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D G = D G o' + RTlnQ. If Q is then D G is > K eq >0 (reverse reaction is favorable) = K eq =0 (at equilibrium) < K eq <0 (reaction favorable as written). Standard States in Biochemistry 1. Activity of water is 1. (really 55 M) 2. Hydrogen ion activity is 1 at pH 7.
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DG = DGo' + RTlnQ If Q isthen DG is > Keq >0 (reverse reaction is favorable) = Keq =0 (at equilibrium) < Keq <0 (reaction favorable as written)
Standard States in Biochemistry 1. Activity of water is 1. (really 55 M) 2. Hydrogen ion activity is 1 at pH 7. Go’
13-2 Table 13-2 p 362 in VVP
Acids, Bases and Buffers!!! • pH = pKa + log [A] • [HA]
Bloody Fact: • If 1 mL of 10 N HCl is added to 1 liter of saline solution at pH = 7.0, the pH will decrease to roughly pH = 2. • If 1 mL of 10 N HCl is added to 1 liter of blood plasma at pH = 7.4, the pH will decrease to pH = 7.2. • Why? Blood is buffered (in this case by the H2CO3/HCO3 system).
This is IMPORTANT!!! • If pH = pKa, then [A-] = [HA] then [deprotonated] = [protonated] • If pH < pKa, then [A-] < [HA] then [deprotonated] < [protonated] • If pH > pKa, then [A-] > [HA] then [deprotonated] > [protonated] Summarized on VVP Fig 2-15
Using Henderson-Hasselbalch • at pH values +3 pH units from pKa the group is essentially fully deprotonated or fully protonated, so the average charge = 0 or +1. • at pH = pKa the group is 50% protonated, thus it carries an average charge = + 0.5 • H-H equation can be used to calculate the average charge on an ionizable group at any pH.
VVP Fig 2-16 pH=pKa3 pH=pKa2 pH=pKa1
BUILDING BLOCKS!!! NUCLEOTIDES AMINO ACIDS
VVP Table 4-1 +0.091 X
amino acid structures See Table 4-1 p80 in VVP
Amino acid structures http://info.bio.cmu.edu/Courses/ BiochemMols/AAViewer/ AAVFrameset.htm
Ionic properties of amino acids impart ionic properties to proteins • in general these are SURFACE properties (i.e. charged sidechains are on solvent-exposed outside of folded structure) • affect protein-ligand binding (e.g. DNA-binding proteins) or catalysis • average charge on protein is an important consideration in the design of a purification process
pKa3 pKa2 pKa1
Other Properties of Amino Acids • Stereochemistry (all biosynthetic proteins made up of L-isomer) • Hydropathy (partitioning between polar and nonpolar solvents as indicator of polarity) (see Table 6-2 in VVP p 150; Take Note p58) these two properties are major determinants of peptide conformation
Example of a protein sequence MANSKINKQL DKLPENLRLN GRTPSGKLRS FVCEVCTRAF ARQEHLKRHY RSHTNEKPYP CGLCNRCFTR RDLLIRHAQK IDSGNLGETI SHTKKVSRTI TKARKNSASS VKFQTPTYGT PDNGGSGGTV LSEGEWQLVL HVWAKVEADV AGHGQDILIR LFKSHPETLE KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH HEAELKPLAQ SHATKHKIPI KYLEFISEAI IHVLHSRHPG DFGADAQGAM NKALELFRKD IAAKYKELGY G N-terminus C-terminus
VVP page 150 “nonpolar” “polar”
VVP Fig 5-1 p 94 C-termini N-termini