chapter 2 : water
DESCRIPTION
Chapter 2 : Water. Learning goals :. What kind of interactions occur between different type of molecules in water. Why water is a good medium for life Why nonpolar moieties aggregate in water How dissolved molecules alter properties of water - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/1.jpg)
Chapter 2 : Water
![Page 2: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/2.jpg)
• What kind of interactions occur between different type of molecules in water.
• Why water is a good medium for life• Why nonpolar moieties aggregate in water• How dissolved molecules alter properties of water• How weak acids and bases behave in water: to be able to
solve weak acid problems with the Henderson-Hasslebalch equation.
• How buffers work and why we need them• How water participates in biochemical reactions
Learning goals:
![Page 3: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/3.jpg)
Structure
![Page 4: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/4.jpg)
ICE
![Page 5: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/5.jpg)
Common H-bonds in Biochemistry
![Page 6: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/6.jpg)
Some Biologically Important H-bonds
![Page 7: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/7.jpg)
H-bond Strength and Alignment
![Page 8: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/8.jpg)
Importance of Hydrogen Bonds
• Source of unique properties of water• Structure and function of proteins• Structure and function of DNA• Structure and function of polysaccharides• Binding of substrates to enzymes• Binding of hormones to receptors• Matching of mRNA and tRNA
“I believe that as the methods of structural chemistry are further applied to physiological problems, it will be found that the significance of the hydrogen bond for physiology is greater than that of any other single structural feature.”
–Linus Pauling, The Nature of the Chemical Bond, 1939
![Page 9: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/9.jpg)
Water as a Solvent
• Water is a poor solvent for nonpolar substances– nonpolar gases– aromatic moieties– aliphatic chains
• Water is a good solvent for charged and polar substances– amino acids and peptides– small alcohols– carbohydrates
![Page 10: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/10.jpg)
![Page 11: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/11.jpg)
Solvation and Hydration Spheres
![Page 12: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/12.jpg)
![Page 13: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/13.jpg)
Flickering Clusters and Clathrate Cages
![Page 14: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/14.jpg)
The Hydrophobic Effect• Refers to the association or folding of nonpolar
molecules in the aqueous solution
• Is one of the main factors behind:– protein folding
– protein-protein association
– formation of lipid micelles
– binding of steroid hormones to their receptors
• Does not arise because of some attractive direct force between two nonpolar molecules
![Page 15: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/15.jpg)
![Page 16: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/16.jpg)
Substrates Must Displace Water to Bind Enzymes
![Page 17: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/17.jpg)
Approximate Bond Strength, kJ/mole
12-30
20
<40
0.4 – 4.0
Distance,nm
0.3
0.25
-
0.2
![Page 18: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/18.jpg)
Water Bound to Hemoglobin
Hb purified from water Hb with Water Removed
![Page 19: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/19.jpg)
Proton Hop and Hydronium
![Page 20: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/20.jpg)
Water Bound in a Protein Channel (Cytochrome f)
Facilitates Proton Hopping – see later in Photosynthesis
![Page 21: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/21.jpg)
![Page 22: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/22.jpg)
Osmotic Pressure
![Page 23: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/23.jpg)
Cell Response to Osmotic Pressures
![Page 24: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/24.jpg)
Plants Use Osmotic Pressure
![Page 25: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/25.jpg)
Plants Use Osmotic Pressure
Protection Against Wind
![Page 26: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/26.jpg)
Ionization of Water
Keq = [H+][OH-] / [H2O] = 1.8 x 10-16 M
Concentration of water - one liter = 1,000g
Mole Wt Water = 18.015
[H2O] = 55.5 M
Kw = [H+][OH-] = Keq x [H2O] = 1 x 10-14 M2
for pure water [H+] = [OH-]
so, [H+] = 10-7 M
pH is negative log [H+] , for pure water = 7.0
![Page 27: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/27.jpg)
![Page 28: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/28.jpg)
![Page 29: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/29.jpg)
Weak Acids
HA ↔ H+ + A-
K e = [H+][A-] / [HA] = Ka
Henderson-Hasselbalch Equation Rearranges Ka
pH = pKa + log ( [A-] / [HA] )
when pKa = pH … [A-] = [HA]
![Page 30: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/30.jpg)
![Page 31: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/31.jpg)
A
![Page 32: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/32.jpg)
![Page 33: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/33.jpg)
Weak acids have different pKas
![Page 34: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/34.jpg)
![Page 35: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/35.jpg)
Enzymes have pH optima Related to their Function
![Page 36: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/36.jpg)
![Page 37: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/37.jpg)
Water as a Reactant
![Page 38: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/38.jpg)
![Page 39: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/39.jpg)
1 liter of 0.1 M glycine.
a. what pH’s is glycine a good buffer due to its amino group:
Problem 18 in Chapter 2
![Page 40: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/40.jpg)
1 liter of 0.1 M glycine.
a. What pH is glycine a good buffer due to its amino group:
NH3+
Glycine = CH2-COO-
pKa’s = 2.34 and 9.6
So it would be good +/- 1.0 from each pKa
which would be from 1.3 to 3.3 and 8.6 to 10.6 for the amino group.
Problem 18 in Chapter 2
![Page 41: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/41.jpg)
I liter of 0.1 M glycine.
b. in a 0.1 M solution, pH 9.0 what fraction has the amino group as –NH3
+ ?
Example of a Clicker Question: R-NH3+ is
A.HA
B.A-
C.H2O
D.H+
E.OH-
Problem 18 in Chapter 2 NH3
+
Glycine = CH2-COO-
pKa’s = 2.34 and 9.6
![Page 42: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/42.jpg)
Problem 18 in Chapter 2 NH3
+
Glycine = CH2-COO-
pKa’s = 2.34 and 9.6I liter of 0.1 M glycine.
b. in a 0.1 M solution, pH 9.0 what fraction has the amino group as –NH3
+?
pH = pKa + log A/HA
9.0 = 9.6 + log A/HA
log A/HA = -0.6 A/HA = 0.25 0.25HA = A
HA + A = 0.1M so HA + 0.25HA = 0.1 M :: 1.25HA = 0.1M
so HA = 0.08 M…and that is 80% of 0.1M so
not asked: A = 0.02 M or 20%
![Page 43: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/43.jpg)
Problem 18 in Chapter 2 NH3
+
Glycine = CH2-COO-
pKa’s = 2.34 and 9.6
I liter of 0.1 M glycine.
c. How much 5M KOH is needed to change pH from 9 to 10 for 1 Liter of 0.1M glycine?
![Page 44: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/44.jpg)
I liter of 0.1 M glycine.
c. How much 5M KOH is needed to change pH from 9 to 10 for 1 Liter of 0.1M glycine?
pH = pKa + log A/HA 10 = 9.6 + log A/HA
so: log A/HA = 0.4 thus A/HA = 2.5 2.5HA = A
HA + A = 0.1 M HA + 2.5 HA = 0.1 M 3.5HA= 0.1M
so HA at pH 10 = 0.029 moles/L
from pH 9 HA is converted to A by adding OH-, that is HA is lowered from 0.08M to 0.029M or a change of 0.051 moles
0.051 moles/5 moles/L = 0.01 L 10 ml of 5M KOH
Problem 18 in Chapter 2 NH3
+
Glycine = CH2-COO-
pKa’s = 2.34 and 9.6
![Page 45: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/45.jpg)
I liter of 0.1 M glycine.
d. When 99% of glycine is in its –NH3+ form, what is the
pH of solution due to it’s amino group? (functionally reworded from the text)
pH = pKa + log A/HA so this is easy HA dominates, so it will be on the acid side of the pKa. A is only 1% or 0.01 so the
log of A/HA ≈ -2 thus pH = 9.6 – 2 = or 7.6
Problem 18 in Chapter 2 NH3
+
Glycine = CH2-COO-
pKa’s = 2.34 and 9.6
![Page 46: Chapter 2 : Water](https://reader033.vdocuments.site/reader033/viewer/2022061617/56815b07550346895dc8b575/html5/thumbnails/46.jpg)
Things to Know and Do Before Class
1. General Chemical Properties of Water.
2. pH definition and what it means+how to calculate it.
3. Strong vs Weak Acids.
4. Henderson-Hasselbalch Equation and how to do calculations with it.
5. Weak bonds and their relative bond strength.
6. Make sure you are able to do EOC Problems calculating pH (2-5, 8), pH affects solubility (14) and uptake of aspirin (15) and rest on buffers (11): They are part of Class Clicker Questions and Case Study (aspirin).