1. Amino acid structure H R C C O O H N H 2 Alpha carbon SIDE CHAIN
CARBOXYLIC ACID N H 2
PRIMARY AMINE

3. 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.

4. Amino acid structure H R C C O O H N H 2 Alpha carbon
(chiral if R is not –H) H
SIDE CHAIN R C C O O H
CARBOXYLIC ACID N H 2
PRIMARY AMINE
IF ALL FOUR SITES ARE OCCUPIED BY DIFFERENT GROUPS THEN THE MOLECULE IS ASYMMETRIC

8. The isomers of amino acids
Only L-isomers are found in proteins; L=LIVING;D = DEAD a a CO CO N N H H R R
L-Alanine
D-Alanine

10. forma acida zwitterione forma basica
AMMINOACIDI
forma acida zwitterione forma basica
pKa1 = ~ 2
pKa2 = ~ 9

15. Interazioni deboli Legami a idrogeno
d- d d-
D H :A
~ 0.9 Å

16. Interazioni deboli
Legami a idrogeno

17. Legami elettrostatici
Interazioni deboli
Legami elettrostatici
E = k * q1* q2 / D * r
k = 332 kcal mol-1 o 1389 kJ mol-1
Dvuoto = DH2O = 80
q1 = 1; q2 = -1; r = 3 Å
E = 1.4 kcal mol-1 (5.9 kJ mol-1)

18. Legami elettrostatici
Interazioni deboli
Legami elettrostatici + +

20. r r

21. Interazione idrofobica
Interazioni deboli
Interazione idrofobica
CH3
CH3
CH2
CH2
CH2
CH2
CH2
CH3 O H
d- d+ d+
CH3 CH
CH2 H

22. R
IDROFOBICI

23. H
Fenolo O H
Indolo N
Benzene
AROMATICI

24. POLARI NON CARICHI

25. BASICI (carichi positivamente)
pKa = ~ 10
pKa = ~ 12
pKa = ~ 6

26. ACIDI (carichi negativamente)
pKa = ~ 4.5
pKa = ~ 4

27. pKa = ~ 8-9
Cisteina
(Cys, C)
Tiolo
Disolfuro

28. 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. H+
Disulphide bond
Zn2+ -:
(anche Hg2+; Cu2+; Fe2+ ecc.)

29. Metionine has a thioether group. binds to metals in proteins. Zn2+ H :3 H C C O O - C H 2 C H 2 S C H 3 H
Zn2+ : S C H C H C C O O H 2 2 C H N H 3 2
(anche Cu2+; Fe2+ ecc.)

30. Histidine is heteroaromatic.
acts as a base - accepts a H+ at neutral pH; is thus positively charged.
can bind metals instead. H+
Zn2+ :

31. Tyrosine Phenol ring is a weak acid (pKa = 10) (can bind metals) H+ N3 H C C O O - C H 2 H H H+ H H OH H
-:O C H C C O O H 2 N H 2

32. 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.

33. Proline ring joins alpha carbon to nitrogen two ways.
no amide formed in proteins = imino group
forms very rigid bend in protein chains a