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What do jellyfish do?
produce enzymes that take a substrate and produce light
Characteristics of enzymes?
Symbol for reaction rate constant?
immense catalytic power
- - lowers Ea
- - speeds up and makes a reaction easier
- - enzymes do not change
Highly regulated: can produce enzymes in proenzyme form, meaning its sythesized in correct order and almost completely folded. But, one change makes it functional. it is activated when needed
What is the fastest enzyme? Or, one that catalyzes the reaction as fast as possible.
What do proteases do?
break peptide bond by adding a cofactor, which is water
- They are highly specific for the bond they break
- ex: One that breaks the bonds that occur after Lys and Arg
Enzymes do what? What are some examples?
convert one form of energy to another
- light--> sugar
- sugar--> ATP
- ATP--> mechanical work
- ATP--> electrical gradients
What is thermodynamics?
science concerned with the relationship between heat and work
First Law of Thermodynamics: __
The total energy of a system (whatever we are trying to study/ anything inside a barrier) and its surroundings is constant
path doesn't matter form A--> B. All that matters are the energies
How to determine change in total energy of a system.
- Esubb: system when we end the process
- Esuba: system when we start process
- Q: heat absorbed by system
- W: work done by system
With a system alone, what can't we determine?
we can't determine whether a reaction is spontaneous or nonspontaneous. So, we look at surroundings.
Second Law of Thermodynamics
When is a system spontaneous if applying this equation?
A process can occur spontaneously only if the sum of the entrophies of the system and its surroundings increase
- all entropy increases.
if disorder increases, then, yes, its spontaneous
In a system with H2 and O2, by its conerting into water, what is it?
It is spontaneous. This is because release of heat increases disorder, making it spontaneous. Even though we created a more ordered system, the entropy of the surroundings increaseed
What are the equations for:
change in total entropy
change in entropy of srroundings
a combo of both
multiplying by T
dStotal=DSsystem+dSsurroundings (we don't always know DSsurroundings)
What is the change in Gibbs free energy?
When does the total entropy increase?
dSsystem > dHsystem/T
When is a reaction spontaneous in terms of the equation?
- when dG is negative= spontaneous
- when dG is positive= nonspontaneous
- when dG equals 0= equilibrium
Why is the folding of a protein possible if you're going from more disordered to more ordered?
Although folding is more ordered, hydrophobin amino acids get inside to hide from the water and hydrophilic amino acids reposition themselves outside. If the hydrophobic amino acids remain outside, it causes water to become ordered adn form a cage around them. When inside, water is free to act with bulk water and get more disordered
Under standard conditions, what relationship occurs?
- a relationship between equilibrium constants and free energy change under standard conditions. Given by:
- The 1.36 comes from multiplying the 2.303 by the RT
Why did biochemists create the standard conditions? And, what is the symbol?
biochemists created standard conditions (denoted with a o sign) for studying the reactions.
Then, they added pH of 7, which is denoted by the apostrophe (')
Relationship between K'eq and dGo
As K'eq increases, dGo decreases at standard conditions at pH 7
What is the comparison of adding an enzyme?
Regardless of whether an enzyme is added, the reaction will still have the same equilibrium point/ end point.
- What an enzyme does is speed up the reaction.
- Therefore, without an enzyme added, it just takes a longer time to reach this equilibrium.
What is free energy?
What is dG≠?
What is the transition state?
how much free energy is associated with various steps
that is Gibbs Free energy of activation
Highest free energy state that a molecule has to go through to be a product
True or False:
There is a great deal of free energy associated with the transition state.
Explain energy and how enzymes help in reactions.
all the weak bonds have energy associated with it. Enzymes help by:
- - bringing enzymes closer together
- - stressing the substrates to make the TS more attainable
Explain the ES complex.
It is the brief period of time that enzymes comes in to react with the substrate
E + S --k1--> ES --k2--> E + P
The ES can continue to convert substrate to product; enzyme not altered
What is the maximal velocity?
when all are bound together
Why is there a parabolic curve for certain enzymes?
the reaction velocity goes up but wouldn't reach the max velocity point because not all can react at the exact same time
What are the ways that we proved that an ES complex existed?
1) the reaction velocity (how much product formed)
2) taking a look at the active sight only to find that amino acids and prosthetic groups surround the side and have ways of interacting with substrate the best; one ideal substrate that can fit in
3) Spectrophotometer to see how enzymes change when mixed with substrate
4) primary sequence of amino acids (6 out of the 29 form the active site and are required for a reaction to take place); the rest of the AAs form the shape that allows them to fit perfectly in the active site
Once in the active site, explain bonding.
Once in the active site, covalent bonds can form eventually, but not initially. Hydrogen bonds, ionic bonds, hydrophobic interactions, etc. form. The higher the amount of weak interactions that occurs, the better the chance for substrate
What are the two models of enzyme and substrate fitting together?
lock and key fit
Explain lock and key.
weak interactions hold the substrate and active site together. The substrate fits perfectly into the active site
Explain the induced fit.
Only the right substrate will react. The enzyme, prior to binding, has all of the components needed to bind, but it isn't positioned properly. When the substrate comes in, it is fit perfectly in via an induced fit.