26:Biomolecules:
Amino Chapter Acids, Peptides, and
Proteins
Based on McMurrys Organic Chemistry, 6th
edition
2003 Ronald Kluger
Department of Chemistry
University of Toronto
Based on McMurry, Organic Chemistry, Chapter 26, 6th edition, (c) 2003
1
Proteins Amides from Amino Acids
Amino acids contain a basic amino group and an
acidic carboxyl group
Joined as amides between the 2 of one amino
NH
acid and the 2H the next
CO
Chains with fewer than 50 units are called peptides
Protein: large chains that have structural or catalytic
functions in biology
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.1 Structures of Amino Acids
In neutral solution, the COOH is ionized and the NH2
is protonated
The resulting structures have + and - charges (a
dipolar ion, or zwitterion)
They are like ionic salts in solution
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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The Common Amino Acids
20 amino acids form amides in proteins
All are -amino acids - the amino and carboxyl are
connected to the same C
They differ by the other substituent attached to the
carbon, called the side chain, with H as the fourth
substituent except for proline
Proline, is a five-membered secondary amine, with N
and the C part of a five-membered ring
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Abbreviations and Codes
Alanine A, Ala
Arginine R, Arg
Asparagine N, Asn
Aspartic acid D, Asp
Cysteine C, Cys
Glutamine Q, Gln
Glutamic Acid E, Glu
Glycine G, Gly
Histidine H, His
Isoleucine I, Ile
Leucine L, Leu
Lysine K, Lys
Methionine M, Met
Phenylalanine F, Phe
Proline P, Pro
Serine S, Ser
Threonine T, Thr
Tryptophan W, Trp
Tyrosine Y, Tyr
Valine V, Val
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Learning the Names and Codes
The names are not systematic so you learn them by using them
(They become your friends)
One letter codes learn them too
If only one amino acid begins with that letter, use it ( Cys,
His, Ile, Met, Ser, Val)
If more than one begins with that letter, the more common
one uses the letter (Ala, Gly, Leu, Pro, Thr)
For the others, some are phonetic: Fenylalanine, aRginine,
tYrosine
Tryp has a double ring, hence W
Amides have letters from the middle of the alphabet ( Q
Think of Qtamine for glutamine; asparagine -contains N
Acid ends in D and E follows (smallest is first: aspartic
aciD, Glutamic acid E)
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Neutral Hydrocarbon Side Chains
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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-OH, SH (Nucleophiles) and -S-CH3
Cysteine C, Cys
Methionine M, Met
Serine S, Ser
Threonine T, Thr
Tyrosine Y, Tyr
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Acids and Amides
Aspartic acid D, Asp
Glutamic Acid E, Glu
Asparagine N, Asn
Glutamine Q, Gln
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Amines
Arginine R, Arg
Histidine H, His
Lysine K, Lys
Tryptophan W, Trp
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Chirality of Amino Acids
Glycine, 2-amino-acetic acid, is achiral
In all the others, the carbons of the amino acids
are centers of chirality
The stereochemical reference for amino acids is the
Fischer projection of L-serine
Proteins are derived exclusively from L-amino acids
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Types of side chains
Neutral: Fifteen of the twenty have neutral side
chains
Asp and Glu have a second COOH and are acidic
Lys, Arg, His have additional basic amino groups side
chains (the N in tryptophan is a very weak base)
Cys, Ser, Tyr (OH and SH) are weak acids that are
good nucleophiles
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Notes on Histidine
Contains an imidazole ring that is partially protonated
in neutral solution
Only the pyridine-like, doubly bonded nitrogen in
histidine is basic. The pyrrole-like singly bonded
nitrogen is nonbasic because its lone pair of
electrons is part of the 6 electron aromatic
imidazole ring (see Section 24.4).
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Essential Amino Acids
All 20 of the amino acids are necessary for protein
synthesis
Humans can synthesize only 10 of the 20
The other 10 must be obtained from food
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.2 Isoelectric Points
In acidic solution, the carboxylate and amine are in
their conjugate acid forms, an overall cation
In basic solution, the groups are in their base forms,
an overall anion
In neutral solution cation and anion forms are present
This pH where the overall charge is 0 is the
isoelectric point, pI
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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pI Depends on Side Chain
The 15 amino acids thiol, hydroxyl groups or pure
hydrocarbon side chains have pI = 5.0 to 6.5
(average of the pKas)
D and E have acidic side chains and a lower pI
H, R, K have basic side chains and higher pI
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Electrophoresis
Proteins have an overall pI that depends on the net
acidity/basicity of the side chains
The differences in pI can be used for separating
proteins on a solid phase permeated with liquid
Different amino acids migrate at different rates,
depending on their isoelectric points and on the pH of
the aqueous buffer
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Titration Curves of Amino Acids
If pKa values for an amino acid are known the
fractions of each protonation state can be calculated
(Henderson-Hasselbach Equation)
pH = pKa log [A-]/[HA]
This permits a titration curve to be calculated or pKa
to be determined from a titration curve
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.3 Synthesis of Amino Acids
Bromination of a carboxylic acid by treatment with Br2
and PBr3 (Section 22.4) then use NH3 or phthalimide
(24.6) to displace Br
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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The Amidomalonate Synthesis
Based on malonic ester synthesis (see 22.8).
Convert diethyl acetamidomalonate into enolate ion
with base, followed by alkylation with a primary alkyl
halide
Hydrolysis of the amide protecting group and the
esters and decarboxylation yields an -amino
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Reductive Amination of -Keto
Acids
Reaction of an -keto acid with NH3 and a reducing
agent (see Section 24.6) produces an -amino acid
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.4 Enantioselective Synthesis of
Amino Acids
Amino acids (except glycine) are chiral and pure
enantiomers are required for any protein or peptide
synthesis
Resolution of racemic mixtures is inherently
ineffecient since at least half the material is discarded
An efficient alternative is enantioselective synthesis
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Chemical Resolution of R,S Amino
Acids
Convert the amino group into an amide and react
with a chiral amine to form diastereomeric salts
Salts are separated and converted back to the amino
acid by hydrolysis of the amide
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Enzymic Resolution
Enzymes selectively catalyze the hydrolysis of
amides formed from an L amino acid (S chirality
center)
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Enantioselective Synthesis of
Amino Acids
Chiral reaction catalyst creates diastereomeric
transition states that lead to an excess of one
enantiomeric product
Hydrogenation of a Z enamido acid with a chiral
hydrogenation catalyst produces S enantiomer
selectively
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.5 Peptides and Proteins
Proteins and peptides are amino acid polymers in
which the individual amino acid units, called residues,
are linked together by amide bonds, or peptide bonds
An amino group from one residue forms an amide
bond with the carboxyl of a second residue
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Peptide Linkages
Two dipeptides can result from reaction between A
and S, depending on which COOH reacts with which
NH2 we get AS or SA
The long, repetitive sequence of atoms
N CH CO
that make up a continuous chain is called the
proteins backbone
Peptides are always written with the N-terminal amino
acid (the one with the free
NH2 group) on the left
and the C-terminal amino acid (the one with the free
2H group) on the right
CO
Alanylserine is abbreviated Ala-Ser (or A-S), and
serylalanine is abbreviated Ser-Ala (or S-A)
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.6 Covalent Bonding in Peptides
The amide bond that links different amino acids
together in peptides is no different from any other
amide bond (see Section Amide 24.4). nitrogens are
nonbasic because their unshared electron pair is
delocalized by interaction with the carbonyl group.
This overlap of the nitrogen p orbital with the
orbitals of the carbonyl group imparts a certain
amount of double-bond character to the CN bond
and restricts rotation around it. The amide bond is
therefore planar, and the NH is oriented 180 to the
C=O.
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.6 Covalent Bonding in Peptides
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Disulfides
Thiols in adjacent chains can form a disulfide RSSR
through spontaneous oxidation (see 18.10)
A disulfide bond between cysteine residues in
different peptide chains links the otherwise separate
chains together, while a disulfide bond between
cysteine residues in the same chain forms a loop
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.7 Structure Determination of
Peptides: Amino Acid Analysis
The sequence of amino acids in a pure protein is
specified genetically
If a protein is isolated it can be analyzed for its
sequence
The composition of amino acids can be obtained by
automated chromatography and quantitative
measurement of eluted materials using a reaction
with ninhydrin that produces an intense purple color
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Amino Acid Analysis Chromatogram
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.8 Peptide Sequencing: The
Edman Degradation
The Edman degradation cleaves amino acids one at
a time from the N-terminus and forms a detectable,
separable derivative for each amino acid
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.9 Peptide Sequencing: C-Terminal
Residue Determination
Carboxypeptidase enzymes cleave the C-terminal
amide bond
Analysis determines the appearance of the first free
amino acid, which must be at the carboxy terminus of
the peptide
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.10 Peptide Synthesis
Peptide synthesis requires that different amide bonds
must be formed in a desired sequence
The growing chain is protected at the carboxyl
terminal and added amino acids are N-protected
After peptide bond formation, N-protection is removed
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Carboxyl Protecting Groups
Usually converted into methyl or benzyl esters
Removed by mild hydrolysis with aqueous NaOH
Benzyl esters are cleaved by catalytic hydrogenolysis
of the weak benzylic CO bond
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Amino Group Protection
An amide that is less stable than the protein amide is
formed and then removed
The tert-butoxycarbonyl amide (BOC) protecting
group is introduced with di-tert-butyl dicarbonate
Removed by brief treatment with trifluoroacetic acid
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Peptide Coupling
Amides are formed by treating a
mixture of an acid and amine
with dicyclohexylcarbodiimide
(DCC)
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Overall Steps in Peptide Synthesis
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.11 Automated Peptide Synthesis: The
Merrifield Solid-Phase Technique
Peptides are connected to beads of polystyrene,
reacted, cycled and cleaved at the end
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Automated Synthesis
The solid-phase technique has been automated, and
computer-controlled peptide synthesizers are
available for automatically repeating the coupling and
deprotection steps with different amino acids
Applied Biosystems Synthesizer
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.12 Protein Classification
Simple proteins yield only amino acids on hydrolysis
Conjugated proteins, which are much more common
than simple proteins, yield other compounds such as
carbohydrates, fats, or nucleic acids in addition to
amino acids on hydrolysis.
Fibrous proteins consist of polypeptide chains
arranged side by side in long filaments
Globular proteins are coiled into compact, roughly
spherical shapes
Most enzymes are globular proteins
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Some Common Fibrous and Globular
Proteins
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.13 Protein Structure
The primary structure of a protein is simply the amino
acid sequence.
The secondary structure of a protein describes how
segments of the peptide backbone orient into a
regular pattern.
The tertiary structure describes how the entire protein
molecule coils into an overall three-dimensional
shape.
The quaternary structure describes how different
protein molecules come together to yield large
aggregate structures
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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-Keratin
A fibrous structural protein coiled into a right-handed
helical secondary structure, -helix stabilized by Hbondsb between amide NH groups and C=O groups
four residues away a-helical segments in their chains
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Fibroin
Fibroin has a secondary structure called a -
pleated sheet in which polypeptide chains line
up in a parallel arrangement held together by
hydrogen bonds between chains
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Myoglobin
Myoglobin is a small globular protein containing 153
amino acid residues in a single chain
8 helical segments connected by bends to form a
compact, nearly spherical, tertiary structure
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Internal and External Forces
Acidic or basic amino acids with charged side chains
congregate on the exterior of the protein where they
can be solvated by water
Amino acids with neutral, nonpolar side chains
congregate on the hydrocarbon-like interior of a
protein molecule
Also important for stabilizing a protein's tertiary
structure are the formation of disulfide bridges
between cysteine residues, the formation of hydrogen
bonds between nearby amino acid residues, and the
development of ionic attractions, called salt bridges,
between positively and negatively charged sites on
various amino acid side chains within the protein
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.14 Enzymes
An enzyme is a protein that acts as a catalyst for a
biological reaction.
Most enzymes are specific for substrates while
enzymes involved in digestion such as papain attack
many substrates
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Cofactors
In addition to the protein part, many enzymes also
have a nonprotein part called a cofactor
The protein part in such an enzyme is called an
apoenzyme, and the combination of apoenzyme plus
cofactor is called a holoenzyme. Only holoenzymes
have biological activity; neither cofactor nor
apoenzyme can catalyze reactions by themselves
A cofactor can be either an inorganic ion or an
organic molecule, called a coenzyme
Many coenzymes are derived from vitamins, organic
molecules that are dietary requirements for
metabolism and/or growth
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Types of Enzymes by Function
Enzymes are usually grouped according to the kind
of reaction they catalyze, not by their structures
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.15 How Do Enzymes Work?
Citrate Synthase
Citrate synthase catalyzes a mixed Claisen
condensation of acetyl CoA and oxaloacetate to give
citrate
Normally Claisen condensation require a strong base
in an alcohol solvent but citrate synthetase operates
in neutral solution
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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The Structure of Citrate Synthase
Determined by X-ray crystallography
Enzyme is very large compared to substrates,
creating a complete environment for the reaction
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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Mechanism of Citrate Synthetase
A cleft with functional groups binds oxaloacetate
Another cleft opens for acetyl CoA with H 274 and D
375, whose carboxylate abstracts a proton from
acetyl CoA
The enolate (stabilized by a cation) adds to the
carbonyl group of oxaloacetate
The thiol ester in citryl CoA is hydrolyzed
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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26.16 Protein Denaturation
The tertiary structure of a globular protein is the result
of many intramolecular attractions that can be
disrupted by a change of the environment, causing
the protein to become denatured
Solubility is drastically decreased as in heating egg
white, where the albumins unfold and coagulate
Enzymes also lose all catalytic activity when
denatured
Based on McMurry, Organic Chemistry, Chapter 26, 6th e
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