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Introduction
1. Modular structure of biomolecules; building blocks of proteins, nucleic acids, cellulose
and starch
Proteins: C, H, O, N, S
Lipids:C,H,O,N,P
Keq = [C][D]/[A][B]
G = -RT ln Keq
o
Free energy change for non-standard state concentrations:
G = G + RT ln [C][D]/[A][B]
o
EX:
o
Water and pH
1. The hydrogen bond; hydrogen bonds in proteins
Bent angle polar
H-bonds occur in highly Eneg atoms
Directional & Saturable
2. The definition of pH; calculation of pH, [H+] and [OH-]
pH = -log10[H+]
10-pH = [H+]
EX:
3. Acid and base theory; conjugate acid and base
A strong acid has a conjugate weak base
A strong base has a conjugate weak acid
4. The definition of pKa and experimental meaning of pKa
pKa defines the acidity of an H+ atom in a solution
pH = pKa when a solution contains 0.5 eq acid & 0.5 eq base
o When there are equal concentrations of acid/base
5. pH calculation using Henderson-Hasselbach equation
pH = pKa + log10 [A-]/[HA]
EX:
6. Buffers; optimum pH of buffer solutions; calculate pH of buffer solutions
pH = pKa + log10 [A-]/[HA]
7. Buffer systems of cells; the titration curve of H3PO4 and related calculation
EX:
Amino acids
1. Stereochemistry of amino acid: L-amino acids are building blocks of proteins
All amino acids are chiral (except Glycine whose side chain is H)
Most naturally occurring amino acids are S, with exception of Cysteine
2. Properties of amino acid: aliphatic, polar, negatively charged, positively charged,
aromatic, disulfide bond and cysteine; UV absorption by aromatic amino acids; average
molecular mass of amino acid residues in proteins (110 Da/residue)
NONPOLAR
o Phenylalanine (Phe, F)
F
o Isoleucine (Ile, I)
I
o Leucine (Leu, L)
L
o Methionine (Met, M)
M
o Tryptophan (Trp, W)
W
o Alanine (Ala, A)
A
o Valine (Val, V)
V
o Proline (Pro, P)
P
POLAR
o Cysteine (Cys, C)
C
o Tyrosine (Tyr, Y)
Y
o Glycine (Gly, G)
G
o Glutamine (Gln, Q)
Q
o Asparagine (Asn, N)
N
o Serine (Ser, S)
S
o Threonine (Thr, T)
T
ACIDIC (neg)
3. Structure of the 20 amino acids; one letter and three letter abbreviations of amino acids
4. Acid base properties of amino acids; titration curve of Gly, Glu, His, Lys
Amino acids are weak polyprotic acids
R-group pKa
o Acidic
Aspartic Acid
Glutamic Acid
Histidine
o Basic
Arginine
Cysteine
Lysine
Serine
Threonine
Tyrosine
Glycine: 2 pKa values
o Trans-conformation
7. Draw structures of short peptides;
identify amino acids and naming of short peptides.
Named from N-terminal to C-terminal
Ser-Gly-Tyr-Ala-Leu OR SGYAL
Protein purification
1. Ion exchange chromatography; principles and applications
Separate molecules by CHARGE by exchanging
ion of interest with salt ion
Increasing salt concentration until protein washed out
Anion exchange resins
o Resins containing positively charged groups
attract NEG charged solute
o If pH > pI: Protein = NEG charged; Use anion exchange
o EX: DEAE cellulose (weakly basic POS)
Max Perutz
o Structure of hemoglobin
2. Planar structure of the peptide group; definition of the dihedral angles and
(phi) = The angle about the C N bond
(psi) = The angle about the C Co (C=O) bond
Planar structure forbids these angles because of steric hindrance:
o = 180 and = 0
o = 0 and = 180
Immunoglobulins
-helices
-sheets