Energetics and enzymes Flashcards
Define enzymes and outline their function mechanisms according to the laws of thermodynamics
Enzyme: A protein that acts as a catalyst to induce chemical changes in other substances, itself remaining apparently unchanged by the process.
- can increase the speed at which a chemical reaction takes place by a factor of at least 1 x 106
- exhibit quite exquisite specificity due to their conformation
Laws of Thermodunamics:
First Law - Energy can neither be created nor destroyed, simply converted from one form to another.
Second Law - In any isolated system, the degree of disorder can only increase. Entropy increases.
Biological systems are ordered. They use energy from the environment to maintain order
The environment becomes more disordered
How do enzymes work?
by lowering the energy barriers that impede chemical reactions taking place
(All the molecules within a cell possess energy in the form of rotation and vibrations and also in the form of the bonds holding the various atoms together)
Free energy and ATP: explain the concept of free energy, how changes in free energy can be used to predict the outcome of a reaction and how ATP is used as a carrier of free energy to drive energetically unfavourable reactions
The Concept of Free Energy:
- Entropy changes during a chemical reaction are very difficult to measure.
- This lead Josiah Gibbs to create the function known as Free Energy.
- (Gibb’s) Free Energy is defined as the amount of energy within a molecule that could perform useful work at a constant temperature.
- It is denoted by the letter G and has units of kilojoules/moles (kJ/mole).
Essentially, molecules have energy that can be used -> Molecules want to get rid of energy
- If the overall amount of energy in the molecules are lost after a reaction, the reaction can occur
A+B –> C + D
ΔG = free energy (C+D) - free energy (A+B)
A reaction can only occur if ΔG is negative
In a biological setting, even this energetically favourable reaction will not occur at a rate useful for life, unless catalysed by enzymes.
Conversely, although enzymes can speed up the rate of this reaction, ΔG°’ for the reaction will still remain the same
Adenosine Triphosphate (ATP):
- Most reactions in our cells involve making things
- By themselves, the reactions can’t occur
- The molecules are gaining energy
- So we combine the reaction with ATP
- ATP loses a lot of energy
- DG°’= - 31 kJ/mole
example: photo
Enzyme catalysis: explain how enzymes act as catalysts of reactions.
Activation Energy
- For substrate to undergo a reaction, you need to invest some energy to make it change to a transition state
- Transition state – atoms in molecules rearranged geometrically and electronically so reaction can happen
- This investment is the activation energy
How do Enzymes Work?
- Enzymes function by lowering the barriers that block a particular reaction
- The high activation energy means most reactions happen very slowly
- Enzymes increase the rate of reaction
- Lower activation energy
- Do not change ΔG or the equilibrium position of a reaction
- Substrate binds to enzymes active site
- Substrate goes into a transition state (photo)
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.
This makes them more amenable to reaction with other molecules.
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) .
2 Models:
Lock and Key
The shape of the substrate (key) matches that of the active site (lock) of the enzyme, forming the enzyme-substrate complex.
Induced Fit
The substrate induces a change in the conformation of the enzyme which results in the formation of the active site.
Lysozyme
- 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.
- 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.
- Two acidic residues Glu35 and Asp52 are essential for catalysis.
How Lysozyme Works
- Glu35 protonates the oxygen in the glycosidic bond breaking the bond holding the two sugar molecules together.
- A water molecule enters and is de-protonated by Glu35.
- Asp52 stabilises the positive charge in the transition state.
- The hydroxide ion attacks the remaining sugar molecule adding an OH group. Both Glu35 and Asp52 are in their original state to continue catalysis.
For Lysozyme, the optimum pH is 5.0
At pH 5.0, Asp52 is ionised (COO-) and Glu35 is unionised (COOH).
This is essential for lysozyme function.
Draw graphs to show the effects of substrate concentration, temperature and pH on reactions catalysed by enzymes.
Substrate Concentration;
- Increasing Substrate Concentration increases the rate of reaction. This is because more substrate molecules will be colliding with enzyme molecules, so more product will be formed.
- However, after a certain concentration, any increase will have no effect on the rate of reaction, since substrate concentration will no longer be the limiting factor.
- The enzymes will effectively become saturated, and will be working at their maximum possible rate.
Temperature
- Chemical reactions speed up as temperature is increased, so, in general, catalysis increases at higher temperatures.
- However, each enzyme has a temperature optimum, beyond which its conformation is said to be denatured and the enzyme is inactive.
pH
- At pH 5.0, Asp52 is ionised (COO-) and Glu35 is unionised (COOH).
- This is essential for lysozyme function.
- This is typical for most enzymes too
Coenzymes: define the term “coenzyme”, and explain the role of the coenzyme NAD in reactions catalysed by dehydrogenases
Some enzymes need the assistance of co-enzymes
NAD+ (Nicotinamide adenine dinucleotide) is a vital component of many dehydrogenation reactions within the body –> NAD+ is a Co-factor for Dehydrogenation Reactions
It has no effect on its own but functions only after binding to a protein
Like all enzymes, they differ with respect to their substrate specificity
NAD+ catalyses the dehydrogenation of substrates by readily accepting a hydrogen atom and two electrons. (image)
Lactate Dehydrogenase
During intense exercise, skeletal muscles have to function anaerobically, as oxygen is a limiting factor. As such, the metabolite pyruvate is converted into lactate. This also generates free NAD+ which is needed by the muscle for other reactions.
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.
Enzyme kinetics: explain how experimental values of reaction velocity at different substrate concentrations can be used to derive Km and Vmax for an enzyme. Explain the effects of competitive and non-competitive inhibitors on Km and Vmax
- Km is the subtrate concentretion when 1/2Vmax
- Km indictes whether an enzyme functions properly
- for non-competitive inhibitors Vmax is lower but Km is the same
- for competitive inhibitors Vmax is the same but Km is higher
Enzyme kinetics: explain how enzyme activity may be measured using spectrophotometry and
