PTT103PTT103 BIOCHEMISTRY BIOCHEMISTRY

Amino AcidsAmino AcidsPn Khadijah Hanim Abdul RahmanPn Khadijah Hanim Abdul Rahman

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 same set of set of 2020 amino acidsamino acids

Polymer of amino acids = polypetidesPolymer of amino acids = polypetides Molecules with fewer than 50 amino acids = peptidesMolecules with fewer than 50 amino acids = peptides More than 50 amino acids = proteinMore than 50 amino acids = protein Proteins consists of 1 or more polypeptides folded and Proteins consists of 1 or more polypeptides folded and

coiled into specific conformationscoiled 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

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

Its amino group is secondaryIts amino group is secondary Formed by ring closure between R group and Formed by ring closure between R group and

the amino nitrogenthe amino nitrogen

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 Neutral molecules which bear an equal number of positive and negative charges number 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 nonpolar (Gly, Ala, Val, Leu, Ile, a) neutral nonpolar (Gly, Ala, Val, Leu, Ile, Phe, Trp, Met, Cys, Pro)Phe, Trp, Met, Cys, Pro)

b) neutral polar (ser, thr, tyr, asn, gln)b) neutral polar (ser, thr, tyr, asn, gln)

c) acidic (Asp, glu)c) acidic (Asp, glu)

d) basic (lys, arg, his)d) basic (lys, arg, his)

a) Neutral nonpolar amino acidsa) Neutral nonpolar amino acids

TermTerm‘Neutral’ – ‘Neutral’ – contains hydrocarbon R contains hydrocarbon R groups- do not bear +ve or –ve chargegroups- do not bear +ve or –ve 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 proteinsdimensional structure of proteins

2 types of hydrocarbon R groups:2 types of hydrocarbon R groups:a) a) aromaticaromatic (contain cyclic structure that (contain cyclic structure that constitute a class of unsaturated hydrocarbons)constitute a class of unsaturated hydrocarbons)

eg. eg. Phenylalanine, tryptophanPhenylalanine, tryptophan

b) b) aliphaticaliphatic (nonaromatic hydrocarbon) (nonaromatic hydrocarbon)

eg. eg. Glycine, alanine, valine, leucine, Glycine, alanine, valine, leucine, isoleucine, prolineisoleucine, proline, , methionine, cysteinemethionine, cysteine

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

In met, the nonbonding electrons of the sulfur atom can In met, the nonbonding electrons of the sulfur atom can form bonds with electrophiles such as metal ions. form bonds with electrophiles such as metal ions.

The nonpolar sulfhydryl group (-SH) of cys can form a The nonpolar sulfhydryl group (-SH) of cys can form a weak H bond with O or N.weak H bond with O or N.

Sulfhydryl groups are highly reactive- important component Sulfhydryl groups are highly reactive- important component in many enzymes. in many enzymes.

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 Are polar and Are polar and positively chargepositively charge at physiological pH. at physiological pH. Therefore can form ionic bonds with acidic amino Therefore can form ionic bonds with acidic amino

acids.acids. Lys contain Lys contain amine R group amine R group which accepts a proton

from water to form conjugate acid (-NH3+) His is a weak base because it partially ionized at pH

7. His act as buffer. Important role in catalytic activity of enzymes.

Biologically active amino acidsBiologically active amino acids

The The 20 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) Chemical messengers

2) Precursors

3) Metabolite intermediates

Chemical 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-amino butyric acids

(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 rootthe root

Precursors

- 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

- Nitrogenous base components of nucleotides - Nitrogenous base components of nucleotides and nucleic acids, chlorophylland nucleic acids, chlorophyll

Metabolic intermediates

- several amino acids act as - several amino acids act as metabolic intermediatesmetabolic intermediates

- eg. Arginine, citrulline, - eg. Arginine, citrulline, ornithine (components of ornithine (components of urea cycle)urea cycle)

- The synthesis of urea, a - The synthesis of urea, a molecule formed in the molecule formed in the livers- principle mechanism livers- principle mechanism for disposal of nitrogenous for disposal of nitrogenous wastewaste

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)

Most asymmetric molecules found in living organisms only Most asymmetric molecules found in living organisms only occur in only 1 stereoisomeric form, either D or L.occur in only 1 stereoisomeric form, either D or L.

Chirality has had a profound effect on the structural and Chirality has had a profound effect on the structural and functional properties of biomoleculesfunctional properties of biomolecules

For eg: the right-handed helices result from the presence of For eg: the right-handed helices result from the presence of L-amino acids.L-amino acids.

In addition, because enzymes are chiral molecules, they only In addition, because enzymes are chiral molecules, they only bind substrate molecules in one enantiomeric form.bind substrate molecules in one enantiomeric form.

Proteases, enzyme that degrade proteins by hydrolyzing Proteases, enzyme that degrade proteins by hydrolyzing peptide bonds, cannot degrade polypeptides composed of D-peptide bonds, cannot degrade polypeptides composed of D-amino acids.amino acids.

QuestionQuestion

Certain bacterial species have outer layers Certain bacterial species have outer layers composed of polymers made of D-amino composed of polymers made of D-amino acids. Immune system cells, whose task is to acids. Immune system cells, whose task is to attack and destroy foreign cells, cannot destroy attack and destroy foreign cells, cannot destroy those bacteria. Suggest a reason for this those bacteria. Suggest a reason for this phenomenon. phenomenon.

Titration of amino acidsTitration of amino acids Amino acids contain Amino acids contain ionizable groupionizable group the predominant ionic form of amino acids in the 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 form exist predominantly in the isoelectric form (no net charge and electrically neutral) (no net charge and electrically neutral)

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)

+H3N-CH2-COO- + HCl +H3N-CH2-COOH + Cl-

(base) (acid) (1)

+H3N-CH2-COO- + NaOH H2N-CH2-COO- + Na+ +H2O (acid) (base) (2)

Titration of alanineTitration of alanine

Consider alanine, a simple amino acid contain Consider alanine, a simple amino acid contain 2 titrable groups2 titrable groups

During titration with strong base, NaOH, During titration with strong base, NaOH, alanine loses 2 protons.alanine loses 2 protons.

In a strongly acidic sol (pH 0), ala present In a strongly acidic sol (pH 0), ala present mainly in the form of in which the carboxyl mainly in the form of in which the carboxyl group is uncharged.group is uncharged.

At this point, alanine net charge = At this point, alanine net charge = +1+1, because , because ammonium group is protonated.ammonium group is protonated.

Lowering of the H+ conc results in the COOH group Lowering of the H+ conc results in the COOH group losing a proton to become COOlosing a proton to become COO--..

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

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

Because no net charge at pI, amino acids are least Because no net charge at pI, amino acids are least soluble at this pH.soluble at this pH.

The pI for ala may be calculated as: pI = pKThe pI for ala may be calculated as: pI = pK11 + pK + pK22

2

pKpK11 and pK and pK22 of alanine are 2.34 and 9.7. of alanine are 2.34 and 9.7. The pI value for alanine :The pI value for alanine :

pI = 2.34 + 9.7 = 6pI = 2.34 + 9.7 = 6

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

This molecule has a net –ve charge because of the This molecule has a net –ve charge because of the carboxylate group.carboxylate group.

2

Amino acid reactionsAmino acid reactions

The functional groups of organic molecules The functional groups of organic molecules determine which reactions they may undergo.determine which reactions they may undergo.

Amino acids with their COOH groups, amino Amino acids with their COOH groups, amino groups and various R groups can undergo groups and various R groups can undergo numerous chemical reactions.numerous chemical reactions.

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. eg. TriTripeptides contain three amino acid peptides contain three amino acid residuesresidues

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

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

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 reactiveThe sulfhydryl group of cysteine is highly reactive Common reaction = reversible oxidation that form Common reaction = reversible oxidation that form

disulfidedisulfide 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) When 2 cys residues form such bond, it is referred When 2 cys residues form such bond, it is referred

to as a disulfide bridge.to as a disulfide bridge. Disulfide bridges help to stabilize many Disulfide bridges help to stabilize many

polypeptides and proteins.polypeptides and proteins.