Lecture 1: Introduction and review

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Lecture 1: Introduction and review
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Quiz 1
Website: http://www.esf.edu/chemistry/nomura/fch530/
Review of acid/base chemistry
Universal features of cells on Earth
Cell types: Prokaryotes and Eukaryotes
Quiz Friday on the 20 amino acids-you need to
know the structures, names, single letter codes,
and pKa’s of the side chains
Review of pH, acids, and bases
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pH is generally defined as the negative logarithm of the hydrogen ion
activities (concentration) expressed over 14 orders of magnitude
pH = -log10 [H+]
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The pH scale is a reciprocal relationship between [H+] and [OH-]
Because the pH scale is based on negative logarithms, low pH values
represent the highest [H+] and thus the lowest [OH-]
At neutrality, pH 7, [H+] = [OH-]
Review of pH, acids, and bases
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Strong electrolytes dissociate completely in water
– Electrolytes are substances capable of generating ions in solution
– Increase the electrical conductivity of the solution
The dissociation of a strong acid in water
H3O+ + Cl-
HCl + H2O
The equilibrium constant is
K=
[H3O+][Cl-]
[H2O][HCl]
[H2O] is constant in dilute aq. Solutions and is incorporated into the equilibrium constant.
giving rise to a new term Ka-the acid dissociation constant = K[H2O], [H3O+] is
expressed as [H+]
[H+][Cl-]
Because Ka is large for HCl,
[H+] in solution = [HCl] added to solution.
a
K=
[HCl]
Thus, a 1M HCl solution has a pH of 0, a
1 mM HCl solution has a pH of 3, and so
on. Conversely, 0.1 M NaOH solution has
a pH of 13.
Ka=
[H+][Cl-]
[HCl]
For a strong acid Ka will approach be large because
the nearly all of the protons will be dissociated.
The [H+] at equilibrium is equal to the initial
concentration of the acid.
Calculate the pH of a 1M HCl solution
HCl + H2O
H3O+ + Cl-
0.0004% at equilibrium
99.996% at equilibrium
Since we are at equilibrium, H3O+ is equal to the initial concentration of acid.
[H+] = [H3O+] = [HCl] = 1M
We know that pH is the -log of [H+], therefore for 1M HCl at equilibrium
pH = -log10 [H+]
pH = -log10 (1)
pH = 0
[H+]
pH
[OH-]
0
(100)
1.0
0.00000000000001
(10-14)
1
(10-1)
0.1
0.0000000000001
(10-13)
2
(10-2)
0.01
0.000000000001
(10-12)
3
(10-3)
0.001
0.00000000001
(10-11)
4
(10-4)
0.0001
0.0000000001
(10-10)
5
(10-5)
0.00001
0.000000001
(10-9)
6
(10-6)
0.000001
0.00000001
(10-8)
7
(10-7)
0.0000001
0.0000001
(10-7)
8
(10-8)
0.00000001
0.000001
(10-6)
9
(10-9)
0.000000001
0.00001
(10-5)
10
(10-10)
0.0000000001
0.0001
(10-4)
11
(10-11)
0.00000000001
0.001
(10-3)
12
(10-12)
0.000000000001
0.01
(10-2)
13
(10-13)
0.0000000000001
0.1
(10-1)
14
(10-14)
0.00000000000001
1.0
(100 )
Review of pH, acids, and bases
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Weak electrolytes only slightly dissociate in water
– Acetic acid, CH3COOH
The dissociation of a weak acid in water
CH3COOH + H2O
H3O+ +
CH3COO-
The acid dissociation constant is
Ka =
[H+][CH3COO-]
[CH3COOH]
= 1.74 X 10-5 M
Ka is also called the ionization constant, because Ka is small, most of the acetic acid is
not ionized.
Acid dissociation constant
– The general ionization of an acid is as follows:
HA
H+ +
A-
So the acid dissociation constant is as follows:
Ka =
[H+][A-]
[HA]
There are many orders of magnitude spanned by Ka values, so pKa is used instead:
pKa = - log10 Ka
The larger the value of the pKa, the smaller the extent of dissociation.
pKa <2 is a strong acid
Henderson-Hasselbalch Equation
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Describes the dissociation of a weak acid in the presence of its
conjugate base
– The general ionization of a weak acid is as follows:
HA
H+ + ASo the acid dissociation constant is as follows:
Ka =
[H+][A-]
[HA]
Rearranging this expression in terms of the parameter of interest [H+] gives the
following:
[H+]
=
Ka [HA]
[A-]
Henderson-Hasselbalch Equation
Take the log of both sides:
log[H+]
=
[HA]
log Ka + log
[A-]
Change the signs and define pKa as -log Ka :
pH = pKa - log
[HA]
[A-]
or
pH = pKa + log
[A-]
[HA]
Titration curves and buffers
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Titration curves can be calculated by the
Henderson-Hasselbalch equation
– As OH- is added to the reaction, it reacts
completely with HA to form A-
[A-] =
x
vol
x = the equivalents of OH- added and V
represents the volume of the solution. If we
let co represent HA equivalents initially
present, then:
[HA] =
(co-x)
vol
We can reincorporate this into the HendersonHasselbalch eqn.
x
(c -x )
pH = pKa + log
o
Buffers
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Buffers are solutions that resist changes in their pH as acid (H+) or base (OH-) is added.
Typically, buffers are composed of a weak acid and its conjugate base.
Acids = Proton (H+) donors
Bases = Proton Acceptors
HA
Acid
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H+ + Aconjugate base
Acids and their conjugate bases are in equilibrium. Equilibria are related to the properties of the
reactants and products, so for weak acids, the tendency to give up its proton determines its
buffering property
+
The tendency to ionize can be put in an equilibrium equation
Ka=
[H ][A ]
[HA]
A solution of a weak acid that has a pH near to its pKa has an equivalent amounts of conjugate
base and weak acid.
Typically a weak acid is in its useful buffer range within 1 pH unit of its pKa.
Polyprotic acids
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Have more than one acid-base group
H3PO4 and H2CO3
The pK’s of two closely associated acid-base groups are not independent - the closer
they are, the greater the effect.
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Examples: oxalic acid and succinic acid
OO
H-O-C-C-O-H
pK differs by 3 pH units
O
O
H-O-C-CH2CH2-C-O-H
pK differs by 1.4 pH units
Polyprotic acids
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The effect of having
successive ionizations
from the same center is
even greater.
However if pK’s of
polyprotic acid differ by
less than 2 pH units, this
reflects the average
ionization of all of the
groups.
Universal features of cells
• “Life possesses the properties of replication, catalysis, and
mutability.” - Norman Horowitz
• Life requires free energy.
– Main energy currency is
• ATP (bond energy, G)
• NADH, NADPH (redox energy)
– All cells obey the same laws of thermodynamics (see Ch.3).
 G (Gibbs free energy) must be negative (spent)
 S (Entropy) increases
– Sources of energy may vary
• Purple sulfur bacteria
• Humans
• Plants
H2S
CH2O
h
So
H2O + CO2
Universal features of cells (cont.)
• Most organisms are composed of only 16 chemical elements
• (H,C,N,O,P,S,Mn, Fe, Co, Cu, Zn, Na, Mg, Cl, K, Ca).
– Chemical makeup appears to be determined partly by the availability of
raw materials and the specific roles of molecules in life processes.
– Do not reflect the composition of the biosphere
– Examples on per atom basis, H in organisms = 49%, H in Earth’s crust
= 0.22 %, Si in organisms = 0.033%, Si in Earth’s crust = 28%)
• H, O, N, and C, make up >99% by weight of living matter are the
smallest atoms that can share 1, 2, 3, and 4 electrons
respectively.
• O, N, and C are the only elements that easily form strong
multiple bonds.
• O2 is soluble in water and readily available to all organisms.
• Phosphorous and sulfur are unstable in the presence of water.
– Require a large amount of energy to form.
– Energy released when they are hydrolyzed.
MW
18-44
N2, H2O, CO2
20 amino
acids
100-250
100-800 Amino acids
104-109
106-1010
Proteins
5 aromatic
bases,
ribose
Nucleotides
Nucleic acids
Glucose
Palmitate, glycerol,
choline
Sugars
Phospholipids
Polysaccharides
Multienzyme complexes, ribosomes, chromosomes,
membranes, structural elements
Organelles, Cells, Tissues, Organs,
Organsims
Universal features of cells (cont.)
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All cells function as biochemical factories and use the same basic
molecular building blocks.
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Proteins (amino acids
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Can be structural or catalytic
Enzymes
Transport (Na+/K+ pump)
Storage (ferritin)
Signals (hormones/toxins), examples insulin or botulinum toxin
Receptors
Structure (collagen, elastin)
Lipids (fatty acids
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polypeptides
lipids)
Membranes
Triglycerides (energy storage)
Phospholipds (membrane structure)
Sphingolipids (found in nerve cells and brain tissue)
Sterols (hormones and membranes)
proteins)
Universal features of cells (cont.)
• Carbohydrates
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Monosaccharides (glucose, fructose)
Disaccharides (sucrose, maltose)
Trisaccharides (raffinose)
Complex carbohydryates
• Starch (energy storage)
• Cellulose (structure, cell wall)
• Cell-cell recognition
• Nucleic acids
– DNA (genetic material)
– RNA (mRNA, tRNA, pre-mRNA or hnRNA, rRNA)
• Proteins and nucleic acids are produced by the same rules
– Central dogma
DNA
RNA
• A living cell can exist with fewer than 500 genes!
Protein
Types of cells
• There are two major cell types: eukaryotes and prokaryotes.
• Eukaryotes have a membrane enclosed nucleus encapsulating
their genomic DNA.
• Prokaryotes do not have a nucleus.
Prokaryotes
Eukaryotes
Bacteria,
Archaea
Fungi, Protists,
Animals, Plants
1-10 µm
10-100 µm
General schematic for a prokaryote cell
General schematic of an animal cell
General schematic of a plant cell
MW
18-44
N2, H2O, CO2
20 amino
acids
100-250
100-800 Amino acids
104-109
106-1010
Proteins
5 aromatic
bases,
ribose
Nucleotides
Nucleic acids
Glucose
Palmitate, glycerol,
choline
Sugars
Phospholipids
Polysaccharides
Multienzyme complexes, ribosomes, chromosomes,
membranes, structural elements
Organelles, Cells, Tissues, Organs,
Organsims

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