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Amino Acids, Peptides & Proteins
amine; basic end
a-amino acid:
H2N
R
carboxylic acid; acidic end
O
OH
H
(S) absolute stereochemistry
side chain
O
H3N
R
O
H
zwitterionic form (internal acid/base reaction):
overall neutral
salt
H2O soluble
pH = 7.3 (within cell; isoelectric point depends on R)
Amino Acids
O
O
• Are >500 naturally
occurring amino acids
identified in living
organisms
• Humans synthesize
10 of the 20 they use.
The other 10 are called
essential amino acids.
H2N
H2N
OH
OH
H
H
H
Valine (hydrophobic,
bulky)
Glycine (achiral)
O
O
H2 N
OH
H2NH2CH2CH2CH2C
H2N
OH
H
H
Lysine (basic, nucleophilic, often
used in catalysis)
O
H2 N
OH
H
CO2H
Aspartic acid (acidic, used in
catalysis)
O
NH
OH
SH
Cysteine (nucleophilic, used in
catalysis, controls shape of
protein)
H
Proline
Amino Acids, Peptides & Proteins
Peptides & proteins:
• Derived from amino acids through peptide or amide bonds.
• The amine and acid ends of amino acids couple to form amide (peptide) bonds
in peptides/proteins/enzymes.
• Proteins fold into well-defined structures. The hydrophobic residues
segregate to the water-free interior, while the polar/charged residues favor
the exterior.
Peptides: Coupling AAs Together
•
Peptides & Proteins: Linear oligomers of the 20 amino acids
•
Peptides ≤ 20 amino acids; Proteins > 20 amino acids
Functions:
1. Catalysis - enzymes
2. Membrane channels
3. Structural support (boundaries)
4. Regulate metabolites (storage & transport)
5. Antibodies; cellular signaling (recognition & binding)
Aspartame
Discovery story:
• In 1965 by Jim Schlatter
working on discovering new
treatments for gastric
ulcers.
• Made a dipeptide intermediate,
which he spilled on his hand
• Tested the dipeptide in coffee
CH3
O
O
Methyl ester
H
Phenylalanine
HN
H3N
O
H
O
• 4 calories per gram
• 180 times sweeter than sugar
Aspartic acid
O
Aspartame
Aspartame: A Dipeptide
CH3
O
O
Methyl ester
H
Phenylalanine
HN
H3N
Two main constituents:
Phenylalanine
Aspartic acid
O
Aspartic acid
H
O
O
Goal:
1. Make the methyl
ester of phenylalanine
2. Make a peptide (amide)
bond between phenylalanine
and aspartic acid
Overall - two main steps to this synthesis
Dipeptides: Coupling of 2 AAs
Consider the synthesis of the dipeptide val-ala (valine-alanine):
O
N-terminus
H2N
CH3
OH
C-terminus
N
H
O
valine
alanine
• Coupling of amino acids is an application of nucleophilic acyl substitution
• Issue of selectivity arises:
val + ala 
val-ala + ala-val +
val-val + ala-ala
A mixture of 4 possible amide
products
Merrifield’s Solid-Phase Synthesis
In order to get the desired peptide (val-ala), the appropriate NH2 and CO2
units must be joined.
O
H2N
CH3
OH
OH
H2N
O
valine's C-terminus
alanine's N-terminus
The selectivity is accomplished through the use of protecting groups.
Merrifield’s approach:
1. Protect N-terminus of valine
2. Protect C-terminus of alanine
3. Couple valine and alanine
4. Deprotect to get dipeptide
Merrifield’s Solid-Phase Synthesis
1. Protection of valine’s N-terminus:
O
Cl
O
H2N
O
OH
(FMOC-Cl)
O
H
N
O
OH
Fmoc group
O
Merrifield’s Solid-Phase Synthesis
2. Protection of alanine’s C-terminus:
Attach the C-terminus to a plastic bead (solid-phase synthesis!)
CH3
CH3
OH
H2N
O
H2N
O
O
Benefits of solid-phase:
• Ease of attachment
• Ease of removal; just filter away from product solution
Merrifield’s Solid-Phase Synthesis
3. Couple valine and alanine:
O
CH3
H
N
O
O
OH
Fmoc group
O
H2N
+
N C N
O
Coupling agent
such as DCC
(dicyclohexylcarbodiimide)
DCC
(Used to derivatize the CO2H
to make it more reactive)
O
CH3
H
N
O
O
N
H
O
O
Merrifield’s Solid-Phase Synthesis
3. Deprotection of Fmoc & bead:
O
CH3
H
N
O
O
N
H
O
O
1. Piperidine (to remove Fmoc)
2. CF3CO2H (TFA, to remove bead)
O
H2N
CH3
OH
N
H
O
valine
alanine
Proteins
•
Amino acid polymers; when long enough, they fold back on themselves to
create intricate, well-defined 3D structures
•
The structure of a protein specifies its function.
•
The AA sequence specifies its structure.
•
The AA chain typically adopts regional sub-structures which sum together
to deliver the overall structure of the protein.
Forces/Factors that dictate protein folding:
1. Planarity of amide bonds
2. H-bonding
3. Hydrophobic interactions
4. Electrostatic Attraction
5. Disulfide linkages
Proteins
1. Planarity of amide bonds:
R
O
H
N
N
H
O
R
O
R
O
H
N
Barrier of rotation
~20 kcal/mol
N
O
R
H
O
Proteins
2. H-bonding:
R
O
H
N
N
O
R
H
H-bond worth ~ 5 kcal/mol
H
O
H-bonds orient the chain
R
O
N
N
H
O
R
O
Proteins
3. Hydrophobic Interactions:
Ph
O
O
H
N
H
N
N
Lots of hydrophobic interactions
between Rs and H2O unstable
H
O
Fold
O
Protein folds to “clump” R
groups together in the
interior of protein to avoid
H2O - very energetically
favored
Hydrophobic
pocket
NH
O
NH
N
H
O
Proteins
4. Electrostatic Attraction:
O
NH3
O
Proteins
5. Disulfide Linkages:
SH
HS
Mild oxidant
S
S
• Covalent S-S
• Drastically alters shape
• Worth ~ 50 kcal/mol
Proteins
Overall, these 5 structural/energetic features leads to the final 3D protein
structure. However, predicting the structure from the amino acid sequence
is still a challenge.
Hierarchy of Structural Elements of Proteins
1. Primary structure: AA sequence
2. Secondary structure: discrete sub-structural elements (modules)
a-helix & b-sheet
a-helix: see board for depiction
b-sheet: see board for depiction
Note:
1. Internal H-bonding
2. The way the side chains line up
3. 3.6 AAs per turn
Note:
1. Chain-to-chain H-bonding
2. Alternating (up-down, up-down)
Pattern of R groups
Proteins
Hierarchy of Structural Elements of Proteins
3. Teritary Structure: the individual secondary structural elements organized
in 3D.
See board for depiction.
4. Quaternary Structure: non-covalent complexation of different proteins.
Lipids
•
•
•
Structurally diverse, derived from living organisms
Functional theme is hydrophobicity - water avoiding due to long alkyl chains
Often found at the interface of aqueous compartments
3 Major Classes of Lipids:
1. Fats and oils
2. Phospholipids
3. Cholesterol & derivatives (steroids)
Lipids
1. Fats & Oils
Derived from glycerol and fatty acids:
CH2OH
H
OH
CH2OH
+
Glycerol: a triol (3 nuc sites)
O
OH
Palmitic acid (C16 fatty acid)
couple
O
O
Weak intramolecular
attractive forces
between chains
O
O
O
O
Triacyl glyceride
Lipids
1. Fats & Oils
•
•
•
In order for a fat to melt, these weak dispersive forces must be broken.
More contacts, the better the packing and the higher the m.p. of the fat
Less contacts, worse packing of chains, the lower the m.p.
O
Unsaturated Fats:
O
O
No contacts here
due to Z-alkene
Oils are polyunsaturated - lots of
alkenes & have low mp due to less packing
Butter has very little unsaturated & has
higher mp
O
O
O
Lipids
Soaps & Detergents
•
•
Hydrolyzed fats
A long chain carboxylate molecule:
O
O-Na+
Polar, hydrophilic end
Non-polar, hydrophobic end
Lipids
Soaps & Detergents
O-Na+
in H2O:
O
O
H2O
O-Na+
O O-Na+
+Na-O
In H2O, forms
a micelle.
O
O
Hydrophobic
Interior
+Na-O
O
O
O-Na+
O
O-Na+
+Na-O
O
H2O
O-Na+
O
O-Na+
+Na-O
O
+Na-O
Grease & dirt get
trapped in the interior.
Micelle is H2O soluble
so can wash out dirt.
O
O-Na+
O
+Na-O
H2O
O
+Na-O
O
O
+
-
Na O
Hydrophilic
Exterior
H2O
Lipids
2. Phospholipids:
• Have hydrophobic and hydrophilic regions
• Forms membranes
• Precursors to prostaglandins
O
O
O
P
O
O
O
O
N
O
H2O insoluble
Phosphatidyl choline
Highly charged
H2O soluble
Lipids
2. Phospholipids:
• Forms membranes: self-organize at certain concentrations to form bilayers
• Membranes are largely impermeable to charged species that exist in
biological environments.
H2O outside of cell
N
N
O
O P O
O
O
O
O
O
O
N
N
O
O P O
O
O
O P O
O
O
O P O
O
O
O
O
O
O
O
O
O
O
O
O
Cell membrane
Hydrophobic interior
O
O
O
O
O
O
O
O
O P O
O
O
O
O
O
O
O P O
O
O
O
O
O
O P O
O
N
N
O
N
H2O inside of cell
O
O
O P O
O
N
Lipids
3. Cholesterol & Steroids
Cholesterol:
27 carbons
4 rings
8 stereocenters
Derived from terpenes
H
H
H
HO
polar
Cholesterol is a precursor to several steroidal hormones:
Testosterone (male hormone)
Estrone (female hormone)
non-polar
Lipids
Cholesterol is a precursor to several steroidal hormones:
Testosterone (male hormone)
Estrone (female hormone)
O
OH
H
H
H
H
H
H
HO
O
Testosterone
Estrone
These hormones operate at the genetic level (turn genes on and off) to
control biochemistry. They are recognized by specific protein receptors.
Antioxidants & Chocolate
Antioxidants:
• Protect against cardiovascular disease, cancer and
cataracts
• Thought to slow the effects of aging
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Chocolate:
• High levels of antioxidants - complex mixtures of phenolic
comounds
• By weight, has higher concentration of antioxidants than red
wine or
Green tea
• 20x higher concentration of antioxidants than tomatoes
Dark chocolate has more than 2x the level of
antioxidants as milk chocolate.
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Side note: The main fatty acid in chocolate, stearic
acid, does not appear to raise blood cholesterol
levels the way other saturated fatty acids do.