Transcript Introduction to Organic Chemistry 2 ed William H. Brown

18
Introduction to
Organic
Chemistry
2 ed
William H. Brown
18-1
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18
Amino Acids
& Proteins
Chapter 18
18-2
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Amino Acids
• Amino acid: a compound that contains both an
amino group and a carboxyl group
• a-Amino acid: an amino acid in which the amino group
is on the carbon adjacent to the carboxyl group
• although a-amino acids are commonly written in the
unionized form, they are more properly written in the
zwitterion (internal salt) form
R- CH- CO2 H
N H2
unionized
form
R- CH- CO2 N H3 +
zwitterion
18-3
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Chirality of Amino Acids
• With the exception of glycine, all protein-derived
amino acids have at least one stereocenter (the acarbon) and are chiral
• the vast majority of a-amino acids have the
L-configuration at the a -carbon
CO 2 H
NH 3 +
CH 3
D-Alanine
CO 2 +
H3 N
H
CH 3
L-Alanine
18-4
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 20 Protein-Derived AA
Nonpolar side chains (predominant form at pH 7.0)
glycine (gly, G)
Halanine (ala, A)
CH3 valine (val, V)
( CH3 ) 2 CH
leucine (leu, L)
( CH3 ) 2 CHCH 2 isoleucine (ile, I)
CH3 CH2 CH( CH3 ) methionine (met, M)
CH3 S CH2 CH2 Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
phenylalanine (phe,F)
tryptophan (trp, W)
N
H
proline (Pro, P)
+
N
H
H
18-5
18 20 Protein-Derived AA
Polar side chains (predominant form at pH 7.0)
asparagine (asn, N)
O
H2 NCCH 2 -
serine (ser, S)
glutamine (glu, G)
O
H2 NCCH 2 CH2 -
threonine (thr, T)
OH
CH3 CH-
HOCH2 -
18-6
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18 20 Protein-Derived AA
Acidic side chains (predominant form at pH 7.0)
aspartic acid (asp, D)
-
O 2 CCH2 -
glutamic acid (glu, E)
-
O 2 CCH2 CH2 -
cysteine (cys, C)
HS CH 2 tyrosine (tyr, Y)
HO
CH2 -
18-7
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 20 Protein-Derived AA
Basic side chains (predominant form at pH 7.0)
arginine (arg, R)
NH2 +
H2 NCNHCH2 CH2 CH2 lysine (lys, K)
histidine (his, H)
N
N
H
CH2 -
+
H3 NCH2 CH2 CH2 CH2 -
18-8
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 20 Protein-Derived AA
• Structural features
• all 20 are a-amino acids
• for 19 of the 20, the a-amino group is primary; for
proline it is secondary
• with the exception of glycine, the a-carbon of each is a
stereocenter
• isoleucine and threonine contain a second
stereocenter
• the sulfhydryl group of cysteine, the imidazole group of
histidine, and the phenolic hydroxyl of phenylalanine
are partially ionized at pH 7.0, but the ionic form is not
the major form at this pH
18-9
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18
AcidBase
Properties
Nonpolar &
polar side
chains
alanine
asparagine
glutamine
glycine
isoleucine
leucine
methionine
phenylalanine
proline
serine
threonine
tryptophan
valine
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
pK a of
pK a of
aCO 2 H
aNH 3
2.35
2.02
2.17
2.35
2.32
2.33
2.28
2.58
2.00
2.21
2.09
2.38
2.29
9.87
8.80
9.13
9.78
9.76
9.74
9.21
9.24
10.60
9.15
9.10
9.39
9.72
+
18-10
18 Acid-Base Properties
Acidic
Side
Chains
aspartic acid
glutamic acid
cysteine
tyrosine
pK a of
Basic
Side
Chains
arginine
histidine
lysine
pK a of
pK a of
aCO 2 H aNH 3
2.10
9.82
2.10
9.47
2.05
10.25
2.20
9.11
pK a of
aCO 2 H aNH 3
2.01
9.04
1.77
9.18
2.18
8.95
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
+
+
pK a of
Side
Chain
3.86
4.07
8.00
10.07
Side
Chain
Group
carboxyl
carboxyl
sufhydryl
phenolic
pK a of
Side
Chain
12.48
6.10
10.53
Side
Chain
Group
guanidino
imidazole
1° amino 18-11
18 Acidity: a-CO2H Groups
• The average pKa of an a-carboxyl group is 2.19,
which makes it a considerably stronger acid than
acetic acid (pKa 4.76)
• the greater acid strength is due to the electronwithdrawing inductive effect of the -NH3+ group
The ammonium ion has an
electron-withdrawing
inductive effect
RCHCO 2 H + H2 O
N H3
+
pK a = 2.19
RCHCO 2
NH 3
-
+ H3 O
+
+
18-12
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Acidity: side chain -CO2H
• Side chain -CO2H groups are stronger acids than
acetic acid
• the greater acid strength is due to the electronwithdrawing inductive effect of the a-NH3+ group,
• the effect decreases with distance from the a-NH3+
group
pK a 2.35
CH3 CHCO 2 H
pK a 3.86
HO 2 CCH 2 CHCO2 -
N H3 +
N H3 +
pK a 4.07
HO 2 CCH2 CH 2 CHCO2 N H3 +
18-13
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Acidity: a-NH3+ groups
• The average value of pKa for an a-NH3+ group is
9.47, compared with an average value of 10.60 for
a 1° alkylammonium ion
RCHCO 2
NH 3
-
+
H2 O
pK a = 9.47
+
NH 2
CH3 CHCH 3 + H2 O
NH3
+
RCHCO2 + H3 O
pK a = 10.76
+
CH3 CHCH 3
+ H3 O
+
NH2
18-14
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Basicity-Guanidine Group
• The side chain of arginine is a considerably
stronger base than an aliphatic amine
• its basicity is due to the large resonance stabilization
of the protonated form relative to the neutral form
••
••
NH2
NH2
••
RNH C
••
+
NH2
+
RNH C
RNH C
••
+
••
NH2
NH2
NH2
••
H2 O
NH
••
+ H3 O
RNH C
••
NH2
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
+
pKa = 12.48
18-15
18 Basicity- Imidazole Group
• The imidazole group on the side chain of histidine
is a heterocyclic aromatic amine
H
+
H
N
N
N
H
CH2 CHCO 2
+
N H3
-
N
this lone pair is
not a part of the
N
aromatic sextet; it is
H
the proton acceptor
2
N + CH2 CHCO
+
NH
3
H
CH2 CHCO 2
+
N H3
-
+ H3 O
-
+
H2 O
pK a 6.10
18-16
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Isoelectric Point
• Isoelectric point, pI: the pH at which the majority
of amino acid molecules in solution have no net
charge
• the pI for glycine, for example, falls between the pKa
values for the carboxyl and amino groups
pI =
1
+
2 (pK a a CO2 H + pK a a NH3 )
= 1
2
(2.35 + 9.78) = 6.06
• given in the following tables are isoelectric points for
the 20 protein-derived amino acids
18-17
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18
Nonpolar &
polar side
chains
alanine
asparagine
glutamine
glycine
isoleucine
leucine
methionine
phenylalanine
proline
serine
threonine
tryptophan
valine
pKa of
Isoelectric
+ Side
aCO2 H aNH3
Chain Point (pI)
---2.35
9.87
6.11
---2.02
8.80
5.41
2.17
9.13
---5.65
2.35
9.78
---6.06
2.32
9.76
---6.04
2.33
9.74
---6.04
2.28
9.21
---5.74
2.58
9.24
---5.91
---2.00
10.60
6.30
2.21
9.15
5.68
---2.09
9.10
---5.60
---2.38
9.39
5.88
2.29
9.72
---6.00 18-18
pKa of
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
pKa of
18
Acidic
Side Chains
aspartic acid
glutamic acid
cysteine
tyrosine
Basic
Side Chains
arginine
histidine
lysine
pKa of
Isoelectric
+ Side
aCO2 H aNH 3 Chain Point (pI)
2.10
9.82
3.86
2.98
2.10
9.47
4.07
3.08
2.05
10.25
8.00
5.02
2.20
9.11
10.07
5.63
pKa of
pKa of
pKa of
Isoelectric
+ Side
aCO2 H aNH 3 Chain Point (pI)
2.01
9.04
12.48
10.76
1.77
9.18
6.10
7.64
2.18
8.95
10.53
9.74
18-19
pKa of
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
pKa of
18 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
18-20
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 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
18-21
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Electrophoresis
• a reagent commonly used to detect amino acid is
ninhydrin
O
O
OH
RCHCO
-
+ 2
OH
+
NH3
An a-amino
acid
O
Ninhydrin
O
O
-
N
O
O
Purple-colored anion
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
O
+ RCH + CO 2 + H3 O +
18-22
18 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 a-carboxyl group of one
amino acid and the a-amino group of another
18-23
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Serylalanine (Ser-Ala)
18-24
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 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
18-25
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Writing Peptides
• by convention, peptides are written from the left,
beginning with the free -NH3+ group and ending at the
right with the free -CO2- group
peptide
bonds
C-terminal
N-terminal
amino acid
amino acid
O
O
+
H3 NCHC- NHCHC- NHCHCO 2
CH2 OH CH2
C6 H5
CH2 CO 2
-
Ser-Phe-Asp
18-26
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Ser-Phe-Asp
18-27
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 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 6 M HCl at elevated temperature
• quantitative analysis of the hydrolysate by ionexchange chromatography
18-28
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Cyanogen Bromide
• Cyanogen bromide, BrCN, is specific for cleavage
of peptide bonds formed by the carboxyl group of
methionine
cyanogen bromide is specific for
the cleavage of this peptide bond
from the
N-terminal
end
O
O
P N -C- NH CH C NH- P C
from the
C-terminal end
CH2
CH2 -S -CH3
18-29
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Cyanogen Bromide
O
O
P N -C- NH CH C NH- P C + Br C N 0.1M HCl
H2 O
Cyanogen
CH2
bromide
CH2 -S -CH3
from the
N-terminal
end
O
from the
C-terminal end
O
C
+ H2 N- PC + CH3 -S -C N
Methyl
CH2 CH2
thiocyanate
(A substituted -lactone)
18-30
P N -C- N H CH
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
O
18 Enzyme Catalysis
• A group of protein-cleaving enzymes can be used
to catalyze the hydrolysis of specific peptide
bonds. Among them are:
Enzyme
Catalyzes Hydrolysis of Peptide Bond
Formed by Carboxyl Group of
trypsin
chymotrypsin
arginine, lysine
phenylalanine, tryptophan, tyrosine
18-31
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Edman Degradation
• Edman degradation: cleaves the N-terminal
amino acid of a polypeptide chain
R
O
H2 N- CH- C- NH- PC + Ph - N= C= S
Phenyl isothiocyanate
R
CH
C O + H2 N- P C
HN
C
N
S
Ph
A phenylthiohydantoin
18-32
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Primary Structure
• Example 18.6 Deduce the 1° structure of this
pentapeptide
Experimental Procedure
Pentapeptide
Edman Degradation
Hydrolysis - Chymotrypsin
Fragment A
Fragment B
Hydrolysis - Trypsin
Fragment C
Fragment D
Amino Acid Composition
Arg, Glu, His, Phe, Ser
Glu
Glu, His, Phe
Arg, Ser
Arg, Glu, His, Phe
Ser
18-33
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Peptide Bond Geometry
• The four atoms of a peptide bond and the two
alpha carbons bonded to it lie in a plane with
bond angles of approximately 120° about C and N
18-34
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 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 a peptide bond is restricted
Ca
••
C
O
+
C
N
Ca
••
••
O
••
••
••
H
(1)
Ca
N
Ca
H
(2)
18-35
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 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
O
Ca
••
••
••
••
H
O
••
C
Ca
••
N
C
H
s-trans
N
Ca
Ca
s-cis
18-36
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 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
• all six atoms of each peptide bond lie in the same plane
and in the s-trans conformation
• there is hydrogen bonding between the N-H group of
one peptide bond and a C=O group of another peptide
bond as shown in the next screen
18-37
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Secondary Structure
18-38
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 Secondary Structure
• On the basis of model building, Pauling and
Corey proposed that two types of secondary
structure should be particularly stable
• the a-helix
• the antiparallel b-pleated sheet
• a-Helix: a type of secondary structure in which a
section of polypeptide chain coils into a spiral,
most commonly a right-handed spiral
18-39
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18 The a-Helix
• polyalanine, cylindrical bonds model, viewed along its
length
18-40
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18 The a-Helix
• polyalanine, cylindrical bonds model, viewed from one
end
18-41
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 The a-Helix
• polyalanine, space filling model, viewed along its
length
18-42
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 The a-Helix
• polyalanine, space filling model, viewed from one end
18-43
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 The a-Helix
• Structural features of the a-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
• C=O groups of all peptide bonds point in the opposite
direction, and also parallel to the axis of the helix
• the C=O 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
18-44
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 b-Pleated Sheet
• The antiparallel b-pleated sheet consists of
adjacent polypeptide chains running in opposite
directions
• each peptide bond is planar and has the s-trans
conformation
• the C=O 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.
18-45
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 b-Pleated Sheet
• polyalanine
18-46
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 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
H
O
H
O
N
N
N
H
CH2 CH2 SH
oxidation
CH2 CH2 S
CH2 CH2 SH
reduction
CH2 CH2 S
O
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
N
H
O
18-47
18 Quaternary Structure
• Quaternary structure: the arrangement of
polypeptide chains into a noncovalently bonded
aggregation
• the major factor stabilizing the aggregation of
polypeptide subunits 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
18-48
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18 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
Protein
Number of Subunits
alcohol dehydrogenase
aldolase
hemoglobin
lactate dehydrogenase
insulin
glutamine synthetase
tobacco mosaic virus protein disc
2
4
4
4
6
12
17
18-49
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.
18
Amino Acids
& Proteins
End of Chapter 18
18-50
Copyright © 2000 by John Wiley & Sons, Inc. All rights reserved.