Amino acid structure

CARBOXYLIC ACID

PRIMARY AMINE

C

H

NH2

COOHRSIDE CHAIN

Alpha carbon

Amino acids• Amino acids are the Lego

Bricks of protein structure.

• Just like these bricks they have a direction with two different types of connection which fit together.

• Each has an N terminus and a C terminus.

• As a result all proteins have the same property and the N terminus is always called the beginning of the protein.

CNH3+ COO-

H

RCNH3

+ COO-

H

R

Amino acid structure

CARBOXYLIC ACID

PRIMARY AMINE

C

H

NH2

COOHRSIDE CHAIN

IF ALL FOUR SITES ARE OCCUPIED BY DIFFERENT GROUPS THEN THE MOLECULE IS ASYMMETRIC

Alpha carbon(chiral if R is not –H)

The isomers of amino acids

L-Alanine D-Alanine

CO

R

N

CO

N

R

Only L-isomers are found in proteins; L=LIVING;D = DEAD

AMMINOACIDI

forma acida zwitterione forma basica

pKa1 = ~ 2 pKa2 = ~ 9

Interazioni deboliLegami a idrogeno

D H :A

~ 0.9 2.5-3.5 Å

Interazioni deboliLegami a idrogeno

O H

H

O H

H

O H

H

O H

H

O H

H

Interazioni deboliLegami elettrostatici

E = k * q1* q2 / D * r

q1 = 1; q2 = -1; r = 3 Å

E = 1.4 kcal mol-1 (5.9 kJ mol-1)

k = 332 kcal mol-1 o 1389 kJ mol-1

Dvuoto = 1 DH2O = 80

Interazioni deboliLegami elettrostatici

R

O

O-

N+

R

H

H

H

O

H

H

OHH

OH

H

O

H HO H

H

OH

H

R

O

O- N

+R

H

H

H

O

H

H

OHH

OH

H

O

HH

OH

H

O

H

H

++

r

r

Interazioni deboliInterazione idrofobica

CH3CH3 CH2 CH2 CH2 CH2 CH2

CH3 CH3

CH3 CH CH2 CH2 CH3

CH3 O H

H

H

H

H

H

H

H

R

IDROFOBICI

H

H

H

H

H

H

Fenolo

O

H

H

H

H

H

H

Indolo

N

H

H

H

HH

H

H

Benzene

AROMATICI

POLARINONCARICHI

BASICI (carichi positivamente)

pKa = ~ 10 pKa = ~ 12

pKa = ~ 6

ACIDI (carichi negativamente)

pKa = ~ 4pKa = ~ 4.5

pKa = ~ 8-9Cisteina(Cys, C)

Tiolo

Disolfuro

• Cysteine• has a thiol/sulphydryl

group. Like -OH but H is lost easily.

• can bond to other cysteines by a disulphide bond.

• binds to metals in proteins.

Cysteine

C

NH3+

H C OO -

SH

C H2

HOOCCHCH2 S

NH2 NH2

CH2CHCOOHS

Disulphide bond

S CH2 COOH

NH2

H

C-:

H+

Zn2+

(anche Hg2+; Cu2+; Fe2+ ecc.)

• Metionine• has a thioether group.

• binds to metals in proteins.

C

NH3+

H COO -

S

CH2

S CH2 COOH

NH2

H

C:Zn2+

(anche Cu2+; Fe2+ ecc.)

CH2

CH3

CH2

CH3

• Histidine• is heteroaromatic.• acts as a base - accepts a H+

at neutral pH; is thus positively charged.

• can bind metals instead.

N N

C

NH3+

H C OO -

C H2

HH+

Histidine

N N

C

NH3+

H C OO -

C H2

HH+

HistidineN

NCH2 C

H

COOH

NH2H

Zn2+

H+

:

• Tyrosine• Phenol ring is a weak acid

(pKa = 10)

• (can bind metals)C

NH3+

H COO -

CH2

OH

H

H

H

H

CH2 C

H

COOH

NH2

H+

-:O

• Glycine• has two hydrogens

attached to the alpha carbon.

• has no D and L form.• is found in flexible

regions of the protein since its side chain is small.

• is a neurotransmitter.

Glycine

C

NH3+

H C OO -

H

Glycine

C

NH3+

H C OO -

H

• Proline• ring joins alpha carbon

to nitrogen two ways.• no amide formed in

proteins = imino group• forms very rigid bend in

protein chains

+N

C OO -

HH2

Proline