Amino Acids and Peptides

Precursors of Proteins

Proteins(Amino Acids)

H2N C C

R1

H

N C COOH

R2

H

H2N C C

R1

H

O

N C COOH

R2

H H

O

OH

H

H

Amino Acid Amino Acid Protein

H2O

Only 20 naturally-occurring amino acids

Only linear structures

Functions of Proteins I

• Catalysts and Metabolic Regulation – Enzymes• Protection

– Serum antifreeze proteins– Blood coagulation– Antibodies

• Membrane Transport – Nutrients• Signal Transduction – Cell Surface Receptors• Structural Support – Collagen

Functions of Proteins II

• Coordinated Motion – Muscle Contraction• Genetic Regulation – DNA Binding Proteins• Transport – Hemoglobin• Generation and Transport of Nerve Impulses• Nutrient Storage

– Seed proteins– Casein in milk

Function of proteins largely due to properties of constituent amino acids

Standard Amino Acids (20)

NH

COOH

Proline

H2N C COOH

R

H

-Amino Acid

Stereochemistry Review

Optical Activity

Figure 4-9

Diagram of a Polarimeter

Rotation of Plane of Polarized Light

Dextrorotatory(rotation to the right) =

“d” or “+”

Levorotatory(rotation to the left) =

“l” or “-”

Empirical

Optically Active Molecules are Asymmetric

(i.e. not superimposible on their mirror image)

Chiral (Asymmetric) Carbon

Four different substituentsStereoisomers

C atoms of amino acids (except glycine) are asymmetric centers!

Chiral Centers Give Rise to Enantiomers

(non-superimposible mirror images)

Distinguishing Stereoisomers

• Rotation of plane of polarized light (not related to absolute configuration)

• Cahn-Ingold-Prelog Method (R/S)

• Fischer Method (projections)

Cahn-Ingold-Prelog Method (R/S)(1956)

COOC NH3

CH2OH

+-

H

(S-2-amino-glycerate)S-Serine

CCOOH3N

CH2OH

+ -

H

(R-2-amino-glycerate)R-Serine

Fischer Convention(1891)

Protein Amino Acids

Fischer Method/Projections (L/D)

H3N C

COO

H

CH2OH

NH3C

COO

H

CH2OH

(S- 2-AMINO-GLYCERATE) (R- 2-AMINO-GLYCERATE)L- SERINE D-SERINE

H3N C

COO

H

CH2OH

NH3C

COO

H

CH2OH

H3N

COO

H

CH2OH

NH3

COO

H

CH2OH

L--Amino Acids

H3N C

COO

H

CH2OH

COOC

CH2OH

H3N

H

Chirality and Biochemistry

Life is Based on Chiral Molecules

Biosynthetic processes almost invariably produce pure

stereoisomers – e.g. L-amino acids

Biological D-amino acids: Bacterial Cell Wall

Pharmaceutical Industry

Racemic Mixtures

Figure 4-12

Benign

Figure 4-13

Devastating

Chiral Synthesis

Goal of Organic Chemistry

Amino Acids

Non-Polar Hydrophobic Amino Acids

Aromatic Amino Acids

H3N C COO–

H

CH2

CH2

S

CH3

H3N C COO–

H

NH

H3N C COO–

H

NH2

COO–CH2 CH2

Proline

PhenylalanineTryptophanMethionine

Non-Polar Polar

H3N C COO–

H

CH2

OH

H3N C COO–

H

CH2

C

NH2

O

H3N C COO–

H

CH2

CH2

C

NH2

O

GlutamineAsparagineTyrosine

Polar Amino Acids

Negatively Charged (Acidic) Amino Acids

Positively Charged (Basic) Amino Acids

Notation for 20 Standard AAs

Three-Letter One-Letter

Amino Acid Symbol Symbol

Alanine Ala A

Arginine Arg R

Asparagine Asn N

Aspartate Asp D

Cysteine Cys C

Glutamate Glu E

Glutamine Gln Q

Glycine Gly G

Histidine His H

Isoleucine Ile I

Leucine Leu L

Lysine Lys K

Methionine Met M

Phenylalanine Phe F

Proline Pro P

Serine Ser S

Threonine Thr T

Tryptophan Trp W

Tyrosine Tyr Y

Valine Val V

Figure 4-8

Greek Nomenclature

Dipolar Ions(Zwitterions)

Amino Acids can be Buffers

Histidine is particularly important for biological function

Isoelectric point (pI)

pH at which the molecule has a net charge of 0.

pI = pKa1 + pKa2

2

– Using the pKa’s on either side of the neutral species

The Peptide Bond

Peptide Bonds

Linear Polymers

N-Terminus

C-Terminus

Peptides

Dipeptides

Tripeptides

Oligopeptides

Polypeptides

Diversity

Number = 20n

Variations in length and sequence contribute to the diversity of shapes and biological functions of

proteins

Nomenclature of Peptides(Primary Structure)

L-alanyl-L-seryl-L-aspartic acid[aspartate]

AlanylserylaspartateAlaSerAsp

ASD

Diversity(Tripeptide: 3 x 2 x 1 = 6

arrrangements)

Ala Ser Asp Ala Asp Ser

Ser Ala Asp Ser Asp Ala

Asp Ser Ala Asp Ala Ser

For 20 amino acids (small peptide):

20! = 2.43 x 1018

Selenocysteine: the 21st Amino Acid

H3N C COO–

H

CH2

SH

H3N C COO–

H

CH2

OH

H3N C COO–

H

CHH3C OH

CysteineThreonineSerine

Pyrrolysine: the 22nd Amino Acid

H3N C COO–

H

CH2

CH2

CH2

CH2

NH3+

H3N C COO–

H

CH2

CH2

CH2

NH

CH2N NH2

H3N C COO–

H

CH2

NH

HN

HistidineArginine

+

Lysine

Protein Amino Acid Derivatives

Figure 4-14

Some Modified Peptidyl Amino Acids

Disulfide Bond Formation(Cystine)

CH

O

CH2

SH

SH

CH2

CHC

O

C

N

H

N

H

CH

O

CH2

S

S

CH2

CHCO

C

N

H

N

H

1/2 O2

Disulf ide Bond

H2O

Cysteine

Cysteine

Cystine

Hydroxylation

NH2

COO–

H

OH

4–hydroxyproline

OH

NH3

CH2

CH

CH2

CH2

CHH3N COO–

5–hydroxylysine

Phosphorylation

Phosphoserine Phosphohistidine

O P O–

O

O–CH2

CHH2N COO–+

N

N

CH2

P O–

O

O–

CHH2N COO–+

Acetylation

H3N C

COO–

H

CH2

CH2

CH2

CH2

NH

C

CH3

O

Acetyllysine

Formylation(amino terminal methionine)

CH 3

S

CH 2

CH 2

CHNH C

O

HC

O

Other Modifications

• Methylation (methyl group)

• Glycosylation (sugar)

Figure 4-15

Biologically Active Amino Acid Derivatives

Non-protein Amino Acids

H3N C

COO–

NH3

CH2

COO–

CH3N

CH2

COO–

CH2

C H3N

CH2

CH2

CH2 H

H

H

H

H

Ornithine -alanine (GABA)-aminobutyric acid

Green Fluorescent Protein

Box 4-3 figure 1

Aequorea victoria

Box 4-3 figure 2

Green Fluorescence Protein (GFP)

• GFP cloned in the early 1990s and expressed in E. coli.

http://www.conncoll.edu/ccacad/zimmer/GFP-ww/GFP2.htm

GFP-like and GFP variants

• GFP-like proteins identified in non-bioluminescent organism (i.e. corals)

• Mutants with faster and brighter fluorescence have since been identified.

http://www.conncoll.edu/ccacad/zimmer/GFP-ww/GFP2.htm

In vivo Imaging

Spatial-temporal imaging of bacterial infection

Zhao, M. et al. PNAS. 2001; 98(17): 9814-9818.

Cool Green Things!

http://www.conncoll.edu/ccacad/zimmer/GFP-ww/GFP4.htm