1 amino acids & peptides. 2 chapter outline amino acids 5.1 amino acids 5.1 –amino acid...

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Amino Acids Amino Acids & Peptides& Peptides

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Chapter OutlineChapter Outline

Amino Acids 5.1Amino Acids 5.1– Amino acid classes (G1)Amino acid classes (G1)– Stereoisomers (G2)Stereoisomers (G2)– Bioactive AABioactive AA– Titration of AA (G3)Titration of AA (G3)– Modified AAModified AA– AA reactionsAA reactions

Peptides 5.2Peptides 5.2

General PropertiesGeneral Properties

There are 20 standard amino acids. There are 20 standard amino acids. With exception of proline, all have With exception of proline, all have primary amino group and a primary amino group and a carboxylic acid bonded to same carboxylic acid bonded to same carbon.carbon.

Carboxyl group and amino group all Carboxyl group and amino group all have pKa values around 2.2 and 9.4 have pKa values around 2.2 and 9.4 respectivelyrespectively

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Note that at physiological pH of 7, amino Note that at physiological pH of 7, amino acids are charged as shown to right. They acids are charged as shown to right. They can act as either acid or base.can act as either acid or base.

Also referred to as zwitterionsAlso referred to as zwitterions This imparts special properties e.g. some This imparts special properties e.g. some

have melting points of 300 C, just like salts. have melting points of 300 C, just like salts. Also very soluble in water and not organics.Also very soluble in water and not organics.

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AMINO AMINO ACIDSACIDSOverviewOverview

The general structure of an amino The general structure of an amino acid molecule, with the amine group acid molecule, with the amine group on the right and the carboxylic acid on the right and the carboxylic acid group on the left. The R group is group on the left. The R group is dependent on the amino acid.dependent on the amino acid.

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AAs overview cont.. AAs overview cont..

In chemistry, an In chemistry, an amino acidamino acid is any is any molecule that contains both amine and molecule that contains both amine and carboxylic acid functional groups. In carboxylic acid functional groups. In biochemistry, this shorter and more biochemistry, this shorter and more general term is frequently used to refer general term is frequently used to refer to alpha amino acids: those amino acids to alpha amino acids: those amino acids in which the amino and carboxylate in which the amino and carboxylate functionalities are attached to the same functionalities are attached to the same carbon, the so-called carbon, the so-called α–carbon..

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An An amino acid residueamino acid residue is what is is what is left of an amino acid once a molecule left of an amino acid once a molecule of water has been lost (an of water has been lost (an H+ from from the nitrogenous side and an the nitrogenous side and an OH- from the carboxylic side) in the from the carboxylic side) in the formation of a peptide bond.formation of a peptide bond.

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Amino acids are the basic structural Amino acids are the basic structural building units of proteins. They form building units of proteins. They form short polymer chains called short polymer chains called peptides or or polypeptides which in turn form which in turn form structures called structures called proteins. The process of . The process of such formation from an such formation from an mRNA template template is known as is known as translation, which is part of , which is part of protein synthesis..

Phenylalanine is one of the standard Phenylalanine is one of the standard

amino acids.amino acids.88

Twenty amino acids are encoded by Twenty amino acids are encoded by the standard the standard genetic code and are and are called called proteinogenic or or standard standard amino acidsamino acids. Combinations of these . Combinations of these amino acids produce every single amino acids produce every single essential protein for the homeostasis essential protein for the homeostasis of the human body. At least two of the human body. At least two others are also coded by DNA in a others are also coded by DNA in a non-standard mannernon-standard manner

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19 standard AAs have the same 19 standard AAs have the same general str. general str.

These molecules contain a central C These molecules contain a central C atom (the atom (the αα-C) to amino group, -C) to amino group, carboxylate group, H atom and R carboxylate group, H atom and R group are attached.group are attached.

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Proline is the only is the only proteinogenic amino acid whose side group cyclizes amino acid whose side group cyclizes onto the backbone: it links to the α-onto the backbone: it links to the α-amino group, and thus is also the amino group, and thus is also the only proteinogenic amino acid only proteinogenic amino acid containing a secondary amine at this containing a secondary amine at this position.position.

1111


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Amino Acid: DefinitionAmino Acid: Definition An alpha amino acid is a carboxylic acid An alpha amino acid is a carboxylic acid

with an amino group on the carbon alpha to with an amino group on the carbon alpha to the carboxylic acid .the carboxylic acid .

The alpha carbon also has an R group side The alpha carbon also has an R group side chain except for glycine which has two Hs.chain except for glycine which has two Hs.

Generic aminoacid at physiologicalpH: zwitterion form

C

CC

R

HNH3

+O

O

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Definition, cont.Definition, cont. If the R group is not H, the AA can If the R group is not H, the AA can

exist in two exist in two enantiomericenantiomeric forms forms (nonsuperimposable mirror (nonsuperimposable mirror image) forms.)image) forms.)

C

C

R1

HNH3

+

OO

C

C

R1

H NH3

+

O O

Mirror plane carbon

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Amino AcidsAmino AcidsGeneral form: 1. an amino General form: 1. an amino

acid (AA); 2. two AA linked to acid (AA); 2. two AA linked to form the peptide bond.form the peptide bond.

NC CR1

H

NH3

+O

C CR1

H

OOH

C

C

R1

HNH3

+

OO

PEPTIDE BONDL-form

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Amino Acids-2Amino Acids-2 Only the L form of amino acids is Only the L form of amino acids is

commonly found in proteins.commonly found in proteins. Depending on the nature of the R Depending on the nature of the R

group, AA are classified into four group, AA are classified into four groups. groups. nonpolarnonpolarpolarpolaracidicacidicbasicbasic

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Hydrophobic Amino Acids 1Hydrophobic Amino Acids 1

C

C

CH3

HNH3

+OO

alanine, Ala

CH2

C

C

HNH3

+OO

phenylalanine, Phe

C

C

CH2

HNH3

+OO

CHCH3

CH3

leucine,Leu

C

C

CH

HNH3

+OO

CH2CH3

CH3

isoleucine, I le


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AA with nonpolar side chains-2AA with nonpolar side chains-2

C

C

CHHNH3

+OO

CH3 CH3CH2

C

C

HNH3

+OO

CH2S CH3

C

C

CH2

HNH2

+OO

CH2

CH2

valine, Val methionine, Met

proline, Pro

C

C

CH2

HNH3

+OO

CCH

NH

tryptophan, Trp


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Neutral Nonpolar AANeutral Nonpolar AA

Contain mostly HC R groupsContain mostly HC R groups Neutral = R groups ≠ ± chargesNeutral = R groups ≠ ± charges They interact poorly with water, They interact poorly with water,

nonpolar (hydrophobic)nonpolar (hydrophobic) Important role maintaining the 3-D Important role maintaining the 3-D

protein strprotein str

2020

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AA with polar side chains-1AA with polar side chains-1

C

C

H

HNH3

+OO

CH2

C

C

HNH3

+OO

OH

C

C

CH2

HNH3

+OO

SH

Glycine, Gly Serine, Ser

cysteine, Cys

C

C

CHHNH3

+OO

CH3

OH

threonine, Thr

Polar Amino Acids 1Polar Amino Acids 1

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AA with polar side chains-2AA with polar side chains-2

glutamine, Gln

tyrosine, Tyr

C NH2O

C

C

HNH3

+OO

CH2

C NH2O

CH2

C

C

HNH3

+OO

CH2

asparagine, Asn

OHC

C

CH2

HNH3

+OO

Polar Amino Acids 2Polar Amino Acids 2

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Polar AAPolar AA

Have functional groups capable of H Have functional groups capable of H bonding; easily interact with waterbonding; easily interact with water

Give significant effect on protein Give significant effect on protein stabilitystability

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AA: acidic and basicAA: acidic and basic

glutamic acid, GluC OO

C

C

HNH3

+OO

CH2

C OO

CH2

C

C

HNH3

+OO

CH2

aspartic acid, Asp

CH2

NH

CH2

CH2

CNH2

+NH2

C

C

HNH3

+OO

CH2

CH2

CH2

C

C

HNH3

+OO

CH2

NH3

+

NHCH

CH2

C

C

HNH3

+OO

C

NH+

CH

histidine, Hislysine, Lysarginine, Arg

Charged Amino AcidsCharged Amino Acids

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2828

The side chains of aspartic acid and The side chains of aspartic acid and glutamic acid are negatively charged above glutamic acid are negatively charged above pH 3.pH 3.

The side chains of basic amino acids are The side chains of basic amino acids are positively charged at physiological pH positively charged at physiological pH values:values:

Lysine – has butylammonium side chainLysine – has butylammonium side chain

Arginine – bears a guanidino groupArginine – bears a guanidino group

Histidine – carries a imidazolium moeityHistidine – carries a imidazolium moeity

Can form ionic bonds with acidic AACan form ionic bonds with acidic AA Play an important role in the catalytic Play an important role in the catalytic

activity of numerous enzymesactivity of numerous enzymes

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Bioactive AAsBioactive AAs

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In addition to protein synthesis, amino In addition to protein synthesis, amino acids have other biologically-important acids have other biologically-important roles. roles. Glycine and and glutamate are are neurotransmitters as well as standard as well as standard amino acids in proteins. Many amino amino acids in proteins. Many amino acids are used to synthesize other acids are used to synthesize other molecules, for example:molecules, for example:

Tryptophan is a precursor of the Tryptophan is a precursor of the neurotransmitter serotonin. neurotransmitter serotonin.

Glycine is one of the reactants in the Glycine is one of the reactants in the synthesis of porphyrins such as heme. synthesis of porphyrins such as heme.

Arginine is used to synthesize the Arginine is used to synthesize the hormone nitric oxide. hormone nitric oxide.

Bioactive AAs cont….Bioactive AAs cont….

Numerous non-standard amino acids Numerous non-standard amino acids are also biologically-important: are also biologically-important: Gamma-aminobutyric acid is another is another neurotransmitter, carnitine is used in neurotransmitter, carnitine is used in lipid transport within a cell, ornithine, lipid transport within a cell, ornithine, citrulline, homocysteine, citrulline, homocysteine, hydroxyproline, hydroxylysine, and hydroxyproline, hydroxylysine, and sarcosine.sarcosine.

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Bioactive AAs cont….Bioactive AAs cont…. The 20 standard amino acids The 20 standard amino acids

undergo a bewildering number of undergo a bewildering number of chemical transformations to other chemical transformations to other amino acids and related compounds amino acids and related compounds as part of their normal cellular as part of their normal cellular synthesis and degradation.synthesis and degradation.

Many organisms use certain amino Many organisms use certain amino acids to transport nitrogen in the acids to transport nitrogen in the form of amino groups.form of amino groups.

Amino acids may also be oxidized as Amino acids may also be oxidized as metabolic fuels to provide energy.metabolic fuels to provide energy.

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Amino acids often function as Amino acids often function as chemical messengers for chemical messengers for communication between cells.communication between cells.

Alpha-aminobutric acid Alpha-aminobutric acid and and dopaminedopamine are neuro transmitters. are neuro transmitters.

HistamineHistamine is a mediator of allergic is a mediator of allergic reactions.reactions.

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ThyroxineThyroxine stimulates vertebrate stimulates vertebrate metabolism.metabolism.

Many peptides (e.g. Many peptides (e.g. glutathioneglutathione) ) have physiological functions as have physiological functions as hormones or regulatory molecules.hormones or regulatory molecules.

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Modified AAs in ProteinsModified AAs in Proteins

The ‘universal’ genetic code specifies The ‘universal’ genetic code specifies only the 20 essential amino acids.only the 20 essential amino acids.

Other amino acids are components of Other amino acids are components of certain proteins resulting from the certain proteins resulting from the specific modification of an amino specific modification of an amino acid residue after the polypeptide acid residue after the polypeptide chain has been synthesized.chain has been synthesized.

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Modified AAs in Proteins Modified AAs in Proteins cont…cont…

These modifications include the These modifications include the simple addition of small chemical simple addition of small chemical groups to certain amino acid chains: groups to certain amino acid chains: hydroxylation, methylation, hydroxylation, methylation, acetylation, and phosphorylation.acetylation, and phosphorylation.

Larger groups, including lipids and Larger groups, including lipids and carbohydrate polymers, are attached carbohydrate polymers, are attached to particular amino acid residues of to particular amino acid residues of certain proteinscertain proteins

Examples: Examples: γγγγ-carboxyglutamate, 4--carboxyglutamate, 4-hydroxyprolinehydroxyproline

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AA StereoisomerAA Stereoisomer

Most amino acids occur in two possible Most amino acids occur in two possible optical isomers, called D and L. The L optical isomers, called D and L. The L amino acids represent the vast majority amino acids represent the vast majority of amino acids found in proteins. of amino acids found in proteins.

D amino acids are found in some D amino acids are found in some proteins produced by exotic sea-proteins produced by exotic sea-dwelling organisms, such as cone dwelling organisms, such as cone snails. They are also abundant snails. They are also abundant components of the proteoglycan cell components of the proteoglycan cell walls of bacteria.walls of bacteria.

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The D-isomer of aspartic acid is The D-isomer of aspartic acid is found in some proteins as the result found in some proteins as the result of a spontaneous post-translational of a spontaneous post-translational modification associated with protein modification associated with protein aging or as the by-product of aging or as the by-product of enzymatic modification catalyzed by enzymatic modification catalyzed by protein L-isoaspartyl protein L-isoaspartyl methyltransferase.methyltransferase.

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All amino acids (except glycine) All amino acids (except glycine) recovered from polypeptides are recovered from polypeptides are optically active and direction of angle optically active and direction of angle of rotation is measured by of rotation is measured by polarimeter.polarimeter.

Optically active molecules are Optically active molecules are asymmetric and the central atoms asymmetric and the central atoms (C-alpha atoms of amino acids) in (C-alpha atoms of amino acids) in such molecules are such molecules are chiral centers chiral centers with property of with property of chirality.chirality.

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These asymmetric centers give rise These asymmetric centers give rise to enantiomers (nonsuperimposable to enantiomers (nonsuperimposable mirror images of one another) or are mirror images of one another) or are stereoisomers (chiral molecules with stereoisomers (chiral molecules with different configurations about at different configurations about at least one of their asymmetric centers least one of their asymmetric centers but which are otherwise identical).but which are otherwise identical).

Life is based on chiral molecules as Life is based on chiral molecules as biosynthetic processes almost biosynthetic processes almost invariably produce pure invariably produce pure stereoisomers.stereoisomers.

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Acid-Base Properties of AAsAcid-Base Properties of AAs Titration curve for glycineTitration curve for glycine Note that one starts with all Note that one starts with all

groups in acid form.groups in acid form. Note how many equivalents are Note how many equivalents are

addedadded Note that at 0.5 and 1.5 Note that at 0.5 and 1.5

equivalents, pH is equal to pK equivalents, pH is equal to pK of group being titrated.of group being titrated.

Note pH which gives zero Note pH which gives zero charge is the isoelectric point. charge is the isoelectric point. Calculated as (pK1+pK2)/2Calculated as (pK1+pK2)/2

Note where the buffering Note where the buffering capacity is bestcapacity is best

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Amino Acid TitrationAmino Acid Titration At physiological pH, the carboxyl group At physiological pH, the carboxyl group

of the AA is negatively charged and the of the AA is negatively charged and the amino group is positively charged.amino group is positively charged.

Amino acids without charged side Amino acids without charged side chains are chains are zwitterionszwitterions and have and have no net no net chargecharge. H. H33

++N-CHR-COON-CHR-COO--.. A titration curve shows how the amine A titration curve shows how the amine

and carboxyl groups react with and carboxyl groups react with hydrogen ion.hydrogen ion.

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Amino Acid TitrationAmino Acid Titration

At low pH a At low pH a nonacidic/nonbasic amino acid nonacidic/nonbasic amino acid is protonated and has the is protonated and has the structure below.structure below.

HH33NN++CHRCOOHCHRCOOHThe charge behavior of acidic The charge behavior of acidic

and basic AAs is more and basic AAs is more complex.complex.

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Titration of AlanineTitration of Alanine

1

mole base added1 2

pH

5

10

1

NH3

+CHR1

CO

OH

NH3

+CHR1

CO

O

NH3

+CHR1

CO

O

A

B

C

A A=BpK1=2.3

B, pI=pH=6.0

B=CpK2=9.73

C

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Isoelectric pointIsoelectric point The isoelectric point (pI) for an AA The isoelectric point (pI) for an AA

occurs when there is no net charge.occurs when there is no net charge. For a neutral AA, the pI is calculated For a neutral AA, the pI is calculated

using the equation pKusing the equation pK11 + pK + pK22/2/2 Eg.: alanine: 2.34 + 9.7 / 2 = 6.0Eg.: alanine: 2.34 + 9.7 / 2 = 6.0 For acidic or basic AAs, the pI is the For acidic or basic AAs, the pI is the

average of the two pKaverage of the two pKaa values values bracketing the isoelectric structure.bracketing the isoelectric structure.

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More Titration CurvesMore Titration Curves AA with ionizable side AA with ionizable side

chains hv complex chains hv complex titration curvetitration curve

Eg. Glutamic acid has Eg. Glutamic acid has a carboxyl side chain a carboxyl side chain groupgroup

At low pH it has net At low pH it has net charge +1. As base is charge +1. As base is added, the added, the αα-carboxyl -carboxyl group loses a proton group loses a proton to become to become carboxylate group.carboxylate group.

Glutamate now has Glutamate now has no net charge. As no net charge. As more base is added more base is added

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More Titration Curves cont…More Titration Curves cont… As more base is As more base is

added, the second added, the second carboxyl group loses a carboxyl group loses a proton and the proton and the molecule has a -1 molecule has a -1 charge.charge.

Adding additional base Adding additional base results in the NHresults in the NH33 ion ion lossing its proton. lossing its proton.

At this point glutamate At this point glutamate has a net charge of -2. has a net charge of -2. the pI value for the pI value for glutamate is the glutamate is the halfway btw the pKa halfway btw the pKa values for the 2 values for the 2 carboxyl groupcarboxyl group

pI = 3.22pI = 3.22

Peptide BondsPeptide Bonds

Peptide bond formed from Peptide bond formed from elimination of water from 2 amino elimination of water from 2 amino acids resulting in CO-NH linkage.acids resulting in CO-NH linkage.

Can have di-, tri-, oligo- and poly-Can have di-, tri-, oligo- and poly-peptides.peptides.

Proteins composed of linear polymer Proteins composed of linear polymer of amino acids.of amino acids.

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Large number of Large number of proteins can exist. A proteins can exist. A small protein of 100 small protein of 100 amino acids can amino acids can have 20have 20100100 or or 1.27x101.27x10130130 possible possible unique polypeptide unique polypeptide chains.chains.

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PeptidesPeptides Peptide: a polymer of about 2-100 AAs linked Peptide: a polymer of about 2-100 AAs linked

by the peptide(amide) bond. As the amino by the peptide(amide) bond. As the amino group and the carboxyl group link, water is group and the carboxyl group link, water is lost.lost.

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C C

R1

H

NH3

+O

O

Peptide bonds

C C

R1

H

NH3

+O

OC C

R1

H

NH3

+O

O

C C

R1

H

NH3

+O

C C

R1

H

NH

OC C

R1

H

NH

OO

-H2O -H2O

PeptidesPeptides A peptide is written with the N-terminal end A peptide is written with the N-terminal end

to the left and the C-terminal end to the to the left and the C-terminal end to the right.right.

HH22N-Tyr-Ala-Cys-Gly-COOHN-Tyr-Ala-Cys-Gly-COOH Name = TyrosylalanylcysteinylglycineName = Tyrosylalanylcysteinylglycine The peptide bond is rigid and planar due to The peptide bond is rigid and planar due to

the resonance contribution shown below.the resonance contribution shown below.

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CC

O

NH

C

CC

O

NH

C

+

-

PeptidesPeptides

The peptide bond The peptide bond angles force angles force specific specific conformations of conformations of proteins and, on proteins and, on extended chains, extended chains, successive R successive R groups are on groups are on opposite sides.opposite sides.

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Physiologically Interesting PeptidesPhysiologically Interesting Peptides

5454

CH

N

C

C

NH

CH2

NH3

+CH2CH2C

O

NH CH COO-

-alanyl-L-histidine

carbon

Common name: carnosinefound in muscle tissue


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SHCH2

CH CH2CH2C

O

NH CH C

OCOO-

NH3

+NH CH2COO

-

-glutamyl-L-cysteineylglycine

Glutathione: the reduced formreduces oxidizing agents by dimerizing toform the disulfide bond with release of 2 H.


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Tyr-Gly-Gly-Phe-LeuN-terminal AA C-terminal AA

Short form description for a peptide.

Leucine enkephalin: a naturalanalgesic found in the brain


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OxytocinInduces labor and aids in forcing milkfrom the mammaryglands.

Vassopressin has a Phe at position 3 instead of Ile and an Arg at position 8instead of a Leu. Its role is in regulatingblood pressure.

3

8

H3N+-Cys-Tyr-Ile

-Cys-Asn

|Gln |

|S |S

|Pro-Leu-Gly-NH2

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Amino Amino Acids & Acids & PeptidesPeptides

THE ENDTHE END

1 amino acids & peptides. 2 chapter outline amino acids 5.1 amino acids 5.1 –amino acid...

Documents

amino acid aa

form of amino acids

standard amino acids

proteinogenic amino

amino acid molecule

alpha amino acids

amino acid residue

hydrophobic amino acids