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Lecture 2 Outline
Chapter 2 Aqueous solutionsAcids and Bases
pHpH
Henderson Hasselbalch
Chapter 4 Amino Acids and PeptidesStructure
Chirality
Non-protein amino acids
Peptide bond
What is the typical molarity of the H+ for maximal
activity in animal tissues?
i.e. ~ pH 7
However a few physiological surroundings are far
from neutrality. Name one: Stomach Contents
Acid Ka p Ka
HCOOH (formic) 1.8 x 10-4 3.75
CH3COOH (acetic) 1.74 x 10-5 4.76
Dissociation of common acids
CH3COOH (acetic) 1.74 x 10-5 4.76
H3PO4 (phosphoric) 7.25 x 10-3 2.14
NH4+ (ammonium) 5.62 x 10-10 9.25
It is important to note that all of the pK values we have talked about
refer to measurements carried out in water.
In biological systems not all of the reactants operate in a purely
aqueous environment.
Box 2-B Acid-base balance in humans.
Table 2-3 (bottom) Dissociation Constants and pK’s at
25°C of Some Acids in Common Laboratory Use as
Biochemical Buffers.
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For reviews of pH and buffers see
http://www.boyerbiochem.com/
and go to Concept Reviews
Deep Diving Apparatus
Chapter 4 Voet & Voet
Figure 4-1General structural
formula for α-amino acids.
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Figure 4-2 Zwitterionic form of the α-amino acids that
occur at physiological pH values.
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Table 4-1 (left)Covalent Structures and Abbreviations of
the “Standard” Amino Acids of Proteins, Their Occurrence,
and the pK Values of Their Ionizable Groups.
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Table 4-1 (right) Covalent Structures and Abbreviations of
the “Standard” Amino Acids of Proteins, Their Occurrence,
and the pK Values of Their Ionizable Groups.
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Ways in Which Amino Acids Differ
• Polarity
• Acidity, Basicity
• Aromaticity
• Bulk• Bulk
• Conformational Flexibility
• Ability to Crosslink
• Ability to Hydrogen Bond
• Chemical Reactivity
Figure 4-9 Greek lettering scheme used to identify
the atoms in the glutamyl and lysyl R groups.
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Figure 4-5 Structure of cystine.
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cystine
Figure 4-4a Structure of
phenylalanine. (a) Ball and stick form.
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Figure 4-4b Structure of
phenylalanine. (b) Space-filling model.
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Figure 4-3 Condensation of two α-
amino acids to form a dipeptide.
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Figure 4-6 Titration curve of glycine.
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Figure 4-7 Titration curves of the
enzyme ribonuclease A at 25°C.
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KCl concentratoion = 0.01M blue, 0.03 red, 0.15 green
Figure 4-8The tetrapeptide Ala-
Tyr-Asp-Gly.
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Figure 4-10 The two enantiomers of
fluorochlorobromomethane.
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Figure 4-11 Schematic diagram of a
polarimeter.
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Figure 4-12 Fischer convention configurations for naming the enantiomers of
glyceraldehyde.
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Figure 4-13 Configuration of L-glyceraldehyde and
L-αααα-amino acids.
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Figure 4-14 “CORN crib” mnemonic for the
hand of
L-amino acids.
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Figure 4-15 Fischer projections of
threonine’s four stereoisomers.
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Only the L-Threonine isomer is found in proteins. Isoleucine is
the only other amino acid found in proteins which has 2
asymmetric centers.
Ways in which an enzyme can interact with substrate
Interaction of prochiral compound with enzyme
Figure 4-20 Views of ethanol.
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Note: The conversion of the serine to selenocysteine
occurs on the tRNA
Figure 4-22 Some uncommon amino acid residues that are components of certain
proteins.
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Figure 4-23: Some biologically produced
derivatives of “standard” amino acids and amino
acids that are not components of proteins.
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Figure 4-3 Condensation of two αααα-amino acids
to form a dipeptide.
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