Lecture 1: Fundamentals Flashcards
What is 1st law of thermodynamics?
Energy is neither created nor destroyed; however energy can change form
Heat is defined as:
How quickly molecules are moving (kinetics)
What is potential energy?
Stored energy (eg. high energy bonds in ATP); energy that will be released when a process occurs
The EXTENT of the reaction is described by ______ and the RATE of the reaction is described by _______
Equilibrium; Kinetics
What is enthalpy? What is it called when H is < 0 or > 0?
The heat of the reaction. When energy is released or consumed in a chemical reaction, this energy is manifested in form of heat. Exothermic (negative number = gives off heat); Endothermic (positive number = absorbs heat)
What is the 2nd law of thermodynamics?
Entropy (S) is always increasing (overall/universal entropy)
What does it mean when Entropy (S) is > 0? When S is < 0?
S > 0 (positive number) is favorable; S < 0 (negative) is unfavorable
Is binding of a flexible ligand entropically favorable or unfavorable and why?
Unfavorable. A flexible peptide can have many different conformations and the receptor can only accept one conformation. The statistical likelihood for getting the right conformation is low. Also, a bound ligand is locked into one conformation (decr entropy). Even though the local entropy is low, the overall system entropy may still be high.
______ determines whether a process/reaction is favorable or will occur spontaneously
Free energy (G)
What is the Free energy equation?
G = H - TS
What does it mean if Free energy (G) is < 0 or > 0?
G < 0 (negative) means a reaction is favorable, spontaneous and exergonic; G > 0 means a reaction is unfavorable, not spontaneous and endergonic
What is G (Free energy) at equilibrium?
Zero
What does it mean for reactions be thermodynamically coupled?
The overall G for a series of reactions equals the sum of the G’s of the individual steps; i.e. a thermodynamically unfavorable reaction can be driven by a thermodynamically favorable one
What is kinetic energy? How does heat affect kinetic energy?
Molecular motion ; Increased heat = increased motion
What kinds of energy do we encounter in biochemical systems?
Kinetic energy and potential energy
What is Entropy?
A measure of the randomness or disorder of a system (S); it is a reflection of statistical probability
What is Entropy?
A measure of the randomness or disorder of a system (S); it is a reflection of statistical probability
Describe the equation for the equilibrium constant (K) and how this relates to reactions.
K = [C][D] / [A][B]
Reactions aren’t all or none and will go back and forth; the concentrations in this expression are at equilibrium not at starting
Describe the equation that relates equilibrium constant to free energy equation.
G = G* + RTlnK (G* is the free energy change under standard conditions; R is the gas constant; T is absolute temperature). At equilibrium, G is 0, so the equation is rearranged as such: G* = -RTlnK
G* = -RTlnK describes what?
It is the link between equilibrium constant and free energy; it describes the extent of the reaction (not the rate)
What does a high equilibrium constant (K) mean?
That G will be more negative and the molecules wants to spend more time in products
Describe first order rates of reactions.
A –> P Rate = k1 [A] Rate is proportional to the concentration of A raised to the first power
Describe second order rates of reations
A + A –> A2 Rate = k2 [A]^2
A + B –> C + D Rate = k3 [A] [B]
Describe psuedo-first order rates of reactions
A + H2O –> X Rate = k4 [A] {H2O]
Water is constant (bc there is so much of it and little is consumed) so equation can be rewritten as first order even though it is second order : Rate = k5 [A]
This applies to situations where concentrations of one of the reactants doesn’t change much during rxn
How is rate of reaction related to equilibrium?
A + B C + D Rate (forward) = k1 [A] [B] Rate (back) = k-1 [C] [D] At equilibrium there is no net change so forward and back are equal: k1 [A] [B] = k-1 [C] [D] K = [C][D]/[A][B] = k1/k-1
What determines the rate constants?
Activation energy (G++)
What is activation energy (G++)?
A measure of energy required to excite molecules into a transition state that is capable of progressing into products. The higher the barrier (transition state), the slower the reaction and the more kinetic energy is needed or a catalyst
What can lower the transition state?
A catalyst like an enzyme
The large difference in ______ between oxygen and hydrogen means that water is a _____ molecule
electronegativity; polar
How do the polar interactions of water affect the physical properties compared to CH4, NH3, H2S?
It greatly increases boiling and melting point compared to other liquids because of high hydrogen bonding
What are hydrogen bonds?
Noncovalent electrostatic interactions in which the electrons on oxygen interact with a hydrogen on another molecule. These are seen in both solid and liquid water and stabilize water immensely.
Besides hydrogen bonds, what are other examples of electrostatic noncovalent bonding?
charge-charge; charge-dipole; dipole-dipole; charge-induced dipole; dispersion
Why are weak interactions important?
The sum of the weak interactions stabilizes molecules; contributes to protein folding, DNA shape and transcription