ERT 106 BIOCHEMISTRYERT 106 BIOCHEMISTRY

Amino AcidsAmino Acids

Pn Syazni Zainul KamalPn Syazni Zainul Kamal

Introduction Introduction Proteins - the most structural, sophisticated Proteins - the most structural, sophisticated

molecules knownmolecules known- vary extensively in structure- vary extensively in structure - are polymer constructed from the - are polymer constructed from the same set of same set of 2020 amino acidsamino acids

Polymer of amino acids = polypetidesPolymer of amino acids = polypetides Proteins consists of 1 or more polypeptides Proteins consists of 1 or more polypeptides

folded and coiled into specific conformationsfolded and coiled into specific conformations

Amino Acids structureAmino Acids structure

Amino Acids contain a central carbon atom (α-carbon) to which an amino group, a carboxylate group, a hydrogen atom and an R (side chain) group are attached

Structure of amino acids commonly found in Structure of amino acids commonly found in proteinprotein

Amino acids shown in their prevailing ionic forms at pH7, approx pH within a cell

Name and three-letter abbreviation of amino acid

The exception : The exception : prolineproline differ from other differ from other standard amino acidstandard amino acid

R group makes up part of a ring which also R group makes up part of a ring which also includes the amino group and the includes the amino group and the αα--carbon carbon atom. atom.

Since the amino group in proline is involved in Since the amino group in proline is involved in two carbon-nitrogen bonds, it is a secondary two carbon-nitrogen bonds, it is a secondary amino group. amino group.

Proline (secondary amino group)

Standard amino acid (primary amino group)

Amino acid structureAmino acid structure The amino and carboxylic groups of amino acids The amino and carboxylic groups of amino acids

readily ionizedreadily ionized At physiological pH (7)At physiological pH (7)

- - carboxyl groupcarboxyl group of an amino acid is unprotonated. of an amino acid is unprotonated. conjugate baseconjugate base form (-COO form (-COO--))- - amino groupamino group of an amino acid is protonated. in its of an amino acid is protonated. in its conjugate acidconjugate acid form ( form (++NHNH33))

Thus, each amino acid can behave as an acid or baseThus, each amino acid can behave as an acid or base referred as referred as amphoteric amphoteric (substance that can act as acid (substance that can act as acid

or base)or base)

Neutral molecules which bear an equal umber Neutral molecules which bear an equal umber of positive and negative charges of positive and negative charges simultaneously are called simultaneously are called zwitterionszwitterions

The R group give each amino acid its unique The R group give each amino acid its unique propertiesproperties

Structure of amino acid at pH7

Amino acid classesAmino acid classes Sequence of amino acids determines the three-Sequence of amino acids determines the three-

dimensional configuration of each proteindimensional configuration of each protein Amino acids classified based on their Amino acids classified based on their capacity capacity

to interact with waterto interact with water 4 classes of amino acids :4 classes of amino acids :

a) neutral nonpolara) neutral nonpolarb) neutral polarb) neutral polarc) acidicc) acidicd) basicd) basic

a) Neutral nonpolar amino acidsa) Neutral nonpolar amino acids TermTerm‘Neutral’ – ‘Neutral’ – R groups do not bear +ve or R groups do not bear +ve or

––ve chargeve charge So they interact poorly with water and play So they interact poorly with water and play

important role in maintaining the three-important role in maintaining the three-dimensional structure of proteindimensional structure of protein

Contain Contain hydrocarbon hydrocarbon R groupsR groups 2 types of hydrocarbon R groups:2 types of hydrocarbon R groups:

a) a) aromaticaromatic (contain cyclic structure) (contain cyclic structure)eg. eg. Phenylalanine, tryptophanPhenylalanine, tryptophan

b) b) aliphaticaliphatic (nonaromatic hydrocarbon) (nonaromatic hydrocarbon)eg. eg. Glycine, alanine, valine, leucine, Glycine, alanine, valine, leucine, isoleucine, proline isoleucine, proline, , methionine, methionine,

cysteinecysteine

Methionine & cysteine Methionine & cysteine contain contain sulfur atomsulfur atom in in the aliphatic side chainthe aliphatic side chain

b) Neutral polar amino acidsb) Neutral polar amino acids Polar amino acids = hydrophilic (water loving)Polar amino acids = hydrophilic (water loving) Have functional group capable of Have functional group capable of forming forming

hydrogen bondinghydrogen bonding, so easily interact with water, so easily interact with water Serine, threonine, tyrosine, asparagine, Serine, threonine, tyrosine, asparagine,

glutamineglutamine Serine, threonine, tyrosineSerine, threonine, tyrosine

- contain polar - contain polar hydroxyl hydroxyl group (-OH)group (-OH)- Thus enable them to from hydrogen bonding - Thus enable them to from hydrogen bonding

(important factor in protein structure)(important factor in protein structure)

Asparagine & glutamineAsparagine & glutamine- are amide derivatives of aspartic acid and - are amide derivatives of aspartic acid and glutamic acid (acidic amino acids)glutamic acid (acidic amino acids)- amide funtional group are highly polar, so - amide funtional group are highly polar, so can form hydrogen bonding (effet on protein can form hydrogen bonding (effet on protein stability)stability)

c) Acidic amino acidsc) Acidic amino acids Contain Contain carboxylate R groupcarboxylate R group The side chains of aspartic acid & glutamic The side chains of aspartic acid & glutamic

acid are polar and acid are polar and negatively chargednegatively charged at at physiological pH, so they often referred as physiological pH, so they often referred as aspartate and glutamateaspartate and glutamate

d) Basic amino acidsd) Basic amino acids Lysine, Arginine, HistidineLysine, Arginine, Histidine Contain Contain amine R groupamine R group Are polar and Are polar and positively chargepositively charge at at

physiological pHphysiological pH Can form ionic bond with acidic amino acidsCan form ionic bond with acidic amino acids Very hydrophilicVery hydrophilic

Biologically active amino acidsBiologically active amino acids

The The 20 standard amino acids20 standard amino acids undergo a bewildering undergo a bewildering number of chemical transformations.number of chemical transformations.

Many amino acids are synthesizes not to be residues Many amino acids are synthesizes not to be residues of polypeptides but to function independently.of polypeptides but to function independently.

Besides being components of protein, amino acids Besides being components of protein, amino acids have several biological roles :have several biological roles :

1)1) Chemical messengersChemical messengers2)2) PrecursorsPrecursors3)3) Metabolite intermediatesMetabolite intermediates

Chemical messengersChemical messengers- - Neurotransmitters Neurotransmitters = substances released from = substances released from one nerve cell that influence the function of a one nerve cell that influence the function of a second nerve cell or a muscle cellsecond nerve cell or a muscle cell-- Glycine Glycine- - γγ-amino butyric acids (GABA)-amino butyric acids (GABA)(derivative of glutamate), (derivative of glutamate), - serotonin & melatonin - serotonin & melatonin (derivative of tryptophan)(derivative of tryptophan)

- - HormonesHormones = chemical signal molecules = chemical signal molecules produced in one cell that regulate the function produced in one cell that regulate the function of other cellsof other cells- Thyroxine (tyrosine derivative), thyroid - Thyroxine (tyrosine derivative), thyroid hormon secreted by thyroid gland hormon secreted by thyroid gland - Indole acetic acid (tryptophan derivative), is - Indole acetic acid (tryptophan derivative), is an auxin plant hormones. Stimulate growth of an auxin plant hormones. Stimulate growth of the root and shootthe root and shoot

PrecursorsPrecursors- a compound that participate in the chemical - a compound that participate in the chemical reaction to produces another compoundreaction to produces another compound- amino acids are precursors of variety of - amino acids are precursors of variety of complex nitrogen-containing moleculescomplex nitrogen-containing molecules- eg. Nucleotides, nucleic acids, chlorophyll- eg. Nucleotides, nucleic acids, chlorophyll

Metabolic intermediatesMetabolic intermediates- several amino acids act as metabolic - several amino acids act as metabolic intermediatesintermediates- eg. Arginine, citrulline, ornithine - eg. Arginine, citrulline, ornithine (components of urea cycle)(components of urea cycle)

Amino acid stereoisomersAmino acid stereoisomers αα-carbon of 19 amino acids -carbon of 19 amino acids

attached to 4 diff. groups, referred attached to 4 diff. groups, referred as asymmetric/chiral carbonsas asymmetric/chiral carbons

Molecule with chiral carbon, can Molecule with chiral carbon, can exist as exist as stereoisomersstereoisomers

StereoisomersStereoisomers - isomeric molecule that have the - isomeric molecule that have the same molecular formula same molecular formula - but differ only in the three-- but differ only in the three-dimensional orientations of their dimensional orientations of their atoms in space.atoms in space.

Molecules with chiral carbon are Molecules with chiral carbon are not superimposablenot superimposable on their mirror image in the same way that a left hand on their mirror image in the same way that a left hand is not superimposable on its mirror image, a right handis not superimposable on its mirror image, a right hand

They are known as enantiomers of one anotherThey are known as enantiomers of one another

L-Alanine and D-Alanine are mirror image to one another

Glyceraldehyde is the reference compound for Glyceraldehyde is the reference compound for optical isomers (to differ between L and D)optical isomers (to differ between L and D)

Titration of amino acidsTitration of amino acids Amino acids contain ionizable group, the Amino acids contain ionizable group, the

predominant ionic form of amino acids in predominant ionic form of amino acids in solution depends on pHsolution depends on pH

Titration of amino acid :Titration of amino acid :- illustrate the effect of pH on amino acids - illustrate the effect of pH on amino acids structurestructure- a useful tool in determining the reactivity of - a useful tool in determining the reactivity of amino acid side chainsamino acid side chains

when amino acid is dissolved in water, it when amino acid is dissolved in water, it exist predominantly in the isoelectric formexist predominantly in the isoelectric form

Upon titration with base, it act as an acid Upon titration with base, it act as an acid (donate proton)(donate proton)

Upon titration with acid, it act as a base Upon titration with acid, it act as a base (accept proton)(accept proton)

eg. titration of glycine with NaOH eg. titration of glycine with NaOH (base)(base)

Glycine has two titratable (ionizable) groups :Glycine has two titratable (ionizable) groups :carboxyl group & ammonium groupcarboxyl group & ammonium group ++NHNH33-CH-CH22-COO-COO--

Upon titration with base, glycine loses two protonsUpon titration with base, glycine loses two protons At pH0 (acidic) – glycine is present in the form which At pH0 (acidic) – glycine is present in the form which

carboxyl group is unchargedcarboxyl group is uncharged++NHNH33-CH-CH22-COOH-COOH

At this point, glycine net charge = +1, because At this point, glycine net charge = +1, because ammonium group is protonatedammonium group is protonated

Gly 0Gly + Gly -

As the pH increase, carboxyl group losing its As the pH increase, carboxyl group losing its proton to become a negatively charged proton to become a negatively charged carboxylate groupcarboxylate group ++NHNH33-CH-CH22-COO-COO--

At this point, glycine has no net charge and is At this point, glycine has no net charge and is electrically neutral.electrically neutral.

The pH at which this occurs is called the The pH at which this occurs is called the isoelectric point (pI). isoelectric point (pI).

Isoelectric point of glycine may be calculated asIsoelectric point of glycine may be calculated as pI = pKpI = pK11 + pK + pK22

2

pKpK11 and pK and pK22 of glycine are 2.34 and 9.6. of glycine are 2.34 and 9.6. The pI value for glycine :The pI value for glycine :

pI = 2.34 + 9.6 = 5.97pI = 2.34 + 9.6 = 5.97

As the titration continues, the ammonium group As the titration continues, the ammonium group will lose its proton, leaving an uncharged will lose its proton, leaving an uncharged amino groupamino group

NHNH22-CH-CH22-COO-COO--

2

eg. Titration of glutamic acid with eg. Titration of glutamic acid with NaOHNaOH

Amino acids with ionizable side chains (acidic & basic a.a) have Amino acids with ionizable side chains (acidic & basic a.a) have more complex titration curve.more complex titration curve.

eg. Glutamic acid has a carboxyl side chain groupeg. Glutamic acid has a carboxyl side chain group At acidic pH (eg. pH0), carboxyl groups are unchargedAt acidic pH (eg. pH0), carboxyl groups are uncharged Glutamic acid net charge = +1Glutamic acid net charge = +1

As base is added, As base is added, αα-carboxyl group loses a -carboxyl group loses a proton to become a carboxylate groupproton to become a carboxylate group

Glutamate now, has no net chargeGlutamate now, has no net charge As more base added, the 2As more base added, the 2ndnd carboxyl group carboxyl group

(side chain) loses a proton(side chain) loses a proton The molecule now has a net charge of -1 The molecule now has a net charge of -1 Adding more base, ammonium ion loses its Adding more base, ammonium ion loses its

protonproton At this point, glutamate has a net charge of -2 At this point, glutamate has a net charge of -2

The pI value for glutamate is the pH halfway The pI value for glutamate is the pH halfway between the pKbetween the pKaa values for the two carboxyl values for the two carboxyl groupgroup

pI = pKpI = pK11 + pK + pK22

2

Note:Note: pI is the pH at which amino acid has a net pI is the pH at which amino acid has a net

charge zero.charge zero. For acidic amino acidsFor acidic amino acids

pI = pKpI = pK11 + pK + pK22

For basic amino acids :For basic amino acids : pI = pKpI = pK22 + pK + pK33

2

2

Amino acid reactionsAmino acid reactions Amino acids with their carboxyl group, amino Amino acids with their carboxyl group, amino

group and various R group can undergo group and various R group can undergo numerous chemical reactionnumerous chemical reaction

i.e i.e peptide bondpeptide bond & & disulfide bridgedisulfide bridge formationformation (effect protein structure)(effect protein structure)

Peptide bond formationPeptide bond formation Polypeptides are linear polymers composed of Polypeptides are linear polymers composed of

amino acids linked together by amino acids linked together by peptide bondspeptide bonds Peptide bonds are amide linkage (CO-NH) Peptide bonds are amide linkage (CO-NH)

formed when the formed when the carboxyl groupcarboxyl group of one amino of one amino acid react with acid react with amino groupamino group of another amino of another amino acidacid

This reaction is a dehydration (mol. water is This reaction is a dehydration (mol. water is removed)removed)

So, the linked amino acids are referred to as So, the linked amino acids are referred to as amino acid residues.amino acid residues.

When When two amino acidtwo amino acid molecules are linked, the molecules are linked, the product is called a product is called a dipeptidedipeptide. .

eg. Serine and glycine can form dipeptides eg. Serine and glycine can form dipeptides glycylserine or serylglycine glycylserine or serylglycine

As amino acids are added and the chain As amino acids are added and the chain lengthens, the prefix reflect the number of lengthens, the prefix reflect the number of residuesresidues

eg. Tripeptides contain three amino acid eg. Tripeptides contain three amino acid residuesresidues

Amino acid residue with the free amino group Amino acid residue with the free amino group is called the N-terminal residue and is written is called the N-terminal residue and is written to the leftto the left

Amino acid residue with free carboxyl group is Amino acid residue with free carboxyl group is called C-terminal residue and is written to the called C-terminal residue and is written to the right right

eg. eg.

Peptides are named by using their amino acid sequence, start from their N-terminal residue

eg. Alanylglycylphenilalanine

Cysteine oxidationCysteine oxidation The sulfhydryl group of cysteine is highly The sulfhydryl group of cysteine is highly

reactivereactive Common reaction = reversible oxidation that Common reaction = reversible oxidation that

form disulfideform disulfide Two molecules of Two molecules of cysteinecysteine oxidized to form a oxidized to form a

cystinecystine (molecule that contain disulfide bond) (molecule that contain disulfide bond)