General comments

This manuscript presents the impact of updates of the chemistry of biogenic organic compounds and other ozone-related reactions in the UKCA model. At reasonable additional computational cost the chemistry-climate interactions mediated by biogenic organics via ozone and organic aerosols can now be investigated  with an up-to-date representation of tropospheric gas-phase chemistry. The manuscript is written very well. The results  and the discussion there of is very well structured and comprehensive. With the help of targeted sensitivity simulations the authors back up their explanations for the differences to the results obtained with previous chemical mechanisms used in the UKCA model. Comparison of model results with observational datasets is also very extensive. Interestingly, the model updates result in a significant higher prediction of tropospheric ozone burden exacerbating the positive bias that is typical of other models.  Hopefully this gives more stimulus to improve the representation of relevant multiphase chemistry and emissionso fo precursors in the UKCA model. 

Specific comments

p2,l54-60: certainly many other studies have investigated these impacts but only two studies from the UKCA are cited. I suggest to cite studies from other modelling communities

p2,l60: the term "chemical behavior" is borrowed from psychology and just triggers an idriosyncrasy. It is sued in other parts of the manuscript. I would not use it. 

p4,l114-116: the authors omit the models developed by  the groups that discovered and first elucidated the OH-recycling in isoprene chemistry (MAGRITTE in Müller et al., 2019; MOM in Sander et al., 2019 and Novelli et al., 2020).

p14,l499: at this point it is not very clear what isop_ox is made of  and that ISOPOOH gives the same PTR-MS signal as MVK and MACR. It would be good it this could be clearly defined.

Technical corrections

p8,l269: the verb "are" is missing

Additional references

Müller, J.-F., Stavrakou, T., and Peeters, J.: Chemistry and deposition in the Model of Atmospheric composition at Global and Regional scales using Inversion Techniques for Trace gas Emissions (MAGRITTE v1.1) – Part 1: Chemical mechanism, Geosci. Model Dev., 12, 2307–2356, https://doi.org/10.5194/gmd-12-2307-2019, 2019.

Sander, R., Baumgaertner, A., Cabrera-Perez, D., Frank, F., Gromov, S., Grooß, J.-U., Harder, H., Huijnen, V., Jöckel, P., Karydis, V. A., Niemeyer, K. E., Pozzer, A., Riede, H., Schultz, M. G., Taraborrelli, D., and Tauer, S.: The community atmospheric chemistry box model CAABA/MECCA-4.0, Geosci. Model Dev., 12, 1365–1385, https://doi.org/10.5194/gmd-12-1365-2019, 2019. 

Novelli, A., Vereecken, L., Bohn, B., Dorn, H.-P., Gkatzelis, G. I., Hofzumahaus, A., Holland, F., Reimer, D., Rohrer, F., Rosanka, S., Taraborrelli, D., Tillmann, R., Wegener, R., Yu, Z., Kiendler-Scharr, A., Wahner, A., and Fuchs, H.: Importance of isomerization reactions for OH radical regeneration from the photo-oxidation of isoprene investigated in the atmospheric simulation chamber SAPHIR, Atmos. Chem. Phys., 20, 3333–3355, https://doi.org/10.5194/acp-20-3333-2020, 2020. 

This paper presents a comprehensive description of the implementation of the CRI v2.2 tropospheric chemistry mechanism into the UKCA model, and provides detailed comparisons to earlier chemistry versions of UKCA.  UKCA is one of the leading global chemistry-climate models, a participant in CMIP6 and widely used by the community, thus it is important to publish documentation such as this.  The focus of this work is on the isoprene oxidation updates, and the impacts on the ozone and nitrogen budgets, as well as discussion of potential implications on secondary organic aerosols although the current implementation was not directly coupled to SOA.  Appropriate comparisons are made to observations for the evaluation of the chemistry schemes.  

The paper is well written, and clearly organized.  It is quite appropriate for publication in GMD. While the results are specific to the UKCA model the results will be of value to other chemistry-climate model developments and interpretation of their results and limitations.  

I recommend publication with only minor corrections as noted below.

Technical comments:

l.273: Should 'new' be 'near'?

l.346: Section S_? (number missing)

Table S3: SE4C4RS -> SEAC4RS

l.464: Should 'latitude' be 'altitude'?

l.492: Instead of 'well-known', it would be more appropriate to say 'major' or 'most significant'.  In general, the PTRMS measurements are reported as the sum of MVK+MACR+ISOPOOH.  Please clarify whether or not that is the case here.  This paragraph is not clear.

l.579: there are 2 Table S3.

Section 5.5:

Are lightning NO emissions identical in all simulations?  Figure 9a looks like it could show a difference in lightning emissions, though I do not doubt it could be explained by the chemistry difference.  It would be good to confirm that it was not caused by an inadvertent change in lightning NO.