Exam 2 Flashcards
First law of thermodynamics
Energy is neither created nor destroyed but it can be transferred
Bioenergeties
How energy gets moved around
Energy
The ability to do work
Second law of thermodynamics
Entropy increases systems tend to become more disordered with each energy transfer
Change that is spontaneous in terms of probability and ordered
Highly ordered- low probability
Disordered- higher probability
Gibbs free energy
Delta G change in final & initial
Endergonic
Delta G is positive
Energy is stored
“Going uphill on a bike “
Also
Exergonic reactions
Delta G is negative
Energy is being released “going down a hill”
Delta o G of chemical reactions makes what kind of bonds
Making covalent bonds tends to be endergonic
Delta G can be affected by
Relative energy levels of reactants & products
Concentration of reactants & products
Temperature & pressure
To look at the energy levels we usually look at the standard free energy
Delta G zero
1M each, 1 atmosphere, 25°C
Biologist prefer delta G zero prime -
as delta G zero but also ph7
Energy charts!
Left to right- exergonic
Right to left-endergonic
Delta G zero prime shows
That the products of this reaction are much more stable
So the product are energetically favored
At equilibrium, there will be more product than reactants
Products move from
Less stable to more stable
Low energy = higher stability
Exergonic at equilibrium
Will leave you with more products than reactants
Spontaneous
When delta G zero prime is less than zero
There Will be more products than reactants at equilibrium
so concentrations don’t change anymore
The rate of the forward reaction is equal to
The rate of the reverse reaction
- equilibrium Constant
’ Products over reactants
Is linked to delta G zero prime
KEQ> 1
Delta G zero prime<o
Exergonic or spontaneous
KEQ< 1
Delta G zero prime>0
Endergonic more reactant than product
Can keq be negative?
No!
Delta G zero prime tells US what about the rate of reaction
Nothing
Rate of reaction & delta G prime zero are
Independent of one another
Reaction rate is controlled
by the energetic path from reactant to products
Activation energy
- Quantitative energy that we need to activate the reaction
Activation energy & delta G prime zero
Are independent of each other
Activation energy
The input energy needed to reach the transition state
Add energy to get to unstable transition state
In chemical reaction that releases energy
Exergonic
This is the mid-point of a chemical reaction which has the highest energy
Transition state
The amount of energy that a chemical must absorb before the reaction can occur
Activation energy
This term describes the state of a chemical reaction when the rate of a forward reaction is equal to the rate of the reverse reaction
‘equilibrium
How does delta G0 prime differ from Delta G value? Why is delta G0 prime more useful to biologist?
With Delta G0 we’re only going to be looking at relative energy levels of reactants and products delta G0 prime will be looked at and a pH of seven because a lot of biological molecules are closest to zero, so adding the prime to G0 will give us an extra constraint 
If the reaction of A~>B has a delta G0, prime= +3.0 kcal/mole, what is the reaction B~>A
-3.0kcal/mole
Molecule be will be more stable because this is an exergonic which is spontaneous and this in terms means that there is going to be more products and reactants and so the KEQ is going to be less than one when we’re going from A to B but when we’re going B to A a it’s going to be bigger than one.
B to A is endergonic non spontaneous
A to B will happen quicker
KEQ is the ratio of the concentration of products to the concentration of reactant under what condition
The condition that the rate of the forward reaction is the same rate as a reverse reaction, due to equilibrium
In what ways is an activation energy barrier of a chemical reaction a lot like a phospholipid bilayer for the movement of an ion
the path of how these barriers work in terms of how easily movement is accessed for some chemicals than with others
Requires energy from one state to get to the other for example, the grasshoppers one might require more energy to get from higher state to another, which requires less energy
How are delta G prime zero and activation energy related to another
They are not. They are independent of one another.
How are the activation energy of a reaction connect to the transition state of the reaction
The activation energy is an input needed in order to reach the transition state so the activation is right before the transition, state,
Are the activation energy is of a forward and reverse reaction equal to each other
No, only the concentrations and the rate of reactions are equal to each other 
How can you speed up a reaction
Applying heat
What is the only piece that controls rate?
Activation, energy
If you heat up glucose and fructose
Vibrate quickly and interact more violently, and some of them will have enough energy to make it over the barrier
Why are you applying heat doesn’t work biologically
Proteins begin to denature membrane membranes become too fluid to permeable and fall apart, can quickly kill the organism
How did we speed up the movement across the hydrophobic zone?
We gave it a different path to go by. There is a transport protein, Lazar different path, and this is for a specific molecules.
Enzymes
Proteins that catalyzes specific chemical reaction
Lower the activation energy and have no effect on Delta zero prime or KEQ
Enzymes in terms of binding
Act upon one substrate or reactant substrate, binds to the enzyme, specific active site face products are released
The good thing about enzymes is that they are unchanged and can act many times
Locke and key model
A substrate is added to an enzyme specific active site 
Induced fit model
Explains catalysis better than lock and key model
In this model of the enzyme and a substrate don’t fit perfectly just close close enough to get some specificity, but they don’t fit and actually have to form into each other the enzyme pushes into the substrate, and the substrate pushes into the enzyme
Doing so stabilizes the transition state 
Transition state
Chemical state between reactant and product
Highly unstable
Enzymes are what kind of catalyst
Bidirectional
Can catalase from reactant to product or product to reactant
By doing so, the enzyme did not affect the change of energy, but rather the affected how quickly we got there
Doesn’t affect the equilibrium just how quickly we get there
Enzymes lower activation energy, but don’t
Affect, Delta Chi zero, prime
No effect on KEQ
Measuring reaction rate
Concentration over time
the curve flattens out or reaches plateaus applied to due to the line, almost reaching an equilibrium
When the curve is flat
When the curve is perfectly flat. The concentration of product is no longer changing because it forward reaction is the same rate as a reverse reaction.
The curve
At zero, there is no product. The reverse reaction can’t happen. Lots of such as the product of beginning a little product to substrate.
As the time goes by the reverse reaction continues to have more and more once the reaction and the product are the same then we are at equilibrium
To find the reaction rate, we’re going to look at the slope of the curve during the early times
Concentration of product over time
We will be defining this, as our initial velocity think of this has reaction rate by looking at the early times we can avoid the complicated factor of the reverse reactor
Initial velocity is a reaction rate, and that is our enzyme activity how active our enzyme is a catalyst during this one reaction
What makes an enzyme, fast or slow? How may we compare enzymes?
The file to undergo reaction. Initial velocity depends on two aspects must be able to find the substrate and once it is bound go to catalysis which causes a reaction to happen.
Michaelis menten kinetics
We will measure the initial velocity by the concentration of substrate
How does the constitution of substrate affect initial velocity?
At zero, substrate concentration we can zero velocity
As a substrate, concentration increases velocity initially increases very quickly, but as concentration of substrate search to get super high velocity isn’t is it affected so much reaches a plateau
The maximum velocity is reached, and that’s why the plateau is reached, but maximum velocity is a theoretical value in order to get to the max. The substrate concentration has to be in a very, very very high.
Maximum velocity
It’s only reached at infinite substrate concentration
The active site is always full
As soon as catalysis happens, product is released instantly and the exercise refilled because there’s infinite amount of substrate available. The only limitation is the speed of the catalysis the faster it happens the faster the velocity is, but there’s a limit because we have gotten to the point that that is as fast as the enzyme it’s gonna go .
More than one way to get to one Vmax
KM is the concentration of substrate needed for half of V max
Km
Reflects substrate binding
Lower KM means tighter substrate binding
lower km means a more effective enzyme with a higher velocity 
KM and V max
Give info about substrate binding and catalysis
How it is achieving its particular velocity under particular conditions
More active enzymes have higher Vmax and lower cam values
But it is always advantageous
Higher KM leads to
More regulation
Most enzymes have a KM above the usual concentration of substrate, and usually acting inside of a cell, because they can show greater degree of regulation that can be adaptive and selected for, and is more useful than a higher enzyme activity
This is the Location on an enzyme that directly binds to the substrate molecules
Active site
What concept helps to explain why enzyme only catalyze on specific reactions
Lock and key model
This variable reflects how well and enzyme and substrate bind each other
Km
This idea helps to explain how an enzyme can lower an activation energy
Induced fit model
Which variable describes the fastest possible read that an enzyme can work out and it’s only achieved when there is an infinite substrate concentration
Vmax
Is it applying heat a good way to speed up a reaction why does it not work well for biological systems?
In chemistry, that might be the solution however, in biology, adding heat, can denature the protein cause the membrane to become too fluid and eventually kill the organism
Why do enzymes generally catalyze only one specific reaction?
Highly specific
How does the lock and key model different from the induced fit model?
Locke and key model expresses that the active site is made specifically for a substrate. However, the induced fit model suggest that the substrate make room for themselves against the active site.
Having too much specificity can be bad but also not good
How do enzymes affect
Delta G 0’ effect
keq no effect
Ea lowers activation energy
Enzymes, lower activation energy
To increase rate, but has no effect on delta G0, prime or KEQ
Vmax reflects
Catalysis rate
KM reflects
Substrate binding 
Other than changing the concentration of substrate how, can we change enzyme activity I terms of regulation
Any enzymes can be regulated by post translational modification  in addition, or subtraction of a phosphorylation can impact how an enzyme is regulated, and their speed phosphorylation has a negative charge, which can impact a 3-D structure of an enzyme that can change the enzyme from an inactive to an active 
Another way that we can change enzyme activity
Regulated by other small molecules
inhibitors
Bind to the active site
Inhibitors can, and are not limited to drugs
Inhibitors are produced by humans to slow down enzymes under the appropriate physiological circumstance 
Competitive inhibitor
A competitive inhibitor is a molecule that looks like the substrate, however, can’t be acted upon by the enzyme
Looks enough like a substrate that you can bind on the active site  call me no catalysis happens once it is found there
Once that inhibitor is bounded to the active site, the substrate can no longer get in there
How does the competitive inhibitor affect the max and KM
No effect on Vmax however, the km is increased
Velocity on inhibitors is
Always lower
Vmax reflects
how fast catalysis is happening after the substrate is bound
Allosteric site
Site that binds to the enzyme outside of the active site
When an allosteric inhibitor binds to an enzyme, it changes the whole structure of the enzyme pushes on the enzyme through induced fit
As a result, this distorts, the active site and this in turn lower the rate of enzyme activity,
How does allosteric inhibitor in fact, the max and KM
There are two sub classes
Pure, non-competitive inhibitors lower Vmax, but have no effect on KM
Have subtle shifts on the active site such that the substrate still binds, but there is no catalysis
Mixed noncompetitive, inhibitors lower Vmax, and raise KM 
Are enzyme binding doesn’t happen, and catalysis doesn’t happen 
Activators
Always work through the allosteric site may be pure or mixed 
If we have any equilibrium of one over two, and the Delta G0 prime is +0.43 kcal per mole how many molecules will we have at equilibrium if we start with 3000 molecules of two peachy
Because the ratio is 2 to 1 in other words for every one product we have two reactants we need to add up to 3000 so 2000+1000 
If we wanted more products,
we would have to add more products
How can we compare enzyme activities?
specific utility
Specific activity
Take the initial, velocity and normalize it right by the total amount of protein present in our lyse
E. coli had an enzyme velocity of 120 µmol per second and 10 µg of protein
S pyogenes a velocity of 40 µmol per second and 4 µg per protein
By dividing for E. coli, you have 120÷10 which equals 12 micromol per second per microgram
40÷4= 10 micro moles per second per microgram
How would pH affect an enzymes function
Not ideal pH denature some of the enzymes however, each enzyme has its own optimal pH 
Pepsin is active in our stomach
Has a pH of two or an acidic environment
Trypsin
Has an optimal pH of eight  or a basic environment 
Howard temperature have an effect on enzyme function
Each enzyme has a different optimum
Denaturation happens at too high temperatures
More heat energy helps overcome the activation energy. Barrier.
on  the other hand less heat, apply less energy to overcome the activation energy barrier
