Background review for Biochemistry

1. Background review for Biochemistry http://www.usm.maine.edu/~rhodes/Biochem/Text/ChapterZero.pdf

2. Acids, Bases and Buffers!!!Here’s a site for remedial work

3. BUILDING BLOCKS!!! NUCLEOTIDES—read Ch 3 (especially Chemists!) We’ll come back to it. AMINO ACIDS

6. DG = DH - TDS If DG isthe reaction is > 0 thermodynamically unfavorable (reverse reaction is favorable) = 0 at equilibrium (forward and reverse reactions equally favorable) < 0 thermodynamically favorable as written

10. See Fig 2-5 in VVP

13. DG = DGo' + RTlnQ If Q isthen DG is > Keq >0 (reverse reaction is favorable) = Keq =0 (at equilibrium) < Keq <0 (reaction favorable as written)

14. 13-2 Table 13-2 in VVP

15. Standard States in Biochemistry 1. Activity of water is 1. (really 55 M) 2. Hydrogen ion activity is 1 at pH 7. Go’

16. Acids, Bases and Buffers!!!

18. What is pH???? pH = -log [H+]

19. What is pK????

21. 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).

22. VVP Fig 2-17 Animation http://www3.interscience.wiley.com: 8100/legacy/college/voet/0471214957/ animated_figures/ch02/f2-15.html

23. Buffers!!! • pH = pKa + log [A] • [HA]

24. 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 2-16

25. 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.

26. VVP Fig 2-18 pH=pKa3 Animation: http://www3. interscience.wiley. com:8100/legacy/ college/voet/ 0471214957/ animated_figures/ ch02/f2-16.html pH=pKa2 pH=pKa1

27. VVP Table 4-1 +0.091 X

28. 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

29. BUILDING BLOCKS!!! NUCLEOTIDES AMINO ACIDS

30. amino acid structures See Table 4-1 p80 in VVP

31. See Table 4-1 p80 in VVP

32. Models Models from Cal Lutheran PDB files

33. Amino acid structures http://info.bio.cmu.edu/Courses/ BiochemMols/AAViewer/ AAVFrameset.htm

34. 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

35. pKa3 pKa2 pKa1

36. See VVP Fig 4-3

38. VVP Fig 6-3 p 126

40. (Rasmol)

41. 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

42. 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

43. VVP page 150 “nonpolar” “polar”

45. VVP Fig 6-1 p 125

46. VVP Fig 5-1 p 94 C-termini N-termini