Bk Structure of Peptide Tu 2012

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

Bk Structure of Peptide Tu 2012

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