Enzymes

Question 1

what 2 ways can a rxn be accelerated?

Answer 1

1) adding heat
-increaes number of reactants with sufficent energy

2) adding a catalyst
-decreases activation energy needed (doesn’t react)

Question 2

what is the difference between an enzyme and a catalyst?

Answer 2

enzymes are catalysts but not all catalysts are enzymes

-enzymes are largely organic in nature and are bio-catalysts, while non-enzymatic catalysts can be inorganic compounds.
Neither catalysts nor enzymes are consumed in the reactions they catalyze.

Question 2

True or False: enzymes are proteins

Answer 2

True however, there are a few exceptions

-typically globular proteins

Question 3

what are characteristics of enzymes?

Answer 3

-accelerate rxn rates
-regenerate at the end of a rxn
-highly specific (no side rxns)

Question 4

is enzyme structure flexible? why or why not?

Answer 4

since they are proteins, enzyme structure is flexible to an extent

Question 5

what does changing the shape of an enzyme do?

Answer 5

change it’s function
-helps with regulation

Question 6

How are some reactions able to proceed if the overall free energy is positive?

Answer 6

They aren’t
-in all systems a rxn will only proceed if the free energy of the products is less than the free energy pf the reactants

Question 7

what determines the speed of a favourable biochemical rxn?

Answer 7

the size of the activation energy barrier

Question 8

how do enzymes affect the free-energy change of a reaction?

Answer 8

They don’t!
-enzymes reduce the free energy of the TS

Question 9

what 4 ways to enzymes contribute to the reduction of free energy for the TS?

Answer 9

1) removal of substrates from an (aq) solution
2) proximity and orientation
3) taking part in rxn
4) stabilizing the TS

Question 10

what is an active site?

Answer 10

region of the enzyme where catalysis occurs
-small portion of the protein

Question 11

what is located in the active site?

Answer 11

key amino acids
-binding and catalysis

Question 12

what do active sites determine?

Answer 12

affinity, specificty and rate

Question 13

what is the relation of the active site to the substrate/TS?

Answer 13

the active site is complementary to the substrate/TS
-shape, hydrophobic interaction, H-bonds and ion pairs

Question 14

what 3 advantages does the exclusion of water provide in a rxn?

Answer 14

1) accelerates rxn
2) enhances polar interactions
3) prevents side rxn’s

Question 15

what does an “induced fit” mean? why is it important?

Answer 15

the enzyme changes shape once bound to the substrate

-closes off active site (excludes more H2O)
-brings catalytic/reactive groups together

Question 16

why is proximity and orientation an important factor in the enzyme active site’s function?

Answer 16

chemical rxn’s only occur if substrates come together in the right orientation and distance

Question 17

how might an enzyme participate in a reaction?

Answer 17

they may work to position functional groups near the substrates in the active site

-acid/base catalysis
-covalent catalysis
-metal ion catalysis

this can be done through AA or cofactors

Question 18

what are cofactors?

Answer 18

molecules/compounds that enhance the reactive potential of proteins by providing new reactive functional groups

Question 19

what is an apoenzyme?

Answer 19

an enzyme that contains a prosthetic group but it is not attatched

Question 20

what is a holoenzyme?

Answer 20

an enzyme that contains a prosthetic group and it is attached to form a functional tertiary structure

Question 21

what does binding the TS do to delta G?

Answer 21

it will help lower delta G of the TRANSITION STATE

Question 22

what is involved in the interaction of transition state stabilization?

Answer 22

parts of the protein interact with the unstable TS

Question 23

does the enzyme active site bind the substrate or the TS better?

Answer 23

the TS

Question 24

what are TS analogs?

Answer 24

A molecule that mimics the transition state of a chemical reaction, effectively "trapping" the transition state. A potent inhibitors of many enzymes -bind to the enzyme with a higher affinity compared to the substrate -basis for drug design

Question 25

what is michaelis constant?

Answer 25

The same as Kd; reflects affinity of enzyme for substrate -small Km = high affinity = better substrate

Question 26

what is a competitive inhibitor?

Answer 26

a substance that binds reversibly to the active site to physcially block active site -resembles the substrate or TS but doesn't react

Question 27

how can competitive inhibition be overcome?

Answer 27

increasing [substrate] -Vmax won't change

Question 28

what is a substrate analog?

Answer 28

a molecule that structurally resembles the substrate of an enzyme-catalyzed reaction. It can bind to the active site of the enzyme, similar to the substrate, but is not acted upon or transformed by the enzyme like the true substrate.

Question 29

why do TS analogs make better competitive inhibitors than substrate analogs?

Answer 29

Transition state analogs typically bind to enzyme active sites much more tightly than substrate analogs because the enzyme binds the substrate in the transition state more strongly than one in the ground state

Question 30

what affect do competitive inhibitors have on affinity for enzyme and substrate?

Answer 30

they decrease affintiy (increase Km)

Question 31

what is an allosteric enzyme?

Answer 31

enzymes that have an additional binding site for effector molecules other than the active site. The binding brings about conformational changes, thereby changing its catalytic properties.

Question 32

how is alloesteric enzyme activity modulated?

Answer 32

by the non-covalent binding of specific molecules at a site other than the active site or at the active site -heteroallostery vs homoallostery

Question 33

what 2 states do allosteric enzymes have?

Answer 33

T state- low activity R state - high activity

Question 34

what state does an allosteric activator favour?

Answer 34

R state

Question 35

what state does an allosteric inhibitor favour?

Answer 35

T state

Question 36

what line represents an allosteric enzyme that has been inhibited?

Answer 36

green

Question 37

what line represents an allosteric enzyme that has been activated?

Answer 37

blue

Question 38

what is the most common type of reversible covalent modification?

Answer 38

phosphorylation -may increase / decrease activity of the target enzyme - may produce slight change in shape

Question 39

what structure level is changed from covalent modification of an AA residue?

Answer 39

tertiary

Question 40

what enzyme catalyzes the phosphorylation of proteins?

Answer 40

protein kinase

Question 41

what enzyme catalyzes the dephosphorylation of proteins by hydrolysis?

Answer 41

protein phosphatases

Question 42

is phosphorylated of enzymes a reversible or irriverisble reaction?

Answer 42

reversible