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Amino Acids and Peptides

Dr. Leisha Mullins

Aug. 29, 2003



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Amino Acids• Amino Acids a compound that contains both an amino group and a

carboxyl group

§§ αα--Amino acidAmino acid:: an amino acid in which the amino group is on thecarbon adjacent to the carboxyl group

• All proteins are composed of 20 standard amino acids

• Amino acids have acid/ base properties

• Amino acids are zwitterionic

• At pH 7, the amino group is protonated and the carboxylic group is

unprotonated



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Stereochemistry of amino acids

• Except forglycine, theα-carbon isattached to

four differentgroups -

chiral center



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Comparison of the stereochemistryof alanine and glyceraldehyde

• The configuration about the Cα atom is generally

described by the Fisher convention• L-amino acids predominate in nature.

H N H3+

COO-

CH3

+H 3 N H

CO O-

CH 3

D-Alanine L-Alanine

H OH

CHO

CH2 OH

HO H

CHO

CH 2 OH

D-Glyceraldehyde L-Glyceraldehyde

the naturallyoccurring form

the naturallyoccurring form



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Chirality of Life• Biosynthetic processes produce pure stereoisomers

• Chemical processes generally produce racemic mixtures

• Most active biological compounds are chiral i.e. only oneenantiomer imparts biological activity



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20 Standard Amino Acids



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Classification of Amino acids• The R group, or side chain, determines the structural range and

general physical characteristics of the amino acids

• The amino acids are generally grouped according to the variouscharacteristics of their R groups

• Non-polar amino acids (hydrophobic)

• Polar, uncharged amino acids

• Polar, charged



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Non-Polar R group: nine amino acids in this group



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Uncharged Polar R Groups : Six amino acids in this groupHydroxyl, Amide and Thiol Groups



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Polar Charged R Groups: 5 amino acids have charged side chains



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Nomenclature• All amino acids have 1 and three letter codes

• The atoms of the side chain are assigned sequential letters in theGreek alphabet beginning with the carbon next to the carboxylgroup



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Spectroscopic Properties• All amino acids absorb in infrared region

• Only Phe, Tyr, and Trp absorb UV• Absorbance at 280 nm is a good diagnostic device forproteins



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Non-standard Amino Acids• Non-standard amino acid can be important components of proteins

and peptides

• The non-standard amino acids generally results from a specificmodification of an amino acid residue after it is incorporated intothe polypeptide strand



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Biologically Active Amino Acids• Amino acids and their derivatives sometimes

function in non-protein roles in cells.

• The most common example are someneurotransmitters and chemical messengers



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Ionizable Groups in amino acids

• Amino Acids are Weak Acids

• All amino acids have at least two acid – base groups – α-carboxyl group

– α-amino group

• Those with ionizable side chains (R groups) have three

– Lysine

– Arginine – Histidine

– Glutamic Acid

– Aspartic Acid



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pKa Values of Free Amino Acids and in Proteins



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Structure varies with pH• At low pH all ionizable groups are protonated – cationic form

• At mid pH range the zwitterionic form dominates

• At high pH the ionizable groups are unprotonated – anionic form



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Isoelectric Point

• The pH at which the molecule carries no netcharge is known as the isoelectric point or pI

• pI = ½ (pKi + pK j)

• The pI is always at an endpoint of an amino

acid titration curve

α-Amino GroupSide ChainPolar Pos

Side Chainα-Carboxyl GroupPolar Neg

α-Amino Groupα-Carboxyl GroupNon-polar

pK jpKiType of AA



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Important Interactions of Amino Acid sidechains

• Hydrogen Bonds

• Ionic Interactions



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Peptides and Peptide Bonds• Amino acids polymerize to form long chains called "peptides"



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Peptides

• Individual amino acids are called amino acid residues once they areincorporated into a peptide

• Polypeptides chains are described by starting at the N-terminus andproceeding to the C-terminus



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Peptide Bond

• Peptide bonds are stable – prolonged exposure to strongacid or base at elevatedtemperature required tohydrolyze

• Peptide bond has two

resonance structures



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Cis vs. Trans• The groups of atoms about the peptide bond can exist in two possible

conformations,cis and trans

• The trans conformation is almost always favored over the cis by ~ 8kJ·mol-1



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Proline – The Exception• ~ 10% of the proline residues in proteins following a cis peptide

bond



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Biologically Active Dipeptides

• Aspartame - NutraSweet



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Biologically Active Tripeptides



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Biologically Active Pentapeptides

Two naturally occuring pain relievers

• Leucine Enkephalin

Tyr – Gly –Gly- Phe – Leu

• Methionine Enkephalin

Tyr – Gly –Gly- Phe – Met



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Cyclic Peptides

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