Organic Chemistry

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Organic Chemistry
William H. Brown Christopher S. Foote
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• Amino Acids
• Proteins

Chapter 27
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Amino Acids

• Amino acid a compound that contains both an
  amino group and a carboxyl group
• ?-Amino acid an amino acid in which the amino
  group is on the carbon adjacent to the carboxyl
  group
• although ?-amino acids are commonly written in
  the unionized form, they are more properly
  written in the zwitterion (internal salt) form

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Chirality of Amino Acids

• With the exception of glycine, all
  protein-derived amino acids have at least one
  stereocenter (the ?-carbon) and are chiral
• the vast majority have the L-configuration at
  their ?-carbon

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Nonpolar side chains
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Polar side chains
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Acidic basic side chains
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Other Amino Acids
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• Acid-
• Base
• Proper-
• ties

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Acid-Base Properties
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Acidity ?-CO2H Groups

• The average pKa of an ?-carboxyl group is 2.19,
  which makes them considerably stronger acids than
  acetic acid (pKa 4.76)
• the greater acidity is accounted for by the
  electron-withdrawing inductive effect of the
  adjacent -NH3 group

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Acidity side chain -COOH

• Due to the electron-withdrawing inductive effect
  of the ?-NH3 group, side chain -COOH groups are
  also stronger than acetic acid
• the effect decreases with distance from the
  ?-NH3 group. Compare
• ?-COOH group of alanine (pKa 2.35)
• ?-COOH group of aspartic acid (pKa 3.86)
• ?-COOH group of glutamic acid (pKa 4.07)

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Acidity ?-NH3 groups

• The average value of pKa for an ?-NH3 group is
  9.47, compared with a value of 10.76 for a 1
  alkylammonium ion

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Basicity-Guanidine Group

• basicity of the guanidine group is attributed to
  the large resonance stabilization of the
  protonated form relative to the neutral form

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Basicity- Imidazole Group

• the imidazole group is a heterocyclic aromatic
  amine

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Ionization vs pH

• Given the value of pKa of each functional group,
  we can calculate the ratio of each acid to its
  conjugate base as a function of pH
• consider the ionization of an ?-COOH
• writing the acid ionization constant and
  rearranging terms gives

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Ionization vs pH

• substituting the value of pKa (2.00) for the
  hydrogen ion concentration at pH 7.0 (1.0 x 10-7)
  gives
• at pH 7.0, the ?-carboxyl group is virtually 100
  in the ionized form and has a net charge of -1
• we can repeat this calculation at any pH and
  determine the ratio of ?-COO- to ?-COOH and
  the net charge on the ?-carboxyl at that pH

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Ionization vs pH

• We can also calculate the ratios of acid to
  conjugate base for an ?-NH3 group for this
  calculation, assume a value 10.0 for pKa
• writing the acid ionization constant and
  rearranging gives

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Ionization vs pH

• substituting values for pKa of an ?-NH3 group
  and the hydrogen ion concentration at pH 7.0
  gives
• thus at pH 7.0, the ratio of ?-NH3 to ?-NH2 is
  approximately 1 to 1000
• at this pH, an ?-amino group is 99.9 in the
  protonated form and has a charge of 1

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Henderson-Hasselbalch

• for the ionization of any weak acid HA
• taking the log and rearranging gives
• substitution pH and pKa gives the
  Henderson-Hasselbalch equation

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Henderson-Hasselbalch

• using the Henderson-Hasselbalch equation
• we see that
• when pH pKa, the concentrations of weak acid
  and its conjugate base are equal
• when pH lt pKa, the weak acid predominates
• when pH gt pKa, the conjugate base predominates

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Isoelectric Point

• Isoelectric point, pI, of an amino acid the pH
  at which the majority of its molecules in
  solution have no net charge
• the pH for glycine, for example, falls between
  the pKa values for the carboxyl and amino groups

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Electrophoresis

• Electrophoresis the process of separating
  compounds on the basis of their electric charge
• electrophoresis of amino acids can be carried out
  using paper, starch, agar, certain plastics, and
  cellulose acetate as solid supports
• In paper electrophoresis
• a paper strip saturated with an aqueous buffer of
  predetermined pH serves as a bridge between two
  electrode vessels

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Electrophoresis

• a sample of amino acids is applied as a spot on
  the paper strip
• an electric potential is applied to the electrode
  vessels and amino acids migrate toward the
  electrode with charge opposite their own
• molecules with a high charge density move faster
  than those with low charge density
• molecules at their isoelectric point remain at
  the origin
• after separation is complete, the strip is dried
  and developed to make the separated amino acids
  visible

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Electrophoresis

• a reagent commonly used to detect amino acid is
  ninhydrin

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Polypeptides Proteins

• In 1902, Emil Fischer proposed that proteins are
  long chains of amino acids joined by amide bonds
  to which he gave the name peptide bonds
• Peptide bond the special name given to the amide
  bond between the ?-carboxyl group of one amino
  acid and the ?-amino group of another

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Serylalanine (Ser-Ala)
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Peptides

• peptide the name given to a short polymer of
  amino acids joined by peptide bonds they are
  classified by the number of amino acids in the
  chain
• dipeptide a molecule containing two amino acids
  joined by a peptide bond
• tripeptide a molecule containing three amino
  acids joined by peptide bonds
• polypeptide a macromolecule containing many
  amino acids joined by peptide bonds
• protein a biological macromolecule of molecular
  weight 5000 g/mol of greater, consisting of one
  or more polypeptide chains

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Writing Peptides

• by convention, peptides are written from the
  left, beginning with the free -NH3 group and
  ending with the free -COO- group on the right

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Primary Structure

• Primary structure the sequence of amino acids in
  a polypeptide chain read from the N-terminal
  amino acid to the C-terminal amino acid
• Amino acid analysis
• hydrolysis of the polypeptide, most commonly
  carried out using 6M HCl at elevated temperature
• quantitative analysis of the hydrolysate by
  ion-exchange chromatography

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Cyanogen Bromide, BrCN

• cleavage of peptide bonds formed by the carboxyl
  group of methionine

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Cyanogen Bromide, BrCN
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Cyanogen Bromide, BrCN

• Step 1 nucleophilic displacement of bromine

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Cyanogen Bromide, BrCN

• Step 2 internal nucleophilic displacement

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Cyanogen Bromide, BrCN

• Step 3 hydrolysis of the imino group

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Enzyme Catalysis

• A group of protein-cleaving enzymes can be used
  to catalyze the hydrolysis of specific peptide
  bonds

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Edman Degradation

• Edman degradation cleaves the N-terminal amino
  acid of a polypeptide chain

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Edman Degradation

• Step 1 nucleophilic addition to the CN group of
  phenylisothiocyanate

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Edman Degradation

• Step 2 nucleophilic addition of sulfur to the
  CO of the adjacent amide group

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Edman Degradation

• Step 3 isomerization of the thiazolinone ring

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Primary Structure

• Example 27.8 Deduce the 1 structure of this
  pentapeptide

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Polypeptide Synthesis

• The problem is join the ?-carboxyl group of aa-1
  by an amide bond to the ?-amino group of aa-2,
  and not vice versa

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Polypeptide Synthesis

• protect the ?-amino group of aa-1
• activate the ?-carboxyl group of aa-1
• protect the ?-carboxyl group of aa-2

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Amino-Protecting Groups

• the most common strategy for protecting amino
  groups and reducing their nucleophilicity is to
  convert them to amides

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Amino-Protecting Groups

• treatment of an amino group with either of these
  reagents gives a carbamate (an ester of the
  monoamide of carbonic acid)

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Amino-Protecting Groups

• a carbamate is stable to dilute base but can be
  removed by treatment with HBr in acetic acid

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Amino-Protecting Groups

• The benzyloxycarbonyl group is removed by
  hydrogenolysis (Section 20.6C)
• the intermediate carbamic acid loses carbon
  dioxide to give the unprotected amino group

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Carboxyl-Protecting Grps

• Carboxyl groups are most often protected as
  methyl, ethyl, or benzyl esters
• methyl and ethyl esters are prepared by Fischer
  esterification, and removed by hydrolysis in
  aqueous base under mild conditions
• benzyl esters are removed by hydrogenolysis
  (Sect. 20.6C) they are also removed by treatment
  with HBr in acetic acid

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Peptide Bond Formation

• The reagent most commonly used to bring about
  peptide bond formation is DCC
• DCC is the anhydride of a disubstituted urea and,
  when treated with water, is converted to DCU

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Peptide Bond Formation

• DCC acts as dehydrating in bringing about
  formation of a peptide bond

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Solid-Phase Synthesis

• Bruce Merrifield, 1984 Nobel prize for Chemistry
• solid support a type of polystyrene in which
  about 5 of the phenyl groups carry a -CH2Cl
  group
• the amino-protected C-terminal amino acid is
  bonded as a benzyl ester to the support beads
• the polypeptide chain is then extended one amino
  acid at a time from the N-terminal end
• when synthesis is completed, the polypeptide is
  released from the support beads by cleavage of
  the benzyl ester

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Peptide Bond Geometry

• the four atoms of a peptide bond and the two
  alpha carbons joined to it lie in a plane with
  bond angles of 120 about C and N

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Peptide Bond Geometry

• to account for this geometry, Linus Pauling
  proposed that a peptide bond is most accurately
  represented as a hybrid of two contributing
  structures
• the hybrid has considerable C-N double bond
  character and rotation about the peptide bond is
  restricted

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Peptide Bond Geometry

• two conformations are possible for a planar
  peptide bond
• virtually all peptide bonds in naturally
  occurring proteins studied to date have the
  s-trans conformation

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Secondary Structure

• Secondary structure the ordered arrangements
  (conformations) of amino acids in localized
  regions of a polypeptide or protein
• To determine from model building which
  conformations would be of greatest stability,
  Pauling and Corey assumed that
• 1. all six atoms of each peptide bond lie in the
  same plane and in the s-trans conformation
• 2. there is hydrogen bonding between the N-H
  group of one peptide bond and a CO group of
  another peptide bond as shown in the next screen

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Secondary Structure

• hydrogen bonding between amide groups

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Secondary Structure

• On the basis of model building, Pauling and Corey
  proposed that two types of secondary structure
  should be particularly stable
• ?-helix
• antiparallel ?-pleated sheet
• ?-Helix a type of secondary structure in which a
  section of polypeptide chain coils into a spiral,
  most commonly a right-handed spiral

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The ?-Helix

• In a section of ?-helix
• there are 3.6 amino acids per turn of the helix
• each peptide bond is s-trans and planar
• N-H groups of all peptide bonds point in the same
  direction, which is roughly parallel to the axis
  of the helix
• CO groups of all peptide bonds point in the
  opposite direction, and also parallel to the axis
  of the helix
• the CO group of each peptide bond is hydrogen
  bonded to the N-H group of the peptide bond four
  amino acid units away from it
• all R- groups point outward from the helix

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The ?-Helix
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?-Pleated Sheet

• The antiparallel ?-pleated sheet consists of
  adjacent polypeptide chains running in opposite
  directions
• each peptide bond is planar and has the s-trans
  conformation
• the CO and N-H groups of peptide bonds from
  adjacent chains point toward each other and are
  in the same plane so that hydrogen bonding is
  possible between them
• all R- groups on any one chain alternate, first
  above, then below the plane of the sheet, etc.

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Tertiary Structure

• Tertiary structure the three-dimensional
  arrangement in space of all atoms in a single
  polypeptide chain
• disulfide bonds between the side chains of
  cysteine play an important role in maintaining 3
  structure

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Quaternary Structure

• Quaternary structure the arrangement of
  polypeptide chains into a noncovalently bonded
  aggregation
• the major factor stabilizing quaternary structure
  is the hydrophobic effect
• Hydrophobic effect the tendency of nonpolar
  groups to cluster together in such a way as to be
  shielded from contact with an aqueous environment

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Quaternary Structure

• if two polypeptide chains, for example, each have
  one hydrophobic patch, each patch can be shielded
  from contact with water if the chains form a dimer

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Prob 27.19

• From what amino acid is histamine derived? By
  what type of reaction is the precursor amino acid
  converted to histamine?

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Prob 27.21

• From which protein-derived amino acid are
  norepinephrine and epinephrine synthesized? What
  types of reactions are involved in each
  biosynthesis?

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Prob 27.22

• From which amino acid are serotonin and
  melatonin derived? What types of reactions are
  involved in the biosynthesis of each?

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Prob 27.39

• Do you expect the modified guanidino group of
  cimetidine to be more basic or less basic that
  the guanidino group of arginine?

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Prob 27.40

• Draw a structural formula for the product formed
  by treating alanine with each reagent.

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Prob 27.45

• A tetradecapeptide (14 amino acids) gives these
  fragments on partial hydrolysis. From this
  information, deduce the primary structure of this
  polypeptide.

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Prob 27.48

• Name the amino acids in glutathione. What is
  unusual about the peptide bond formed by the
  N-terminal amino acid?

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Prob 27.49

• Name the amino acids in aspartame. Estimate the
  isoelectric point of this dipeptide.

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Prob 27.51

• Write a structural formula for the product
  formed by treating the N-terminal amino acid of a
  polypeptide chain with 2,4-dinitrofluorobenzene,
  and for the derivatized amino acid formed when
  the polypeptide chain is hydrolyzed in acid.

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• Amino Acids
• Proteins

End of Chapter 27