Protein - Revised 2010

Biochemistry for Health Science Amino acid, Peptide and Protein
Amino acid, Peptide and Protein
Chymotrypsin
Chatchawin Petchlert,
Petchlert, Ph.D.
The light produced by firefly → protein luciferin and ATP, catalyzed by
Department of Biochemistry the enzyme luciferase.
luciferase.
Faculty of Science, Burapha University Petchlert C. 2
Erythrocytes contain large amounts of the O2-transporting protein, The protein keratin is the chief structural component of hair, scales, horn,
hemoglobin. wool, nails, and feathers.
Petchlert C. 3 Petchlert C. 4
Petchlert C. 1
L-Form Amino Acid Structure
Carboxylic group -
COO
Amino group
+
H3 N α H
R group H = Glycine
CH3 = Alanine
Petchlert C., 2004
Stereoisomers of Alanine.
Alanine. L-
L- and D-
D-alanine are nonsuperimposable mirror
images of each other (ENANTIOMERS).
(ENANTIOMERS).
Petchlert C. 2
Petchlert C. 3
Northwest line North line

-C-C-C-N-C-N Aromatic Amino Acid Subway Map
=
N+
Trp W -C-
Arg R N Northeast line
Basic -C- -OH
-C-CONH2 -C-C-CONH2
Lys K Tyr Y
Asn N Gln Q Amide
-C-C-C-C-NH3+ -C-
-C-C C His H Phe F Asp D Glu E Acidic

N N+
-C-COOH -C-C-COOH
Aliphatic
Central line Gly G Ala A
A Val V Ile I Leu L
-H -CH3 C C C C
-C -C-C-C -C-C-C
-C-OH Ser S Cys C -C-SH
Circular line C
C
C
South line HN C-COOH
-C-C α
Non-polar Thr T Met M -C-C-S-C
Pro P
OH Imino,
Petchlert C. 15 Polar Petchlert C. 16
Hydroxy Sulfur Circular
Petchlert C. 4
Absorbance of UV light by aromatic

amino acids.
Note that the absorbance maxima for
both Trp and Tyr occur near a
wavelength of 280 nm.
nm
The light absorbance of Trp is as much
as fourfold higher than that of Tyr.
Reversible formation of a disulfide bond by the oxidation of two molecules of

cysteine.
cysteine. Disulfide bonds between Cys residues stabilize the structures of many
proteins.
Absorption of Light by Molecules: The Lambert-

Lambert-Beer’
Beer’s Law
Some nonstandard amino acids found in proteins. Desmosine is formed from 4 Lys
Petchlert C. 19 residues. Petchlert C. 20
Petchlert C. 5
Ornithine and Citrulline,

Citrulline, which are not found in proteins, are
intermediates in the biosynthesis of Arg and in the urea cycle.
Titration of an amino acid.

Shown here is the titration curve of
0.1M Gly at 250C. The ionic species
predominating at key points in the
titration are shown above the
graph.
The shaded boxes indicate the
regions of greatest buffering
power.
Effect of the chemical environment on pKa. The pKa values for the ionizable groups in
Gly are lower than those for simple, methyl-substituted amino and carboxyl groups.
These downward perturbations of pKa are due to intramolecular interaction. Similar
effects can be caused by chemical groups that happen to be positioned nearby-for
example, in the active site of an enzyme.
Petchlert C. 6
Formation of Peptide Bonds by Dehydration
Amino acids are connected head to tail
NH2 1 COOH NH2 2 COOH
Carbodiimide Dehydration
-H2O
O
NH2 1 C N 2 COOH
H Peptide bond is a covalent bond.
Petchlert C. 7
Free α-amino group
This tetrapeptide has 1

free α-amino group, 1 free
α-carboxyl group, and 2
ionizable R groups.
Ionizable R groups
How many peptide bonds are there?

Name of amino acids in this peptide.
Petchlert C. 29
Free α-carboxyl group
Petchlert C. 30
Petchlert C. 8
The composition of the amino acid

mixtures obtained on complete
hydrolysis of bovine cytochrome c
and chymotrypsinogen. These 2
proteins, with very different
functions, also differ significantly
in the relative numbers of each
kind of amino acid they contain.
Level of Structure in Proteins Level of Protein Structure
Juang RH (2004) BCbasics
Petchlert C. 9
Petchlert C. 10
A comparison of the structures of myoglobin and the β subunit of

hemoglobin.
QUATERNARY STRUCTURE OF HEMOGLOBIN
Heme.
Heme. The iron atom of heme
has 6 coordination bonds: 4 in
the plane of, and bonded to, the
flat porphyrin ring system, and
2 perpendicular to it.
Petchlert C. 11
Normal erythrocytes Sickle-

Sickle-shaped erythrocytes
As the result of the change, deoxyHbS has a

hydrophobic patch on its surface, which
causes the molecules to aggregate into
strands that align into insoluble fibers.
Subtle differences between the conformations of HbA and HbS result from
a single amino acid change in the β chains.
Petchlert C. 12
Hair is an array of many α-

keratin filaments, made up of
the substructures shown in the
previous picture.
Structure of hair. Hair α-keratin is an elongated α helix with somewhat thicker

elements near the amino and carboxyl termini. Pairs of these helices are interwound in a
left-handed sense to form two-chain coiled coils. These then combined in higher-order
structures called protofilaments and protofibrils. About 4 protofibrils-32 strands of α-
keratin altogether-combine to form an intermediate
Petchlert C. filament. 49 Petchlert C. 50
Structure of collagen fibrils.

Collagen (M (Mr 300,000) is a rod- rod-shaped
molecule, about 3,000 Å long and only 15 Å
thick. Its 3 helically interwined α chains may
have different sequences, but each has about
1,000 amino acid residues. The specific
alignment and degree of cross-cross-linking vary
with the tissue and produce characteristic
cross-
cross-striations in an electron micrograph. In
the example shown here, alignment of the
head groups of every fourth molecule
produces striations 640 Å apart.
Structure of collagen. (a) The α repeating sequence adopts a left-

left-handed helical structure
(Gly-
Gly-Pro-
Pro-HyPro).
HyPro). (b) Space-
Space-filling model of the same α chain. (c) Three of these helices wrap around
one another with a right-
right-handed twist. (d) The three-
three-stranded collagen superhelix shown from one end,
in a ball-
ball-and-
and-stick representation. Gly residuesPetchlert
are shown
C. in red. They is required at the tight 51
junction
junction Petchlert C. 52
where the three chains are in contact.
Petchlert C. 13
Structure of silk.
(b) Strands of fibroin (blue)
emerge from the spinnerets of a
spider in this colorized electron
micrograph.
Structure of silk.
(a) Fibroin consists of layers of antiparallel β sheets rich in Ala (purple) and Gly (yellow) residues.
Petchlert C. 14

Protein - Revised 2010

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Biochemistry for Health Science Amino acid, Peptide and Protein

Amino acid, Peptide and Protein

L-Form Amino Acid Structure

Northwest line North line

-C-C C His H Phe F Asp D Glu E Acidic

Absorbance of UV light by aromatic

Reversible formation of a disulfide bond by the oxidation of two molecules of

Absorption of Light by Molecules: The Lambert-

Ornithine and Citrulline,

Titration of an amino acid.

Formation of Peptide Bonds by Dehydration

Amino acids are connected head to tail

NH2 1 COOH NH2 2 COOH

Free α-amino group

This tetrapeptide has 1

How many peptide bonds are there?

The composition of the amino acid

Level of Structure in Proteins Level of Protein Structure

A comparison of the structures of myoglobin and the β subunit of

QUATERNARY STRUCTURE OF HEMOGLOBIN

Normal erythrocytes Sickle-

As the result of the change, deoxyHbS has a

Hair is an array of many α-

Structure of hair. Hair α-keratin is an elongated α helix with somewhat thicker

Structure of collagen fibrils.

Structure of collagen. (a) The α repeating sequence adopts a left-

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