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Amino acid structure CARBOXYLIC ACID PRIMARY AMINE C H NH 2 COOH R SIDE CHAIN Alpha carbon.

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Presentation on theme: "Amino acid structure CARBOXYLIC ACID PRIMARY AMINE C H NH 2 COOH R SIDE CHAIN Alpha carbon."— Presentation transcript:

1 Amino acid structure CARBOXYLIC ACID PRIMARY AMINE C H NH 2 COOH R SIDE CHAIN Alpha carbon

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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 CARBOXYLIC ACID PRIMARY AMINE C H NH 2 COOH R SIDE 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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8 The isomers of amino acids L-Alanine D-Alanine CO R N N R Only L-isomers are found in proteins; L=LIVING;D = DEAD

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10 AMMINOACIDI forma acida zwitterione forma basica pK a1 = ~ 2pK a2 = ~ 9

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15 Interazioni deboli Legami a idrogeno D H :A ~ 0.9 2.5-3.5 Å

16 Interazioni deboli Legami a idrogeno

17 Interazioni deboli Legami elettrostatici E = k * q 1 * q 2 / D * r q 1 = 1; q 2 = -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 D vuoto = 1 D H2O = 80

18 Interazioni deboli Legami elettrostatici + +

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20 r r

21 Interazioni deboli Interazione idrofobica CH 3 CH 2 CH 3 CHCH 2 CH 3 O H H H H H H H H

22 R IDROFOBICI

23 H H H H H H Fenolo O H H H H H H Indolo N H H H H H H H Benzene AROMATICI

24 POLARI NON CARICHI

25 BASICI (carichi positivamente) pK a = ~ 10 pK a = ~ 12 pK a = ~ 6

26 ACIDI (carichi negativamente) pK a = ~ 4 pK a = ~ 4.5

27 pK a = ~ 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. Disulphide bond -:-: H+ Zn 2+ (anche Hg 2+ ; Cu 2+ ; Fe 2+ ecc.)

29 Metionine has a thioether group. binds to metals in proteins. C NH 3 + HCOO - S CH 2 SCH 2 COOH NH 2 H C : Zn 2+ (anche Cu 2+ ; Fe 2+ ecc.) CH 2 CH 3 CH 2 CH 3

30 Histidine is heteroaromatic. acts as a base - accepts a H + at neutral pH; is thus positively charged. can bind metals instead. Zn 2+ H+H+ :

31 Tyrosine Phenol ring is a weak acid (pK a = 10) (can bind metals) C NH 3 + HCOO - CH 2 OHOH H H H H CH 2 C H COOH NH 2 H+H+ -:O-:O

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

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