amino acids, peptides, and proteins.. classification of amino acids

Amino Acids, Peptides, Amino Acids, Peptides, and Proteins.and Proteins.

Classification of Amino AcidsClassification of Amino Acids

FundamentalsFundamentals

While their name implies that amino acids are While their name implies that amino acids are compounds that contain an —NHcompounds that contain an —NH2 2 group and a group and a

—CO—CO22H group, these groups are actually H group, these groups are actually

present as —NHpresent as —NH33++ and —CO and —CO22

–– respectively. respectively.

They are classified as They are classified as , , , , , , etcetc. amino acids . amino acids according the carbon that bears the nitrogen.according the carbon that bears the nitrogen.

Amino AcidsAmino Acids

NNHH33

++

CCOO22––

an an -amino acid that is an-amino acid that is anintermediate in the biosynthesisintermediate in the biosynthesisof ethyleneof ethylene

++HH33NNCHCH22CHCH22CCOO22

––a a -amino acid that is one of-amino acid that is one ofthe structural units present inthe structural units present incoenzyme Acoenzyme A

++HH33NNCHCH22CHCH22CHCH22CCOO22

–– a a -amino acid involved in-amino acid involved inthe transmission of nervethe transmission of nerveimpulsesimpulses

The 20 Key Amino AcidsThe 20 Key Amino Acids

More than 700 amino acids occur naturally, but More than 700 amino acids occur naturally, but 20 of them are especially important.20 of them are especially important.

These 20 amino acids are the building blocks of These 20 amino acids are the building blocks of proteins. All are proteins. All are -amino acids.-amino acids.

They differ in respect to the group attached to They differ in respect to the group attached to the the carbon. carbon.

These 20 are listed in Table 27.1 (p 1054-1055).These 20 are listed in Table 27.1 (p 1054-1055).

Table 27.1Table 27.1

CC CC

OO

OO––

RRRR

HH

HH33NN++

The amino acids obtained by hydrolysis of The amino acids obtained by hydrolysis of proteins differ in respect to proteins differ in respect to R R (the side chain).(the side chain).

The properties of the amino acid vary as the The properties of the amino acid vary as the structure of structure of RR varies. varies.

Table 27.1Table 27.1

CC CC

OO

OO––

HH

HH

HH33NN++

Glycine is the simplest amino acid. It is the only Glycine is the simplest amino acid. It is the only one in the table that is achiral.one in the table that is achiral.

In all of the other amino acids in the table the In all of the other amino acids in the table the carbon is a stereogenic center.carbon is a stereogenic center.

GlycineGlycine

(Gly or G)(Gly or G)

Table 27.1Table 27.1

CC CC

OO

OO––

CHCH33

HH

HH33NN++

AlanineAlanine

(Ala or A)(Ala or A)

Table 27.1Table 27.1

CC CC

OO

OO––

CH(CHCH(CH33))22

HH

HH33NN++

ValineValine

(Val or V)(Val or V)

Table 27.1Table 27.1

CC CC

OO

OO––

CHCH22CH(CHCH(CH33))22

HH

HH33NN++

LeucineLeucine

(Leu or L)(Leu or L)

Table 27.1Table 27.1

CC CC

OO

OO––

CHCH33CHCHCHCH22CHCH33

HH

HH33NN++

IsoleucineIsoleucine

(Ile or I)(Ile or I)

Table 27.1Table 27.1

CC CC

OO

OO––

CHCH33SSCHCH22CHCH22

HH

HH33NN++

MethionineMethionine

(Met or M)(Met or M)

Table 27.1Table 27.1

ProlineProline

CC CC

OO

OO––

CHCH22

HH

HH22NN++

HH22CCCCHH22

(Pro or P)(Pro or P)

Table 27.1Table 27.1

PhenylalaninePhenylalanine

CC CC

OO

OO––

CHCH22

HH

HH33NN++

(Phe or F)(Phe or F)

Table 27.1Table 27.1

TryptophanTryptophan

CC CC

OO

OO––

CHCH22

HH

HH33NN++

NN

HH

(Trp or W)(Trp or W)

Table 27.1Table 27.1

AsparagineAsparagine

CC CC

OO

OO––

HH

HH33NN++

HH22NCCHNCCH22

OO

(Asn or N)(Asn or N)

Table 27.1Table 27.1

GlutamineGlutamine

CC CC

OO

OO––

HH

HH33NN++

HH22NCCHNCCH22CHCH22

OO

(Gln or Q)(Gln or Q)

Table 27.1Table 27.1

CC CC

OO

OO––

CHCH22OHOH

HH

HH33NN++

SerineSerine

(Ser or S)(Ser or S)

Table 27.1Table 27.1

CC CC

OO

OO––

CHCH33CHOHCHOH

HH

HH33NN++

ThreonineThreonine

(Thr or T)(Thr or T)

Table 27.1Table 27.1

Aspartic AcidAspartic Acid

CC CC

OO

OO––

HH

HH33NN++

OCCHOCCH22

OO

––

(Asp or D)(Asp or D)

Table 27.1Table 27.1

Glutamic AcidGlutamic Acid

CC CC

OO

OO––

HH

HH33NN++

OCCHOCCH22CHCH22

OO

––

(Glu or E)(Glu or E)

Table 27.1Table 27.1

TyrosineTyrosine

CC CC

OO

OO––

CHCH22

HH

HH33NN++

OHOH

(Tyr or Y)(Tyr or Y)

Table 27.1Table 27.1

CC CC

OO

OO––

CHCH22SSHH

HH

HH33NN++

CysteineCysteine

(Cys or C)(Cys or C)

Table 27.1Table 27.1

CC CC

OO

OO––

CHCH22CHCH22CHCH22CHCH22NNHH33

HH

HH33NN++

LysineLysine

++

(Lys or K)(Lys or K)

Table 27.1Table 27.1

CC CC

OO

OO––

CHCH22CHCH22CHCH22NNHCHCNNHH22

HH

HH33NN++

ArginineArginine

++ NNHH22

(Arg or R)(Arg or R)

Table 27.1Table 27.1

HistidineHistidine

CC CC

OO

OO––

HH

HH33NN++

CHCH22

NHNHNN

(His or H)(His or H)

27.227.2Stereochemistry of Amino AcidsStereochemistry of Amino Acids

Configuration of Configuration of -Amino Acids-Amino Acids

Glycine is achiral. All of the other amino acids Glycine is achiral. All of the other amino acids in proteins have the in proteins have the LL-configuration at their -configuration at their carbon.carbon.

HH33NN++

HH

RR

COCO22––

27.727.7PeptidesPeptides

PeptidesPeptides

Peptides are compounds in which an amide Peptides are compounds in which an amide bond links the amino group of one bond links the amino group of one -amino acid -amino acid and the carboxyl group of another.and the carboxyl group of another.

An amide bond of this type is often referred to An amide bond of this type is often referred to as a peptide bond.as a peptide bond.

Alanine and GlycineAlanine and Glycine

CHCH33

OO

CC++

HH

CC OO––

HH33NN

OO

CC

HH

HH

CCHH33NN++

OO––

AlanylglycineAlanylglycine

CHCH33

OO

CCHH33NN++

HH

CC

OO

CCNN

HH

HH

CC OO––

HH

Two Two -amino acids are joined by a peptide bond -amino acids are joined by a peptide bond in alanylglycine. It is a in alanylglycine. It is a dipeptidedipeptide..

AlanylglycineAlanylglycine

CHCH33

OO

CCHH33NN++

HH

CC

OO

CCNN

HH

HH

CC OO––

HH

Ala—GlyAla—Gly

AGAG

N-terminusN-terminus C-terminusC-terminus

Alanylglycine and glycylalanine are Alanylglycine and glycylalanine are constitutional isomersconstitutional isomers

CHCH33

OO

CCHH33NN++

HH

CC

OO

CCNN

HH

HH

CC OO––

HH

HH

OO

CCHH33NN++

HH

CC

OO

CCNN

HH

CHCH33

CC OO––

HH

AlanylAlanylglycineglycineAlaAla——GlyGly

AAGG

GlycylGlycylalaninealanineGlyGly——AlaAla

GGAA

AlanylglycineAlanylglycine

CHCH33

OO

CCHH33NN++

HH

CC

OO

CCNN

HH

HH

CC OO––

HH

The peptide bond is The peptide bond is characterized by a characterized by a planar geometry.planar geometry.

Higher PeptidesHigher Peptides

Peptides are classified according to the number Peptides are classified according to the number of amino acids linked together.of amino acids linked together.

dipeptides, tripeptides, tetrapeptides, etc.dipeptides, tripeptides, tetrapeptides, etc.

Leucine enkephalin is an example of a Leucine enkephalin is an example of a pentapeptide.pentapeptide.

Leucine EnkephalinLeucine Enkephalin

Tyr—Gly—Gly—Phe—LeuTyr—Gly—Gly—Phe—LeuYGGFLYGGFL

OxytocinOxytocin

Oxytocin is a cyclic nonapeptide.Oxytocin is a cyclic nonapeptide.

Instead of having its amino acids linked in an Instead of having its amino acids linked in an extended chain, two cysteine residues are extended chain, two cysteine residues are joined by an joined by an S—S S—S bond.bond.

N-terminusN-terminus

C-terminusC-terminusIle—Gln—AsnIle—Gln—Asn

TyrTyr

CysCys SS SS

Cys—Pro—Leu—GlyNHCys—Pro—Leu—GlyNH22

11

22

3344 55

66 77 88 99

OxytocinOxytocin

S—S bond

An S—S bond between two cysteines isAn S—S bond between two cysteines isoften referred to as a often referred to as a disulfide bridgedisulfide bridge..