Chapter 4: Amino Acids • All peptides and polypeptides are polymers of alpha-amino acids. lipid polysaccharide enzyme 1940s 1980s. Lipids membrane 1960s. Polysaccharide • Are energy metabolites and many of them are essential nutrients. • Several of the amino acids found in proteins also serve functions distinct from the formation of peptides and proteins, e.g., tyrosine in the formation of thyroid hormones or glutamate acting as a neurotransmitter. Epinephrine Tryptophan Tyrosin Dopamine General Features of Amino Acids • -amino acids in peptides and proteins (excluding proline) consist of a carboxylic acid (-COOH) and an amino (-NH 2 ) functional group attached to the same tetrahedral carbon atom. • Distinct R-groups, that distinguish one amino acid from another, also are attached to the alpha-carbon (except in the case of glycine where the R-group is hydrogen). • The fourth substitution on the tetrahedral a-carbon of amino acids is hydrogen. • In physiological condition, both the carboxylic acid and the amino groups of a-amino acids are completely ionized. pK 1 a-carboxylic acid, 2.2 pK 2 a-amino group, 9.4 pK R functional group ampholytes (amphoteric property)
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Chapter 4: Amino Acids• All peptides and polypeptides are polymers of alpha-amino acids.
lipid polysaccharideenzyme
1940s 1980s.Lipids membrane 1960s. Polysaccharide
• Are energy metabolites and many of them are essential nutrients.• Several of the amino acids found in proteins also serve functions
distinct from the formation of peptides and proteins, e.g., tyrosine in the formation of thyroid hormones or glutamate acting as a neurotransmitter.
EpinephrineTryptophan
TyrosinDopamine
General Features of Amino Acids• �-amino acids in peptides and proteins (excluding proline) consist of a
carboxylic acid (-COOH) and an amino (-NH2) functional group attached to the same tetrahedral carbon atom.
• Distinct R-groups, that distinguish one amino acid from another, also are attached to the alpha-carbon (except in the case of glycine where the R-group is hydrogen).
• The fourth substitution on the tetrahedral a-carbon of amino acids is hydrogen.
• In physiological condition, both the carboxylic acid and the amino groups of a-amino acids are completely ionized.
pK1 a-carboxylic acid, 2.2pK2 a-amino group, 9.4pKR functional group
ampholytes(amphoteric property)
Physical Properties
• The melting point of most amino acids are near 300 ºC
• More soluble in polar solvents (H2O etc.)• At pH 7.0, both carboxyl and amino
group are completely ionized.
There are 20 Amino Acids encoded by codons in the genetic code.
Similar to ionic compound because of charged groups of opposite polarity.(
zwitterionsdipolar ions)
Peptide BondsPeptide bond formation is a condensation reaction leading to the polymerization of amino acids into peptides and proteins.(Peptide: hormones, neurotransmitters, several antibiotics and antitumor agents)
The presence of the carbonyl group in a peptide bond allows electron resonance stabilization to occur such that the peptide bond exhibits rigidity not unlike the typical -C=C- double bond. The peptide bond is, therefore, said to have partial double-bond character.
Amino Acid Structure/FunctionThese 20 AAs can be divided into the above 3 groups (non-polar, flexible and polar)and then subdivided by their chemical character. I prefer to divide them based on the R-functional group.
Aliphatic: Gly, Ala, Val, Leu, Ile, ProAromatic: Phe, Tyr, TrpPolar but uncharged: Ser, Thr, Asn, GlnSulfur containing: Cys, MetCharged: Asp, Glu, His, Lys, Arg
Amino Acid: Aliphatic-R Group
Gly, Ala, Val, Leu, Ile, ProRefer to the structure
Amino Acid: Aromatic R-Group
Refer to the structurePhe, Tyr, Trp
The aromatic R-groups in amino acids absorb ultraviolet light with an absorbance maximum in the range of 280nm. The ability of proteins to absorb ultraviolet light is predominantly due to the presence of the tryptophan which strongly absorbs ultraviolet light.
Amino Acid: Polar but uncharged
Refer to the structureSer, Thr, Asn, Gln
Amino Acid: Sulfur containing
Refer to the structureCys, Met
Amino Acid: Charged R-Group
Refer to the structureAsp, Glu, His, Lys, Arg
Uncommon amino acids• Hydroxylysine,
hydroxyproline - collagen• Carboxyglutamate - blood-
clotting proteins• Pyroglutamate –
bacteriorhodopsin• Phosphorylated amino acids
- signaling device
Other uncommon amino acids
• Carboxyl groups form amides & esters
• Amino groups form Schiff bases and amides
• Side chains show unique reactivities– Cys residues can form
disulfides and can be easily alkylated
– Few reactions are specific to a single kind of side chain
Reactions of Amino acids
Optical Properties of the Amino Acids
A tetrahedral carbon atom with 4 distinct constituents is said to bechiral.
Chirality:Describe the mirror images of a molecule are not superimposable.These molecules are designated as enantiomers of one another.
( superimposable )( optical isomers
)
Optical Activity
Polarimeter is used to measure the specific rotation of optical isomer
The handedness of a chiral molecule is observable by the ability of a molecule to rotate the plane of polarized light either to the right(dextrorotatory, + or d) or to the left (levorotatory, - or l ).
)25][ 3-conc.(g.cmX(dm)lengthpathoptical
(degree)rotationobserved�D�
The physical and chemical propertiesof optical isomers are almost identical except for the opticalactivity.
Why L-�-amino acids?All of the amino acids in proteins exhibit the same absolute stericconfiguration as L-glyceraldehyde. Therefore, they are all L-�-aminoacids.
D-amino acids are never found in proteins, although they exist in nature. D-amino acids are often found in polypeptide antibiotics.
hydroxyl, aldehyde, CH2OH amino, carboxyl, R
More about Chiral MoleculesFor molecule with more than one chiral center:N chiral centers has 2n possible stereoisomers and 2n-1 enantiomericpairs.
Diastereisomer:• The optical isomers are not mirror image of each other.• The diastereomers are physically and chemically distinguishable from one another.
•A solution contained equal amount of –d and –l isomer is known as racemic. It is optical inactive.
Chiral molecules but no optical activity?
A molecule which has an internal mirror symmetry plane, is known as meso compound.Even though meso compound has either one or more chiral centers, the molecule does not have enantiometic isomer.
Absolute ConfigurationDilemma: Given a optical isomer, one can not tell whether it’s in –d
or –l form .: Cahn-Ingold-Prelog System optical isomer
: The four groups attached to the chiral center are ranked according to their atomic number.
SH > OH > NH2 > COOH > CHO > CH2OH > C6H5 > CH3 > 2H > 1H
If the first atom in groups are the same, then the rank is based on the second atom in groups and so on.
W > X > Y > ZRotate the molecule so that the lowest priority group (Z) faces toward you.The order of the groups W�X�Y is clockwise, assigned R.The order of the groups W�X�Y is counter-clockwise, assigned S.
Absolute Configuration
The configuration of a molecule with multiple asymmetric centers can be described unambiguously.
W > X > Y > Z R, Sconfiguration.
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 for amino acids
• NMR spectra are characteristic of each residue in a protein, and high resolution NMR measurements can be used to elucidate three-dimensional structures of proteins
UV spectrum
Superimposible
chemical formula( )
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Illustration of the chiral molecule
return
optical isomers
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