mechanisms and the stuff i'm shit at

Question 1

draw the michael reaction mechanism with conditions

Answer 1

see notes

Question 2

draw the oxazolone formation mechanism with condition

Answer 2

see notes

Question 3

draw the imine formation reaction

Answer 3

see notes

Question 4

draw the maleimide coupling reaction mechanism

Answer 4

see notes

Question 5

draw decoupling of maleimide

Answer 5

see notes

Question 6

draw a coupling mechanism with DCC

Answer 6

see notes

Question 7

Draw Fmoc

Answer 7

see notes

Question 8

Draw Boc

Answer 8

see motes

Question 9

draw the reaction to form a dipeptide via DiPEA and HATU

Answer 9

see notes

Question 10

draw the process of protection via methyl ester

Answer 10

see notes

Question 11

how does the actual Xray part of crystallography work for proteins

Answer 11

-scattering arises from individual atoms
-crytal introduces gaps into the pattern as convolution of object and lattice cause diffraction
-pattern phase is identical to scattering pattern
-can have discrete spots as planes must have correct interplane distance .
-> as correct distance in plane is required some xrays have to move extra distance (explained by Braggs law) causing spots from the reflection of braggs planes

Question 12

how to interpret x-ray crystal structures

Answer 12

A number of different poses of the target can be observed.
Many classes have clear symmetry and this may indicate a dimer.
Particularly dense cofactors show up as dots.
Secondary structure is visible typically
Some of the classes are better resolved than others, this may indicate underlying
heterogeneity or different population sizes.

Question 13

what is differential scanning fluorimetry and how is it used

Answer 13

its a technique used to determine protein stability
-> it works well with tryptophan as it reacts differently depending if its in hydrophobic or hydrophilic conditions
cross over is melting point
measure change as a subject of temperature using DSF

can be used experimentally to:
-> check for the presence of folding
-> the impact of mutation to determine stability can work out which regions are important for stability

Question 14

Describe how the Fourier Shell Correlation (FSC) is used to assess the resolution of maps.

Answer 14

The data are split into half-sets ,
and their correlation in the Fourier domain calculated.
The reported resolution is where the correlation drops below a certain point

Question 15

what features are observable at different resolutions?

Answer 15

10-20A - outline of protein structure
5-6A - separate alpha helices
3-4A - separate b sheets
2-3A - clear sidechains
0.5-1A - atoms are visible

Question 16

how to know whether something is a good resolution from a diffration pattern

Answer 16

Reflections at high θ angles (2A) from very finely-spaced planes contain high-resolution information
low res shows up (16A)
big blobs are likely salt crystals NOT protein contaminants

Question 17

Explain how you could use NMR spectroscopy to validate an AlphaFold2 model suggesting folding via an inflexible and unstructured linker

Answer 17

Would need to produce a 13C,15N-labelled sample and assign backbone nuclei of polypeptide spectrum.
Low chemical shift dispersion of amide proton nuclei would confirm the linker region is unfolded.
Flexibility could be determined using 15N relaxation measurements or through linewidth analysis .
The dispersion of chemical shifts of amide proton nuclei for domain C would indicate that the domain is folded.

Question 18

mechanism for oxazolone formation into undesired stereoisomer

Answer 18

see notes

Question 19

mechanism for oxazolone formation into desire stereoisomer

Answer 19

see notes