Download Amino Acids

Guest Lecturer: Prof. Jonathan L. Sessler
Carbohydrates
• Carbohydrate: A polyhydroxyaldehyde, a
polyhydroxyketone, or a compound that gives either of
these compounds after hydrolysis.
• Monosaccharide: A carbohydrate that cannot be
hydrolyzed to a simpler carbohydrate.
– They have the general formula CnH2nOn, where n
varies from 3 to 8.
– Aldose: a monosaccharide containing an aldehyde
group.
– Ketose: a monosaccharide containing a ketone group.
Monosaccharides
• Monosaccharides are classified by their number
of carbon atoms:
Name
Triose
Tetrose
Formula
C3 H6 O3
C4 H8 O4
Pentose
Hexose
C5 H1 0 O5
C6 H1 2 O6
Heptose
Octose
C7 H1 4 O7
C8 H1 6 O8
Names and Structures
• Monosaccharide: aldehyde or ketone containing at least two additional
hydroxy groups
– Aldehyde - aldose
– Ketone - ketose
– Also named by number of carbons
Monosaccharides
• There are only two trioses:
CHO
CH2 OH
CHOH
C= O
CH2 OH
Glyceraldehyde
(an aldotriose)
CH2 OH
Dihydroxyacetone
(a ketotriose)
• Often the designations aldo- and keto- are omitted and
these compounds are referred to simply as trioses,
tetroses, and so forth.
– Although these designations do not tell the nature of
the carbonyl group, they at least tell the number of
carbons.
Monosaccharides
• Glyceraldehyde contains a stereocenter and
exists as a pair of enantiomers.
CHO
CHO
H
C
OH
CH2 OH
(R)-Glyceraldehyde
HO
C
H
CH2 OH
(S)-Glyceraldehyde
Fischer Projections
• Fischer projection: A two dimensional representation for
showing the configuration of carbohydrates.
– Horizontal lines represent bonds projecting forward.
– Vertical lines represent bonds projecting to the rear.
– The only atom in the plane of the paper is the
stereocenter.
– The more highly oxidized carbon is shown at the top.
CHO
H
C
OH
convert to a
Fischer projection
CH2 OH
(R)-Glyceraldehyde
(three-dimensional
representation)
CHO
H
OH
CH2 OH
(R)-Glyceraldehyde
(Fischer projection)
.
D,L Monosaccharides
• In 1891, Emil Fischer made the arbitrary assignments of
D- and L- to the enantiomers of glyceraldehyde.
• This is an older stereochemical designation that is still
used for amino acids and sugars that antedates the
Cahn-Ingold-Prelog R/S system.
CHO
H
OH
CH2 OH
CHO
HO
H
CH2 OH
D-Glyceraldehyde L-Glyceraldehyde
(R)-Glyceraldehyde (S)-Glyceraldehyde
25
25
[]D
= +13.5
[]D
= -13.5
D,L Monosaccharides
• According to the conventions proposed by Fischer:
– D-monosaccharide: A monosaccharide that has the
same configuration at its penultimate carbon as Dglyceraldehyde; that is, its -OH is on the right when
written as a Fischer projection.
– L-monosaccharide: A monosaccharide that has the
same configuration at its penultimate carbon as Lglyceraldehyde; that is, its -OH is on the left when
written as a Fischer projection.
Note that this designation refers to only one carbon in molecules that
often have many stereocenters.
Names and Structures
• Sugars are optically active (D vs. L)
– Almost all naturally occurring sugars are D
Fischer projections
make it easy to see
the “last” carbon.
It is one reason we
use them!
D,L Monosaccharides
• Here are the two most abundant D-aldotetroses and the
two most abundant D-aldopentoses in the biological
world:
CHO
CHO
H
OH
HO
H
OH
H
CH2 OH
D-Erythrose
CHO
CHO
H
OH
H
H
H
H
OH
H
OH
OH
H
OH
H
OH
CH2 OH
D-Threose
CH2 OH
D-Ribose
CH2 OH
2-Deoxy-Dribose
You must know these compounds and their chemistry
(and their normal Fischer and Haworth projections)
D,L Monosaccharides
• And the three most abundant hexoses:
CHO
H
OH
HO
H
H
OH
H
OH
CH2 OH
D-Glu co s e
CHO
H
OH
HO
H
HO
H
H
OH
CH2 OH
D -Gala cto s e
CH2 OH
C O
HO
H
H
OH
H
OH
CH2 OH
D -Fru cto s e
You must know these compounds and their chemistry
(and their normal Fischer and Haworth projections)
Amino Sugars
• Amino sugar: A sugar that contains an -NH2 group in
place of an -OH group.
– Only three amino sugars are common in nature
– N-Acetyl-D-glucosamine is a derivative of Dglucosamine.
H
HO
H
H
CHO
NH2
H
OH
OH
CH2 OH
CHO
H2 N 2 H
HO
H
H
OH
H
OH
CH2 OH
CHO
H
NH2
HO
H
4
HO
H
H
OH
CH2 OH
D-Glucosamine D-Mannosamine D-Galactosamine
H
HO
H
H
CHO O
NHCCH3
H
OH
OH
CH2 OH
N-Acetyl-Dglucosamine
Physical Properties
• Monosaccharides are colorless crystalline solids, very
soluble in water, but only slightly soluble in ethanol.
– sweetness relative to sucrose:
Sweetness
Relative to
Carbohydrate
Sucrose
Fructose
1.74
Invert sugar
1.25
Sucrose (table sugar) 1.00
Honey
0.97
Glucose
0.74
Maltose
0.33
Galactose
0.32
Lactose (milk sugar) 0.16
Sweetness
Relative to
Artificial
Sweetener
Sucrose
Saccharin
450
Acesulfame-K
200
Aspartame
160
Cyclic Structure
• Monosaccharides have hydroxyl and carbonyl
groups in the same molecule and those with five
or more carbons exist almost entirely as fiveand six-membered cyclic hemiacetals.
– Anomeric carbon: The new stereocenter
created as a result of cyclic hemiacetal
formation.
– Anomers: Carbohydrates that differ in
configuration at their anomeric carbons.
Haworth Projections
• Haworth projections
– Five- and six-membered hemiacetals are represented
as planar pentagons or hexagons, as the case may
be, viewed through the edge.
– They are most commonly written with the anomeric
carbon on the right and the hemiacetal oxygen to the
back right.
– The designation - means that the -OH on the
anomeric carbon is cis to the terminal -CH2OH;
- means that it is trans to the terminal -CH2OH.
Haworth Projections
1
CHO
H
OH
HO
H
H
OH
H5
OH
redraw to show the -OH
on carbon-5 close to the
aldehyde on carbon-1
CH2 OH
OH
H5
O
H
OH H C
1 H
HO
H
CH2 OH
D-Glucose
Hint: Drawn this way,
the “non-D” OH’s to
the right in a standard
Fischer Projection go
“down” in the
Haworth Projection
anomeric
carbon
CH2 OH
O OH()
H
H
OH H
HO
H
H OH
-D-Glucopyranose
(-D-Glucose)
OH
anomeric
carbon
CH2 OH
OH
H
H
+
OH H
HO
OH()
H OH
-D-Glucopyranose
( -D-Glucose)
Haworth Projections
– Six-membered hemiacetal rings are shown by the
infix -pyran-.
– Five-membered hemiacetal rings are shown by the
infix -furan-.
O
O
Furan
Pyran
Conformational Formulas
– Five-membered rings are so close to being planar
that Haworth projections are adequate to represent
furanoses.
HOCH2
H
H
O
H
OH ( )
OH
OH
-D-Ribofuranose
(-D-Ribose)
H
HOCH2
H
H
OH ( )
O
H
H
OH
H
-2-Deoxy-D-ribofuranose
(-2-Deoxy-D-ribose)
Conformational Formulas
– Other monosaccharides also form five-membered
cyclic hemiacetals.
– Here are the five-membered cyclic hemiacetals of Dfructose.
1
1
HOCH2
5
O
H HO
H
HO
CH2 OH
2
CH2 OH
2
OH( )
H
 -D-Fructofuranose
( - D-Fructose)
C=O
HO
H
4
H
OH
H 5 OH
3
6
CH2 OH
D-Fructose
HOCH2
5
O
H HO
H
OH ( )
2
CH2 OH
HO
H
1
 - D-Fructofuranose
(- D-Fructose)
Ascorbic Acid (Vitamin C)
• L-Ascorbic acid (vitamin C) is synthesized both
biochemically and industrially from D-glucose.
H
HO
H
H
CHO
biochemial
OH and industrial
H
syntheses
OH
OH
CH2 OH
D-Glucose
CH2 OH
H
OH O
O
H
HO
OH
L-Ascorbic acid
(Vitamin C)
Ascorbic Acid (Vitamin C)
– L-Ascorbic acid is very easily oxidized to Ldehydroascorbic acid.
– Both are physiologically active and are found in most
body fluids.
CH2 OH
H
CH2 OH
OH O
O
H
HO
OH
L-Ascorbic acid
(Vitamin C)
oxidation
reduction
H
OH O
O
H
O
O
L-Dehydroascorbic acid
Conformational Formulas
– For pyranoses, the six-membered ring is more
accurately represented as a chair conformation.
H OH
H
H O
HO
HO
H
H
OH
H
OH
OH
H OH
HO
HO
H
H
O
OH
H
-D-Glucopyranose
(-D-Glucose)
rotate about
C-1 to C-2 bond
H OH
H OH
H OH
HO
HO
H
H
OH
H
O
HO
HO
H O
H
H
OH
OH
H
-D-Glucopyranose
(-D-Glucose)
Conformational Formulas
– If you compare the orientations of groups on carbons
1-5 in the Haworth and chair projections of -Dglucopyranose, you will see that in each case they
are up-down-up-down-up respectively.
6 CH OH
2
H
4
5
H
OH
HO
3
H
O
6
1
H
H
2
OH
-D-Glucopyranose
(Haworth projection)
CH2 OH
4
OH()
O
HO
HO
5
3
OH( )
2
OH 1
-D-Glucopyranose
(chair conformation)
Cyclic Forms of Monosaccharides - details
• Sugars often have a choice in forming intramolecular hemiacetals
Cyclic Forms of Monosaccharides - cont.
• Sugars form intramolecular hemiacetals
– New stereocenter formed at anomeric carbon
– For D sugars, S centers are termed  and R centers are 
– These diastereomers are termed anomers
Cyclic Forms of Monosaccharides - cont.
Which conformation do you think is the most stable? Why?
Mutarotation
• Mutarotation: The change in specific rotation that occurs
when an  or  form of a carbohydrate is converted to an
equilibrium mixture of the two.
[]
Monosaccharide
-D-glucose
-D-glucose
[] after
% Present at
Mutarotation Equilibrium
+112.0
+18.7
+52.7
+52.7
36
-D-galactose +150.7
-D-galactose
+52.8
+80.2
28
72
HO
HO
CH2 OH
O
OH
-D-Glucopyranose
[] D2 5 +18.7
OH ( )
64
+80.2
HO
HO
CH2 OH
O
HO
OH ( )
-D-Glucopyranose
[] D 25 +112
Mutarotation of Monosaccharides
•Conversion of anomers is termed mutarotation and goes through an open chain form
Glycosides
• Glycoside: A carbohydrate in which the -OH of the
anomeric carbon is replaced by -OR.
– methyl -D-glucopyranoside (methyl -D-glucoside)
glycosidic
bond
CH2 OH
CH2 OH
CH2 OH
O OH
OH
O OCH3
H
H
+
H
H
H
H
H
+
CH
OH
+
OH H
3
OH H
OH H
-H
O
2
HO
H
HO
OCH3
H
HO
H OH
H OH
H OH
-D-Glucopyranose
Methyl -D-glucoMethyl -D-gluco(-D-Glucose)
pyranoside
pyranoside
( Methyl -D-glucoside) (Methyl -D-glucoside)
Glycosides
• Glycosidic bond: The bond from the anomeric carbon of
the glycoside to an -OR group.
• Glycosides are named by listing the name of the alkyl or
aryl group bonded to oxygen followed by the name of the
carbohydrate with the ending -e replaced by -ide.
– methyl -D-glucopyranoside
– methyl -D-ribofuranoside
N-Glycosides
• The anomeric carbon of a cyclic hemiacetal also
undergoes reaction with the N-H group of an amine to
form an N-glycoside.
– N-glycosides of the following purine and pyrimidine
bases are structural units of nucleic acids.
O
NH2
HN
O
N
H
Uracil
N
O
N
H
Cytosine
O
HN
O
NH2
CH3
N
H
Thymine
O
N
N
N
H
Adenine
N
N
HN
H2 N
N
Guanine
N
H
N-Glycosides
– The -N-glycoside formed between D-ribofuranose
and cytosine.
NH2
N
O
HOCH2
O
H
H
N
a -N-glycosidic
bond
H
H
HO
OH
anomeric
carbon
Reduction to Alditols
• The carbonyl group of a monosaccharide can be
reduced to an hydroxyl group by a variety of reducing
agents, including NaBH4 and H2/M.
HO
HO
CH2 OH
O
OH
OH
-D-Glucopyranose
CHO
H OH
HO H
H OH
H OH
CH2 OH
D-Glucose
NaBH4
CH2 OH
H OH
HO H
H OH
H OH
CH2 OH
D-Glucitol
(D-Sorbitol)
Reduction to Alditols
– Other alditols common in the biological world are:
CH2 OH
H
OH
H
OH
CH2 OH
Erythritol
CH2 OH
HO
H
HO
H
H
OH
H
OH
CH2 OH
D-Mannitol
CH2 OH
H
OH
HO
H
H
OH
CH2 OH
Xylitol
Oxidation to Aldonic Acids
• The -CHO group can be oxidized to -COOH (reducing
sugars). Oxidizing agents for this transformation include
bromine in aqueous CaCO3 (Br2, CaCO3, H2O),
copper(II) in base (Fehling’s solution), and Tollens’
solution (Ag(NH3)2+). -- Copper bricks and silver mirrors!
H
O
C
HO
CH2 OH
O
HO
OH
OH
- D-Glucopyranose
( -D-Glucose)
OH oxidizing
agent
H
OH
basic
solution
OH
CH2 OH
D-Glucose
H
HO
H
H
-
O
O
C
H
HO
H
H
OH
H
OH
OH
CH2 OH
D-Gluconate
Oxidation to Aldonic Acids
• 2-Ketoses (also reducing sugars) are also oxidized to
aldonic acids. 3-Ketoses, 4-ketoses, etc. are not. Nor
are compounds where the carbonyl is tied up in a
glycosidic bond.
– Under the conditions of the oxidation, 2-ketoses
equilibrate with isomeric aldoses (Step 1 & 2) by ketoenol tautomerization. The aldose is then oxidized to
the aldonic acid (Step 3).
CH2 OH
(1)
C= O
( CHOH ) n
CH2 OH
A 2-ketose
CHOH
C-OH
(2)
( CHOH ) n
CH2 OH
An enediol
CHO
CHOH
(3)
( CHOH ) n
CH2 OH
An aldose
COOH
CHOH
( CHOH ) n
CH2 OH
An aldonic acid
Oxidation to Uronic Acids
• Enzyme-catalyzed oxidation of the terminal -OH group
gives a -COOH group.
CHO
CHO
H
OH enzyme-catalyzed
H
OH
COOH
O
oxidation
HO
H
HO
H
HO
H
OH
H
OH
HO
OH
H
OH
H
OH
CH2 OH
COOH
D-Glucose
D-Glucuronic acid
(a uronic acid)
OH
Oxidation to Uronic Acids
– In humans, D-gluconic acid is an important
component of the acidic polysaccharides of
connective tissue.
– It is also used by the body to detoxify foreign
hydroxyl-containing compounds, such as phenols and
alcohols; one example is the intravenous anesthetic
propofol.
COOHO
HO
HO
O
O
OH
Propofol
A urine-soluble glucuronide
Carbohydrates
End of Chapter 25
Triglycerides
Beeswax contains a
component which is an
ester of a fatty acid
Vegetable oils contain
mostly unsaturated
fatty acids
A Triglyceride
Tristearin, a
saturated triglyceride
A polyunsaturated
triglyceride
Soaps and Detergents
Steroids
Tetracycylic ring system
characteristic of steroids
Cholesterol
Human gallstones are almost pure
cholesterol
(continued)
Biosynthesis of
Cholesterol
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 neutral -amino acids are commonly written
in the unionized form, they are more properly written
in the zwitterion (internal salt) form. Needless to say,
adding acid or base can lead to conversion to other
O
O
forms.
RCHCOH
N H2
-Amino Acid
RCHCO -
N H3 +
Zwitterion
form
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.
COOH
N H3 +
CH3
D-Alanine
COOH 3N
H
CH3
L-Alanine
Nonpolar side chains
COO- Alanine
(Ala, A)
N H3 +
COO- Phenylalanine
(Phe, F)
+
N H3
COO- Glycine
(Gly, G)
N H3 +
COO- Isoleucine
(Ile, I)
N H3 +
-
COO
N H3 +
S
Leucine
(Leu, L)
COO- Methionine
(Met, M)
N H3 +
- Proline
COO
N
(Pro, P)
H H
N
H
COO- Tryptophan
(Trp, W)
N H3 +
COO- Valine
(Val, V)
+
N H3
Polar side chains
COO-
H 2N
O
N H3 +
Asparagine
(Asn, N)
O
H 2N
COON H3 +
Glutamine
(Gln, Q)
HO
COO-
Serine
(Ser, S)
N H3 +
OH
COO- Threonine
(Thr, T)
N H3 +
Acidic & Basic Side Chains
-
COO-
O
O
N H3
+
Aspartic acid
(Asp, D)
N H2 +
H2N
O
-
COO-Glutamic acid
N H3 + (Glu, E)
O
N
H
3
N
-
HS
COO
N H3 +
Cysteine
(Cys, C)
-
COO
HO
N H3 +
Tyrosine
(Tyr, Y)
N
H
+
H 3N
COO- Arginine
(Arg, R)
NH +
COON H3
+
COON H3
+
Histidine
(His, H)
Lysine
(Lys, K)
Some Other Amino Acids
O
-
+
H 3N
COO
H 2N
N H3 +
N
H
Ornithine
I
HO
N H3 +
Citrulline
I
O
I
COO-
I
Thyroxine, T4
O
-
CH2 CHCOO
N H3 +
-
O
N H3 +
4-Aminobutanoic acid
(-Aminobutyric acid, GABA)
Acid-Base properties
Nonpolar &
polar side
chains
alanine
asparagine
glutamine
glycine
isoleucine
leucine
methionine
phenylalanine
proline
serine
threonine
tryptophan
valine
pK a of
pK a of
-COOH
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
-NH 3
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
+
Acid-Base Properties
Acidic
pKa of
pKa of
Side
+
-COOH -NH3
Chains
aspartic acid
2.10
9.82
glutamic acid
2.10
9.47
cysteine
2.05
10.25
tyrosine
2.20
9.11
pKa of
Side
Chain
3.86
4.07
8.00
10.07
Side
Chain
Group
carboxyl
carboxyl
sufhydryl
phenolic
Basic
Side
Chains
arginine
histidine
lysine
pKa of
Side
Chain
12.48
6.10
10.53
Side
Chain
Group
guanidino
imidazole
1° amino
pKa of
pKa of
-COOH -NH3
2.01
9.04
1.77
9.18
2.18
8.95
+
Acidity: -COOH 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 electronwithdrawing inductive effect of the adjacent -NH3+
group.
RCHCOOH
NH3 +
+
H2 O
RCHCOONH3
+
+
+
H3 O
pKa = 2.19
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)
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.
RCHCOO + H2 O
+
NH3
RCHCOO + H3 O+
NH2
-
CH3 CHCH3 + H2 O
+
NH3
CH3 CHCH3 + H3 O
NH2
pKa = 9.47
+
pKa = 10.60
The Guanidine Group of Arg
– This is a special side chain.
– The basicity of the guanidine group is attributed 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
H2 O
NH2
:
NH2
+
+ H3 O
RN C
:
NH2
pKa = 12.48
Basicity - Imidazole Group
– The imidazole group is a heterocyclic aromatic amine.
H
••
N
N+
H
H
NH3
+
+
N
-
COO
NH3 +
••
N
COO-
H2 O
H3 O+
H
Not a part of the
aromatic sextet;
the proton acceptor
••
N
••
N
H
NH3 +
+
COO- + H 3 O
pKa 6.10
Titration of Amino Acids
• Titration of glycine with NaOH.
Isoelectric Point
• Isoelectric point (pI): The pH at which an amino acid,
polypeptide, or protein has a total charge of zero.
– The pH for glycine, for example, falls between the pKa
values for the carboxyl and amino groups.
1
pI = 2
+
( pKa -COOH + pKa -NH3 )
= 1 (2.35 + 9.78) = 6.06
2
Isoelectric Point
Nonpolar &
pKa of
pKa of
polar side
+
-COOH -NH3
chains
alanine
2.35
9.87
asparagine
2.02
8.80
glutamine
2.17
9.13
glycine
2.35
9.78
isoleucine
2.32
9.76
leucine
2.33
9.74
methionine
2.28
9.21
phenylalanine 2.58
9.24
proline
2.00
10.60
serine
2.21
9.15
threonine
2.09
9.10
tryptophan
2.38
9.39
valine
2.29
9.72
pKa of
Side
Chain
----------------------------------------
pI
6.11
5.41
5.65
6.06
6.04
6.04
5.74
5.91
6.30
5.68
5.60
5.88
6.00
Isoelectric Point
Acidic
Side Chains
aspartic acid
glutamic acid
cysteine
tyrosine
Basic
Side Chains
arginine
histidine
lysine
pKa of
+ Side
-COOH -NH3 Chain
2.10
9.82
3.86
2.10
9.47
4.07
2.05
10.25
8.00
2.20
9.11
10.07
2.98
3.08
5.02
5.63
pKa of
+ Side
-COOH -NH3 Chain
2.01
9.04
12.48
1.77
9.18
6.10
2.18
8.95
10.53
pI
10.76
7.64
9.74
pKa of
pKa of
pKa of
pI
pKa of
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, polyacrylamide and agarose
gels, and cellulose acetate as solid supports.
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.
– After derivitization with ninhydrin, 19 of the 20 amino acids
give the same purple-colored anion; proline gives an
orange-colored compound.
Electrophoresis
– The reagent commonly used to detect amino acid is
ninhydrin.
O
O
OH
-
RCHCO + 2
NH3
OH
+
An -amino
acid
O
Ninhydrin
-
O
O
N
O
O
Purple-colored anion
O
+ RCH + CO2 + H3 O+
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.
Peptide bonds
Peptide bonds
Serinylalanine (Ser-Ala)
A dipeptide
HOCH2 H
H 2N
O
O
O
Serine
(Ser, S)
H
+ H 2N
O
H
H CH3
Alanine
(Ala, A)
peptide bond
HOCH2 H H
O
N
H
H 2N
O
O H CH
3
Serinylalanine
(Ser-Ala, (S-A)
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 or greater, consisting of one or
more polypeptide chains.
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.
+
H 3N
N-terminal
amino acid
O
C6 H5
O
H
N
N
OH
O
OH
COOSer-Phe-Asn
C-terminal
amino acid
Writing Peptides
– The tetrapeptide Cys-Arg-Met-As
– At pH 6.0, its net charge is +1.
pKa 8.00
N-terminal
amino acid
+
H3 N
SH
H
N
SCH3
O
H
N
N
H
O
O
NH
H2 N
NH2 +
C-terminal
amino acid
O
-
O
NH2
O
pKa 12.48
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 ionexchange chromatography.
Ion Exchange Chromatography
• Analysis of a mixture
of amino acids by ion
exchange
chromatography
Edman Degradation
• Edman degradation: Cleaves the N-terminal amino acid
of a polypeptide chain.
N-terminal
amino acid
R
+
H3 N
NH
O
COO-
+ S=C=N-Ph
Phenyl isothiocyanate
R
HN
S
O + H2 N
N
Ph
A phenylthiohydantoin
COO-
Edman Degradation Mechanism – It will be on the final!
Cytochrome C
And, we are done!!