Chemistry Chapter 7: Acid-Base Chemistry Flashcards
Log trick for pH
1) put concentration value into scientific notation
2) move decimal one to the left
3) positive value exponent - coefficient
Ie 0.003M
3 x 10^-3
0.3
3-0.3
pH = 2.7
pI
The isoelectric point where the pH of an amino acid has no net charge (a zwitterion)
zwitterion
is a molecule that has both positive and negative charges on different atoms but is overall electrically neutral
At the equivalence point on a titration curve (strong base or acid) added
moles of the analyte = moles of strong acid/base
Henderson-Hasselbalch Equation.
Relates pH to pKa for a weak acid
Relationship between pH and pKa @ the midpoint
pH = pKa. because midpoint is where 1/2 of the weak acid (HA) has been neutralized by the base. Therefore, pH = pKa + log(1)
Why are BF3, BCL3, AlCl3 and AlF3 lewis acids
They don’t have a full octet and therefore electron deficient. They all accept e-
For example, these acids could form a coordinate covalent bond with NH3, a lewis base (resulting in no conjugate base)
Definition of Arrhenius Acid/Base
Acids dissociate to form H+ ions
Bases dissociate to form OH- ions
least broad defintion
Bronsted Lowry
Acid = proton donor
Base = Proton acceptor
middle broad definition
*** MCAT is typically referring to this definition
Lewis Definition
Acid = Electron acceptor
Base = Electron donor
***helps explain redox
Most broad
Amphoteric species
can either accept or donate a proton
Acid-Base Equilibria
Equilibria of reactions in which protons are gained and lost
Kw defintion
autoionization equilibrium constant
Autoionization of water
Doesn’t go to completion, vastly favors the reactants. H3O+ and OH- are 1:1 therefore, solution stays neutral
Kw = ?
don’t include liquid water because you don’t use pure liquids in equilibrium equations
1 x 10^-14 @ standard conditions
If temperature changes, does the pH of water change
yes. because H3O+ and OH- are always equal, pH can change from 7 but the solution will always be neutral
Simple Acid reaction in water
Simple Base reaction in water
High Ka favors products or reactants?
Products because Ka = [products]/[reactants]
Strong acids/strong base and dissociation
fully dissociate. Ka/Kb higher than 1
weak acids/weak base
don’t fully dissociate Ka/Kb lower than 1
Strong acids to know for the MCAT
Stromg bases to know for the MCAT
For strong acids/base you can assume what about the concentration of starting reactants and end products
reaction goes to completion, meaning that for example 3M HCl (reactant) will be equal to 3M H3O+ (product)
acid-base chemistry is subject to
common ion effect ***watch out for this!
Common Ion effect Acid + acidic solution =
Acid ionizes less
Common Ion effect Base + acidic solution =
Base ionizes less
pKw =
pH + pOH
pH + pOH =
14
pKa =
-logKa
pKb =
-logpKb
pKa + pKb =
-logKw = 14
Ka*Kb =
Kw = 1 x 10^=14. here Ka = acid and Kb = conjugate base
True or false: Acidic side chain amino acids can also exhibit basic properties
True - depending on the pH
in acidic conditions (example pH) of 1, does protonation or deprotonation happen?
Protonation because there is excess H+ in solution
in basic conditions (example pH) of 14, does protonation or deprotonation happen?
Deprotonation because excess OH- want another H+
Amine group is charged or neutral when it’s protonated?
Charged (+1)
Carboxylic acid group is charged or neutral when protonated?
Neutral
why does pH denature acidic and basic amino acids?
preventing interactions between charged side chain
Decreases in pH can change the protonation state of acidic and basic amino acids, preventing ionic attractions between oppositely charged pairs. This can cause major tertiary structural changes in proteins that contain a high proportion of acidic and basic residues
written definition of pKa
willingness of a compound to give up its proton
definition of pH
measures the acidity of a solution, specifically the concentration of hydrogen ions in the environment.
Difference between pKa and pH
pKa - compound specific and describes how a compound responds to the environment
pH - solution-wide and describes the environment
what happens if pKa > pH
The environment is more acidic, so the compound tends to remain protonated.
what happens is pKa < pH
The environment is more basic so the compound will become deprotonated
what happens when pKa = pH
50% of molecules are protonated and 50% deprotonated
Alanine side chain pKa is 2.34. What does that mean at pH below 2.34, above and equal to?
When pH = 2.34 50% protonated, 50% deprotonated
pH<2.34 More are protonated (positively charged)
pH>2.34 More are deprotonated (negatively charged)
Titration with AA is what kind of titration?
Weak acid + strong base
As you add more base to a titration (move up a titration curve), what trend occurs with the charge of the amino acid?
Tends to become more negative because base deprotonates
Half equivalence point
mid point, flat because 1/2 compound exist protonated and deprotonated. pH = pKa of group
@ the equivalence point
, all compounds from specific group have been deprotonated
difference between pKa and pI
pKa = acidity of a single group, pI = where a full peptide is neutral
True or false: here is always a 1:2 ratio of acid to base at the second equivalence point in a titration, regardless of which amino acid was titrated.
true
how to find pI from pKa values (no curve) - acidic
pI - average of the 2 lowest pKas
how to find pI from pKa values (no curve) - basic
pI - average of the 2 highest pKas
pI occur at the
For a simple amino acid with only one acidic and one basic group, the isoelectric point will generally coincide with the equivalence point on a titration curve, as this is the pH where the net charge of the amino acid is zero; however, for amino acids with more complex side chains, the isoelectric point may not align exactly with a single equivalence point depending on the pKa values of the different ionizable groups. points
For the titrations performed in the study of acetic acid, a weak acid, and sodium hydroxide the endpoint of the titration will occur at a pH ____________ than 7
Greater
Rule of thumb for picking indicators based on pKas
When effectively chosen, an indicator undergoes a color change near the desired pH (solution pH). The pKa (acidity of the compound) of a chosen indicator should be within ±1 unit of the target pH.
Weak acid titrations equivalence points
Typically higher than 7
Below isoelectric point, amino acids are more likely to be ___________ Below isoelectric point, amino acids are more likely to be __________
Positive below isoelectric (PROTONATION DOMINATES)
Negative above isoelectric (DEPROTONATED DOMINATES)
THIS IS NAOH - NOT AN ACID!!! So pH is 12
How to find pKa for each oligonucleotide
pKa corresponds to the pH where 50% of the DNA is folded and 50% is unfolded.
This occurs at the midpoint of the unfolding transition in the graph.
To find pKa, locate the pH where the normalized CD signal is approximately 0.5 for each oligonucleotide.
IE WT (solid line): pKa ≈ 6.3
5mC-WT (dashed line): pKa ≈ 6.5 (highest pKa)
5hmC-WT (dotted line): pKa ≈ 5.9 (lowest pKa)
Equilibrium equation for Ka
Equilibrium equation for Kb
