The Church has questioned the legality of the proposed law that could introduce suicide clinics to Scotland and see those as young as 16 given the right to decide to have their lives ended.
The End of Life Assistance Bill was published in the Scottish Parliament yesterday, after months of consultation.
But a spokesman for the Catholic Church in Scotland said the legislation "would cross a moral boundary that no society should ever breach".
He added: "It would completely invert and threaten the relationship between patient and doctor and undermine the role of medicine in society."
He argued the Human Rights Act would override MSPs' ability to pass the bill, raising the possibility of a legal challenge.
"Ultimately, it is questionable whether the Scottish Parliament even has the power to legislate in this area," the spokesman said. "The European Convention on Human Rights recognises the right to life as inalienable, that is, it cannot be removed by any authority or relinquished by any person."
Ms MacDonald said: "The Church may want to challenge this in the courts, but what about the abortion law? That would seem to undermine their claim."
There is anger within the Catholic hierarchy that the bill has been allowed to proceed at all.
It has received a certificate of competency from Presiding Officer Alex Fergusson – that means it has been judged by parliamentary lawyers as legal for MSPs to vote it through as legislation.
The Catholic Church spokesman described Mr Fergusson's decision as "extremely concerning".
However, Ms MacDonald said she was confident the bill was competent for MSPs to pass. She has had help in drawing it up from a support unit for members' bills within the parliament.
She said: "It's absolutely appalling that people should have to leave their homes and their families and friends and everything that's familiar to them, and end their life in a foreign country in what has to be a relatively clinical atmosphere.
"Dying is part of living, it's the last act of your life, and if we accept the responsibility of how we live our lives, then I really fail to see where there is any demarcation of how we should die.
"This bill is meant to try and redress that unfairness, to give those people the autonomy to exercise some control over how they die, to give them the legal right to seek assistance and to protect the people that give assistance."
The independent Lothians MSP dismissed criticisms that the proposed new law threatened the lives of the weakest and most vulnerable, who might come under pressure to follow the route of assisted suicide.
She pointed out safeguards in the bill, including the need for the decision to be signed off by a GP, who must have received two separate requests, and for a psychiatric report to be received. The patient would also need to have been registered with a Scottish GP for 18 months.
The law would apply only to those with severe degenerative disorders or terminal diseases, and those whose lives had become unbearable through a severe, disabling accident. It would not apply to those with dementia, or to anyone unable to make a decision for themselves.
The bill has come as a direct result of debate across the UK over whether assisted suicide should be allowed.
The campaigner Diane Pretty won a case at the High Court in London, forcing the Director of Public Prosecutions to spell out the circumstances under which he would take somebody to court for assisting suicide.
There was also the case of the Daniel James, 23, whose parents escaped prosecution after taking him to the Dignitas clinic in Switzerland after he was paralysed in a rugby accident.
Ms MacDonald has said she wants the chance to be helped to end her life should her Parkinson's disease make life unbearable.
However, she insisted the bill was "not personal".
She said she doubted whether Scotland would become the new Switzerland, but added: "If folk can get a dignified death in Scotland, then they are welcome as far as I am concerned."
She was unsure how many would choose to end their lives if the law changed, but said figures showed 50 or 60 a year made that choice in Scotland.
Sheila Duffy, from the Friends at the End campaign group, which backs the bill, said there would not be queues of people wanting help to die.
She said experience in Switzerland, the Netherlands and the US state of Oregon, where assisted suicide is legal, showed this was not the case.
Doubts have been raised over public support for assisted suicide, which supporters say is moving in their direction.
But Dr Calum MacKellar, director of research at the Scottish Council on Human Bioethics, said an analysis of the figures revealed that support dropped dramatically when people were given the full facts.
At Holyrood, all parties will allow a free vote on the bill, with all ministers also able to vote with their consciences, although First Minister Alex Salmond has said he is not persuaded.
Ms McDonald said she was more confident of support and of getting the bill passed than she had been previously.
But many of the 25 MSPs who signed up to support the bill said they had done so mainly so that a debate could take place.
Many of them said they were not convinced about legalising assisted suicide, but felt that the issue should be considered in parliament.
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