The talk in the US is of constitutional crisis. It’s been looming for a while, thanks to the Mueller investigation into suspected collusion between the Trump campaign and Kremlin efforts to swing the 2016 election. At some point – perhaps when special counsel Robert Mueller issues a subpoena, demanding Donald Trump answers his questions – a clash was bound to come. But it may already be upon us.

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That’s because of a move Trump made within hours of seeing his party take a beating in the midterm elections, losing the House of Representatives as Democrats notched up what should be, once the final tally is in, their biggest gains since the post-Watergate landslide of 1974. The president fired his attorney-general and replaced him with a reliable partisan named Matt Whitaker, who has loyally echoed Trump’s denunciations of Mueller’s probe as a “witch-hunt”. It is this man who is now charged with fairly and impartially supervising the Mueller investigation. He will have access to all Mueller’s findings, which he could pass on to Trump, and has the power to block Mueller any way he likes, including by starving him of funds.

Condemnation for the move has been swift, including by a pair of constitutional lawyers who wrote a New York Times op-ed denouncing it as “illegal” on the grounds that Whitaker had not gone through a Senate confirmation process for a senior role in the justice department. “Constitutionally, Matthew Whitaker is a nobody,” they wrote. To add extra piquancy, one of the authors is George Conway, husband of Kellyanne, the Trump adviser whose gift to the world was “alternative facts”.

Such dissent is encouraging. But there’s a problem. For who has the power to make the crucial decisions on all this, either by confirming Whitaker in his post or by passing a law to to protect Mueller, including from being fired? The answer is the US Senate. And on Tuesday, Republicans retained their grip on that body.

Similarly, what if the Mueller-Trump standoff ends up in court and ultimately the supreme court, as the great Watergate battles did 44 years ago? That body is also safely in the hands of Republican appointees, its conservative majority boosted by the recent arrival of Trump favourite Brett Kavanaugh. There is no easy consolation that a neutral referee stands ready to blow the whistle: there is no such person.

This situation points to the true constitutional crisis that afflicts the United States. The fact that Trump is president and the fact that the Senate and supreme court are, if not in his hands, then at least likely to back him, are not the cause of this crisis – they are symptoms of it.

Now, this may get technical but stick with it. Because what can seem mechanical and nerdy is shaping the most powerful country in the world - and affecting all of us in the process. The problem, stated simply, is a democratic deficit. Its most overt expression is Trump himself. In 2016 he won nearly 3m fewer votes than Hillary Clinton, yet he is in the White House and she is not. That was not a freak event. Four elections earlier, George W Bush won fewer votes than Al Gore, yet it was he who got to call himself Mr President. That’s because of America’s electoral college system, which awards the presidency to the winner of the right combination of states rather than the popular vote. That mechanism gives disproportionate power to smaller, rural states, which – as we saw again on Tuesday – are almost unvaryingly conservative.

The same is truer still of the Senate, in which a nearly empty, rural state such as Wyoming – population 580,000 – has the same representation as California, home to 39 million people. Both get two seats. Which is how Democrats could win 11m more votes than Republicans in Tuesday’s Senate contests yet Republicans still come out ahead. That matters. It means a majority of Americans could oppose Kavanaugh, but he still had enough Senate votes to be elevated to the top court. And, in a month that has seen more horrific mass shootings, it’s worth recalling that the Republican-held Senate has regularly voted down even the mildest gun control measures. Compulsory background checks are favoured by 94% of Americans, but in 2013 the Senate rejected them 54 to 46.

Defenders of the Senate say this is the price of a federal system, which must accord equal status to its constituent parts. They suggest it cannot be changed because it’s part of the near-sacred settlement devised by the US’s founders. But those men could see the dangers from the start. Alexander Hamilton, no less, was a fierce opponent of granting two senators to each state, regardless of population, accurately prophesying that “it may happen that this majority of States is a small minority of the people of America”.

If Hamilton was offended by the imbalances back then, how much more appalled would he be now. In 1790 the most populous state, Virginia, was a mere 20 times larger than the least, Tennessee. Today, the equivalent ratio – Californians to Wyomingites – is 67 to 1. Besides, the Founding Fathers deliberately set out to make the Senate undemocratic, if not anti-democratic: it was meant as a “cooling saucer”, drawing the heat of the popular mood. Few would want to offer that defence now.

Still, realistically, small states are not going to vote for a change that would diminish their influence. So democrats – and Democrats – may need to look beyond the Senate for remedy. There has rightly been a focus on combating voter suppression and gerrymandering in House contests. But other reforms are worth exploring, and would entail no great rewriting of the constitution. They relate to the electoral college.

There are a range of options. States could allocate their electoral college votes not on today’s winner-takes-all basis, but in proportion to the popular vote in that state. So Trump would have got some of, say, Wisconsin’s electoral college votes in 2016 but not all of them – and not enough to win an election in which he got fewer actual votes than his opponent. Others suggest increasing the number of seats in the House to reflect the increase in US population since the chamber was last expanded a century ago. That would boost the more populous states and give them greater weight in the electoral college.

There are a variety of moves Americans could make, but they need to move. A system that repeatedly gives power to the losing side – favouring the white, rural minority over the expanding and diverse majority – will soon lose legitimacy in the eyes of its citizens. That is America’s true constitutional crisis.

• Jonathan Freedland is a Guardian columnist