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If there is some ongoing investigation into some matter involving the president, the Attorney General heads the Justice department and therefore would be involved in running the investigation.
However, the president can just fire the Attorney General at will, so isn't there a conflict of interest there? How can the Attorney General be expected to investigate a matter with the knowledge that a certain matter know risk getting himself fired?
Ultimately, the legal check on the President is not the Department of Justice, nor the FBI etc., as these are all arms of the Executive Branch, and so are ultimately under the President's control. The constitutional and legal check on the President is Congress itself. Congress has the power to impeach and investigate the president, and remove him from office.
This is why some people are so adamant about creating a Special Prosecutor: one who is not subject to the President's whims and cannot simply be fired or otherwise intimidated by such, nor is subject to partisan and party-line politics that might influence the Congressional chambers. It's also why the House and Senate investigations are under such intense scrutiny, with any perceived procedural oddities leading to intense and sometimes broadly bipartisan criticism. With continued refusal from Congress to appoint an independent investigation, Congress is the closest thing we've got to an investigative team that can't be intimidated or obstructed by the President (assuming, of course, that he attempts to do so, or already has).
The aforementioned party-line politics makes this questionable, to both sides of the political fence: Republicans seem prone to think the Democrats are on a witch-hunt, while Democrats seem prone to think the Republicans are engaging in a cover-up.
Some reasons:
Damage: the AG, and most top level officials, are usually people with an extensive résumé, well-qualified and with experience and contacts in the upper echelons of the administration and the political parties. So, many of them are highly sought for important jobs1 (from executives to lobbyists, and even as conference speakers).
The AG being fired does not (usually) mean that he will be without a job/unable to house and feed the family. For example, McNamara recounted that when he was offered the post of Secretary of Defense, he had to discus it with his family because it meant a significantly reduction of income.
Prestige: As the above states, AGs and the like have their own personal prestige. As top public officers their actions are widely reported, so if they do not do the right thing their personal prestige will suffer from it. And that prestige is what will help the official to get one of those high level jobs stated above.
Additionally, that combines nicely with Maslow's hierarchy of needs; the job opportunities for a dismissed top official means that they are less worried about the lower levels of the pyramid (basically, getting money to get food, shelter and a minimum of comfort) and more with the upper levels (public recognition).
Mutual Assured Destruction: As the Comey case shows, firing one of such top level officials can be very damaging to the president him/herself, unless the action is beyond all doubt2. Of course, the President being under investigation by such official makes it near impossible to claim that the President action had no hidden motives.
Of course all of that does not mean that, just for being AG, an individual will be immune from pressure (from the President or other parties); those are just reasons to make a point that a proper AG has motives not to bend to those pressures. Chose a spineless person and none of the above will prevent that s/he becomes a pawn of whoever is a President.
And also, despite all of the above, no sane AG or other official would make such a move as opening an investigation on the President unless they are truly convinced that there might be something to be found out. It is not the kind of thing that one should begin without enough evidence supporting it.
The information coming from the Comey's or Yates' affairs are good examples; both could have submitted to the pressures but chose not to; and the President's actions are being heavily criticized.
2 As in "the official posted in Youtube a video of himself snorting coke next to the body of a dead, underage prostitute".
