Transcript Ch13 Lect

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 aa’s
- D-amino acids and L-amino acids
13.2 The Peptide
- Reaction of aa’s to form Peptide, peptide bond
- The peptide structure; terms to describe the numbers of aa’s 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 (aa’s)
H O

H2N C C OH
R
H O

H2N C C OH
C
C
C
C
All aa’s 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 aa’s behave like this way.
+
H O
H H O
-
H 3N C C O
+
H N C C O-
or
R
H R
H O
H O
+
+
H 3N
H3N C C OH
R
C C OR
H+
Acidic form
H O
Zwitterion form
H2N C C OH+
R
basic form
3
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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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Protein
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.
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Protein Structure
The structure of proteins is
understood in terms of four levels
of organization:
1) primary (the aa sequence)
2) secondary
3) tertiary
4) quaternary
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Secondary Structure:
The -helix.
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Secondary Structure:
The -sheet; parallel
-sheet and anti-parallel
-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 aa’s 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 threedimensional 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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Adehyde
dehydrogenase
O
CH3
O
CH3
C H
H2 O
NAD+
Examples of some real
enzyme catalyzed
reactions :
NADH + H+
HOH2C
HOH2C
O
O
OH
OH
OH
O
HO
How does
maltase cut
(hydrolyze)
maltose?
C OH
OH
OH
H2O, Maltase
HOH2C
HOH2C
O
O
OH
+
OH
OH
HO
OH
OH
HO
OH
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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 !)
Asp
Asp
HOH2C
-
HOH2C
C O CH2OH
O
O
O
OH
O
O
O
O
OH
1
C O
O
OH
O
O
O
OH
OH
OH
CH2OH
OH
O
H
H
OH
-
O C O
O C O
Asp
Asp
H2O
2
Asp
HOH2C
Asp
HOH2C
-
O
C O
OH
3
O
O
O
O H
O
H
OH
OH
O H
O
H
OH
O C O
C O
O C OAsp
Asp
Original state of
the E
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Enzyme Inhibition:
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