chapter 27 amino acids, peptides, and proteins slides copy

Amino Acids, Peptides, and Proteins

27

Ribbon model of human myoglobin

27.1 STRUCTURES OF THE α-AMINO ACIDSFigure 27.1 Chirality of the α-Amino Acids(a) Planar projection of an L-amino acid in unionized form. (b) !e α-carboxyl group and the α-amino group are ionized in aqueous solution at pH 7. (c)!e con"guration of the α-amino acids isolated from proteins is opposite to the con"guration of the reference compound D-glyceraldehyde. (d) Molecular model of L-serine, whose side chain is a CH2OH group.

C

CO2H

R

HNH2α C

CO2

R

HNH3α

(a) (b)

Cα

Cβ

N H

C OO

(c)α−Amino group

Side chain

(c)

α−Carboxyl group

CHO

HHO

CH2OH

CHO

OHH

CH2OH

mirror plane

CO2H

HNH2

CH2OH

CO2H

NH2H

CH2OH

D-glyceraldehyde

D-serineL-serine

L-glyceraldehyde

(d)

27.1 STRUCTURES OF THE α-AMINO ACIDSNonpolar (hydrophobic) side chains

CO2-

C H+NH3

CH3

Alanine (A) (Ala)

CO2-

C

CH

H+NH3

CH3

CO2-

C H+NH3

CH2

CHCH3

CH3

Valine (V) (Val)

CH3

Leucine (L) (Leu)

CO2-

C H

C

CH2

CH3

+NH3

CH3H

Isoleucine (Ile) (I)

CN+

H-O2CH

H

Proline (P) (Pro)

CO2-

C H+NH3

CH2

Phenylalanine (F) (Phe)

CO2-

C H+NH3

CH2

Tryptophan (W) (Trp)

NH

Methionine (M) (Met)

CO2-

C H

CH2

S

CH2

CH3

+NH3

Cysteine (C) (Cys)

CO2-

C H

CH2

SH

+NH3

Glycine (G) (Gly)

CO2-

C H

H

+NH3

CO2-

C H+NH3

CH2

Tyrosine (Y) (Tyr)

OH

CO2-

C H

C

CH3

+NH3

OHH

Threonine (Thr) (T)

CO2-

C H+NH3

CH2

C

Asparagine (N) (Asn)

O NH2

Glutamine (Q) (Gln)

CO2-

C H

CH2

CH2

C

+NH3

O NH2

CO2-

C H+NH3

CH2

OH

Serine (S) (Ser)

Polar, neutral (hydrophilic) side chains

CO2-

C H

CH2

CH2

CH2

+NH3

Lysine (Lys) (K)

CH2

NH3+

CO2-

C H

CH2

CH2

CH2

+NH3

Arginine (Arg) (R)

NH

CH2N NH2

CO2-

C H

CH2

+NH3

N

NH

Histidine (His) (H)

CO2-

C H

CH2

CH2

+NH3

Aspartate (Asp) (D)

CO2-

C H

CH2

CH2

CO2-

+NH3

Glutamate (Glu) (E)

Acidic Amino AcidsBasic Amino Acids

Figure 27.2 Structures of theα-Amino Acids at pH 7At pH the α-amino and α-carboxyl groups are both ionized. !e amino acids are classi"ed by their side chain polarities. !e amino acids have both on-letter and three-letter abbreviations.

27.2 ACID-BASE EQUILIBRIA OF α-AMINO ACIDSIonic Form of Amino Acids

CO2-

C H

R

+NH3

structure of a dipolar ion (zwitterion)

CO2-

C H

R

+NH3

zwitterion

+ OH-

CO2-

C H

R

NH2

conjugate base

+ HOH

CO2-

C H

R

+NH3

zwitterion

+ H3O+

CO2H

C H

R

NH2

conjugate acid

+ H2O

27.2 ACID-BASE EQUILIBRIA OF α-AMINO ACIDSpKa Values of α-Amino Acids

CO2H

C H

H

+NH3

conjugate acid of glycine

+ H2O

CO2-

C H

R

NH2

dipolar form of glycine

+ H3O+ Ka = 5 x 10-3

pKa = 2.35

CO2-

C H

H

+NH3

dipolar form of glycine

+ H2O

CO2-

C H

R

NH2

conjugate baseof glycine

+ H3O+ Ka = 1.6 x 10-10

pKa = 9.78

27.1pKa Values of Acidic and Basic Groups in α−Amino AcidsAmino Acid α−CO2H group α−NH3+ group Side chain

Glycine 2.35 9.78Alanine 2.35 9.87Valine 2.29 9.72Leucine 2.33 9.74Isoleucine 2.32 9.76Methionine 2.17 9.27Proline 1.95 10.64Phenylalanine 2.58 9.24Tryptophan 2.43 9.44Serine 2.19 9.44#reonine 2.09 9.10Cysteine 1.89 10.78 8.53Tyrosine 2.20 9.11 10.11Asparagine 2.02 8.80Glutamine 2.17 9.13Aspartate 1.99 10.00 3.96Glutamate 2.13 9.95 4.32Lysine 2.16 9.20 10.80Arginine 1.82 8.99 12.48Histidine 1.81 9.15 6.00

27.2 ACID-BASE EQUILIBRIA OF α-AMINO ACIDSpKa Values of α-Amino Acids

27.3 ISOIONIC POINT AND TITRATION OF α-AMINO ACIDSIsoionic Points of Amino Acids

Table 27.2Isoionic PointsAmino Acid pHI

Glycine 5.97Alanine 6.10Valine 5.96Leucine 5.98Isoleucine 6.02Methionine 5.74Proline 6.30Phenylalanine 5/48Tryptophan 5.89Serine 5.68!reonine 5.60Cysteine 5.07Tyrosine 5.66Asparagine 5.41Glutamine 5.65Aspartic acid 2.77Glutamic acid 3.22Lysine 9.74Arginine 10.76Histidine 7.59

27.3 ISOIONIC POINT AND TITRATION OF α-AMINO ACIDSTitration of Amino Acids

Figure 27.3 Titration Curve of Glycine

pK1 = 2.35

pK2 = 9.78

pHI = 6.02

Equivalents OH-2.01.00.0 0.5 1.5

pHH3NCH2CO2H

+

H3NCH2CO2+ –

H2NCH2CO2–

27.4 SYNTHESIS OF α-AMINO ACIDSAmination of α-Halocarboxylic Acids

CH2 CO2HRBr2PBr3

NH3CH

NH2

R CO2HCH

Br

R CO2H

The Strecker Synthesis

NaCN

NH4Cl

H3O+

CH

NH3+

R CO2HCH

NH2

R CN

(an α-amino nitrile)

C HR

O

NH3H2OC HR

O

C HR

NH

+

CNC HR

NH

+ H CHR CN

NH2

27.4 SYNTHESIS OF α-AMINO ACIDSReductive Amination and Acetamidomalonate Synthesis

Reductive Amination

NH3C CO2HR

O

C CO2HR

NH

CHR CO2H

NH2

NH4Cl

H2

Pd

Acetamidomalonate Synthesis

CHNH CO2CH2CH3

CO2CH2CH3

CCH3

O

(diethyl acetamidomalonate)

C CO2CH2CH3

CO2CH2CH3

R

NHCCH3

OH3O+

heatC CO2H

CO2H

R

NH2 CH

R

NH2 CO2H

CHNH CO2CH2CH3

CO2CH2CH3

CCH3

O

(diethyl acetamidomalonate)

CH3CH2O-

CH3CH2OHCNH CO2CH2CH3

CO2CH2CH3

CCH3

OR Cl

C CO2CH2CH3

CO2CH2CH3

R

NHCCH3

O

27.5 CHIRAL SYNTHESIS OF α-AMINO ACIDSFigure 27.4 Structure of (R,R)-degphos

N

PH

PH

(R,R)-degphos

C C

H CO2H

N C

H

O

CH3

Rh(R,R)-degphos

H2

C CH CO2H

N C

H

O

CH3

H H

(Z)-2-acetamido-3-phenylpropenoic acid (S)-N-acetylphenylalanine

H3O+ C CH CO2H

NH2

H H

(S)-phenylalanine

27.6 REACTIONS OF α-AMINO ACIDSEsterification of the α-Carboxyl Group

C HNH2

CH3

CO2CH2C6H5

alanine benzyl ester

H2 / PdC HNH2

CH3

CO2H

+ C6H5CH3

alanine

C HNH3

CH3

CO2H

+ CH3CH2OHHCl (g)

C HNH3

CH3

CO2CH2CH3

alanine alanine ethyl ester

C HNH3

CH(CH3)2

CO2H

+ C6H5CH2OHHCl (g)

C HNH3

CH(CH3)2

CO2CH2C6H5

valine valine benzyl ester

27.6 REACTIONS OF α-AMINO ACIDSAcetylation of the α-Amino Group

OCO

O

(CH3)3C C O

O

C(CH3)3

di-tert-butyldicarbonate (Boc)2O

CNH3

CH3

CO2

alanine

H NHCO

O

(CH3)3C

N-tert-butoxycarbonyl alanine (Boc alanine)

(Boc)2OC H

CH3

CO2H

CNH2

CH3

CO2

alanine

H + ClCO

O

C6H5CH2pyridine

NHCO

O

C6H5CH2

N-benzyloxycarbonyl alanine (Cbz alanine)

benzyl chloroformate

C H

CH3

CO2H

27.6 REACTIONS OF α-AMINO ACIDSAcetylation of the α-Amino Group

NHCO

O

C6H5CH2


C H

CH3

NH C H

CH3

CO2H

a carbamic acid

C H

CH3

CO2H

NH2 + CO2CHO

OCO2H

NHCO

O

C6H5CH2


C H

CH3

NH C H

CH3

CO2H

C H

CH3

CO2H

NH2 + C6H5CH3CHO

OCO2HH2

Pd

CO2

NHCO

O

(CH3)3C

N-tert-butoxycarbonyl alanine (Boc alanine)

C H

CH3

CO2HCF3CO2H

NHCHO

O

C H

CH3

CO2H

+ C(CH3)2CH2

27.7 PEPTIDESPeptide Nomenclature

Figure 27.4 Peptide Nomenclature(a) Structure of glycylalanine. !e N-terminal α-amino group and the C-terminal α-carboxyl group and are ionized in aqueous solution at pH 7. !ree-letter and one-letter abbreviations for the amino acids are commonly used. (b) Structure of alanylglycine. (c) An aminoacyl group consists of the —NH—CHR—CO— group of each amino acid in the peptide.

H

C C

H

+NH3

N-terminal residue

NH

O

C C

H

CH3

O

OC-terminal residue

glycylalanine(Gly-Ala or GA)

peptide bond

H

C C

CH3

+NH3

N-terminal residue

NH

O

C C

H

H

O

OC-terminal residue

alanylglycine(Ala-Gly or Ag)

H

C C

R1

+NH3 NH

O

C C

H

R2

NH

O

aminoacyl group

C

R3

α1 α2 α3

(a) (b)

(c)

27.8 OVERVIEW OF PEPTIDE SYNTHESIS

CHNH2 C

R1

OH

OPC

CHNH2 C

R2

O

O

PC

CHNH2 C

R1

OH

OPN

CHNH C

R2

OH

O

PN

CHNH C

R1

OH

O

PN CHNH2 C

R2

O

O

PC+ CHHN C

R1

NH

O

PN CH C O

O

R2

PC

27.8 OVERVIEW OF PEPTIDE SYNTHESISProtecting the Carboxyl Group

C HNH3

R

CO2H

+ C6H5CH2OHHCl (g)

C HNH3

R

CO2CH2C6H5

benzyl ester

C HNH2

R

CO2CH2C6H5

amino acid (or peptide) benzyl ester

H2 / PdC HNH2

R

CO2H

+ C6H5CH3

deprotected amino acid (or peptide)

27.8 OVERVIEW OF PEPTIDE SYNTHESISProtecting the Amino Group

CNH3

R

CO2

H NHCO

O

(CH3)3C

N-tert-butoxycarbonyl amino acid (a Boc-amino acid)

(Boc)2OC H

R

CO2H

NHCO

O

(CH3)3C

N-tert-butoxycarbonyl amino acid (Boc-amino acid)

C H

R

CO2BzCF3CO2H

NHCHO

O

C H

R

CO2Bz

+ C(CH3)2CH2

unstable carbamate derivative ofan amino acid

NH C H

R

CO2Bz

+ CO2

27.8 OVERVIEW OF PEPTIDE SYNTHESISPeptide Bond Synthesis

N C N

dicyclohexylcarbodiimide (DCCI)

C

O

HN

HN

dicyclohexylurea

CHNH C

R1

OH

O

PN CHNH2 C

R2

O

O

PC+ CHHN C

R1

NH

O

PN CH C O

O

R2

PCDCCI

27.8 OVERVIEW OF PEPTIDE SYNTHESISPolypeptide Synthesis

CHHN C

R1

NH

O

O CH C O

O

R2

BzC(CH3)3C

O

CF3CO2H

CHNH2 C

R1

NH

O

CH C O

O

R2

BzBoc-Amino acid

DCCIBoc-tripeptide-CO2Bz

27.9 SOLID PHASE PEPTIDE SYNTHESIS

NHCO

O

Boc

(N-protected Boc-amino acid)

C CO2

H

R

+ polymerClCH2 NHCO

O

Boc C C

H

R

OCH2

O

polymer

(polymer bound N-protected Boc-amino acid)

Step 1.

Step 2.

NHCO

O

Boc C C

H

R

OCH2

O

polymer

(polymer bound N-protected Boc-amino acid)

1. CF3CO2H

2. (CH3CH2)3NNH2 C C

H

R

OCH2

O

polymer

(polymer bound amino acid)

NH2 C C

H

R'

OCH2

O

polymer

polymer bound amino acid

+NHCBocO

O

a Boc-amino acid

C CO2

H

R

DCCI

NHCBocO

O

C C

H

R O

NH C C

H

R'

OCH2

O

polymer

N-protected polymer bound dipeptide

Step 3.

27.10 DETERMINATION OF THE AMINO ACID COMPOSITION OF PROTEINS

NH3 C C

H

R1 O

NH3 C C

H

R2

NH3

O

C C

R3

H

OH

O

NH3 C C

H

R1 O

NH C C

H

R2

NH

O

tripeptide

C C

R3

H

OH

O

6 M HCl

OHOH + +

NH2 C C

H

R1 O

OH + N C S NHCHN

S

C CO2H

H

R1

phenylisothiocyanate (PICT)

phenylisothiocarbamyl amino acid (PCT amino acid )


Figure 27.5 HPLC Separation of PCT Amino Acids

Abs

orba

nce,

254

nm

Min5 10 15

DE S G H

RH TP

YV

M

C

I

LF

K

Table 27.4Amino Acid Composition of Human LysozymeAmino Acid

Number of Amino Acids

Per Cent Composition

Ala 5 4.1Arg 1 0.8Asn 4 3.3Asp 12 9.8Cys 8 6.5Gln 7 4.9Glu 8 6.5Gly 6 9.8His 2 11.4Ile 12 9.8Leu 14 11.4Lys 12 9.8Met 2 1.6Phe 4 3.3Pro 2 1.6Ser 8 6.5!r 7 5.7Trp 3 2.4Tyr 4 3.3Val 2 1.6


Figure 27.6 Edman DegradationFirst, the peptide is converted to its N-terminal PCT derivative by treatment with phenylisothiocyanate. Next, the PCT protein is treated with tri!uoroacetic acid, then with water to give the phenylthiohydanto-in derivative. "e N-terminal amino acid is released in this step. "e other peptide bonds are not a#ected.

NH2 C C

H

CH3 O

NH C C

H

H

NH

O

C C

R3

H

protein

O

Ala Gly

PICT/base

NHCHN

S

C

H

CH3

C6H5 NH C C

H

H

NH

O

C C

R3

H

protein

O

Gly

C

O

N-terminal PCT derivative of the protein

N-terminal PCT group

1. CF3CO2H2. H+, H2O

NH3 C C

H

H

NH

O

C C

R3

H

protein

O

Gly

+N

NH

S

OCH3

phenylthiohydantoin derivative of alanine

27.11 DETERMINATION OF THE AMINO ACID SEQUENCE OF PROTEINSThe Edman Degradation

27.11 DETERMINATION OF THE AMINO ACID SEQUENCE OF PROTEINSBlocking Cystine Residues

CH2SH

CNH C

H

CH2SH

NH

O

C

H

NHC

O

+

cysteine residues

I CH2CH2CO2-

iodoacetate

CH2SCH2CH2CO2-

CNH C

H

SCH2CH2CO2-

NH

O

C

H

NHC

O

+

S-Carboxymethylcysteine residues

CH2

CNH C

H

cystine residue

SS

CH2

NH

O

C

H

NHCNH

O

2 HSCH2CH2OH

(β-mercatpethanol)CH2SH

CNH C

H

CH2SH

NH

O

C

H

NHC

O

+

2 cysteine residues

+SCH2CH2OH

SCH2CH2OH

27.11 DETERMINATION OF THE AMINO ACID SEQUENCE OF PROTEINSPeptide Cleavage at Methionine Residues

-Ala-Phe-Arg-Gly-Lys-Met-Val-Leu----H3N CO2-

BrCN

-Val-Leu----CO2--Ala-Phe-Arg-Gly-Lys NH

O

O

C-terminal homoserine lactone (HSL)

+ NH3NH3

27.11 DETERMINATION OF THE AMINO ACID SEQUENCE OF PROTEINSEnzymatic Cleavage of Polypeptide Chains

(H3N—)Ala—Arg—Phe—Gly—Lys—Trp—Val(—CO2H)Trypsin

(H3N—)Ala—Arg(—CO2H) (H3N—)Phe—Gly—Lys(—CO2H)+ (H3N—)Trp—Val(—CO2H)+

(H3N—)Ala—Arg—Phe—Gly—Lys—Trp—Val(—CO2H)

Chymotrypsin

+ (H3N—)Val(—CO2H)+(H3N—)Ala—Arg—Phe(—CO2H) (H3N—)Gly—Lys—Trp(—CO2H)

ValAla—Arg—Phe Gly—Lys—Trp

Ala—Arg Phe—Gly—Lys Trp—Val

27.11 DETERMINATION OF THE AMINO ACID SEQUENCE OF PROTEINSPrimary Structures and Evolutionary Relationships

Figure 27.7 Evolutionary Family Tree for Cytcochrome c

Bacteria

Yeast

Candidakrusei

Neurosporacrasa

Baker’s yeast

Fruit !ySilk moth

Hornwormmoth

Insects

Plants

WheatMung bean Pumpkin

Tomato

Sun!ower

Paci"clamprey

CarpTuna

Bonito

Snapping turtleDuck

Chicken, TurkeyPenguin

Human, chimpanzeeMonkey

Zebra,Horse

Cow, pig, sheepDog

BullfrogGrey whale

CC

NC

O

H

αα' C

CN

C

O

H

αα'

contributing structure 1 contributing structure 2

CC

NC

O

H

αα'

resonance hybrid

δ

δ

27.12 BONDING IN PROTEINSStructure of the Peptide Bond

27.12 BONDING IN PROTEINSStructure of the Peptide Bond

Figure 27.8 Structure of the Peptide Bond(a) Rotation around the C—N bond, which has 50% double bond character, does not occur at room temperature. However, rotation around the N—Ca bond (φ) and the C—Ca bond (ψ) is possible, and many conformations are possible in peptides and proteins. (b) we can think of the α-carbon as a “hinge” between two planar peptide bonds. If one takes two note cards, and links them with a swivel, it is easy to see that many arrangements are possible. However, some φ and ψ are not possible because of steric interference of the side chain R group. Glycine, for example, can assume many more conformations than amino acids like proline and tryptophan.

(a)

O

Cα

N

H

C

O

N

Cα

ψφ

Cα

ONH

HCα

N

HR

ψ

φ

O

C

C

Cα

(b)

Figure 27.8 Dimensions of an α-Helix!e distance between amino acid residues in an α-helix is 0.15 nm. !e distance required for one turn of the helix, its pitch, is 5.4 nm.

27.12 BONDING IN PROTEINSThe α-Helix

0.15 nm Rise per aminoacid residue

Pitch: distancefor one turn

0.54 nm

Figure 27.9 Ribbon Diagram of an α-HelixHydrogen bonds in an α-helix are approximately parallel to long axis of the helix. !ey from between carbonyl oxygen and amide hydrogens separated by 3.6 residues. Side chains radiate outward from the helix. !e α-helix is right-handed.

27.12 BONDING IN PROTEINSThe α-Helix

Lys

Asp

Gln

Met

Leu

Ala

Ala

H-bond

H-bond

27.12 BONDING IN PROTEINSβ-Pleated Sheets

Figure 27.10 Hydrogen Bonding In Parallel β-Pleated Sheet

CR

C O

N

C

CO

N H

CR

H

HRH

H

CR

C O

N

C

CO

N H

CR

H

HRH

H

CR

C O

N

C

CO

N H

CR

H

HRH

H

27.12 BONDING IN PROTEINSDisulfide Bonds

C

CO2

HNH3

CH2SH

2 [O]

SCH2 S CH2

CCNH3 H

CO2

HNH3

CO2

cysteine cystine

Figure 27.12 Conformation of an s-trans Disulfide Bond

s-trans disul!de bond

27.13 PROTEIN STRUCTURE

Table 27.5Examples of Proteins Having Quatenary StructureProtein Molecular

WeightNumber ofSubunits

Function

alcohol dehydrogenase

80,000 4 enzymatic reaction in fermentation

aldolase 150,000 4 enzymatic reaction in glycolysisfumarase 194,000 4 enzymatic reaction in citric acid cyclehemoglobin 65,000 4 oxygen transport in bloodinsulin 11,500 2 hormone that regulates metabolism of glucose

Figure 27.13 Ribbon Diagram of the Membrane Region of the Serotonin Receptor!e seven helix region of the serotonin receptor is the site of serotonin binding. !e serotonin receptor is a member of the G-coupled receptor protein family. !ese proteins have similar structures. !eir di"erent speci#cities depend upon di"erences in primary structure at the ligand bindings site.



Figure 27.14 Structure of 1GB1

Figure 27.15 Parallel b Strands and an α-Helix in a β-α-β Arrangement


Figure 27.16 Tertiary Structure of Triose Phosphate Isomerase!e α-helices are shown in red, β-pleated sheets are blue, and less structured “loops” are shown in green.


27.14 OXYGEN STORAGE AND TRANSPORT: MYOGLOBIN AND HEMOGLOBINMyoglobin

Figure 27.18 Heme

N

N N

N

OOO O

FeII

heme

27.14 OXYGEN STORAGE AND TRANSPORT: MYOGLOBIN AND HEMOGLOBINMyoglobin

Figure 27.17 Structure of Oxymyoglobin.(a) !e α-helices are shown in red, and less structured “loops” are shown in green. (b) Structure of the heme group bound to myoglobin via a bond from a nitrogen on histidine 93 and the FeII ion. Oxygen binds on the opposite side of the histidine.

Heme

O2(a)

His 93

O2FeII

(b)

27.14 OXYGEN STORAGE AND TRANSPORT: MYOGLOBIN AND HEMOGLOBINHemoglobin

Figure 27.19 Structure of Deoxyhemoglobin.!e α and β subunits of hemoglobin interact cooperatively, and when one heme binds O2, the each of the others rapidly bind O2.

27.14 OXYGEN STORAGE AND TRANSPORT: MYOGLOBIN AND HEMOGLOBINSickle Cell Hemoglobin

1 2 3 4 5 6 7 8Hemoglobin A Val-His-Leu-!r-Pro-Glu-Glu-Lys-

Hemoglobin S Val-His-Leu-!r-Pro-Val-Glu-Lys-

27.14 OXYGEN STORAGE AND TRANSPORT: MYOGLOBIN AND HEMOGLOBINSickle Cell Hemoglobin

Figure 27.20 Structure of Deoxyhemoglobin Dimer.!e β subunits of hemoglobin interact by van der Waals contact between the isopropyl side chains at residue 6 of sickle cell hemoglobin (HbS). Since each HbS has two β subunits on opposite sides of the tetramer, a "brous polymer forms. HbS polymerizes when HbS releases O2, which disorts the red blood cells into the shape of a sickle.

chapter 27 amino acids, peptides, and proteins slides copy

Documents