1. Buffers Ka= HA H+ + A- [H+][A-] [HA]
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
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
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.
HA H+ + A-
Acid conjugate base
[H+][A-]
Ka=
[HA]

2. H-O-C-C-O-H H-O-C-CH2CH2-C-O-H
Polyprotic acids
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.
Examples: oxalic acid and succinic acid O O O O
H-O-C-C-O-H H-O-C-CH2CH2-C-O-H
pK differs by 3 pH units
pK differs by 1.4 pH units
Note that the curves have similar shapes but are shifted vertically according to pH
The pH at the equivalence point of each titration is where the equavalents of OH- = equivalents of HA is greater than 7. Because of the reaction of A- with water to form HA and OH-. Also note that the initial pH for all is below 7.
The pH at the midpoint of each titration is numberically equal to the pK of the corresponding acid, remember for Henderson-Hasselbalch, HA = A-
Ths slope of each titration curve is musch les near the midpoint than near the wings.

3. Polyprotic acids
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.
This is the titration curve of a 1-L solution of 1 M phosphoric acid. The two intermediate equivalence points occur at the steepest parts of the curve. Note the flatness of the curve near its starting and end points in comparison with the titration curves in the previous figure. This indicats that phosphoric acid is close to a strong acid and phosphate a strong base.

4. 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 H2S So
Humans CH2O H2O + CO2
Plants h
Norman Horowitz worked with Beadle and Tatum on the one gene one enzyme hypothesis.

5. 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 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.

6. Palmitate, glycerol, choline 100-250 GlucoseMW
N2, H2O, CO2
18-44
5 aromatic bases, ribose
20 amino acids
Palmitate, glycerol, choline
Glucose
Amino acids
Phospholipids
Nucleotides
Sugars
Proteins
Nucleic acids
Polysaccharides
Multienzyme complexes, ribosomes, chromosomes, membranes, structural elements
Organelles, Cells, Tissues, Organs, Organsims

7. Universal features of cells (cont.)
All cells function as biochemical factories and use the same basic molecular building blocks.
Proteins (amino acids polypeptides proteins)
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 lipids)
Membranes
Triglycerides (energy storage)
Phospholipds (membrane structure)
Sphingolipids (found in nerve cells and brain tissue)
Sterols (hormones and membranes)

8. Universal features of cells (cont.)
Carbohydrates
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
A living cell can exist with fewer than 500 genes!
hnRNA - heterogeneous nuclear RNA (with introns and exons)
Pelagibacter ubique has 1354 genes and is free living in the oceans (non parasitic)
Mycoplasma genitalium has about 400 genes but it is a parasite
Craig Ventner is trying to make an articial organism with about 300 genes
DNA RNA Protein

9. Types of cells Prokaryotes Eukaryotes Bacteria,
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
Bacteria,
Archaea
1-10 µm
Eukaryotes
Fungi, Protists, Animals, Plants µm

10. Prokaryotes Most numerous and widespread organisms on Earth
Wide variety of metabolic energy sources
Relatively simple anatomy
Shape is sometimes used to determine a particular type of bacteria