I am not in possession of my mothers birth certificate. Will this affect my application for portuguese nationality. I have all my fathers documents who was born in funchal.

Yes, you will need your mother's birth certificate to apply.

If your mother was a Portuguese citizen you can obtain a copy of her birth certificate through Portal do Cidadão (Portuguese Citizen's Portal) .

You must sign up to use their website (the only section that is in English) and know what concelho (municipality/district) and freguesia (subdivision of concelho) she was born in. If you know where she was born but don't know the concelho and freguesia that would be in, it can be found by looking at these terms in Wikipedia. I do not understand Portuguese but didn't have any problem using an online translator and a credit card. In Feb. of this year it took 3 weeks and cost €17 (aka $22).

Best of luck to you.

Portal do Cidadão registration page in English:
https://www.portaldocidadao.pt/portal/templates/areautilizadores/ajuda/en/registo.html

Page in Portuguese to request the birth certificate after you register:
https://www.portaldocidadao.pt/PORTAL/pt/certidoes_online/HP?JS=true