metabolism 2- energetics and enzymes

Question 1

What are enzymes.

Answer 1

A protein that acts as a catalyst to induce chemical changes in other substances, itself remaining apparently unchanged by the process. i.e. they can increase the speed at which a chemical reaction takes place by a factor of at least 1 x 106 yet at the same time, they exhibit quite exquisite specificity due to their conformation- don’t change equilibrium or free energy of reaction.

Question 2

What is Von Gierke’s disease

Answer 2

The most common glycogen storage
disorder (1 in 100,000).

Autosomal recessive deficiency of
Glucose-6-Phosphatase

Clinical outcomes:

Hypoglycaemia, poor growth,
distended abdomen, seizures when
blood glucose is low- difficulty maintaining blood glucose conc.

Question 3

Why is glucose-6-phosphatase important.

Answer 3

Glycogen is broken down into glucose-6-phosphate in the liver where it must then be broken down into glucose before it can enter the bloodstream.

Question 4

In which forms do molecules in the cell posses energy

Answer 4

energy in the form of rotation and vibrations and also in the form of the bonds holding the various atoms together.

Question 5

What is the first law of thermodynamics

Answer 5

Energy can neither be created nor destroyed. i.e. it is simply converted from one form to another.

Question 6

What is the second law of thermodynamics

Answer 6

In any isolated system, e.g. a single cell or the universe, the degree of disorder can only increase.

Question 7

What is entropy

Answer 7

The amount of disorder in a particular system

Question 8

How do spontaneous reactions take place

Answer 8

Reactions proceed spontaneously towards products with greater entropy (i.e. more disorder). i.e when delta G is negative.

Question 9

How are cells well ordered.

Answer 9

This is achieved by taking energy from the environment surrounding the cell and investing it in chemical reactions which maintain order- such as making peptide bonds.

Question 10

What happens as cells become more ordered

Answer 10

Reactions which create order release heat- which increases the disorder of the surroundings.

Question 11

Define Gibbs’ free energy

Answer 11

(Gibb’s) Free Energy is defined as the amount of energy within a molecule that could perform useful work at a constant temperature. (kJ/mole)

Question 12

Why do we need to couple reactions.

Answer 12

Pathways within the cell that synthesise molecules are generally energetically unfavourable e.g. peptide synthesis- order is created- hence cannot take place spontaneously.

They take place because they are coupled to an energetically favourable one- hydrolysis of ATP does this.

Providing that the sum of the DG for the overall reaction is still negative, the reaction will proceed.

The majority of energetically unfavourable biochemical reactions rely on the hydrolysis of high-energy phosphate bonds such as those found in ATP.

Question 13

What are phosphoanhydride bonds

Answer 13

Anhydride bonds (in red) link the terminal phosphate groups.

Question 14

What is the delta G of ATP hydrolysis

Answer 14

-31 kJ/mole

Question 15

Describe the coupling of the reaction to convert glucose to sucrose with the hydrolysis of ATP

Answer 15

Glucose + ATP — Glucose-1-phosphate + ADP

G1P + Fructose — Sucrose

Question 16

Describe the changes in free energy in a reaction

Answer 16

Increases from substrate to transition state of substrate- difference in free energy is the activation energy. Free energy decreases from transition state of substrate to product. Enzymes lower the activation energy for the reaction.

Question 17

What is the transition state of the substrate.

Answer 17

The transition state is the particular conformation of the substrate in which the atoms of the molecule are rearranged both geometrically and electronically so that the reaction can proceed.

Enzymes work by bending their substrates in such a way that the bonds to be broken are stressed and the substrate molecule resembles the transition state- lowers the transition state.

This makes them more amenable to reaction with other molecules.

Question 18

How does the active site interact with the substrate

Answer 18

Enzymes bind one or more substrate molecules tightly within a part of the protein known as the active site.

Enzymes arrange the substrate(s) in such a way that certain bonds are strained. Key residues within the enzyme participate in either the making or breaking of bonds by altering the arrangement of electrons within the substrate(s).

This can often take the form of either oxidation reactions, (in which electrons are removed from an molecule) or reduction reactions (in which electrons are added to a molecule) .

Since the cellular environment is generally aqueous, often, when a molecule gains an electron, it also simultaneously
gains a proton. e.g. A + e- + H+ AH

Question 19

Describe the lock and key model

Answer 19

In this model, the shape of the substrate (key) matches that of the active site (lock) of the enzyme. This model explains the specificity of most enzymes for a single substrate.

Question 20

Describe the induced fit model

Answer 20

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

Question 21

How do we know that the induced fit model is valid

Answer 21

From crystallographic analysis of enzymes with and without substrate bound, we now hold the induced fit model to be valid. There is a change in conformation of the enzyme when the substrate is bound- showing that there is an interaction between the substrate and enzyme.

Question 22

What is the function of lysozyme

Answer 22

Lysozyme is a component of tears and nasal secretions and is one of the first lines of defence against bacteria.

It catalyses the hydrolysis of sugar molecules within bacterial cell walls that are necessary for their structure. With this bond broken, the bacteria lyse and die.

Question 23

What exactly does lysozyme hydrolyse

Answer 23

Lysozyme hydrolyzes 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.

Lysozyme cleaves at the b(1-4) glycosidic linkage, connecting the C1 carbon of NAM to the C4 carbon of NAG.

Question 24

What is the function of Glu35 in the non-polar environment in the action of lysozyme

Answer 24

protonates the Oxygen in the glycosidic bond between NAM and NAG- breaking it- it then deprotonates an approaching water molecule- returning to its original state to continue catalysis. Hydroxide ion attacks the NAM

Question 25

What is the function of Asp52 in the polar environment of lysozyme

Answer 25

stabilises the positive charge in the transition state.

Question 26

Why is pH 5 the optimum pH for lysozyme

Answer 26

Asp52 is ionised and Glu32 is unionised.

Question 27

Why do we have fevers

Answer 27

Fever is part of this process- speeding up immune reactions- whilst worsening the activity of bacteria enzymes.

Question 28

What is NAD (Nicotinamide adenine dinucleotide)

Answer 28

A cofactor/coenzyme

Question 29

How does NAD catalyse dehydrogenation reactions

Answer 29

by readily accepting a hydrogen atom and two electrons.

Question 30

What is the difference between NAD and redNAD

Answer 30

No double bond between N atom and carbon atom in nicotinamide ring.

Question 31

Describe the action of lactate dehydrogenase

Answer 31

Converts pyruvate into lactate in anaerobic respiration. - redNAD donates H atom which creates more NAD which allow glycolysis to continue. Lactate diffuses from the muscle into the blood stream and is picked up by the liver, where the high levels of NAD+ can be used by lactate dehydrogenase to regenerate pyruvate.

Question 32

How does alcohol dehydrogenase work

Answer 32

alcohol + NAD — redNAD + Ketone