Amino acids the monomer of proteins

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Last updated Sept. 20, 2008
PROTEINS
Amino acids (the monomer of proteins)
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At pH 7, ,most amino acids are zwitterions

(charged, but electrically neutral)
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Equilibrium state of the carboxyl group lies far
towards the ionized molecule at pH7
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OH- ( -H)
R OH
/ H3N - C CO H
R O- /
H2N - C CO H
R O-
/ H3N - C CO H
pH Net charge
1 1
11 -1
7 0
H
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Numbering (lettering) amino acids
e-amino group
e
d
?
ß
alpha-carboxyl (attached to the a-carbon)
alpha-amino
alpha-carbon
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Shown uncharged (as on exams)
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H ? H 50 at pH7
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Ball and stick physical model of an amino acid
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Amino acids in 3 dimensions

• Asymmetric carbon (4 different groups attached)
• Stereoisomers
• Rotate polarized light
• Optical isomers
• Non-superimposable
• Mirror images
• L and D forms

From Sadava text
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Condensation of amino acids to form a
polypeptide (must be catalyzed)
dehydration again
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Parts of a polypeptide chain
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Handout 3-3
(Without showing the R-groups)
The backbone is monotonous
It is the side chains that provide the variety
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Polypeptides vs. proteins

• Polypeptide amino acids connected in a linear
  chain (polymer)
• Protein a polypeptide or several associated
  polypeptides (discussed later)
• Often used synonymously
• Peptide (as opposed to polypeptide) is smaller,
  even 2 AAs (dipeptide)

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The backbone is monotonous
(Without showing the R-groups)
It is the side chains that provide the variety
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Proteins do most of the jobs in the cell E.g.,
egg albumin, hemoglobin, keratin, estrogen
receptor,immunoglobulins (antibodies), enzymes
(e.g., beta-galactosidase) Each is a polymer or
assemblage of polymers made up of amino
acidsEach particular protein polymer
(polypeptide) has a unique sequence of amino
acids . . . . and an English name.Each molecule
of a particular protein has the same sequence of
amino acids. E.g., met-ala-leu-leu-arg-glu-leu-v
al- . . . . How is this sequence determined?
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Primary (1o) Structure the sequence of the
amino acids in the polypeptide chain
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Determining the sequence
Carboxypeptidase hydrolyzes the peptide bond
One way use an enzyme (an old method, but
useful for teaching)
,
identify
e.g., . arg-leu-leu-val-gly-ala-gly-phe-trp-lys-g
lu-asp-ser . arg-leu-leu-val-gly-ala-gly
-phe-trp-lys-glu-asp
. arg-leu-leu-val-gly-ala-gly-phe
-trp-lys-glu
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METHODS . . .
AA mixture
(-)
()
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A paper electrophoresis apparatus
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Handout 3-4
Side view
AAs applied at lower end
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After stopping the paper chromatography
and staining for the amino acids
Rf 0.82 0.69 0.45 0.27 0.11
1.00
front
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Paper chromatography apparatus
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• Treatment of a polypeptide with trypsin
• Trypsin is a proteolytic enzyme.
• It catalyzes cleavage (hydrolysis) after lysine
  and arginine residues

Polypeptide chain
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But the order of the subpeptides is unknown. . .
. The sequence is reconstructed by noting the
overlap between differently produced subpeptides
Trypsin (lys, arg)
(1)
Chymotrypsin (trp, tyr, phe)
N
C
(2)
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The order of the subpeptides is unknown. The
sequence is reconstructed by noting the overlap
between differently produced subpeptides
Trypsin (lys, arg)
(1)
Chymotrypsin (trp, tyr, phe)
N
C
(2)
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The order of the subpeptides is unknown. The
sequence is reconstructed by noting the overlap
between differently produced subpeptides
Trypsin (lys, arg)
(1)
Chymotrypsin (trp, tyr, phe)
N
C
(2)
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Fingerprinting a protein analysis of the
sub-peptides (without breaking them down to
their constituent amino acids)
Sub-peptides
No further digestion to amino acids left as
sub-peptides
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Oligopeptides behave as a composite of their
constituent amino acids

-
-
Net charge -1 moves toward the anode in paper
electrophoreses Fairly hydrophobic (5/6)
expected to move moderately well in paper
chromatography
Nomenclature ala-tyr-glu-pro-val-trp or
AYEPVW or alanyl-tyrosyl-gluta
myl-prolyl-valyl-tryptophan
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Hb
In fingerprinting, these spots contain peptides,
not amino acids
trypsin
Negatively charged
------valine------ (sickle)
Positively charged
More hydrophobic
------glutamate----- (normal)
More hydrophilic
Negatively charged
Positively charged
Negatively charged
Positively charged
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Every different polypeptide has a different
primary structure (sequence). Every polypeptide
will have different arrangement of spots after
fingerprinting.
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3-dimensional structure of proteins
One given purified polypeptide

• Molecule 1 N-met-leu-ala-asp-val-val-lys-....
• Molecule 2 N-met-leu-ala-asp-val-val-lys-...
• Molecule 3 N-met-leu-ala-asp-val-val-lys-...
• Molecule 4 N-met-leu-ala-asp-val-val-lys-... etc

.
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3-D structure of polypeptides
Arrangement 3 at one momentin time?
Arrangement 2 at one momentin time?
Arrangement 1 at one momentin time?
Arrangement 3 at one momentin time?
Rope models here
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Primary structure itself results in some folding
constraints
See bottom of handout 3-3
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And these 4 atoms in one plane
These 4 atoms in one plane
? so 6 atoms in one plane
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Theres still plenty of flexibility
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Secondary structure the alpha helix
Amino acids shown simplified, without side
chains and Hs.
Almost every N-H and CO group can participate
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Alpha helix depictions
C grays N blue O red
Poly alanine Side chains -CH3 (lighter
gray) Hs not shown
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Linus Pauling and a model of the alpha helix.1963
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Secondary structure
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Beta sheet
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Beta-sheets
Anti-parallel
Parallel
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secondary structure (my definition) structure
produced by regular repeated interactions between
atoms of the backbone.
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Tertiary structure The overall 3-D structure of
a polypeptide.
These ribbon depictions do not show the side
chains, only the backbone
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Tertiary structure (overall 3-D)
ionic
hydrophobic
H-bond
cys
Ion - dipoleinteraction
covalent
Van der Waals
Weak bonds also occur throughout the polypeptide,
between the amino acid side chains in regions of
secondary structure as well as the looped regions
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Disulfide bond formation
Disulfide bond
Sulfhydryl group
R-CH2-SH
HS-CH2-R

R-CH2-S-S-CH2-R
HOH
cystine
cysteine
cysteine
Two sulfhydryls have been oxidized (lost
Hs) Oxygen has been reduced (gained Hs). Oxygen
was the oxidizing agent.
An oxidation-reduction reaction Cysteines are
getting oxidized (losing H atoms, with the
electron NOT losing a proton, not like
acids. Oxygen is getting reduced, gaining H-atoms
and electrons Actually its the loss and gain of
the electrons that constitutes oxidation and
reduction, respectively. No catalyst usually
needed.
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Overall 3-D structure of a polypeptide is
tertiary structure
Stays intact in the jacuzzi at 37 deg C
Usually does not require the strong covalent
disulfide bond to maintain its 3-D structure
Tuber model ?
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Protein structures are depicted in a variety of
ways
Backbone only
Ribbon
(Small molecule bound)
Space-filling
Space-filing, With surface charge
blue red -
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Information for proper exact folding (How does a
polypeptide fold correctly?)
Predicting protein 3-dimensional structure
Determining protein 3-dimensional structure
Where is the information for choosing the correct
folded structure?
Is it in the primary structure itself, or being
provided by another source?