Protein design (Max)

Question 1

Why is directed evolution better than normal?

Answer 1

create new proteins quicker by mutation

Question 2

why is PS ineffective

Answer 2

5% of light converted to glucose
as temperature increase RUBISCO fix O2

Question 3

how can PS be improved

Answer 3

increase light range absorption of chlorophyll
engineer rubsico

Question 4

outline direct evolution cycle

Answer 4

• Random mutageni PCR produce seq library
• library express in e.coli
  -activity assay to find the fittest varient

Question 5

what is gene shuffling?

Answer 5

digets target gene with DNase to get fragmented DNA
PCR w/out primer to anneal and extend frag
PCR w/ fragment to produce shuffled genes

Question 6

how has directed evolution with RUBSICO took place

Answer 6

random mutagenic PCR produces seq library
express in ecoli
activity assay to find fittest varient

Question 7

what are the 2 types of mutations

Answer 7

synonymous: change 1 base not change amino acid seq
non synonymous: change 1 base, change amino acid seq

Question 8

dN/ dS ratios

Answer 8

> 1 advantageous, +’ve selection
=1neutral
<1disadvantageous, -“ve selection

Question 9

why does RUBISCO differ between plants?

Answer 9

global distribution
climate plants in

Question 10

how can machine learning apply to RUBISCO

Answer 10

Alphafold- predict structure
models- predict kinetics a snot much known about varying RUBISOC kinetics.

Question 11

alpha fold +/-‘ve

Answer 11

+ Accurate
+ handle missing physical context
- miss non-protein elements
- miss protein interactions

Question 12

diff between red and green RUBSICO

Answer 12

Convergent evolution: same structure/ function but different genetic info

Question 13

How does oxygenation take place?

Answer 13

RUBISCO fix O2, not CO2. Produces 2 phosphoglycolate
2PG not regen RUBP needed for calvin cycle - inefficient.
2PG need convert to 3PGA but needs ATP.
3PGA regen RUBP.