
Histidine with a pKA near physiological pH
32
Covalent Catalysis
As a part of the reaction mechanism the substrate is covalently bound to the enzyme to form a reactive intermediate Covalent Catalysis often involves 2 steps, the first which forms a covalent linkage to the enzyme, the second to regenerate the free enzyme
33
Step one of Covalent Catalysis of Sucrose Phosphorylase
Glucosyl residue is transferred to enzyme Glucose - Fructose + Enz -> Glucosyl-Enz + Fructose
34
Step two
Glucose is transferred to Phosphate Glucosyl-Enz + P -> Glucose 1-Phosphate +Enz
35
Velocity of Reaction
V= P/t
36
The activity of enzymes is
Temperature and pH sensitive
37
Kinetics of enzymes
Initial velocity at the beginning of an enzyme catalyzed reaction prior to product accumulation K1 and k-1 represent rapid non covalent interactions between enzyme and substrate K2 is rate constant of formation of product from ES. Vo = [ES]k2
38
Michaelis Menton Kinetics
Rate of formation is equal to the rate of its breakdown [E][S]k1=[ES]K-1+[ES]k2
39
Michaelis Menton Plot
Describes the relationship between substrate concentration and initial velocity Vo = Vmax[S] / Km+[S]
40
Km
Concentration of substrate requires to reach 1/2 Vmax Km provides an accurate approximation of the in vivo substrate concentration It means enzymes are working at half their maximum velocity
41
Max
Maximum Velocity of an enzyme
42
When [S] < Km
Enzymes are highly sensitive to changes in substrate but have very little activity
43
When [S] > Km
Enzymes have high activity but are insensitive to changes in substrate concentration
44
When [S] = [Km]
Enzyme has significant activity and is responsive to changes in substrate concentration
45
Lineweaver Burk Plots
Also describe the relationship between [S] and Vo Are a double reciprocal plot of 1/Vo vs 1/[s] Are a more precise method of analysis of kinetic data are used to determine Vmax and Km 1/Vo = km/Vmax[S] + 1/Vmax
46
Enzyme turnover number
Also called kcat Equals the number of molecules of substrate converted to product per unit time under saturating conditions Is calculated by Vmax / [Et]
47
Reversible Enzyme Inhibition
An inhibitor is a compound that binds to an enzyme to interfere with its activity Inhibitor can prevent formation of ES or the breakdown to E and P Reversible inhibitors bind to enzyme by non covalent interactions
48
Competitive inhibitor
Competitive Inhibitors resemble the substrate and compete with the substrate for binding the active site Competitive inhibitors bind only the free enzyme The effect of competitive inhibitors can overcome with an excess of substrate Vmax is same bit Km is increased
49
Uncompetitive Inhibitor
Only bind to ES complex Vmax is decreased by conversion of ES to ESI which cannot form a product Uncompetitive inhibitors reduce [ES] As E binds S to replenish ES this apparent increase in affinity of the E for S causes a decrease in Km
50
Non Competitive Inhibitor
Non competitive binds to E and ES Vmax is decreased with no change in Km Do not influence S so no change in Km Reduces the number of active enzyme molecules
51
Serine Proteases
Serve as digestive enzymes, including trypsin chymotrypsin and elastase that cleave peptide bonds in protein structures Members of this family share similar sequences and active site residues Are synthesized and stored in the pancreas as inactive zymogens to prevent damage to cellular proteins
52
Thrombin Cleaves
Arg-Gly (RG)
53
Trypsin Cleaves
Lys Arg (RL)
54
Chymotrypsin cleaves
Phe, Tyr or Met (FYM)
55
Elastase cleaves
Glycine and Alanine (GA)
56
Papain
Cuts all peptide bonds
57
Serine protease (Catalytic Triad)
Asp, His, Ser Each residue plays a specific role in the catalytic triad
58
histidine
Acts to accept and donate a proton at each of the two stages of the reaction mechanism (Acid base catalysis)
59
Aspertate
Stabilizes the positively charged Histidine to facilitate serine ionization
60
Serine
Attacks the carbonyl group of the peptide bond to be cleaved (Covalent Catalysis)
61
Chymotryosin Phase 1 step 1
Acid/base: Histidine acts as a base to extract proton from hydroxyl of Ser. This activates the oxygen of the hydroxyl group
62
Phase 1 Step 2
Covalent: Formation of a covalent linkage from the hydroxyl group of the Ser to the carbonyl carbon of the peptide bond to be cleaved in the structure
63
Phase 1 Step 3
Acid/Base: Histidine acts as an acid to donate a proton to the amine group of the peptide bond to be cleaved, this cuts the substrate peptide into 2 pieces
64
Phase 2 Step 1
Acid/Base: Histidine acts as a base to extract a proton from a water molecule, activating the oxygen of this molecule
65
phase 2 step 2
Covalent: Activated water molecule attacks the point of covalent linkage between enzyme and substrate
66
Phase 3 step3
Acid/base: Histidine acts as an acid to donate a proton to reform the hydroxyl group of serine
67
Allosteric Enzymes
Serves as information sensors to coordinate cellular metabolism Are regulated by interaction with metabolic intermediates Are regulated by allosteric modulators that bind non covalently at sites other than the active site Are quaternary Structures Slow Do not obey Michaelis kinetics

BMSC 200 (10 decks)

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