Proteins - Lecture Nine

Question 1

∆G < 0

Answer 1

Energy released, products dominate

Question 2

∆G > 0

Answer 2

Energy required, substrates dominate

Question 3

∆G = 0

Answer 3

At equilibrium, substrates and products at equal concentration

Question 4

∆H

Answer 4

Enthalpy

Question 5

∆S

Answer 5

Entropy

Question 6

To favour forward reaction (∆G < 0)

Answer 6

Either enthalpy must decrease (∆H < 0) or entropy must increase (∆S > 0)

Question 7

Cellular integrity

Answer 7

Decrease in entropy in the cell, so energy from elsewhere is required. Enzymes control where and when energy is released to maintain the cell.

Question 8

Activation energy (∆G˚‡)

Answer 8

Enquired to reach the transition state, this determines rate

Question 9

Free energy (∆G˚)

Answer 9

Sets ratio [P]/[S] at equilibrium

Question 10

Aldolase

Answer 10

Very positive ∆G˚, but big rate enhancement

Question 11

Adenylate kinase

Answer 11

∆G˚ near zero, big rate enhancement

Question 12

Cleavage of DNA phosphodiester backbone

Answer 12

Negative ∆G˚

Question 13

Classes of enzymes

Answer 13

Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligases

Question 14

Oxidoreductases

Answer 14

Redox

Question 15

Transferases

Answer 15

Transfer of a functional group

Question 16

Hydrolases

Answer 16

Hydrolysis reactions (using water), this includes many things that break down peptide bonds (proteases), or burn ATP

Question 17

Lyases

Answer 17

Non-hydrolytic breaking or making of bonds (not using water)

Question 18

Isomerases

Answer 18

Transfer to atoms/groups within a molecule to yield an isomeric form

Question 19

Ligases

Answer 19

Join two molecules together

Question 20

Enzyme-substrate binding

Answer 20

Occurs at a specific site on the enzyme, the active site

Question 21

The active site

Answer 21

Has amino acid side chains projecting into it
Binds the substrate via several weak interactions
Determines the specificity of the reaction

Question 22

Types of enzyme-substrate bonds

Answer 22

Ionic bonds, hydrogen bonds, van der Waals interactions and covalent bonds

Question 23

Ionic bonds (aka salt bonds)

Answer 23

Make use of charged side chains

Question 24

Hydrogen bonds

Answer 24

Side chain or backbone O and N atoms can often act as hydrogen bond donors and acceptors

Question 25

Van der Waals interactions

Answer 25

Between any protein and substrate atoms in close proximity, weakest of the interactions, but abundant

Question 26

Covalent bonds

Answer 26

Relatively rare but much stronger than the other bonds

Question 27

Lock and Key model

Answer 27

When the active site is already perfectly shaped for the substrate to fit, they are already complementary

Question 28

Induced Fit model

Answer 28

When the active site isn’t completely complementary but they can make small adjustments as the substrate fits into the active site

Question 29

Many, weak interactions ensure specificity and reversibility;

Answer 29

Several bonds are required for substrate binding - specificity.
Weak bonds can only form if the relevant atoms are precisely positioned.
Weak bonds allow reversible binding.

Question 30

How is ∆G˚‡ lowered?

Answer 30

1. Ground state destabilisation
2. Transition state stabilisation (picture)
3. Alternate reaction pathway with a different (lower-energy) transition state
   1 and 2 can be achieved by having an active site that has shape/charge complementarity to the transition state, not the substrate.

Question 31

Strategies for catalysis

Answer 31

Acid-base catalysis, adding or removing a protein to/from a substrate
Covalent catalysis, substrate ends up making a covalent bond with the protein
Redox and radical catalysis (metal ions), moving protons/electrons around
Geometric effects (proximity and orientation),
Stabilisation of the transition state
Cofactors with activated groups, e.g. electrons, hydride ion (H-), methyl groups (CH3), amino groups (NH2). Acts as carriers

Question 32

Proximity and Orientation Effect

Answer 32

For two molecules to react they need to be close together AND in the right orientation

Question 33

Cofactors

Answer 33

Many enzymes require other non-protein 􏰀factors􏰁 to help them catalyse reactions, there are two classes; metal ions and coenzymes

Question 34

Metal ion catalysis

Answer 34

More than a third of known enzymes require metal ions
Specific coordination geometry orients substrates
As Lewis acids, metals accept an electron pair to polarise H2O and functional groups
Transfer electrons in oxidation-reduction reactions

Question 35

Mg2+

Answer 35

DNA polymerase; hexokinase; pyruvate kinase

Question 36

Zn2+

Answer 36

Alcohol dehydrogenase; carbonic anhydrase

Question 37

Fe2+ or Fe3+

Answer 37

Cytochrome oxidase; peroxidase

Question 38

Mn3+ or Mn4+

Answer 38

Photosystem II

Question 39

Hexokinase using Mg2+ as a cofactor

Answer 39

Establishes orientation of phosphates of ATP by octahedral coordination of Mg2+ ion
‘Electron withdrawing’ Lewis acid: stabilises electrons on oxygen, making phosphorous a better electrophile

Question 40

Coenzymes

Answer 40

Are small organic molecules
Are co-substrates
Are carriers (of electrons, atoms, or functional groups)
Are often derived from vitamins

Question 41

Pyruvate dehydrogenase

Answer 41

Provides acetyl-CoA in aerobic conditions:
Multienzyme complex composed of 30 copies of enzyme E1, 60 copies of E2 and 12 copies of E3, each with cofactors.
Net reaction is an oxidative decarboxylation.