Do Catholics believe everything in the bible is true as written? I thought I remember at some point learning that Catholics believed everything that was mentioned int he bible actually happened. Things like Noah actually having 2 of every animal on one ark, Jonah living inside of a whale, etc. 

Is this true? Are there groups that believe things in the bible happened as written?
OP asks: 


  Do Catholics believe everything in the bible is true as written?


&lt;meme&gt;You keep using that word, "true". It does not mean what you think it means.&lt;/meme&gt;

The short answer is "Yes, and not quite", if by "true" is intended a flatly literalistic understanding of everything written in the Bible. (On the problem of "literalism", not restricted to Catholic interpretation of Scripture, see James Barr, "Literality", Faith and Philosophy 6(4) (1989): 412-428.)

Dei Verbum

A good way to get a handle on Catholic understanding of Scripture is to read the document from the Second Vatican Council (which met throughout 1962-1965) entitled Dei Verbum (which also has a helpful article on Wikipedia). That document both affirms that


  the books of Scripture must be acknowledged as teaching solidly, faithfully and without error that truth which God wanted put into sacred writings for the sake of salvation (Ch. III ¶ 11).


It also immediately goes on to acknowledge that 


  since God speaks in Sacred Scripture through men in human fashion, the interpreter of Sacred Scripture, in order to see clearly what God wanted to communicate to us, should carefully investigate what meaning the sacred writers really intended, and what God wanted to manifest by means of their words" (Ch. III ¶ 12). 


[Emphasis added by me.] In practice, then, one needs to consult approved teachers of the church to know in any particular case whether such-and-such a case is to be taken as literally true. (And the church has a teaching office in this regard: "It devolves on sacred bishops 'who have the apostolic teaching' to give the faithful entrusted to them suitable instruction in the right use of the divine books, especially the New Testament and above all the Gospels" [Dei Verbum, Ch. VI ¶ 25].)

Examples

OP gives two examples: "...Noah actually having 2 of every animal on one ark, Jonah living inside of a whale...". Between them, they suggest the scope of possibilities open to Catholic "belief" about the Bible, as displayed by the Jerome Biblical Commentary, published in the wake of Vatican II, and having the nihil obstat (explanation) and imprimatur  (also explained):


Noah - The article on Genesis describes its stories as "history", but in a heavily qualified way, since this "history" has a divine origin, purpose, and unity:


  Because it is supernatural, the purpose is beyond the effective control of modern scientific history. Therefore, the ultimate meaning of Genesis, like that of the other books of the Bible, will always elude the historian who works outside its religious postulates. (p. 8)


Meanwhile, the events of the "primitive history" (Genesis 1-11) are "facts", "events of a cosmic order that affected universal man", so that the "first 11 chapters of Genesis present truths based on historical facts" (p. 8). In practice, for the flood story, the composite nature of the biblical account -- made up of material from "J" and "P" -- is a given, and the source of the story found in Mesopotamian flood accounts, with parallels noted and discussed: "The non-biblical versions reflect pagan mythology... In the biblical story, the one God, supreme lord of the situation, decrees the flood because of man's sin" (p. 15). The "cosmic" nature of the whole story is repeatedly stressed.

There is no special consideration given as to the pairs of animals (6:20; nor the tension with there also being "seven pairs" instructed in 7:2-3).
Jonah - is taken to be a product of the period 400-200 BC (p. 633; and roughly Hellenistic, then), and asserts


  Although scholars differ as to the term that should be used in determining the literary form of Jonah, they would agree that the book is not to be classified as history. ... Jonah is to be classified as a didactic narrative, satirical in tone with a profound theological purpose. (p. 634)



Conclusion

Hopefully this makes clear how it is that Catholic teaching affirms that the Bible is true, but that at the same time, this is not to be understood in terms of taking all its statements "literally".