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A young boy cries out as his head is firmly gripped, a large thumb pressing into his cheek as his father's mighty palm grasps him by the throat. That moment from The Sacrifice of Isaac visits the Florentine museum, evoking unease through Caravaggio's harrowing portrayal of the suffering youth from the scriptural narrative. It appears as if the patriarch, instructed by God to kill his son, could snap his spinal column with a single twist. Yet the father's preferred method involves the silvery steel blade he grips in his remaining hand, ready to cut the boy's throat. A certain element remains – whoever posed as Isaac for this breathtaking work demonstrated extraordinary expressive ability. Within exists not just fear, surprise and pleading in his darkened eyes but also profound grief that a protector could abandon him so completely.

He adopted a familiar scriptural story and transformed it so fresh and raw that its terrors seemed to happen directly in front of the viewer

Standing in front of the painting, observers recognize this as a real countenance, an precise depiction of a adolescent subject, because the same youth – recognizable by his tousled hair and nearly black eyes – appears in several other works by the master. In every case, that richly expressive visage dominates the scene. In John the Baptist, he gazes mischievously from the darkness while holding a lamb. In Amor Vincit Omnia, he smirks with a hardness learned on Rome's alleys, his dark plumed appendages sinister, a naked child creating chaos in a affluent dwelling.

Amor Vincit Omnia, presently exhibited at a London gallery, represents one of the most embarrassing masterpieces ever painted. Viewers feel totally disoriented looking at it. Cupid, whose darts inspire people with frequently painful longing, is shown as a extremely tangible, vividly illuminated unclothed figure, straddling toppled-over objects that include musical devices, a musical score, plate armor and an architect's ruler. This heap of possessions echoes, deliberately, the mathematical and construction equipment strewn across the ground in the German master's print Melencolia I – save in this case, the melancholic disorder is caused by this smirking deity and the turmoil he can unleash.

"Affection sees not with the eyes, but with the mind, / And therefore is winged Love depicted sightless," wrote Shakespeare, shortly before this painting was created around 1601. But Caravaggio's god is not unseeing. He stares directly at the observer. That countenance – sardonic and ruddy-faced, looking with bold confidence as he poses unclothed – is the same one that screams in fear in Abraham's Test.

When Michelangelo Merisi da Caravaggio painted his three portrayals of the identical distinctive-looking youth in the Eternal City at the dawn of the seventeenth century, he was the highly acclaimed religious painter in a metropolis ignited by Catholic revival. Abraham's Offering reveals why he was sought to adorn sanctuaries: he could take a scriptural narrative that had been portrayed numerous times previously and render it so fresh, so unfiltered and visceral that the horror seemed to be occurring directly in front of the spectator.

However there was another side to Caravaggio, apparent as soon as he came in Rome in the cold season that concluded 1592, as a painter in his early twenties with no mentor or patron in the city, only skill and audacity. Most of the paintings with which he captured the sacred metropolis's eye were anything but holy. That could be the absolute first hangs in the UK's art museum. A young man opens his red mouth in a scream of agony: while stretching out his filthy digits for a cherry, he has rather been bitten. Boy Bitten By a Lizard is eroticism amid poverty: viewers can see the painter's gloomy room reflected in the murky liquid of the transparent container.

The adolescent wears a rose-colored flower in his hair – a symbol of the erotic commerce in early modern painting. Northern Italian painters such as Tiziano and Jacopo Palma depicted prostitutes holding blooms and, in a painting destroyed in the second world war but known through images, the master represented a famous woman prostitute, clutching a posy to her chest. The message of all these botanical indicators is obvious: intimacy for purchase.

How are we to make of Caravaggio's sensual depictions of youths – and of one adolescent in particular? It is a question that has split his interpreters ever since he gained mega-fame in the 1980s. The complex past truth is that the painter was not the queer hero that, for example, the filmmaker presented on screen in his 1986 film Caravaggio, nor so entirely devout that, as some art historians unbelievably claim, his Boy With a Basket of Fruit is actually a portrait of Jesus.

His early works do make explicit sexual implications, or even offers. It's as if the painter, then a destitute youthful artist, identified with Rome's sex workers, offering himself to live. In the Uffizi, with this thought in mind, observers might turn to an additional initial creation, the 1596 masterpiece Bacchus, in which the deity of alcohol gazes calmly at the spectator as he begins to untie the dark sash of his garment.

A several annums after the wine deity, what could have driven Caravaggio to paint Victorious Cupid for the artistic patron Vincenzo Giustiniani, when he was at last growing almost established with prestigious church commissions? This profane pagan deity resurrects the sexual challenges of his initial works but in a increasingly powerful, unsettling manner. Fifty years later, its secret seemed clear: it was a representation of Caravaggio's lover. A English traveller viewed Victorious Cupid in about 1649 and was told its subject has "the physique and countenance of [Caravaggio's|his] own boy or servant that laid with him". The name of this adolescent was Francesco.

The artist had been dead for about forty years when this account was documented.