Amino Acids

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Chapter 4 Amino Acids
Read entire chapter
Learn to draw the 20 standard amino acids. Learn
both the 3 letter and the 1 letter codes. (pages
66 67)
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• Proteins
• Abundant biomolecules
• Occur in all cells and all parts of cells
• Occur in great variety (small to really large)
• Polymers of amino acids
• Joined by a specific type of covalent bond
• Almost all proteins are built from the same set
  of
• 20 amino acids
• Covalently linked in characteristic linear
  sequence
• Exhibit diversity in biological functions

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General Structure of an a-Amino Acid
All amino acids have this general structure
except proline which is cyclic
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Phenylalanine R -CH2-Ph
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Amino acids can act as acids and bases
Forms of amino acids
Predominates at neutral pH
Does not occur in significant amounts in aqueous
solution
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Can act as acid or base Subtances with dual
nature are called ampholytes or amphoteric
Dipolar Ion
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Amino acid
R

• carbon is bound to four different groups
• carbon atom is a chiral center

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Page 66
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Page 67
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You need to know the one- and three-letter
abbreviations for each AA. You also
need to know which group each one is in.
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Nonpolar side chains with different degrees of
hydrophobicity
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Unchanged, polar side chains Hydrogen bond donors
and acceptors
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Changed, polar side chains Acidic and basic groups
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Reversible formation of a disulfide bond by the
oxidation of two molecules of cysteine
Disulfide bonds stabilize the structure of many
proteins
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The condensation of 2 a-amino acids to form a
dipeptide
Peptide bond is shown in RED
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Condensation and hydrolysis
From Lehninger Principles of Biochemistry
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The Pentapeptide
Ser-Gly-Tyr-Ala-Leu or Serylglycyltyrosylalanyll
eucine
Learn to draw peptides and calculate net charge
at a given pH
N or
C or
From Lehninger Principles of Biochemistry
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Nonstandard amino acids
These are found in proteins.
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These are derived from the standard AAs but are
not found in proteins.
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Stereoisomerism in a-amino acids
The object and its mirror image are not
superimposable
From Lehninger Principles of Biochemistry
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Project out of the plane of the paper
behind it
From Lehninger Principles of Biochemistry
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Assumed to project out of the plane of the paper
behind it
From Lehninger Principles of Biochemistry
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Steric relationship of the stereoisomers of
alanine to the absolute configuration of L- and
D- glyceraldehyde
L-amino acids have a amino group on left
a
R group below a C
l and d designations were used historically for
levo and dextro rototary Not all L-amino acids
are levorotatory
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Looking down the H-C bond, toward the a-carbon,
clockwise you get "CORN".
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The amino acid residues in proteins are
exclusively L stereoisomers

• Formation of stable repeating substructures in
  proteins require the amino acids to be only one
  stereo isomer
• Cells can specifically synthesize L isomers of
  amino acid because the active site of the enzymes
  are asymmetric causing the reactions catalyzed to
  be stereospecific

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Amino acids have characteristic titration curves
At this pH predominant species is species 2
(dipolar ion)
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2
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At midpoint in the first stage of titration
species 1 species 2
pKa of Carboxyl group 2.34 pKa of amino group
9.6
At low pH predominant species is species 1
Know the pKa roughly for various groups
From Lehninger Principles of Biochemistry
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Titration of Glycine
Isoelectric point pH at which net charge is zero
From Garrett Grisham
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From Lehninger Principles of Biochemistry
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Titration of Glutamic Acid
From Garrett Grisham
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Titration of Lysine
From Garrett Grisham