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7/31/2019 Bk Structure of Peptide Tu 2012
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STRUCTURE OF PEPTIDE
Tyas Utami2012
C CCH3
H
NH2
O
OH
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Peptides are chains of Amino Acids
Peptide bond
N terminal residue C terminal residu
Amino acid residues
connected by
peptide bonds
DIPEPTIDE
Amino acid 1 Amino acid 2
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Peptides are chain of Amino Acids
Two amino acid molecules can be covalently joined
through a substituted amide linkage, termed a
peptide bond to yield a dipeptide
Such a linkages is formed by removal of the elements
of H2O from the carboxyl group of one amino acid
and the -amino group of the other by the action of
strong condesing agents.
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Groups available foradding more amino acids
Three amino acids can be joined by two peptide
bonds in a similar manner to form a tripeptide.
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Number ofamino acidjoined by
peptidebond
Numberof
peptide
bond
Peptide
2 1 Dipeptide
3 2 Tripeptide
4 3 Tetrapeptide
5 4 Pentapeptide
Many Polipeptide
Protein Partial hydrolysis Peptides
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Pentapeptide: Ser-Gly-Tyr-Ala-Leu
Peptides are named from the sequence of their constituentamino acids beginning from the N-terminal residu.
Ser-Gly-Tyr-Ala-Leu = Serylglycyltyrosinylalanylleucine
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Pentapeptide
Ser-Gly-Tyr-Ala-Leu
Amino acid residues
connected by peptide bonds
Groups available for
adding more amino acids
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The amino acid units in a peptide are usuallycalled residues. They are no longer amino acids
since they have lost a hydrogen atom from theiramine groups and a portion of their carboxylgroups.
The amino acid residue at the end of a peptide
having a free -amino group is the amino-terminal residue (N terminal residue).
The residue at the opposite end, which has a
free carboxyl group is the carboxyl-terminal or Cterminal residue.
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Peptides formed by partial hydrolysis ofproteins occur in enormous variety.
A given amino acid can form a differentpeptide with each of the 20 standard amino
acids in two different sequences to give a totalof 39 dipeptides
The number of possible tripeptides and
tetrapeptides of different composition andsequences is very much greater
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20 Amino AcidsAmino acid Three-letter
abbreviation
One letter
abbreviation
Alanine Ala A
Arginine Arg R
Asparagine Asn N
Aspartic
acid
Asp D
Cysteine Cys C
Glutamine Gln Q
Glutamic
acid
Glu E
Glysine Gly G
Histidine His H
Isoleucine Ile I
Amino acid Three-letter
abbreviation
One letter
abbreviation
Leucine Leu L
Lysine Lys K
Methione Met MPhenylalani
ne
Phe F
Proline Pro P
Serine Ser S
Threonine Thr T
Tryptophan Trp W
Tyrosine Tyr Y
valine Val V
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Acidic Amino Acids
Acidic
R group = carboxylic acid
Donates H+
Negatively charged
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Nonpolar Amino Acids Hydrophobic, neutral, aliphatic
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Polar Amino Acids Hydrophilic, neutral, typically H-bond
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Aromatic Amino Acids
Bulky, neutral, polarity depend on R
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Basic Amino Acids
Basic
R group = amine
Accepts H+
Positively charged
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Peptides can be separated on the basis of
their ionization behavior
Peptides contain only one free -amino group and one free -
carboxyl group at their terminal residue which ionize as they do insimple amino acids.
All the other-amino and -carboxyl groups of the constituent aminoacids are covalently joined in the form of peptide bonds, which do notionize and thus do not contribute to the total acid-base behavior of
peptides.
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Dipeptide alanine
Cationic form (pH < 3,0)
Isoelectric form (pH 6,0)
Anionic form (pH >10)
CH3 H CH3+NH3 CH C N CH COOH
O
CH3 H CH3+NH3 CH C N CH COO
O
CH3 H CH3
NH3 CH C N CH COO
O
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R groups of some amino acids can
ionize
Aspartic acid : COO-
Glutamic acid : COO-
Lysine : +NH3
Arginine : +NH3
Histidine : NH
Tyrosine : OH
Cysteine: SH
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pK values for the ionizing groups of
some amino acids at 25 C
Amino acid pK1-COOH
pK2-NH3
+
pKRR group
Alanine 2.34 9.69
Serine 2.21 9.15
Aspartic acid 2.09 9.82 3.86
Glutamic acid 2.19 9.67 4.25
Histidine 1.82 9.17 6.0
Cysteine 1.71 10.78 8.33
Tyrosine 2.20 9.11 10.07
Lysine 2.18 8.95 10.53
Arginine 2.17 9.04 12.46
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K R
H
R groups of some amino acids can ionize
+H
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FY
R groups of some amino
acids can ionize
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The ionization state of aas.
Some aas can be
protonated/deprotonated
depending on the pH. Themidpoint of this process is
called the pK. You can ignore
pK1 and pK2 since they dont
occur in proteins (except forthe N and C termini
respectively).
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R groups of some amino acids can ionize:
When such amino acids are present in a peptide, their
R groups contribute to its acid-base properties
Thus the total acid-base behaviour of peptide can be
predicted from its single free -amino and -carboxylgroups at the ends of the chain and the nature and
number of its ionizing R groups.
Like free amino acids, peptides have characteristictitration curves
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Alanylglutamylglycyllysine, a tetrapeptide with two
residues having ionizing R groups
+NH3
CH2
COO- CH2
CH2 CH2
CH3 H CH2 H H CH2
+NH3 CH C N CH C N CH2 C N CH COO-
O O O
Ala Glu Gly Lys
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Peptides have characteristic Chemical
Reaction
Peptides undergo chemical reactions that are
characteristic of their functional groups (the free
amino acid and carboxyl groups), and also of their R
groups
Two very useful reactions of peptides:
1. Hydrolysis of peptide bonds2. Reaction with 1-fluoro-2,4-dinitrobenzene to yield
yellow derivative
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Peptide bonds can be hydrolyzed by booling with either
strong acid or base to yield te constituent amino acids in free
form
Peptide bonds can also be hydrolyzed by certain enzymes:
Trypsin (carboxyl group: lysine or arginine residue)
Chymotrypsin (craboxyl group: phenylalanine, tryptophan,
tyrosine),
H2O
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Peptide bonds can also be hydrolyzed by
certain enzymes
Proteolytic enzymes: selective in their catalysis of peptidehydrolysis
Trypsin:hydrolyse only those peptide bonds in which thethe carboxyl group has been contributed by a lysine or
arginine residue
Chymotrypsin: ......... Phenylalanine, tryptophan, andtyrosine residu
ala-gly-lys dan met-tyr-pro-cys
Ala-gly-lys-met-tyr-pro-cys
ala-gly-lys-met-tyr and pro-cys
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Peptides have characteristic chemical
Reactions
-amino group of free amino acid (or of the
amino-terminal residu of peptides) can react
with 1-fluoro-2,4-dinitrobenzene to yield a
2,4-dinitrophenylamino acid
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1-fluoro-2,4-dinitrobenzene reagent reactswith the -amino group of a free aminoacid to yield a 2,4-dinitrophenylamino acid.
It is also reacts with the -amino group ofthe amino-terminal residue of peptides toform a dinitrophenylpeptide.
The amino-terminal residue of peptide islabeled.
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Some Peptides have specific
Biological Functions
Many peptides occur in free form in living matter notassociated with protein structure.
Many free peptides have intense biological activityeg:
Hormones are chemical messenger, secreted byspecific cells of endocrine glands, such as pancreas,pituitary, or adrenal cortex and sent via blood tostimulate specific functions of other tissues ororgans. (insulin, glucagon, bradykinin)
Antibiotics
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Hormon Insulin
It is secreted by the B cells of thepancreas, is a chemical messenger carried
by the blood to other organs, especially
the liver and muscles, where it becomes
bound to receptors on cell surfaces and
stimulates the capacity of cells to use
glucose as a metabolic fuel.
It contains two polypeptide chains: 30amino acid residues and 21 amino acid
residues
-S-S-
-S-S-
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stop
Structure of Proteins:
Primary structure
Secondary structure
Tertiary structure
Quaternary structure