Bioscience: Protein Structure Function BS20001 Section 2

Books Followed: Biochemistry (Lubert Stryer) Introduction to protein structure (Carl Branden & John Tooze)

Central Dogma of life

Storage Medium

DNA
transcription

CCTGAGCCAACTATTGATGAA

mRNA

Transmission Medium

CCUGAGCCAACUAUUGAUGAA
Text composed of 3-letter words (with 4 unique letters) gets mapped into a seq of 20 unique letters

translation

Protein

PEPTIDE

What is a Protein
Proteins are polymers built up from 20 different amino-acids linked end to end by peptide bonds
CGVPAIQPVLSGLXXIVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGV TTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSA VCLPSASDDFAAGTTCVTTGWGLTRYXXANTPDRLQQASLPLLSNTNCKKYWGTKIKDAM ICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQ TLAAN*

More directly linked to function Better conserved than sequence

All amino acids in protein have the L-form

Structure of Cys ( C )

His can bind or release protons near physiological pH

Proteins are polypeptide chains

Successful polypeptide bonds: main chain or backbone

The peptide bond

(----ALA-HIS-GLY-ILE-LEU-PHE-TYR-LYSGLY---)n

Peptide units are building blocks of protein structures

The only degrees of freedom: N-C bond: phi () C -C bond: psi () rotation angle

Ramachandran Plot

G. N. Ramachandran

Glycine residues can adopt many different conformations

Properties of Gly
Glycine with only a H-atom as side chain can adopt a much wider range of conformations than the other residues It thus plays a structurally important role; it allows unusual main chain conformations proteins This is the main reasons why a high proportion of Glycine residues are conserved among homologous protein sequences