User:Benjah-bmm27/degree/2/DNW

=Proteins, DNW= "Amino Acids, Peptides and Proteins: Chemistry, Structure and Function"

Polyamides

 * Nylon (polyamides) from condensation polymerisation, e.g.
 * nH2N-(CH2)6-NH2 + nClOC-(CH2)4-COCl → (-HN-(CH2)6-NH-CO-(CH2)4-CO-)n (nylon 6,6 with amide bond in bold) + 2nHCl


 * Aramids e.g. Kevlar

Amino acids

 * Amino acids
 * All naturally-occurring amino acids have the (S) configuration, except cysteine which is (R): (because of its C-S side chain, which unlike all other side chains, has a higher priority than the CO2H group)


 * Cysteine-and-serine-stereochemistry-compared-2D-skeletal.png

Proteins

 * Peptide bonds
 * Peptides
 * Proteins
 * Hormones, signaling molecules
 * Peptide synthesis, Protein synthesis, Protein biosynthesis

Protein structure

 * Protein structure, Protein folding, Protein structure prediction, Membrane protein
 * Keratin, especially β-keratins (a kind of scleroprotein [AKA fibrous protein], thus a type of quaternary structure alongside globular proteins)
 * π-π stacking interactions
 * Ubiquitin (PDB 1UBQ ubiquitin), Proteasomes

Amino acids by polarity and structure

 * Chemical polarity of amino acids: FAMILYVW - hydrophobic, DEHKNQRST - polar, GPC - special
 * Proline (Pro, P) is special:
 * It's a secondary amino acid (AKA imino acids, although this nomenclature is disputed)
 * It's conformationally locked (backbone dihedral angle φ fixed to about −75°) → very rigid, loses less conformational entropy upon folding, found in turns

Primary structure

 * Primary structure: sequence of amino acid backbone (plus cross-linking such as disulfide bonds)

Secondary structure

 * Secondary structure: alpha helices, beta strands (plus rare others)

Tertiary structure

 * Tertiary structure: three-dimensional structure (full set of atomic coordinates in 3D space) - determined by protein crystallography or protein NMR


 * all α-structures (αα) - buffers, triggers, allostery
 * calbindin - (2 × EF hand) mops up loose Ca2+
 * myoglobin - baby brother of haemoglobin - 8 helices, haem group binds Fe and thus O2
 * all β-structures (ββ) - hard-as-nails brick walls → rigidity
 * viral capsids
 * plastocyanin
 * antibodies

Quaternary structure

 * Quaternary structure: arrangement of multiple folded protein molecules in a multi-subunit complex - XRD again

Ramachandran plots

 * Ramachandran plot


 * UV-Vis spectroscopy can be used to determine protein concentration - aromatic amino acid side chains (K, Y, W, H) absorb UV

Supersecondary structure

 * Supersecondary structure
 * EF hand - chiral, right-handed enantiomer only (with one exception). Aspartic acid residues bind Ca2+ (important in calcium signaling) in loop between two alpha helices.
 * Beta hairpin - major structural unit, two beta strands antiparallel
 * βαβ motif - two beta strands parallel, chiral (alpha helix either above or below plane of beta strands), only right-handed enantiomer found in nature
 * Coiled coil - left-handed(!) - HPPHPPP repeat gives 3.5 not 3.6 residues per turn, so hydrophobic seam slowly curves - myosin, keratin
 * Polyproline helix?
 * Collagen helix?


 * Plastocyanins - Cu redox centre converts between Cu(I) and Cu(II), coordination geometry of Cu is not optimal for either oxidation state, making neither favoured and thus interconversion facile. Structures: PDB 3BQV, PDB 1PNC.


 * TIM barrel

Reactions

 * Strecker amino acid synthesis
 * Peptide synthesis
 * Peptide synthesis
 * Protecting groups
 * Fmoc