L9-w5-Enzymes:Basic principles

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1. enzymes

1.1. biological catalyst

1.2. molecular devices that determine the patterns of chemical transformations

1.3. mediate the transformation of one form of energy to another

1.4. almost all enzymes are proteins

1.4.1. exception=RNases

1.4.1.1. enzymatic activity

1.4.1.2. ribozymes

1.5. most striking features

1.5.1. catalytic power

1.5.1.1. catalysis takes place at the active site of the enzyme

1.5.1.2. catalyze reactions by stabilizing transition states =highest energy species in rxn pathways

1.5.2. specificity

1.5.2.1. selectively stabilizing a transition state

1.5.2.1.1. enzyme determines which one of several potential rxns take place

1.6. highly effective because of their capacity to specifically bind a very wide range of molecules

2. Function of enzymes

2.1. accelerate biological rxns

2.2. rate enhancement by enzymes

2.2.1. measured in units of (kcat/kun)

2.2.2. Kcat

2.2.2.1. max # of enzymatic rxns by catalyzed/s

2.2.2.2. used to define enzyme rxns

2.3. e.g. carbonic anhydrase

2.3.1. catalyses hydration of CO2

2.3.1.1. removes CO2

2.3.1.2. rxn

2.3.1.2.1. CO2+H20=H2CO3

2.3.2. one of fastest enzymes known

2.3.3. each enzyme molecule can hydrate 10^6 molecules of CO2/second

2.3.4. catalyzed rxn is 10^7 x as fast as the uncatalyzed rxn

2.4. enzymes are highly specific in choice of reactants=substrates

2.4.1. enzyme usually catalyzes a single chemical rxn/a set of closely related rxns

2.5. example

2.5.1. catalase

2.5.1.1. 2H2O2>2H2O+O2

2.5.1.2. one of most rapid in the body

2.5.1.3. catalyzes reactive oxygen species (ROs)

2.5.2. proteolytic enzymes

2.5.2.1. enzymes catalyze proteolysis in vivo

2.5.2.2. proteolysis=hydrolysis of a peptide bond

2.5.2.2.1. into a carboxyl component and an amino component

2.5.2.3. also catalyzes a diff. but related rxn

2.5.2.3.1. hydrolysis of an ester bond

2.5.2.4. differ in degree of substrate specificity

2.5.2.4.1. e.g papain

2.5.2.4.2. trypsin

2.5.2.4.3. Thrombonin

2.5.3. DNA polymerase I

2.5.3.1. template directed enzyme

2.5.3.2. highly specific catalyst

2.5.3.2.1. precise in carrying out instructions given by the template

2.5.3.2.2. error rate = 1/1000 x

2.5.3.2.3. specificity due to

2.5.3.3. function

2.5.3.3.1. adds nucleotide strand to a DNA strand that is being newly synthesised

2.5.3.3.2. sequence of addition is based on sequence of nucleotides in template strand

2.5.3.4. example of why specificity is important

3. 6 major classes of enzymes

3.1. 1. Oxidoreductases

3.1.1. catalyzes oxidation and reduction rxns

3.1.2. e.g. lactate dehydrogenase

3.2. 2. Transferases

3.2.1. catalyzes grp transfers

3.2.2. e.g. NMP(nucleotide monophosphate) kinase

3.2.2.1. transfers a phosphate grp

3.3. 3. Hydrolases

3.3.1. hydrolysis rxns

3.3.1.1. transfer of functional grps to water

3.3.1.2. e.g. chymotrypsin

3.4. 4. Lyases

3.4.1. + or - of grps to form double bonds

3.4.2. e.g. Fumarase

3.5. 5. Isomerases

3.5.1. catalyzes isomerization rxns

3.5.1.1. intramolecular transfer of grps

3.5.2. e.g. triose phosphate isomerase

3.6. 6. Ligases

3.6.1. Ligation of two substances at the expense of ATP hydrolysis

3.6.1.1. amino acyl tRNA synthase

4. Cofactors

4.1. many enzymes require cofactors for activity

4.2. cofactors

4.2.1. small molecules that are essential for the catalytic activity of many enzymes

4.3. precise role varies with cofactor and enzyme

4.4. able to carry out rxns that cannot be performed by the standard set of 20 AAs

4.5. apoenzyme

4.5.1. an enzyme without its cofactor

4.6. holoenzyme

4.6.1. complete catalytically active enzyme

4.7. apoenzyme + cofactor=holoenzyme

4.8. subdivided into 2 grps

4.8.1. metal ions

4.8.1.1. e.g. K+,Zn2+

4.8.2. coenzymes

4.8.2.1. small organic molecules

4.8.2.2. vitamin derivatives

4.8.2.2.1. many diseases are associated with vitamin deficiencies

4.8.2.3. can be

4.8.2.3.1. tightly bound

4.8.2.3.2. loosely bound

5. Energy Transformation

5.1. enzymes can transform energy from one form into another

5.2. key activity in all living systems= ability to transform energy from one form to another

5.2.1. photosynthesis

5.2.1.1. Light>chemical bond energy

5.2.2. cellular respiration

5.2.2.1. mitochondria

5.2.2.2. free energy in small molecules(food)>free energy of ionic gradient>free energy of ATP

5.3. enzymes play key role in energy transformation

5.3.1. enzymes use the chemical bond E in ATP in diverse ways

5.3.1.1. examples

5.3.1.1.1. pumps in organelle and cell membranes

5.3.1.1.2. electrochemical gradients

5.3.2. play vital roles in

5.3.2.1. photosynthesis

5.3.2.1.1. Rubisco

5.3.2.2. cellullar respiration

5.3.2.2.1. adenylyl cyclase

5.4. ATP=universal currency

5.4.1. Light >ATP

5.4.2. Food>ATP

5.4.3. ATP>work

6. Free energy(G) + free energy difference (ΔG)

6.1. properties of the rxn-if it can take place and degree to which enzyme accelerates the rxn

6.1.1. depends on energy differences between reactants and products

6.2. free energy (G)

6.2.1. measure of useful energy/energy that is capable to do work

6.3. free energy difference ( ΔG)

6.3.1. differences in free energy between its reactants and products

6.3.2. tells us if the rxn can take place spontaneously

6.3.3. ΔG=negative=<0

6.3.3.1. rxn can take place spontaneously

6.3.3.2. exergonic rxn

6.3.3.2.1. example

6.3.3.3. energy diagram

6.3.3.3.1. energy levels of reactants >energy levels of products

6.3.3.3.2. energy is released in this rxn

6.3.4. ΔG=0

6.3.4.1. system is at equilibrium

6.3.4.2. no net change takes place

6.3.5. ΔG=positive=>0

6.3.5.1. non spontaneous rxn

6.3.5.2. endergonic rxn

6.3.5.3. energy diagram

6.3.5.3.1. energy of products>energy of reactants

6.3.5.3.2. energy input needed to drive rxn

6.3.5.3.3. equilibrium constant for endergonic rxn <1

6.3.6. depends only on (Gproducts(final state)-Greactants(initial state)

6.3.6.1. ΔG of rxn is independent of the path(molecular mechanism) of the transformation

6.3.6.2. e.g. ΔG of oxidation of glucose>O2 same if it takes place by combustion/by series of enzyme catalyzed steps in cell

6.3.6.3. ΔG=Gproducts-Greactants

6.3.7. provides no info about the rate of rxn

6.3.7.1. rate of rxn depends on free energy of activation( ΔG‡)

6.3.7.2. negative ΔG=spontaneous rxn

6.3.7.2.1. but does not tell us rate at which it will take place

6.4. 2 thermodynamic properties of rxn need to be considered to understand how enzymes work

6.4.1. ΔG between products and reactants

6.4.1.1. determines whether the rxn will take place spontaneously

6.4.1.2. doesn't tell us about the rate of rxn

6.4.2. energy required to initiate the conversion of reactants into products

6.4.2.1. activation energy

6.4.2.2. determines the rate of rxn

6.4.2.3. affected by enzymes

7. ΔG0 and equilibrium constant

7.1. rate of rxn is defined by the equilibrium constant Keq

7.2. ΔG=0

7.2.1. system is at equilibrium

7.2.2. not net change can occur

7.3. need to be able to determine the ΔG 4 an enzyme catalyzed rxn

7.3.1. know whether the rxn is spontaneous/not

7.3.2. how to determine ΔG

7.3.2.1. use equilibrium constant

7.3.2.1.1. Keq=equilibrium constant

7.3.2.1.2. [A],[B],[C],[D]

7.3.2.2. calculating ΔG

7.3.2.2.1. delta G rxn

7.3.2.2.2. simple way is to determine ΔG°′

8. Catalysis

8.1. enzymes alter rxn rate only not rxn equilibrium

8.1.1. an enzyme cannot alter the laws of thermodynamics

8.1.1.1. cannot alter equilibrium of a chemical rxn

8.1.2. amount of product formed is the same whether an enzyme is present or absent

8.1.2.1. amount of product is formed more rapidly in presence of an enzyme

8.1.3. Example

8.1.3.1. in absence of enzyme

8.1.3.1.1. kF=forward rate constant for conversion of S>P

8.1.3.1.2. kR=reverse rate constant for the conversion of P>S

8.1.3.1.3. K=equilibrium constant

8.1.3.1.4. working out

8.1.4. rate of product formation levels off with time

8.1.4.1. rxn has reached equilibrium

8.1.4.2. Substrate still being converted into product

8.1.4.3. Product is being converted into S at a rate such that the amount of P remains the same

8.1.4.4. same equilibrium point reached

8.1.4.4.1. more rapidly reached in presence of an enzyme

8.1.4.5. New Topic

8.1.5. enzymes accelerate the attainment of equilibrium

8.1.5.1. do not shift equilibria position

8.1.5.1.1. if more P is made than S

8.1.5.2. equilibrium position is a function only of ΔG between reactants and products

8.1.5.3. consider the equilibrium

8.1.5.3.1. K+1=conversion of A-E

8.1.5.3.2. K-1=reverse conversion

8.1.5.3.3. with enzyme and without enzyme

8.2. Why do exergonic rxns do not occur spontaneously

8.2.1. Activation energy

8.2.1.1. Gibbs free energy of activation/activation energy

8.2.1.1.1. =difference in free energy between the transition state and the substrate

8.2.1.1.2. symbol= ΔG ‡

8.2.1.1.3. equation

8.2.1.1.4. doesnt enter into final ΔG calculation

8.2.1.2. how enzyme enhances rate of rxn without altering ΔG

8.2.1.2.1. enzymes function by lowering the activation energy

8.2.1.2.2. enzymes facilitate the formation of the transition state

8.2.1.3. the higher the activation energy the slower the rate of rxn

8.2.1.4. rate of rxn depends on ΔG‡

8.2.1.4.1. bigger ΔG‡=slower rate of rxn

8.2.1.4.2. smaller ΔG‡=faster rate of rxn

8.2.1.4.3. enzymes work by lowering ΔG‡

8.2.2. Transition state

8.2.2.1. chemical rxn of substrate to form product goes through a transition state=(X‡)

8.2.2.2. denoted by ‡ symbol

8.2.2.3. =transitory molecular structure that is no longer the substrate but is not yet a product

8.2.2.4. least stable and most seldom occupied species along the rxn pathway

8.2.2.4.1. one with highest energy

8.2.2.5. Transition state theory

8.2.2.5.1. `substrate + enzyme>rxn pathway whose transition state energy is lower than the rxn with no enzyme

8.2.2.6. essence of catalysis is stabilization of the transition state

9. Summary

9.1. enzymes are biological catalysts

9.2. enzymes are highly specific

9.3. enzymes alter the rate of rxn but has no effect on equilibrium of rxn

9.4. enzymes stabilize the transformation state

9.4.1. lower the activation energy

9.4.1.1. increase the rate of rxn