Bioinformatics

Biological Basics

1. Amino acids I 2. Peptide bond I 3. Proteins I 4. DNA I 5. Miscellaneous

1. Amino acids

1a.) What are amino acids ?

basic structural units of proteins
consist of an amino group (-NH2, basic), a carboxyl group (-COOH, acidic), a hydrogen atom (-H), and a side chain group (residue R) bonded to a carbon atom (Cα-atom)
	20 naturally occuring amino acids, proteinogenic ones, in (L)-configuration + selenocysteine
	non-proteinogenic amino acids, i.e. ornithine or citrulline, are metabolites and not occur in proteins
	chiral molecules main carbon (Cα-atom) is asymmetrical exception: glycine (R = H)
ampholytes ionizableness of the carboxyl and/or amino group form zwitter-ions under physiological conditions two pka's ! buffer characteristics (titration curves)	group type typical pKa range1 α-COOH (carboxyl) 3.5 - 4.0 side chain -COOH of aspartic and glutamic acid 4.0 - 4.8 imidazole (histidine) 6.5 - 7.4 α-NH2 (amino) 8.0 - 9.0 cysteine (-SH) 8.5 - 9.0 phenolic (tyrosine) 9.5 - 10.5 side chain -NH2 (lysine) 9.8 - 10.4 guanidinyl (arginine) ~ 12 1 Values outside these ranges are observed, for example, -COOH side chains have been reported with pka values as high as 7.3.
differences between the amino acids are in the nature of the R group R group varies in: size hydrophobicity shape reactivity charge

1b.) Amino acids classification

• different ways of grouping amino acids together, for example, by their structure, their size, their hydrophobizity ...

Charged residues

• normally found on the surface of the protein
  • interact with water and other important biological molecules
• seldom buried in the interior of a folded protein
• important in the recognition (binding) of oppositely charged groups on molecules that interact with proteins

  positive charged	arginine, histidine, lysine
  	basic sidechains NH-groups protonated at physiological pH
  negative charged	aspartic acid, glutamic acid
  	acidic sidechains carboxyl groups (COO-) with a negative charge at physiological pH

Polar residues (hydrophilic)

• possess hydrophilic groups, like carbonyl (C=O), hydroxyl (OH) or amine (NH) groups
• both buried as well as on the protein surface
• often found in active sites of proteins
• either form hydrogen bonds with other polar residues in the protein or with water
  • for example, the OH group of serine can both donate as well as accept a hydrogen bond

Non-polar residues (hydrophobic)

• possess CH-bonds
• not favorably interact with water
• central core of most proteins is composed almost exclusively of non-polar residues, stabilized by numerous van der Waals interactions
• significant number of non-polar residues are also found on the surface of the protein



hydrophobic / non-polar side chain:	alanine, isoleucine, leucine, methionine, phenylalanine, tryptophan, valine, (glycine), (proline)
hydrophilic / weakly polar side chain:	serine, tyrosine, threonine, (cysteine), glutamine, asparagine

1c.) The 20 proteinogenic amino acids and their properties

amino acid	structure	3-letter code	1-letter-code	properties
alanine		Ala	A	aliphatic hydrophobic neutral
arginine		Arg	R	polar hydrophilic positive charged (+) strongly polar !
asparagine		Asn	N	polar hydrophilic neutral
aspartic acid (aspartate)		Asp	D	polar hydrophilic negative charged (-)
cysteine		Cys	C	polar hydrophilic neutral not very polar ! able to form a disulfide bridge (S-S) with other cysteines !
glutamine		Gln	Q	polar hydrophilic neutral
glutamic acid (glutamate)		Glu	E	polar hydrophilic negative charged (-)
glycine		Gly	G	aliphatic neutral no side chain ! smallest amino acid can adopt conformations which are sterically forbidden for other amino acids amphiphilic (exits in any surroundings)
histidine		His	H	aromatic polar hydrophilic positive charged (+) strongly polar ! imidazole ring act either as a proton donor or an acceptor at physiological pH frequently found in reactive center of enzymes
isoleucine		Ile	I	aliphatic hydrophobic neutral
leucine		Leu	L	aliphatic hydrophobic neutral
lysine		Lys	K	polar hydrophilic positive charged (+) strongly polar !
methionine		Met	M	hydrophobic neutral fairly hydrophobic !
phenylalanine		Phe	F	aromatic hydrophobic neutral highly hydrophobic !
proline		Pro	P	hydrophobic neutral cyclic only one with a secondary amine (imino acid) ! most rigid amino acid shares many properties with aliphatic amino acids can disrupt protein folding structures (α-helix or β-sheet)
serine		Ser	S	polar hydrophilic neutral OH group can act as a nucleophile during enzymatic catalysis
threonine		Thr	T	polar hydrophilic neutral OH group can act as a nucleophile during enzymatic catalysis
tryptophan		Trp	W	aromatic hydrophobic neutral little less hydrophobic than phenylalanine !
tyrosine		Tyr	Y	aromatic polar hydrophobic very weakly acidic !
valine		Val	V	aliphatic hydrophobic neutral
additional codes
any amino acid			X
asparagine / aspartic acid		Asn / Asp	B	polar hydrophilic neutral / negative charged (-)
glutamine / glutamic acid		Gln / Glu	Z	polar hydrophilic neutral / negative charged (-)

important characteristics for protein structure


charge	formation of salt bridges or ion pairs, total charge of the protein
polarity	formation of hydrogen bonds (in the chain or with the solvens)
hydrophobicity	hydrophobic amino acids stabilze the protein core (protein folding)
aromaticity	π-π stacking and interaction with amide or amino groups
size	important for the packing within the protein, complementarity of the van der Waals surfaces

1d.) Essential amino acids

• 8 amino acids are essential for humans, that means, they must take up in adequate amounts with the food
  • phenylalanine, threonine, tryptophan, valine, isoleucine, leucine, lysine, methionine
    • infants additionally histidine !
• can't be synthesized form other precursors

1e.) Additional information

More information and some nice pictures of amino acids you wil find under the following links:

• LIFE - The Science of Biology (7th edition) (by W.K. Purves, D. Sadava, G.H. Orians, H. Craig Heller)

• L-Amino Acid Structures part of The Online Macromolecular Museum
• Side-by-Side Images of Amino Acids (by W. McClure, Carnegie Mellon University)
• Structure of Amino Acids (University of Leicester)
• The Amino Acid Collection (by M.W. Davidson, Florida State University)
• The Amino Acid Repository-Site on the Jena Library of Biological Macromolecules - Website

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