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Chapter 2: Chemical Properties of Water

This document summarizes key concepts about the chemical properties of water and amino acids: 1) It describes water ionization and defines important constants like Kw and pH. Pure water has a pH of 7 when [H+] = [OH-]. 2) It introduces acid-base chemistry concepts like Brønsted-Lowry acids and bases, conjugate pairs, and the acid dissociation constant Ka. 3) It explains how the pH of a solution relates to the charge of acids and bases depending on whether pH is below, equal to, or above the pKa. The Henderson-Hasselbalch equation relates pH, pKa, and concentrations. 4) Buffers are defined

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Kyle Broflovski
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53 views28 pages

Chapter 2: Chemical Properties of Water

This document summarizes key concepts about the chemical properties of water and amino acids: 1) It describes water ionization and defines important constants like Kw and pH. Pure water has a pH of 7 when [H+] = [OH-]. 2) It introduces acid-base chemistry concepts like Brønsted-Lowry acids and bases, conjugate pairs, and the acid dissociation constant Ka. 3) It explains how the pH of a solution relates to the charge of acids and bases depending on whether pH is below, equal to, or above the pKa. The Henderson-Hasselbalch equation relates pH, pKa, and concentrations. 4) Buffers are defined

Uploaded by

Kyle Broflovski
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© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
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Chapter 2: Chemical Properties of Water

Ionization of water K, pH Acid-base chemistry pK, Henderson-Hasselbalch equation Buffers titration curves

Water Ionization: H+ and OHH2O H+ + HO H+ (proton), HO- (hydroxide), H3O+ (hydronium ion)

K = [H+] [OH-] [H2O]


Recall that K is an dissociation constant, and [A] represent the concentration of species A Recall also that [H2O] is 55.5M by definition but we ignore it since it remains constant, so the equation simplifies to:

K[H2O] = Kw = [H+] [OH-]


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Water Ionization: H+ and OHH2O H+ + HO-

Pure water has equal concentrations of H+ and HO[H+]=[HO-]=(Kw)1/2=10-7M for a neutral solution Therefore, KW =[H+][HO-] = 10-14 M2 pH = -log[H+], therefore, pure water pH = 7 If [H+]> 10-7M, then pH < 7, the solution is acidic If [H+]< 10-7M, then pH > 7, the solution is basic

Acid-Base Chemistry
HA + H2O CH3COOH + H2O
Acid

H3O+ + AH3O+ + CH3COOConjugate base

Brnsted-Lowry An acid is a substance that can donate a proton A base is a substance that can accept a proton In the above equation, HA is the acid and H2O is the base Also, A- is the conjugate base of HA (an acid) and H3O+ is the conjugate acid of H2O (a base)
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Acid-Base Chemistry
HA + H2O
Simplified Version:

H3O+ + A-

HA + H2O

H+ + A -

Ka

H A K[H O]
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HA

pKa = -log Ka
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Charge of Acid/Base as Function of pH


Acid (R-COOH): If pH<pKa, acid protonated, neutral (0) If pH=pKa, (50% ionized, -0.5) If pH>pKa, acid unprotonated, charged (-1) Base (R-NH2): If pH<pKa, base protonated, charged (+1) If pH=pKa, (50% ionized, +0.5) If pH>pKa, base unprotonated, neutral (0)
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Charge of Acid/Base as Function of pH


Acid

HA

H+ + ACharge = 0 Charge = -1

pH < pKa = H+ pH > pKa = H+


Base pH < pKa = H+ pH > pKa = H+

B + H+

HB+
Charge = +1 Charge = 0

REMEMBER: pH = -log [H+], so high [H+] = low pH! IN BOTH CASES, THE pKa DEFINES THE pH WHERE HALF OF THE ACID OR BASE IS IONIZED!
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Henderson-Hasselbalch Eq.

A - pH pK log HA
HA H K A -

A - pH -logK log HA

ONE OF THE MOST IMPORTANT EQUATIONS IN BIOCHEMISTRY! It can be used to compute the pH of a solution of a weak acid (HA) and its conjugate base (A-) 10

Buffers
A buffer is a solution that resists changes in pH when small quantities of a strong acid or strong base are added. Any weak acid (or base) can act as a buffer if the pH of the solution is near the pK midpoint for the compound (i.e. BY DEFINITION, pH=pK at the midpoint of the titration curve) Note on the figure on the next slide that the slope of the titration curve is relatively flat near the midpoint Therefore, addition of small quantities of a strong acid or base has little effect on the pH of the solution. You can use the Henderson-Hasselbalch Equation to explain this!
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Titration curves for some weak acids Note that the slope of each curve is quite flat near the midpoint and very sharp at the end points Note also that different compounds have different pK midpoints and pH profiles
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Here is the titration curve for a polyprotic acid (i.e. an acid that has more than one ionizable proton) Each proton has a different pKa. Each proton acts as a buffer near its pKa.
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Chapter 4: Amino Acids


Amino acid structure
General properties Peptide bonds Classification and characteristics Acid-base properties Nomenclature

Stereochemistry Nonstandard amino acids


Amino acid derivatives D-amino acids Biologically active amino acids
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Amino acid
Backbone of an amino acid is composed of the N, Ca, and C Amino acid structures and sequences are written from left to right, starting with the N-terminus (amino) and finishing with the C-terminus (carboxyl) The thing that differentiates each amino acid is the R group Ca is chiral, except in Gly
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Please carefully note the charged ends (termini). At physiological pH, the ends of an amino acid are charged. Certain R groups will also be charged at pH 7.

The backbone of individual amino acids are zwitterionic (i.e. has both a positively charged and a negatively charged group) Some amino acids have ionizable (i.e., charged) side chains Because of these ionizable groups (backbone and some side chains), amino acids can have a number of different charge states The R group in an amino acid is called the side chain An amino acid is often called a residue (i.e., an amino acid residue, especially in polypeptides and proteins) There are 20 standard amino acids - they all differ in R
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General Properties

Peptide Bonds
As mentioned previously, amino acids can be connected together (i.e. condensed) to form a bigger molecule, now containing two amino acids The bond formed is a peptide bond and the molecule is a dipeptide. If we add another amino acid, then we would have a tripeptide
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Condensation Reaction

Classification
Non-polar Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Methionine (Met, M), Proline (Pro, P), Phenylalanine (Phe, F), Tryptophan (Trp, W) Polar Serine (Ser, S), Threonine (Thr, T), Asparagine (Asn, N), Glutamine (Gln, Q), Tyrosine (Tyr, Y), Cysteine (Cys, C) Charged Aspartic acid (Asp, D, -1); Glutamic acid (Glu, E, -1) Lysine (Lys, K, +1); Arginine (Arg, R, +1), Histidine (His, H, +1)

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Amino acids
An amino acid is shown below in line, stick, ball and stick, and CPK (space filling) representations. What amino acid is it?

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Amino acids

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Amino acids

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Amino acids

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Amino acids
A tripeptide is shown below in stick (left) and CPK (right) representations quite a different impression, huh?! What is the sequence of amino acids?

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For next time:


We are not going through Chapter 3. It is not a bad idea to read (i.e. MCAT). Read Chapter 4, All Sections. Finish working through all problems you in Chapter 2. Start working through problems in Chapter 4. Keep memorizing amino acids structure, names (3 and 1 letter also), pKas for polar protonated side chains
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