Lecture 11: Enzymes

Question 1

Enzymes have varying degrees of —- for their substrate

Answer 1

specificity

Question 2

Papin (3)

Answer 2

• low specificity
• cleave any peptide bond of any peptide
• Add water to bond to release carboxylic acid/ amino group

Question 3

Trypsin (2)

Answer 3

• found in small intestine and degrades protein after a meal
• Bind next to lys or Arg and cleave peptide bond on carboxy side of those residue

Question 4

Thrombin （2）

Answer 4

• More specific
• Only cleave peptide bond on the carboxyl side of Arg

Question 5

Group specificity

Answer 5

• Enzyme is specific for substrates with a particular functional group in common
• It can catalyze reaction for a number of different substrate as long as those substrate have some functional group in common

Question 6

Absolute specificity +ex

Answer 6

• Enzyme is specific for only one substrate (ex: lactase cleaves galactose and glucose)

Question 7

Enzymes do not shift the —– of a reaction. Explain….

Answer 7

• equilibrium
• The same equilibrium point is reached but it is reached faster with an enzyme

Question 8

Equilibrium

Answer 8

• The concentration of your product is not changing but the reaction is still happening in both direction

Question 9

Gibbs free energy (2)

Answer 9

• The difference in free energy between products and reactants
• a measure of useful energy, or the energy that is capable of doing work

Question 10

ΔG is negative (3):

Answer 10

• The reaction is spontaneous
• Exergonic
• More energy in the reactants then products

Question 11

At equilibirum, ΔG is —, cells want to ….

Answer 11

• 0
• Avoid this as theres no energy to do work

Question 12

ΔG is independent of

Answer 12

the path of transformation. Its value is dependent on the product and reactant difference.

Question 13

ΔG tells us nothing about

Answer 13

The rate of the reaction

Question 14

Standard free energy change ΔG0

Answer 14

• at standard conditions
• Reactants and products have concentration of 1M
• 1 atm for gas
• Temperature is 298K

Question 15

Standard free energy change ΔG0’ (2)

Answer 15

• Convention for biochemistry: ΔG0’
• PH of 7- when H+ is a reactant, it has a concentration of 1M

Question 16

How to determine ΔG0’

Answer 16

• By measuring concentration of products and reactants at equilibrium

Question 17

K’eq + formula (2)

Answer 17

Equlibirum concentration of products and reactants

Question 18

Whether ΔG is larger, smaller or the same as ΔG0’ depends on —

Answer 18

the concentration of reactants and products

Question 19

For a reaction to be energectically favourable (spontaneous), ΔG must be

Answer 19

negative

Question 20

Spontaneous reactions are not

Answer 20

Instantaneous

Can take hundreds of years to happen

Question 21

Enzymes can make spontaneous reactions happen faster so they are —–

Answer 21

kinectically favourable

Question 22

How do enzymes accelerate reactions?

Answer 22

• Enzymes decrease the activation energy to overcome the activation energy barrier
• Enzymes lower the activation energy by stabilizing the transition state

Question 23

With enzymes, —- doesnt change, only —-

Answer 23

• free energy
• activation energy

Question 24

Where does the energy come from to lower the activation energy (4)?

What it is+ also called+ maximize it?+ tightly?

Answer 24

• There is free energy released when many weak interactions form between the enzyme and substrate (H-bond, electrostatic, vander waals). The negative binding energy compensates for the positive energy necessary to “bend” the substrate into the higher energy transition state
• This free energy is called binding energy
• Only the correct substrate can maximize the amount of binding energy (specificity) by making the maximium # of weak binding
• Maximal binding energy occurs during the transition state (bind tightly) as in the begining its bound loosely)

Question 25

Features of the Enzyme’s active site (5)

Answer 25

• Residues forming the active site come from different positions in the sequence
• Small volume of the total protein
• Unique micro-environment (active site compatible with substrate, ex: hydrophobic)
• Forms multiple weak interactions with substrates (electrostatic, H-bond, electrostatic)
• Specificity of substrate binding depends on percise arrangement of atoms in the active site

Question 26

Lysozyme

Answer 26

Enzyme present in tear, saliva, helps protect us against bacteria as it destryoys the carbohydrates in the cell wall of the bacteria

Question 27

Co-factors (2)

Answer 27

• non-protein compounds that bind to proteins and are needed for biological activity
• can be organic or inorganic (co-enzyme or metals)

Question 28

Co-enzyme

Answer 28

• vitamin-derived organic molecules

Question 29

Apoenzyme

Answer 29

Enzyme without the cofactor

Question 30

Holoenzyme

Answer 30

Enzyme with the cofactor

Question 31

Prosthetic group

What it is/removability+ what can it be

Answer 31

• Co-factor is very tightly bond to active site
• can be small organic molecules or metal ions. Due to the tight binding to the enzyme, prosthetic groups are difficult to remove from the enzymes. Hence, it is considered that the bond between prosthetic group and enzyme is permanent unlike in coenzymes.

Question 32

Co-substrate

Answer 32

Cofactor bind losely, and with every chemical reaction, the cofactor and product is released

Question 33

NAD+ and NADH cofactor/coenzyme + ex (2)

Answer 33

• an important coenzyme for redox reactions
• Ex: electron from NADH transferred with H+ to reduce pyruvate to lactate

Question 34

Lock and key

Answer 34

The substrate is a perfect fit for the enzyme’s active site. The lock-and-key model portrays an enzyme as conformationally rigid and able to bond only to substrates that exactly fit the active site.

Question 35

Induced fit

Answer 35

The induced fit model portrays the enzyme structure as more flexible and is complementary to the substrate only after the substrate is bound. Enzyme’s active site becomes complementary to substrate after substrate binding.

Question 36

The enzyme’s atcive site stabilizes the ——. This lowers the —– which allows enzymes to speed up the reaction. —- provides most of the energy used to lower the atcivation energy

Answer 36

• transition state
• activation energy
• binding energy