Energetics and enzymes

Question 1

What is the First and Second Law of Thermodynamics?

Answer 1

1st: energy is not created or destroyed, it can only be changed from one form to another e.g. thermal to kinetic and light to chemical
2nd: Energy spontaneously tends to flow from being concentrated in one place to becoming diffused and spread out e.g. hot cup of coffee going cold

Question 2

What is the concept of Free Energy?

Answer 2

• Free energy is the amount of energy within a molecule that could perform useful work at a constant temperature
• It measures the change in entropy and the change in the order at a given temperature
• The changes in free energy for a reaction are defined by the difference between the free energy of the products and reactants
• Reaction can only occur if ΔG is negative

Question 3

Chemical structure of ATP

Answer 3

• ATP includes a ribose sugar linked to adenine and 3 phosphate groups.
• The phosphates are linked via phosphoanhydride bonds which have a large negative value of ΔG of hydrolysis and are hence high energy bonds.

Question 4

How to make a reaction energetically favourable? Use an example

Answer 4

They take place because they are coupled to an energetically favourable one.
Majority of energetically unfavourable biochemical reactions rely on the hydrolysis of high energy phosphate bonds such as ATP.

Question 5

What are enzymes and why are they important?

Answer 5

• Enzymes increase the rate of reaction and lower the activation energy of a reaction, but they never
  change ΔG or the equilibrium position
• In a biological setting, even some favourable reactions will not take place at a rate that is useful for
  life unless they are catalysed by an enzyme

Question 6

What does a deficiency of glucose-6-phosphatase result in?

Answer 6

Von Gierke’s disease - sufferers inherit two mutant copies of the G6Pase gene, one from each parent.
It is rare but those afflicted suffer from low blood sugar levels, slow growth, large livers and short stature.

Question 7

How do you calculate free gibbs energy?

Answer 7

A+B——>C+D

DeltaG= (C+D)-(A+B)

Question 8

what bonds do ATP contain?

Answer 8

Phophoanhydride bonds which have a large negative deltaG of hydrolysis- said to have high energy bonds

Question 9

Where is lysozyme found and how does it provide defence against bacteria?

Answer 9

Tears and nasal secretions. Hydrolyses the bond between the repeating disaccharide NAG (N-acetylglucosamine) and NAM (N-acetyl muramic acid) in the bacterial cell wall making it lyse.

Question 10

State the two essential residues in lysozyme.

Answer 10

Glu-35 and Asp-52

Question 11

Describe the mechanism of action of lysozyme.

Answer 11

Glu-35 protonates the oxygen in the glycosidic bond thus breaking it. Asp-52 stabilises the positively charged intermediate that’s formed. Water becomes de protonated by Glu-35 which returns the Glu-35 to its original state. The hydroxide ion then attacks the positively charged intermediate adding an OH to it.

Question 12

What is the optimum pH of lysozyme and why?

Answer 12

5.0

because at this pH Glu-35 (COOH) is unionised and Asp-52 is ionised (COO-)

Question 13

What type of reaction is NAD+ regularly involved in?

Answer 13

Dehydrogenation – it is able to readily accept one hydrogen and two electrons
(H-).

Question 14

Describe the action of NAD+ in Lactate Dehydrogenase.

Answer 14

In anaerobic respiration, pyruvate is converted to lactate which generates lots of NAD+. The lactate travels to the liver where the NAD+ converts the lactate back to pyruvate

Question 15

Order in biological systems is achieved by taking energy from the surrounding environment and investing it in chemical reactions which maintain order. In so doing, how is the second law of thermodynamics obeyed?

Answer 15

By an increase in the entropy of the environment

Question 16

The change in Gibbs’ free energy (Delta G) for the hydrolysis of a phosphoanhydride bond within the molecule Adenosine Triphosphate (ATP) is:

Answer 16

-31 kJ/mol
The ΔG for hydrolysis of a single phosphoanhydride bond of ATP has a large negative value of -31 kJ/mole. This allows ATP hydrolysis to couple energetically unfavourable reactions to energetically favourable reactions.

Question 17

The enzyme lactate dehydrogenase (pictured) catalyses which reaction?

Answer 17

reduction of pyruvate to lactate, thereby generating NAD+

Question 18

What happens to Glu-35 when temp increased and what happens to asp-32 when temp lowered

Answer 18

Asp-52 is protonated ( shifted to the left)

Glu-35 is ionised (COO-) leading to a loss of function.

Question 19

Crystallographic analysis of enzymes with and without substrate bound, support an ‘Induced fit’ model of enzyme function in which the enzyme’s substrate induces a change in the conformation of the enzyme and results in the formation of the ACTIVE SITE. Upon release of products, the enzyme reverts back to its original conformation.

Answer 19

TRUE

Question 20

How do enzymes work

Answer 20

Enzymes break bonds by bending their substrates in such a way that the bonds to be broken are stressed and the substrate molecule resembles the transition state, a particular conformation in which the atoms of the molecule are rearranged both geometrically and ELECTRON configuration changes so that the reaction can proceed.