2. Energetics and Enzymes

Question 1

1st Law of Thermodynamics

Answer 1

Energy can neither be created nor destroyed

Simply converted from one form to another

Question 2

2nd Law of Thermodynamics

Answer 2

In any isolated system the degree of disorder can only increase.

Question 3

Entropy

Answer 3

Amount of disorder in a system

Question 4

Reactions proceed spontaneously towards

Answer 4

products with greater entropy

Question 5

Gibb’s Free energy

Answer 5

amount of energy within a molecule that could perform useful work at a constant temperature.
Denoted by G with units kJ/mole§

Question 6

Delta G

Answer 6

measures amount of disorder that results from a particular reaction

Question 7

Calculate delta G

Answer 7

Free energy (Products) - Free energy (Reactants)

Question 8

A reaction can only proceed spontaneously if

Answer 8

Delta G is negative

Question 9

Pathways in cells that synthesise molecules are generally energetically unfavourable, how do they still occur?

Answer 9

Take place because they are coupled to an energetically favourable one.
Providing sum of delta G for overall reaction is still negative, reaction will proceed.

Question 10

What do the majority of energetically unfavourable biochemical reactions rely on?

Answer 10

Hydrolysis of high-energy phosphate bonds e.g. those in ATP.

Question 11

Phosphoanhydride bonds have a large negative delta G of hydrolysis

Answer 11

= High energy bonds

Question 12

Delta G when converting ATP to ADP + Pi

Answer 12

-31 kJ/mol

Question 13

In a biological setting, some energetically favourable reactions won’t occur at a rate useful for life

Answer 13

Unless catalysed by enzymes

Question 14

Why is combustion of glucose energetically favourable?

Answer 14

It has a highly negative delta G

Question 15

Why does glucose not spontaneously combust?

Answer 15

Because it has activation energy

Question 16

Activation energy

Answer 16

Minimum energy required for a reaction to occur

Question 17

How can activation energy be overcome?

Answer 17

Enzymes provide an alternative reaction pathway

Lowering activation energy required

Question 18

Enzyme

Answer 18

A protein that acts a as a catalyst to induce chemical changes in other substances
Itself remaining apparently unchanged by the process

Question 19

What effect do enzymes have on rate of reaction?

Answer 19

Drastically increase rate of reaction

Lower energy barriers impeding chemical reactions

Question 20

Enzyme shape

Answer 20

Extremely specific due to their conformation

Question 21

What do enzymes do to their substrate?

Answer 21

Bend their substrates in such a way that bonds to be broken are stressed
Substrate molecule resembles transition state

Question 22

Transition state

Answer 22

Particular conformation of substrate in which atoms of the molecule are rearranged geometrically and electronically so the reaction can proceed
Makes them more amenable to reaction with other molecules

Question 23

How do enzymes work?

Answer 23

Substrate molecule binds tightly to enzyme active site
Arrange substrate in such a way that bonds are strained.
Key residues within enzyme participate in either the making or breaking of bonds by altering arrangement of electrons within substrate in the form of oxidation (-electrons from molecule) or reduction reactions (+ electrons).

Question 24

When enzymes cause oxidation/ reduction, as cellular environment is generally aqueous

Answer 24

Substrate molecule gains an electron & simultaneously gains a proton

Question 25

Lock and Key model

Answer 25

Shape of substrate (key) matches active site (lock) of enzyme.
Explains specificity of most enzymes for a single substrate.

Question 26

Induced fit model

Answer 26

Substrate induces a change in conformation of the enzyme which results in formation of the active site. Upon release of products, enzyme reverts back to its original conformation

Question 27

What is an enzyme found in nasal secretions and tears?

Answer 27

Lysozyme

Question 28

What does lysozyme do?

Answer 28

Catalyses hydrolysis of sugar molecules in bacterial cell wall necessary for their structure.
With this bond broken, bacteria lyse & die.
1st line of defence against bacteria

Question 29

What does lysozyme hydrolyse?

Answer 29

Alternating polysaccharide copolymers of N-acetyl glucosamine (NAG) and N-acetyl muramic acid (NAM) which represent the “unit” polysaccharide structure of many bacterial cell walls.

Question 30

Where does lysozyme cleave?

Answer 30

At Beta(1-4) glycosidic linkage, connecting C1 carbon of NAM to C4 carbon of NAG.

Question 31

Which acidic residues are essential for catalysis by lysozyme?

Answer 31

Glu-35 and Asp-52

Question 32

Mechanism of action for lysozyme

Answer 32

1. Glu-35 protonates Oxygen in glycosidic link between the 2 sugars- breaking glycosidic bond.
2. A water molecule enters & is deprotonated by Glu-35.
3. Asp-52 stabilises the positive charge in the transition state.
4. Hydroxide ion attacks remaining sugar molecule adding an OH group to it.
5. Proton is transferred to Glu-35 to return it to it’s original state.
6. Glu-35 & Asp-52 are both in their original state to continue catalysis.

Question 33

Chemical reactions speed up as temperature is increased

Answer 33

Catalysis increases at higher temperatures

Question 34

Each enzyme has a temperature and pH optimum

Answer 34

beyond which its conformation is denatured

Enzyme becomes inactive

Question 35

Coenzyme

Answer 35

an organic non-protein compound that binds with an enzyme to catalyse a reaction

Question 36

Example of a coenzyme:

NAD+ (Nicotinamide adenine dinucleotide)

Answer 36

No effect on its own but functions only after binding to a protein.
Vital component of many dehydrogenation reactions

Question 37

How does NAD+ catalyse dehydrogenation of substrates?

Answer 37

By readily accepting a hydrogen atom & 2 electrons