1. Amino Acids, Peptides

2. Amino Acids Amino acids are the building blocks of proteins.
contain a carboxylic acid group and an amino group on the alpha () carbon.
are ionized in solution.
each contain a different side group (R).

3. Amino acids are derivatives of carboxylic acids formed by substitution of -hydrogen for amino functional group.
Composed of C, H, O, N usually S, P
Always has a NH2

4. All the standard amino acids except (glycine) the α carbon is asymmetric.
α carbon is bonded to four different substituent groups:
carboxyl group
amino group
R group
hydrogen atom.

5. All amino acids start with this structure
The “R” stands for “anything”

6. Classification of Amino Acids

7. CLASSIFICATION: Classified based on the properties of their R groups.
Tendency to interact with water at biological pH (near pH 7.0).

8. those whose R groups are:
nonpolar and aliphatic )aromatic (generally nonpolar)
3) polar but uncharged
4) negatively charged
5) positively charged.
Within each class, there are gradations of polarity, size, and shape of the R groups.

9. nonpolar (hydrophobic) with hydrocarbon side chains.
polar (hydrophilic) with polar or ionic side chains.
acidic (hydrophilic) with acidic side chains.
basic (hydrophilic) with –NH2 side chains.
Nonpolar Polar
Acidic
Basic

10. Nonpolar Polar
Acidic
Basic

11. 1) Nonpolar Aliphatic R group:
The hydrocarbon R groups are nonpolar and hydrophobic.
The bulky side chains of alanine, valine, leucine, and isoleucine, promote hydrophobic interactions within protein structures.

12. Nonpolar Amino Acids
An amino acid is nonpolar when the R group is H, alkyl, or aromatic.

13. Amino acids can be classified by R groups

14. 2) Polar, Uncharged R Groups :
Are more soluble in water than nonpolar amino acids, because they contain functional groups that form hydrogen bonds with water.
Includes:
Serine(OH)
Threonine(OH)
Cysteine( S)
Methionine(S, sulphur atom)
Asparagine(NH2, amide group)
Glutamine. (NH2)

15. Polar Amino Acids
An amino acid is polar when the R group is an alcohol, thiol, or amide.

17. Tryptophan and tyrosine, and phenylalanine absorb ultraviolet light.
3) Aromatic R Groups:
Phenylalanine (Phe), Tyrosine (tyr), and Tryptophan (Trp), are relatively nonpolar.
The OH group of tyrosine can form hydrogen bonds, hence important functional group in the activity of some enzymes.
Tyrosine and tryptophan are more polar than phenylalanine because of the tyrosine hydroxyl group and the nitrogen of the tryptophan indole ring.
Tryptophan and tyrosine, and phenylalanine absorb ultraviolet light.

18. indole
ring

20. 4) Negatively Charged (Acidic) R Groups:
Include:
1) Aspartate
2) Glutamate
Each have a second carboxyl group.
These are the parent compounds of asparagine and glutamine.

22. 5) Positively Charged (Basic) R Groups:
Includes:
lysine, has a second amino group at the e position on its aliphatic chain;
Arginine, which has a positively charged guanidino group;
Histidine, has an imidazole group.

23. imidazole
guanidino

24. Acidic and Basic Amino Acids
An amino acid is
acidic when the R group is a carboxylic acid.
basic when the R group is an amine.

25. Essential Amino Acids Clue to remember: PVT TIM HALL
Proteinaceous AA − proteins consist of 20 AA.
Essential − organism is not able to synthesize these AA but accept from food.
Nonessential − organism produced from essential AA by transamination.
Methionine
Histidine
Arginine
Lysine
Leucine
Phenylalanine
Valine
Threonine
Tryptophan
Isoleucine

26. Description – general properties

27. GENERAL PROPERTIES OF AMINO ACIDS:
Isomerism:
Two types:
1) L form
2) D forms.
stereo-isomerism: all amino acids except glycine exist as D and L- isomers.
In D-amino acids, -NH2 group (right). In animals and plants.
In L-amino acids (left) ,occur in bacteria.

28. Amino Acids
Steric relationship of the stereoisomers of Alanine to the absolute configuration of L- and D-glyceraldehyde
The amino acid residues in proteins are the L isomers

29. AA are optically active molecules and asymmetry of their mirror images is not superimposable (except in the case of glycine where the R-group is hydrogen)
according new UIPAC nomenclature L- D- forms were replaced for (S)- and (R)- system

30. 2) Ionization:
Amino acids in aqueous solution are ionized and can act as acids or bases.
Those having a single amino group and a single carboxyl group crystallize from neutral aqueous solutions as fully ionized species known as zwitterions (German for "hybrid ions"), each having both a positive and a negative charge.

32. Zwitterionic structure is neutral and its value of pH is called isoelectric point.

33. Amino Acids Can Act as Acids and as Bases.
3) Amphoteric nature:
Amino Acids Can Act as Acids and as Bases.
When a crystalline amino acid, such as alanine, is dissolved in water, it exists in solution as the dipolar ion, or zwitterion, which can act either as an acid (proton donor), or as a base (proton acceptor)

34. majority of amino acids has amphoteric character – functional group –COOH is the reason of acidity and –NH2 group causes basic properties.
in basic environment AA dissociate proton to form carboxyl anion –COO-. Basic surround defends –NH2 against dissociation.

35. in basic environment AA dissociate proton to form carboxyl anion –COO-
in basic environment AA dissociate proton to form carboxyl anion –COO-. Basic surround defends –NH2 against dissociation.
in acidic environment AA accept proton to form amonium cation –NH3+. Acidic environment defends –COOH against dissociation.

37. Physical propeties – AA are colourless crystalline substances soluble in water and insoluble in organic solvents with high melting point.
Arginine
Valine
Alanine
Lysine

38. Reactions of amino acids

39. Polymerization – form peptides, proteins and enzymes
A condensation reaction between the carboxyl of one amino acid and the amino group of another forms a peptide bond.
Peptides
Oligopeptides − condensation of 2 – 10 AA units
Polypeptides − condensation of 11 – 100 AA units
Proteins − more than 100 AA units

40. Disulfide linkage – conversion of cysteine to cystine is like a conversion of thiols to disulfides by mild oxidizing agents. This conversion can be reversed by mild reducing agents.
Disulfide bonds stabilize protein structure by providing cross-link.

41. e.g. two polypeptide chains of insuline
Reversible formation of disulfide bond by the oxidation of two molecules of cysteine
e.g. two polypeptide chains of insuline

42. Peptides

43. The Peptide Bond Amino acids can be linked together by covalent bonds
The bonds are formed between the -carboxyl group of one amino acid and the -amino group of the next one
Water is removed in the process and the linked amino residues remain attached to one another

44. This bond is called a peptide bond and peptides are formed
When hundreds of amino acids are joined in this process, a polypeptide is formed
The compound formed may also be referred to as an amide
The bond formed between the carbon and nitrogen is a single bond

45. The Peptide Bond
Pentapeptide
hydrolysis
condensation
Serylglyciltyrosylalanylleucine or
Ser-Gly-Tyr-Ala-Leu
SGYAL
Two amino acid molecules can be covalently joined through a substituted amide linkage, termed a peptide bond, to yield a dipeptide
Peptides are named beginning with the amino-terminal
residue, which by convention is placed at the left.
just a few residues  oligopeptide
many residues  polypeptide

46. Some Small Peptides of Physiological Interest
Simplest combination of amino acids are dipeptides in which two amino acids are linked together
An example is the dipeptide carnosine which is found in muscle tissue
The compound is also known as -alanyl-L-histidine
The peptide bond is formed between the carboxyl group of the -alanine and the amino group of histidine
Aspartame is another dipeptide which has health implications
Glutathione a tripeptide is a scavenger for oxidizing agents

47. Glutathione is -glutamyl-L-cystenylglycine
Two pentapeptides found in the brain are enkaphalins which are natural analgesics
Tyr-Gly-Gly-Phe-Leu (leucine enkaphalin)
Tyr-Gly-Gly-Phe-Met (Methionine enkaphalin)
Opiates bind to the same receptors in the brain intended for the enkaphalins and hence produce their physiological activities
Oxytocin and vasopressin have cyclic structures
Each has 9 amino acid residues and an amide group at the C-terminal and disulfide bonds at positions 1 and 6

48. There are several levels of protein structure
Multisubunit proteins
Arrangement is space of
polypeptide subunits
Particularly stable arrangements of
amino acid residues giving rise to
recurring structural paterns
All aspects of the 3-D folding
of a polypeptide
Includes disulfide bonds

50. ~ 300 additional amino acids have been found in cells
Uncommon amino acids also have important functions 1 2 3 4 5 a b g
plant cell wall,
collagen
myosin
prothrombim,
a # of Ca+ binding proteins
elastin
Lysine
residues
Residues created by modification of common residues already incorporated into a polypeptide
rare, introduced during protein
synthesis rather than created
through a postsynthetic modification
~ 300 additional amino acids
have been found in cells

51. Reversible amino acid modifications involved in regulation of protein activity

52. Examples of Clinical Aminoacidurias
Metabolic defects: Phenylketonuria (Phe), Tyrosinemias (Phe,Tyr), Maple Syrup Urine Disease (Leu, Val, Ile), Alcaptonuria (Tyr)
Absorption/transport defects: cystinuria (Cys), Hartnup disease , Fanconi’s Syndrome
These diseases are generally diagnosed from indicators in the urine or plasma.