Energetics and dynamics of protein action Flashcards
What is cleaving?
Removing the functional group or splitting metabolites into chunks.
What are hydrolases?
Hydrolytic cleavages
Nucleases - cleave nucleic acids
Proteases - cleave proteins
What are polymerases?
Polymerisation reactions - expanding RNA or DNA.
What are synthases?
Catalyses synthetic processes
What are kinases?
Important for signalling by phosphatases.
Adding or removing phosphate changes its interactions with other things.
What are isomerases?
Intermolecular rearrangment into other isomers.
What are oxido-reductases?
Oxidise or reduce substrates - dehydrogenases or oxidases
What are ATPases?
Use ATP to drive across membranes through motors and pumps.
What is the effect of high temperature on enzymes?
Heating an enzyme makes the molecules vibrate so it is harder to hold the substrate in place and collide and for the enzyme-substrate complex to take place.
At a high enough temperature the bonds will denature and structure degrade.
What does the graph for temperature and enzyme action look like?
Vo on y axis
Temperature on x axis
Gradual increase, sharp decline after peak.
What is the effect of low temperature on enzyme activity?
When cold the substrate and enzyme are moving slowly so are in the correct orientation less often and won’t bind as often so low rate.
The side chains move slower to accomodate substrate.
What is the effect of pH on enzyme activity?
The charges on amino acids change so the structure changes and the substrate binds less easily.
At extreme pH the protein is denatured.
What does the graph of pH on enzyme activity look like?
Vo on y axis
pH on x axis
2 lines - first peak is narrow at low pH.
broad peak at high pH
What is the progress of a reaction?
Substrate + enzyme –> enzyme substrate complex –> enzyme product complex –> release enzyme + product
What does the free energy of a reaction look like?
Free energy on y axis
Progress of reaction on x axis
Activation energy peak
Free energy of enzyme and product is lower than enzyme and substrate at start
What does the free energy look like when an enzyme is added?
Peak at activation energy is lower
Enzyme and product energy is at same point as original line.
How does an enzyme affect the free energy in a reaction?
Lowers the activation energy so it is easier to form the transition state.
What is an exergonic reaction?
Spontaneous - ΔG is negative and energy is given out.
What is an endergonic reaction?
Not spontaneous
Energy is taken in and ΔG is positive.
What is a freely reversible reaction?
When ΔG = 0 it is freely reversible.
see graph
What is an energetically unfavourable reaction?
Endergonic because ΔG is positive
There is a transition state, with a peak which needs overcoming.
An enzyme will lower the peak of the activation energy to the transition state but still requires energy.
See graph
What is an example of coupling exergonic and endergonic reaction?
Phosphorylation of glucose to produce glucose-6 phosphate.
Large ΔG so not spontaneous so couple with a spontaneous reaction.
Add ΔG together to form an overall negative ΔG so the reaction will be favourable.
What is the induced fit model?
Proposes distortion of enzyme and substrate to favour product formation.
Active site has similar structure to substrate, forms transition state, substrate binds to enzyme and substrate takes a form so it is easier to form products.
What is catalysis dependent on?
Localisation, orientation and binding energy of substrate.
Catalytic residues on protein framework.
These all contribute to a lower energy of the transition state.
Why is the enzyme complementary to the transition state?
Because this lowers the activation energy.
How does hexokinase show enzyme function?
When there is nothing bound, hexokinase has an open structure.
When glucose and then ATP bind, it forms a closed structure around it, which brings the catalytic residues closer together so the reaction can happen.
