Re: what controls what flows in and out of the nucleus?

The nucleus is surrounded by a membrane which serves to keep some molecules in (like proteins that interact with DNA) and some moleucules out (proteins that are required elsewhere in the cell). Other molecules have to be both inside the nucleus and outside the nucleus. Messenger RNA (mRNA) for instance, gets made inside the nucleus and then leaves the nucleus for use by ribosomes. In order to let certain molecules out and to keep other molecules in, the nucleus is studded with holes (called pores) which are filled with a large protein complex called the nuclear pore complex (NPC). NPCs are therefore the sole site of flow into and out of the nucleus. Being such a large structure, the NPCs create plugs or barriers. But, given their structure (see image of a single NPC-in color, embedded in the membrane of the nucleus-the "U" shapes at either side of the NPC), some small molecules can sneak through. These would be ions (like calcium) and small proteins (less than 40 kiloDaltons). Larger molecules must make their way through the central channel of the NPC. To do so, these larger molecules must contain within their sequence particular stretches of amino acids (these are called NLSs for nuclear localization sequences or NESs for nuclear export sequences). NLSs and NESs are recognized by import or export receptors (proteins which recognize the amino acid sequences of other proteins), depending on which way (in or out) the transport is happening. It's not totally clear how these receptors allow large molecules to go through the central NPC channel but it probably has to do with causing a change in the NPC which makes the channel bigger, say by removal of the central plug (shown in red). There are also other proteins (called transport factors) which use energy (ATP/GTP) to help the receptors to dock proteins and RNAs at the NPC and then to translocate them through.