User:Benjah-bmm27/degree/2/DNW
Proteins, DNW[edit]
"Amino Acids, Peptides and Proteins: Chemistry, Structure and Function"
Polyamides[edit]
- 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
Amino acids[edit]
- 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)
Proteins[edit]
- Peptide bonds
- Peptides
- Proteins
- Hormones, signaling molecules
- Peptide synthesis, Protein synthesis, Protein biosynthesis
Protein structure[edit]
- 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[edit]
- 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
More protein structure[edit]
Primary structure[edit]
- Primary structure: sequence of amino acid backbone (plus cross-linking such as disulfide bonds)
Secondary structure[edit]
- Secondary structure: alpha helices, beta strands (plus rare others)
Tertiary structure[edit]
- 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[edit]
- Quaternary structure: arrangement of multiple folded protein molecules in a multi-subunit complex - XRD again
Ramachandran plots[edit]
- UV-Vis spectroscopy can be used to determine protein concentration - aromatic amino acid side chains (K, Y, W, H) absorb UV
Supersecondary structure[edit]
- 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.
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Ribbon diagram of plastocyanin -
Residues coordinating Cu in plastocyanin -
Cu coordination geometry
