Download - Amino acid structure CARBOXYLIC ACID PRIMARY AMINE C H NH 2 COOH R SIDE CHAIN Alpha carbon
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Amino acid structure
CARBOXYLIC ACID
PRIMARY AMINE
C
H
NH2
COOHRSIDE CHAIN
Alpha carbon
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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
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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)
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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
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AMMINOACIDI
forma acida zwitterione forma basica
pKa1 = ~ 2 pKa2 = ~ 9
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Interazioni deboliLegami a idrogeno
D H :A
~ 0.9 2.5-3.5 Å
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Interazioni deboliLegami a idrogeno
O H
H
O H
H
O H
H
O H
H
O H
H
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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
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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
++
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r
r
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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
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R
IDROFOBICI
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H
H
H
H
H
H
Fenolo
O
H
H
H
H
H
H
Indolo
N
H
H
H
HH
H
H
Benzene
AROMATICI
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POLARINONCARICHI
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BASICI (carichi positivamente)
pKa = ~ 10 pKa = ~ 12
pKa = ~ 6
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ACIDI (carichi negativamente)
pKa = ~ 4pKa = ~ 4.5
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pKa = ~ 8-9Cisteina(Cys, C)
Tiolo
Disolfuro
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• 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.)
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• 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
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• 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+
:
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• 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
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• 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
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• 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
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