Spring Quarter 1998 Chem 115 General Chemistry

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Background review for Biochemistry
http//www.usm.maine.edu/rhodes/Biochem/Text/Chap
terZero.pdf
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Acids, Bases and Buffers!!!Heres a site for
remedial work
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BUILDING BLOCKS!!! NUCLEOTIDESread Ch 3
(especially Chemists!) Well come back to it.
AMINO ACIDS
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DG DH - TDS

• If DG is the reaction is
• gt 0 thermodynamically unfavorable (reverse
  reaction is favorable)
• 0 at equilibrium (forward and reverse
  reactions equally favorable)
• lt 0 thermodynamically favorable as written

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See Fig 2-5 in VVP
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DG DGo' RTlnQ

• If Q is then DG is
• gt Keq gt0 (reverse reaction is favorable)
• Keq 0 (at equilibrium)
• lt Keq lt0 (reaction favorable as written)

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13-2
Table 13-2 in VVP
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Standard States in Biochemistry 1. Activity of
water is 1. (really 55 M) 2. Hydrogen ion
activity is 1 at pH 7. ?Go
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Acids, Bases and Buffers!!!
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What is pH????
pH -log H
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What is pK????
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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).

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VVP Fig 2-17
Animation http//www3.interscience.wiley.com 810
0/legacy/college/voet/0471214957/ animated_figures
/ch02/f2-15.html
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Buffers!!!

• pH pKa log A
• HA

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This is IMPORTANT!!!

• If pH pKa, then A- HA
• then deprotonated protonated
• If pH lt pKa, then A- lt HA
• then deprotonated lt protonated
• If pH gt pKa, then A- gt HA
• then deprotonated gt protonated

Summarized on VVP Fig 2-16
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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.

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VVP Fig 2-18
pHpKa3
Animation http//www3. interscience.wiley. com8
100/legacy/ college/voet/ 0471214957/ animated_fig
ures/ ch02/f2-16.html
pHpKa2
pHpKa1
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VVP Table 4-1
0.091
X
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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

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BUILDING BLOCKS!!! NUCLEOTIDES AMINO ACIDS
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amino acid structures
See Table 4-1 p80 in VVP
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See Table 4-1 p80 in VVP
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Models
Models from Cal Lutheran
PDB files
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Amino acid structures
http//info.bio.cmu.edu/Courses/ BiochemMols/AAVie
wer/ AAVFrameset.htm
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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

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pKa3
pKa2
pKa1
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See VVP Fig 4-3
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VVP Fig 6-3 p 126
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(Rasmol)
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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

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Example of a protein sequence
N-terminus

• 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

C-terminus
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VVP page 150
nonpolar
polar
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VVP Fig 6-1 p 125
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VVP Fig 5-1 p 94
C-termini
N-termini