Imines (Schiff bases) look kind of like carbonyls. Except instead of O, there is N. and attached to N is a
methyl group. Once again, acid catalyzed.
Process: amine attacks the carbonyl carbon. Carbonyl O becomes O-. N+ formed and O- takes proton
Carbonyl is electrophilic. i.e. the carbon has a partial positive charge. Bcs inductive fx. And also there is a
resonance form with O- and C+. Rmb you can attack this carbon from two sides.
Electrophilicity (reactivity) of aldehydes vs ketones. Aldeh
20.3. How to make aldehydes/ketones
Primary alcohol = PCC, secondary alcohol = na2cr2o7 + h2so4 +h20 oxidizes. only goes to aldehyde,
ketone, respectively. Stops before cx. Acid.
O3 (Ozone)/DMS cut through the double bond (alkene), put oxygen
Secondary structure = doesnt care about conformation of side chains. If it didthen what?
Tertiary struct does care about conformation of side chain (everything)
Peptide bond = 40% double bond character
Trans = neighbouring a-Carbons on oppos
Collagen fibrils appear banded
Most abundant types of collagen? 3 types, for different function
1 skin bone tendon blood
3 blood vessels
Four different arrangements for different functions
Tendon = parallel bundles
Skin sheets of fibrils. I
Silk fibroin = b-sheet structure. i.e. silk and cocoons
Antiparallel b sheets parallel to fiber axis, stacked
Contain domains of 6 residue repeats (gly-ser-gly-ala-gly-ala). i.e. small a.a. only, how does this matter,
Allows for max
B-Bends include B turns and reverse turns?
Non rep structure. Usually involves 4 a.a. sharp turn in pp chain. Pic only shows 3. Type 1 vs 2do I need
If C=O is I, HN is i+3. H bond. What?
Gly and Pro very common in B-turns. Gly is flexible and
Sheets represented by thick arrows. Arrows show parallel/antiparallel
Right-handed twist to minimize steric interaction btn residue. What?
2-15 strands/sheet (average = 6)
Bovine carboxypeptidase A
Right handed twist. Cant see it.
Mixture of 8 strands
Mostly L-amino acids; bacteria cell wall has D-aa.
Average polypeptide has 50-9000 amino acids. Avg amino acid has molc wt of 110 Da.
Since average pp has 5500 residues, about 1 mil daltons
Protein can be more than 1 pp
Pp can be joined by n
Amide bond = 120 degrees around C=O carbon, sp2
R group = trans conf more stable
Limited rotation around N-C alpha and C- C alpha bonds bcs steric interference
Ramachandran diagram = shows allowed NC and CC bond rotations of pp. CCalpha = psi, fork, N
Anions anode (+ terminal)
Cations cathode (- terminal)
Uses electric field
Direction and rate depends: net charge > size (prop to M^(-1/3), sticking (adsorption) btn amino acid
Ninhydrin. Upper limit = 3 E-4 M. what?
Protein Separation and Purification
Size-exclusion (gel-filtration) chromatography
Column/matrix = porous bead, channels of well defined size
Beads can be made from various materials, and various exclusion limits (channel size)
Larger proteins pass
Separation of A.A.
Nature AND strength of sticking btn a.a. and resin important to sep
a.a. interact with fn groups of resin
ionic strength AND pH can be manipulated to release (elute) a.a.
importance: charge>size or polarity
e.g. cation xchang