Chapter Outline

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Chapter Outline

• 13.1 Amino Acid Structures
• General structure of the aa Groups bonded to
  the alpha carbon structure of aa in water
  zwitterion
• Classification of aas
• D-amino acids and L-amino acids
• 13.2 The Peptide
• Reaction of aas to form Peptide, peptide bond
• The peptide structure terms to describe the
  numbers of aas in the peptide (dipeptide,
  tripeptide, tetrapeptide, oligopeptide)
• 13.4 Polypeptide and Protein
• Polypeptide
• Protein, levels of protein structure,
• 13.5 Denaturation
• 13. 6 Enzymes, enzyme reactions, mechanism of
  enzyme reaction.

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13.1 Structures of Amino Acids (aas)
All aas have this general structure, except the
side chains are different. You need to know the
general structure of the aa, but not the side
chain structure of each specific aa.
What is the name of each group or atom bonded to
the alpha C?
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In water the aa exists as a dipolar ion called
Zwitter ion. All aas behave like this way.
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Classifying Amino Acids

• The water solubility and the chemistry of amino
  acids vary to some extent, depending on the
  makeup of the side chain.
• It is useful to use side chains to classify each
  amino acid as being either
• 1) nonpolar
• 2) polar-acidic
• 3) polar-basic
• 4) polar-neutral.

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Classifying Amino Acids

• 1) nonpolar - the side chain is usually an alkyl
  group, an aromatic ring, or a nonpolar collection
  of atoms.
• 2) polar-acidic - the side chain contains a
  carboxyl group. At pH 7, the carboxyl group is
  found in its conjugate base form (-COO-), which
  means that the side chain carries a negative
  charge at this pH.
• 3) polar-basic - the side chain contains an amine
  group. At pH 7 the amines exist in their
  conjugate acid form and therefore carry a
  positive charge at this pH.
• 4) polar-neutral - the side chain is usually an
  alcohol, a phenol, or an amine. They do not
  carry a charge at
• pH 7.

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Stereoisomers (remember what enantiomers are?)
What is one purpose of amino acids?
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Peptide bond formation
H2O
This bigger molecule is called a Pepetide.
Which bond is the amide bond? Or peptide bond?
Can you find it?
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Dipeptide, tripeptide, oligopeptide
Ala-Gly
Ala-Gly-Ser
C-terminus
N-terminus
Ala-Gly-Ser-Val-Gly
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Examples of two real peptides in our bodies.
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13.4 Protein Structure
backbone
What is a polypeptide?
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1) Fibrous proteins - These proteins exist as
long fibers or strings. These proteins including
collagen (in skin) and keratin (in hair), are
usually tough and water insoluble.2) Globular
proteins - These proteins are spherical in shape,
highly folded, and tend to be water soluble.
Protein
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The structure of proteins is understood in terms
of four levels of organization1) primary (the
aa sequence)2) secondary3) tertiary4)
quaternary
Protein Structure
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Secondary Structure The a-helix.
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Secondary Structure The b-sheet parallel
b-sheet and anti-parallel b-sheet.
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Secondary structures compare to tertiary
structure
Tertiary structure
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Another look at tertiray structure.
Where are the aas in the protein above? What
are we looking at?
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Non-covalent interactions and S-S- bond
important for maintaining the protein
structure (Can you name each one?)
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Tertiary Structure

• The tertiary structure refers to the overall
  three-dimensional shape of a protein, including
  the folding of the ?-helices or ?-sheets with
  respect to one another.
• Of the many folding patterns (conformations)
  possible for a protein, there is usually only one
  that leads to a native (biologically active)
  molecule.
• The sequence of amino acids (primary structure)
  ultimately determines which folding pattern is
  selected, so both secondary and tertiary
  structure depend on primary structure.

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Tertiary Structure

• In an aqueous environment, the native form of a
  globular protein typically has its nonpolar amino
  acid side chains folded into the hydrophobic
  interior and its polar side chains on the
  hydrophilic surface.
• This folding rule, known as nonpolar in, polar
  out is the most stable arrangement because it
  allows polar side chains on the surface of the
  protein to interact with water molecules and
  allows nonpolar side chains to avoid water.

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Quarternary Structure of protein
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13.5 Denaturation

• Denaturation is any change in protein
  conformation caused by disruption of the
  noncovalent forces responsible for maintaining
  the native conformation.
• A loss of biological activity normally
  accompanies denaturation, and this process is
  reversible only if minor changes in conformation
  take place.

Denaturation can be caused by heat,
denaturants, extreme pH, sonication, dehydration,

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13.6 Enzymes
(Enzyme catalysis)

• Enzymes are often referred to as biological
  catalysts.
• Most enzymes are globular proteins.

Model of enzyme catalysis.
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Examples of some real enzyme catalyzed reactions
How does maltase cut (hydrolyze) maltose?
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Examples of other enzyme catalyzed reactions.
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Real catalytic mechanism of reaction of maltase
How does maltase cut (hydrolyze) maltose? (This
is exactly how !)
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Enzyme Inhibition
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