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
The ________ can drive self-assembly in biological systems
hydrophobic effect
Describe the hydrophobic effect
nonpolar substances in water can’t interact with water and, at an entropic cost, water must surround the nonpolar substance in an ordered fashion (unfavorable). Water is not repelled by nonpolar substance but will form cages around them. Ampipathic molecules will self-assemble into layers or micelles (or proteins must fold to hide nonpolar portions) to increase the entropy of water
Molecules that have both polar and nonpolar regions are known as _______
amphipathic
Is the hydrophobic effect spontaneous or not spontaneous?
spontaneous
What is the Bronsted-Lowry definition of Acid and Base?
Acid is a proton donor and Base is a proton acceptor.
Water can dissociate into ____ and ____ ions.
Protons and hydroxyl ions
The equilibrium of water dissociation is described by the ______
Product of water (Kw)
Kw = [H+] [OH-] = 1 x 10^-14
The concentration of protons is usually expressed as ___
pH
pH = -log [H+]
When an acid dissociates, it produces a _____ and a _____.
Proton and an anion (conjugate base)
The acid and the corresponding anion (conjugate base) are known as the _________
Conjugate pair
Bases join with protons to make a _____.
Conjugate acid.
The STRENGTH of an acid (its tendency to give up its proton) is expressed by the ________
Acid dissociation constant (Ka);
What is the Ka in a strong acid vs. a weak acid?
Strong acids have high Ka values vs. weak acids have small Ka values
What is the equation for the acid dissociation constant (Ka)?
For the acid HA, HA H+ + A-
Ka = [H+] [A-] / [HA]
Define pKa
The pH of the solution when the molar concentrations of the acid and its conjugate base are equal. It is the -logKa which is log(1/Ka)
What is the purpose of the Henderson-Hasselbach equation and what is the actual equation?
Useful for estimating the pH of a buffer solution and finding the equilibrium pH in an acid-base reaction. The equation is derived from taking the acid dissociation constant equation (Ka) and rearranging it, then taking the logarithms of that equation:
pH = pKa + log ([A-]/[HA])
Some acids carry __________ which can dissociate sequentially at different pKa.
Multiple protons; The first proton dissociates more readily than the second.
What is the pKa for a strong and weak acid (high or low)?
Strong acid (low pKa); Weak acid (high pKa)
True or false: water is capable of dissociating
True
What is a buffer and when is the buffering capacity at its best.
Buffers are composed of weak acids and their conjugate bases (or weak bases and their conjugate acids) used to make systems less sensitive to the addition of strong acids or bases. They function greatest when they are at the pKa of the acid or base (no more than +/- 1 pH unit away from the pKa value.
_______ are the building blocks of proteins.
Amino acids
What are some functions of amino acids?
Precursors for biologically important compounds (heme, purines, pyrimidines, neurotransmitters, hormones); utilized as fuel for metabolism
What is the general structure of an amino acid
An alpha (central) carbon surrounded by four substituents: Amino group (NH2), Carboxylic acid (COOH), Side chain (R), Hydrogen
Since there are four different substituents attached to the alpha carbon, this carbon is _______. This means two different versions of any amino acid are possible. These are called ______ or _____ and are mirror images of one another also called ______
asymmetric; optical isomers or stereoisomers; enantiomers
True or false: only D-amino acids are found in proteins.
False; only L-amino acids are found in proteins. D-amino acids are found in nature (bacterial cell walls) but are not incorporated into proteins.
How do the 20 amino acids side chains differ and what determines how a protein will fold and function?
Side chains differ in size, polarity and charge. The proteins amino acid sequence determines how it will fold and function.
The 20 amino acids based on side chain structure can be classified as _____ or ______
apolar or polar
What is a characteristic about the apolar (nonpolar) side chains and name all of the apolar amino acids.
Hydrocarbons; Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline
Which amino acid is achiral? Why?
Glycine; Its side chain is a single hydrogen
_____ is an apolar amino acid in which the side chain is covalently linked to the amino group forming a cyclic structure.
Proline
Polar amino acids can be subdivided based upon _____ exhibited by their side chains at physiologic pH. The three groups are: ____, ____ and _____.
Charge; neutral, basic, acidic
Which amino acids contain hydroxyl groups in their side chains? Why are hydroxyl groups important?
Serine, threonine, tyrosine; They can serve as phosphorylation sites for kinases or attachment points for other modifiers (sugars)
What are the polar neutral amino acids?
Serine, Threonine, Tyrosine, Asparagine, Glutamine, Cysteine
The side chains of cysteine contains a ______ group that is quite reactive. These groups of two cysteine residues can be oxidized to form a covalent ______.
sulfhydryl (thiol) group; disulfide bond
Two covalently bonded cysteines form a species known as ______
Cystine
What are the polar basic amino acids? Which are strongly basic and weakly basic
Lysine, Arginine, Histidine
Lysine and Arginine are strongly basic. Histidine’s side chain contains the weak base imidazole and is close to physiological pH. Small changes in pH will change the histidine side chain’s protonation state from uncharged to charged and vice versa.
What are the polar acidic amino acids?
aspartate and glutamate; they readily donate protons leaving them with net negative charge as physiological pH. The uncharged forms (protonated) are known as aspartic acid and glutamic acid
What is the difference between aspartic acid and asparagine?
They are different amino acids. Aspartic acid contains a carboxylic acid, asparagine contains an amide.
What part of the amino acids are peptide bonds formed?
The hydroxyl group on the carboxylic acid covalently bonds to the amino group on another amino acid (condensation reaction; loses H2O)
Peptides and pH: what happens when you link amino acids together into a peptide?
You lose the acidic or basic groups (ionizable groups)
What is the “net charge” of the peptide?
The SUM of the charge states of ALL ionizable groups
What is Isoelectric point (pI)?
The pH value at which all positive and negatively charged groups of a protein are balanced, yielding a net charge of zero.
What charge does the protein have if the pH < pI; when the pH > pI?
pH < pI: protein has a net positive charge
pH > pI: protein has a net negative charge
How many ionizable groups does an amino acid have?
Two or three. At least two (amino group and carboxylic acid); three if the side chain is ionizable as well
What is the pKa for the carboxylic acid group and the amino group? What kind of graph or curve does this create?
carboxylic acid (2-3); amino group (9-10); biphasic titration curve.
True or false: the peptide bond is readily ionizable
False; formation of the peptide bond makes it not easily ionizable compared to the separate amino acids
When basic groups on amino acids with a pKa of 9-12 are placed into solution of pH 7.5, will the groups be protonated or deprotonated and what will their charge be?
Protonated; positively charged.
When acidic groups on amino acids with pKa of 2-4 are placed into a solution of pH 7.5, will the groups be protonated or deprotonated and what will their charge be?
deprotonated; negatively charged
Below its pI, a protein will have a net ____ charge, above its pI, a protein carries a net _____ charge.
Positive, negative
At its pI value, a protein will typically be at its _______(lowest/highest) solubility in aqueous solution
Lowest (no net charge)
