"How long is now," the giant mural on the side of the Kunsthaus Tacheles in Berlin's Mitte district asks. The answer, it appears, is not very long at all. The former department store, turned prison and then squat and alternative culture centre, appears to be on the verge of shutting down.

"We are expecting to be closed any day," says Yvonne Hildebrandt, a jewellery designer in a studio named Kalerie. After years of legal appeals, she admits, the occupants of the colourful graffiti-covered Tacheles in what was once the Jewish quarter of Berlin have finally run out of road.

When its occupants have been pushed out and the building pulled down, another Berlin landmark of the post-Wall era will have gone. All that will be left behind on Oranienburger Strasse, once at the heart of East Berlin's counter-cultural scene, will be the C/O photography gallery, a block down from Tacheles. And its days are also numbered.

Tacheles and C/O may be the highest-profile symbols of the battle to define the shape of the new Berlin, but they are not the only ones, nor are they the most important.

It is the urban poor who have suffered most from the gentrification of the old neighbourhoods in the city's east, and their resistance to the changes has been anything but passive.

Instead, wealthy newcomers to districts like the now fashionable Prenzlauer Berg have been treated to an often weekly ritual of car torching, a practice that peaked a year ago. Police and criminology experts have yet to identify the culprits, alternately settling on members of the radical "autonomous" movement or largely non-ideological young people simply angered by the visibility of the new wealth in once poor districts.

Whoever they are, they are not without a mouthpiece. The struggle to save something of the old Berlin entered a new phase shortly before Christmas with the threat in Interim, a small radical magazine, to target the tourists whom it blames, among others, for the city's yuppification. Berlin's police are taking the threat seriously.

A stroll down Prenzlauer Berg's Greifswalder Strasse towards Alexanderplatz and the central Mitte district reveals the pace of renovation: old blocks of flats being turned into colourfully painted New York-style lofts above organic food markets.

As buildings have been transformed, rents have been pushed up, driving a double urban exodus. Former residents, many on benefits, who had once lived on cheap rent-controlled agreements, have been driven out to the periphery, including the prefab estates of Spandau and Marzahn. At the same time artists and other "creatives", who had been attracted to Berlin by low-cost housing, have also been pushed out.

In Kalerie, with two dogs lying at her feet, Hildebrandt describes her own problems. "I've been here in Tacheles for 20 years," she says. "I used to live across the road, but the rents went up and it became a monoculture." When I ask what she means she describes the influx of wealthy young couples pushing buggies.

Yvonne was displaced to Kreuzberg, where she found a cheap flat in an 18th-century building. But now wealthy speculators have their eye on that home, too.

It is a typical tale, but others are worse. People who have long lived in the east recount being put under pressure from unscrupulous landlords who, looking to cash in on rising prices, have let their flats to other people while the original tenants are away travelling. Others have been offered money to leave low-rent contracts so that landlords can refurbish and push up rental prices.

The advent of the Schickimicki – the wealthy in-crowd – in the formerly run-down and edgy areas of East Berlin has not only been resisted but mocked. In 2009 they were satirised in a comic song translated loosely as Hey, You Beautiful Hipster, which portrayed them as gauche and phony interlopers.

With elections due in the city in the autumn, it is no longer a matter for laughter. Instead, the issue of the city's gentrification has entered the political debate as a serious issue, with both the Greens and Social Democrats offering proposals to blunt the edge of Berlin's yuppification.

Johannes Novy, one of the authors of Searching for the Just City, a book on urban planning, believes that gentrification in Berlin has come as a shock to those who are horrified by the prospect of it becoming "a more ordinary city".

"For many years people saw Berlin [which in the 1990s had 100,000 empty flats] as a place with opportunities and enough space to move to," he says. "When Mitte was gentrified people there felt they could move on. I think what has happened is that people no longer feel there is that space.

"That is what has turned it into a political issue. And it is touching on a different milieu. People such as teachers and those in the creative industries who are not on big salaries have become articulate about the threat."

It is this, Novy believes, that inspired the substantial demonstrations against the proposed massive riverside MediaSpree media development in central Berlin two years ago – the growing feeling among Berliners that they should have a say in the future shape of their city.

He blames the city and the government for some of the current problems. Can it be right, he wonders, that they subsidise huge renovation in some areas, benefiting landlords and owners, while failing to provide protection for the original community? "People moved to areas like Kreuzberg originally for the social mix. The danger now is that places like Kreuzberg are becoming yuppie ghettoes," says Novy.

All of which presents something of a mystery: in a city lacking industry, where unemployment is higher than many cities in the old west and the government is the biggest employer, where exactly are Berlin's wealthy young inhabitants coming from?

Andrej Holm, author of a blog entitled "Gentrification", believes a substantial number are from the so-called "inheritance generation" and can buy into Berlin's new chi-chi neighbourhoods by selling family property in the affluent south west. "Their work lives may not be any less precarious than many Berliners'," he says, "but they have money and wealth in their family backgrounds."

In Prenzlauer Berg, where a government-backed renovation amounting to €1bn ($843m) has given way to a market-driven approach, the impact of this creeping gentrification is clear. In the last two decades, more than 60% of the old inhabitants have been driven out. And a clash of cultures has ensued. Holm was arrested three years ago on what he says were trumped-up terrorism charges when the police tried to link his writing to the activities of some of the militants opposed to gentrification. These days, however, what Holm has to say is part of the political mainstream.

He believes that there has been a change in the terms of the debate among those most involved in anti-gentrification activism. "I think there has been a recognition that while the car burnings, which peaked in 2009, brought the issue into the debate at first, politicians quickly moved to talking about policing and security and that was counter-productive," he says.

Now, he believes, radical activists are moving more towards a strategy of making Berlin "unattractive" to the incomers distorting its social fabric, taking a leaf out of the book of the famous Kupi squat in Kreuzberg, which has rallied aggressively against each threat to eject its inhabitants.

Holm suggests it does reflect a new trajectory among Berlin's activists. "The feeling," he says, "is that we have to de-attract the city to the middle classes and investors."