protein_ revised 2010

8/9/2019 Protein_ Revised 2010

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iochemistry for Health Science Amino acid, Peptide and Protein

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Amino acid, Peptide and Protein

ChatchawinChatchawin PetchlertPetchlert, Ph.D., Ph.D.Department of BiochemistryDepartment of BiochemistryFaculty of Science, Burapha UniversityFaculty of Science, Burapha University

ChymotrypsinChymotrypsin

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The light produced by fireflyThe light produced by firefly proteinprotein luciferinluciferin and ATP, catalyzed byand ATP, catalyzed bythe enzymethe enzyme luciferaseluciferase..

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Erythrocytes contain large amounts of the OErythrocytes contain large amounts of the O22--transporting protein,transporting protein,hemoglobinhemoglobin..

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The proteinThe protein keratinkeratin is the chief structural component of hair, scales, horn,is the chief structural component of hair, scales, horn,wool, nails, and feathers.wool, nails, and feathers.


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COO-

R group

Amino group

Carboxylic group

L-Form Amino Acid Structure

H = Glycine

CH3 = Alanine

H N3+

H

Petchlert C., 2004

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StereoisomersStereoisomers ofof AlanineAlanine. L. L-- and Dand D--alaninealanine areare nonsuperimposablenonsuperimposable mirrormirrorimages of each otherimages of each other (ENANTIOMERS)(ENANTIOMERS)..

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Leu L

-C-C-CONH2-C-CONH2

-C-COOH -C-C-COOH

-H -CH3

-C-OH -C-SH

-C-C-S-C PPro

-C-C CN N+

-C-C-C-C-NH3+

-C-

-C- -OH

-C-

N

South line

Circular line

Central line

Northeast line

North lineNorthwest line

Aliphatic

Amide

Acidic

Imino,Circular

Basic

SulfurHydroxy

Aromatic-C-C-C-N-C-NN+=

C

-C-C-C

C

-C-C-C

C C

-C

CC C

HN C-COOH

-C-C

OH

Gln QAsn N

Asp D Glu EPhe F

Arg R

Lys K

His H

Gly G AAAla VVal IIle

YTyr

Ser S

Thr T Met M

Cys C

Amino Acid Subway Map

Trp W

Non-polar

Polar


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Absorbance of UV light by aromaticAbsorbance of UV light by aromaticamino acids.amino acids.

Note that the absorbance maxima forboth Trp and Tyr occur near awavelength of 280 nm280 nm.

The light absorbance of Trp is as muchas fourfold higher than that of Tyr.

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Reversible formation of a disulfide bond by the oxidation of twoReversible formation of a disulfide bond by the oxidation of two molecules ofmolecules ofcysteinecysteine. Disulfide bonds between. Disulfide bonds between CysCys residues stabilize the structures of manyresidues stabilize the structures of manyproteins.proteins.

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Absorption of Light by Molecules:Absorption of Light by Molecules: The LambertThe Lambert--BeerBeers Laws Law

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Some nonstandard amino acids found in proteins.Some nonstandard amino acids found in proteins. DesmosineDesmosine is formed from 4is formed from 4 LysLysresidues.residues.


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OrnithineOrnithine andand CitrullineCitrulline, which are not found in proteins, are, which are not found in proteins, areintermediates in the biosynthesis ofintermediates in the biosynthesis of ArgArg and in the urea cycle.and in the urea cycle.

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Titration of an amino acid.Titration of an amino acid.

Shown here is the titration curve of0.1M Gly at 250C. The ionic speciespredominating at key points in thetitration are shown above thegraph.

The shaded boxes indicate theregions of greatest bufferingpower.

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Effect of the chemical environment on pKa. The pKa values for the ionizable groups inGly are lower than those for simple, methyl-substituted amino and carboxyl groups.These downward perturbations of pKa are due to intramolecular interaction. Similareffects can be caused by chemical groups that happen to be positioned nearby-forexample, in the active site of an enzyme.


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NH2 COOH1 NH2 COOH2

NH2 C N COOH

O

H

21

Amino acids are connected head to tail

Formation of Peptide Bonds by Dehydration

Dehydration-H2O

Carbodiimide

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Peptide bond is a covalent bond.


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How many peptide bonds are there?How many peptide bonds are there?

Name of amino acids in this peptide.Name of amino acids in this peptide.

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This tetrapeptide has 1free -amino group, 1 free-carboxyl group, and 2ionizable R groups.

Free -amino group

Free -carboxyl group

Ionizable R groups



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The composition of the amino acidmixtures obtained on completehydrolysis of bovine cytochrome cand chymotrypsinogen. These 2proteins, with very differentfunctions, also differ significantlyin the relative numbers of eachkind of amino acid they contain.

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Level of Structure in ProteinsLevel of Structure in Proteins

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Level of Protein Structure

Juang RH (2004) BCbasics


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A comparison of the structures of myoglobin and the subunit ofhemoglobin.

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QUATERNARY STRUCTURE OF HEMOGLOBINQUATERNARY STRUCTURE OF HEMOGLOBIN

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HemeHeme.. The iron atom ofThe iron atom of hemehemehas 6 coordination bonds: 4 inhas 6 coordination bonds: 4 inthe plane of, and bonded to, thethe plane of, and bonded to, the

flatflat porphyrinporphyrin ring system, andring system, and2 perpendicular to it.2 perpendicular to it.


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Normal erythrocytesNormal erythrocytesPetchlert C. 46

SickleSickle--shaped erythrocytesshaped erythrocytes

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Subtle differences between the conformations ofSubtle differences between the conformations of HbAHbA andand HbSHbS result fromresult froma single amino acid change in thea single amino acid change in the chains.chains.

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As the result of the change,As the result of the change, deoxyHbSdeoxyHbS has ahas ahydrophobic patch on its surface, whichhydrophobic patch on its surface, whichcauses the molecules to aggregate intocauses the molecules to aggregate intostrands that align into insoluble fibers.strands that align into insoluble fibers.


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Structure of hair.Structure of hair. Hair -keratin is an elongated helix with somewhat thicker

elements near the amino and carboxyl termini. Pairs of these helices are interwound in aleft-handed sense to form two-chain coiled coils. These then combined in higher-orderstructures called protofilaments and protofibrils. About 4 protofibrils-32 strands of -keratin altogether-combine to form an intermediate filament. Petchlert C. 50

Hair is an array of many -keratin filaments, made up ofthe substructures shown in theprevious picture.

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Structure of collagen.Structure of collagen. (a)(a) TheThe repeating sequence adopts a leftrepeating sequence adopts a left--handed helical structurehanded helical structure((GlyGly--ProPro--HyProHyPro).). (b)(b) SpaceSpace--filling model of the samefilling model of the same chain.chain. (c)(c) Three of these helices wrap aroundThree of these helices wrap aroundone another with a rightone another with a right--handed twist.handed twist. (d)(d) The threeThe three--stranded collagenstranded collagen superhelixsuperhelix shown from one end,shown from one end,in a ballin a ball--andand--stick representation.stick representation. GlyGly residues are shown in red. They is required at the tight junctiresidues are shown in red. They is required at the tight juncti ononwhere the three chains are in contact.where the three chains are in contact.

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Structure of collagen fibrils.Structure of collagen fibrils.Collagen (Collagen (MMrr 300,000) is a rod300,000) is a rod--shapedshapedmolecule, about 3,000molecule, about 3,000 long and only 15long and only 15 thick. Its 3 helicallythick. Its 3 helically interwinedinterwined chains maychains mayhave different sequences, but each has abouthave different sequences, but each has about1,000 amino acid residues. The specific1,000 amino acid residues. The specificalignment and degree of crossalignment and degree of cross--linking varylinking varywith the tissue and produce characteristicwith the tissue and produce characteristiccrosscross--striations in an electron micrograph. Instriations in an electron micrograph. Inthe example shown here, alignment of thethe example shown here, alignment of thehead groups of every fourth moleculehead groups of every fourth moleculeproduces striations 640produces striations 640 apart.apart.


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Structure of silk.Structure of silk.(a) Fibroin consists of layers of(a) Fibroin consists of layers of antiparallelantiparallel sheets rich in Ala (purple) andsheets rich in Ala (purple) and GlyGly (yellow) residues.(yellow) residues.

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Structure of silk.Structure of silk.(b) Strands of fibroin (blue)(b) Strands of fibroin (blue)emerge from the spinnerets of aemerge from the spinnerets of aspider in this colorized electronspider in this colorized electronmicrograph.micrograph.

protein_ revised 2010

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