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BMSC 200 > Module 6 > Flashcards

Module 6 Flashcards

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
Q

Transition State Stabilization

A

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

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26
Q

Transition state analogs (TSAs)

A

Stable compounds that resemble unstable transition states

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27
Q

Competitive inhibitors

A

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
Q

Chemical effects

A

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
Q

Side chains include

A

Polar ionizable such as Asp, Glucose, His, Cys, Tyr, Lys, Arg, Ser

30
Q

Acid Base Catalysis

A

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
Q

What is often involved with Acid / base Catalysis

A

Histidine with a pKA near physiological pH

32
Q

Covalent Catalysis

A

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
Q

Step one of Covalent Catalysis of Sucrose Phosphorylase

A

Glucosyl residue is transferred to enzyme
Glucose - Fructose + Enz -> Glucosyl-Enz + Fructose

34
Q

Step two

A

Glucose is transferred to Phosphate
Glucosyl-Enz + P -> Glucose 1-Phosphate +Enz

35
Q

Velocity of Reaction

A

V= P/t

36
Q

The activity of enzymes is

A

Temperature and pH sensitive

37
Q

Kinetics of enzymes

A

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
Q

Michaelis Menton Kinetics

A

Rate of formation is equal to the rate of its breakdown

[E][S]k1=[ES]K-1+[ES]k2

39
Q

Michaelis Menton Plot

A

Describes the relationship between substrate concentration and initial velocity

Vo = Vmax[S] / Km+[S]

40
Q

Km

A

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
Q

Max

A

Maximum Velocity of an enzyme

42
Q

When [S] < Km

A

Enzymes are highly sensitive to changes in substrate but have very little activity

43
Q

When [S] > Km

A

Enzymes have high activity but are insensitive to changes in substrate concentration

44
Q

When [S] = [Km]

A

Enzyme has significant activity and is responsive to changes in substrate concentration

45
Q

Lineweaver Burk Plots

A

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
Q

Enzyme turnover number

A

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
Q

Reversible Enzyme Inhibition

A

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
Q

Competitive inhibitor

A

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
Q

Uncompetitive Inhibitor

A

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
Q

Non Competitive Inhibitor

A

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
Q

Serine Proteases

A

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
Q

Thrombin Cleaves

A

Arg-Gly (RG)

53
Q

Trypsin Cleaves

A

Lys Arg (RL)

54
Q

Chymotrypsin cleaves

A

Phe, Tyr or Met (FYM)

55
Q

Elastase cleaves

A

Glycine and Alanine (GA)

56
Q

Papain

A

Cuts all peptide bonds

57
Q

Serine protease (Catalytic Triad)

A

Asp, His, Ser
Each residue plays a specific role in the catalytic triad

58
Q

histidine

A

Acts to accept and donate a proton at each of the two stages of the reaction mechanism (Acid base catalysis)

59
Q

Aspertate

A

Stabilizes the positively charged Histidine to facilitate serine ionization

60
Q

Serine

A

Attacks the carbonyl group of the peptide bond to be cleaved (Covalent Catalysis)

61
Q

Chymotryosin Phase 1 step 1

A

Acid/base: Histidine acts as a base to extract proton from hydroxyl of Ser. This activates the oxygen of the hydroxyl group

62
Q

Phase 1 Step 2

A

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
Q

Phase 1 Step 3

A

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
Q

Phase 2 Step 1

A

Acid/Base: Histidine acts as a base to extract a proton from a water molecule, activating the oxygen of this molecule

65
Q

phase 2 step 2

A

Covalent: Activated water molecule attacks the point of covalent linkage between enzyme and substrate

66
Q

Phase 3 step3

A

Acid/base: Histidine acts as an acid to donate a proton to reform the hydroxyl group of serine

67
Q

Allosteric Enzymes

A

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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