Bioinformatics

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Biological Basics

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

3. Proteins

macromolecules / polymers
'workhorses of the cell'
made up of various L-amino acids connected by peptide bonds
linear chains (unbranched)
- protein molecule that consists of a single polypeptide chain is said to be monomeric
- proteins made up of more than one polypeptide chain are called oligomeric
interact with other proteins, nucleic acids, small molecules, ions, etc.

Bonds

Classification

Denaturation

Purification

Structure

Quantitation

Protein Bonds

folded protein structure
- stabilized by a variety of chemical interaction
- in some cases stabilized by covalent (disulfide) bonds between cysteine residues

several types of bonds involved in the formation of spatial configurations

peptide bonds

backbone of the molecule

hydrogen bonds

attraction between H-atoms

amino acids side chains capable of forming hydrogen bonds will typically found on the surface of proteins (may interact with water)

although the energy of the hydrogen bond is fairly weak when compared to covalent interactions, they are numerous, and together contribute a significant amount of energy and stability to protein conformation

covalent disulfide bonds

SH-group of two cysteine side chains react to form a covalent bond between the two sulfur atoms (formation of a disulfide bridge -S-S-)

electrostatic interactions between ionized groups

attraction of opposite charges

charged groups are normally found on the exterior of the protein

strength of interaction depends on the concentration of dissolved salts (dielectric)

hydrophobic bonding

hydrophobic interactions

amino acids with hydrophobic side chains are almost exclusively located in the protein interior

van der Waals interactions

intermolecular forces between non-polar molecules

contribute significantly to conformational stability in the interior of the protein

Additional information

LIFE - The Science of Biology (7th edition) (by W.K. Purves, D. Sadava, G.H. Orians, H. Craig Heller)
Cozzone, A.J.; Encyclopedia of Life Sciences 2002, 1-10. Proteins: fundamental chemical properties. [PDF]

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several types of bonds involved in the formation of spatial configurations
peptide bonds	backbone of the molecule
hydrogen bonds	attraction between H-atoms amino acids side chains capable of forming hydrogen bonds will typically found on the surface of proteins (may interact with water) although the energy of the hydrogen bond is fairly weak when compared to covalent interactions, they are numerous, and together contribute a significant amount of energy and stability to protein conformation
covalent disulfide bonds	SH-group of two cysteine side chains react to form a covalent bond between the two sulfur atoms (formation of a disulfide bridge -S-S-)
electrostatic interactions between ionized groups	attraction of opposite charges charged groups are normally found on the exterior of the protein strength of interaction depends on the concentration of dissolved salts (dielectric)
hydrophobic bonding	hydrophobic interactions amino acids with hydrophobic side chains are almost exclusively located in the protein interior
van der Waals interactions	intermolecular forces between non-polar molecules contribute significantly to conformational stability in the interior of the protein