install markdown (which is a perl script) from here: http://daringfireball.net/projects/markdown/
(Alternately you can use homebrew (Link) to install markdown, or one of the many enhanced markdown utilities)
Then once you have your markdown text file (say it's
text.md) you can simply run:
$ perl *pathto*/markdown.pl text.md > text.html in the terminal
then open the resulting text.html in Safari (or any other web browser) and Print to PDF.
If you are extensively converting markdown to pdf you can simplify this by using pandoc: http://johnmacfarlane.net/pandoc/
Better yet, there are a number of text editors designed specifically for Markdown that seem to do the job for you. (Though you may want to check for pdf export... for example iA Writer only exports to RTF or HTML... the conversion of one of those to PDF is trivial, but it's an extra step).
Many general purpose text editors (TextMate, BBEdit) can be used well for Markdown. (For example in the latest TextMate 2 Beta you can select Preview from the Markdown bundle and then export the formatted document to PDF from the Print dialog.)
.mdsuffix is just a convention, there is no difference to