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A young boy cries out as his head is firmly gripped, a massive thumb digging into his face as his father's powerful hand holds him by the throat. That scene from The Sacrifice of Isaac appears in the Florentine museum, evoking distress through Caravaggio's chilling rendition of the suffering youth from the scriptural narrative. The painting appears as if the patriarch, instructed by the Divine to sacrifice his offspring, could break his neck with a single twist. Yet Abraham's preferred approach involves the metallic grey knife he grips in his other palm, prepared to cut Isaac's neck. A certain aspect stands out – whomever posed as the sacrifice for this breathtaking piece demonstrated extraordinary expressive ability. Within exists not just fear, shock and begging in his shadowed gaze but also deep sorrow that a protector could abandon him so utterly.

He took a well-known scriptural story and made it so fresh and raw that its terrors seemed to unfold directly in view of you

Viewing in front of the painting, observers identify this as a real countenance, an precise depiction of a young subject, because the identical youth – identifiable by his tousled locks and nearly dark pupils – appears in two additional paintings by Caravaggio. In each case, that highly emotional visage dominates the composition. In John the Baptist, he gazes mischievously from the shadows while embracing a lamb. In Amor Vincit Omnia, he grins with a hardness acquired on Rome's streets, his dark plumed appendages demonic, a naked adolescent running riot in a affluent residence.

Victorious Cupid, presently exhibited at a London gallery, represents one of the most discomfiting masterpieces ever created. Viewers feel totally disoriented looking at it. Cupid, whose darts fill people with frequently painful desire, is portrayed as a very tangible, vividly illuminated nude form, straddling toppled-over objects that comprise stringed devices, a musical score, plate armour and an architect's T-square. This pile of possessions echoes, intentionally, the mathematical and architectural equipment scattered across the floor in Albrecht Dürer's engraving Melencolia I – save here, the gloomy disorder is caused by this smirking deity and the mayhem he can release.

"Affection looks not with the eyes, but with the mind, / And therefore is feathered Love depicted sightless," penned Shakespeare, just prior to this work was produced around 1601. But Caravaggio's god is not unseeing. He stares straight at you. That countenance – sardonic and ruddy-cheeked, staring with brazen assurance as he poses naked – is the same one that shrieks in fear in Abraham's Test.

As Michelangelo Merisi da Caravaggio created his multiple images of the same distinctive-appearing youth in the Eternal City at the dawn of the seventeenth century, he was the highly acclaimed religious painter in a metropolis enflamed by Catholic revival. The Sacrifice of Isaac demonstrates why he was commissioned to adorn churches: he could take a biblical narrative that had been portrayed numerous occasions before and render it so new, so raw and visceral that the terror seemed to be happening directly in front of the spectator.

However there was another side to Caravaggio, evident as quickly as he came in the capital in the winter that concluded 1592, as a painter in his early twenties with no mentor or patron in the urban center, only skill and audacity. Most of the paintings with which he caught the holy metropolis's eye were anything but devout. What could be the very earliest hangs in London's art museum. A young man opens his red mouth in a scream of agony: while stretching out his dirty fingers for a fruit, he has rather been attacked. Boy Bitten By a Lizard is sensuality amid poverty: viewers can see the painter's gloomy chamber mirrored in the cloudy liquid of the transparent container.

The adolescent wears a rose-colored blossom in his hair – a emblem of the erotic trade in early modern painting. Venetian artists such as Tiziano and Jacopo Palma portrayed courtesans grasping flowers and, in a work lost in the WWII but known through photographs, Caravaggio portrayed a famous woman courtesan, clutching a bouquet to her chest. The message of all these floral indicators is clear: sex for sale.

How are we to interpret of Caravaggio's sensual depictions of youths – and of one boy in specific? It is a inquiry that has divided his commentators ever since he gained mega-fame in the 1980s. The complicated historical reality is that the artist was neither the homosexual hero that, for instance, Derek Jarman put on film in his 1986 film about the artist, nor so completely devout that, as some art scholars unbelievably assert, his Boy With a Basket of Fruit is in fact a likeness of Jesus.

His early paintings do make overt sexual suggestions, or including offers. It's as if the painter, then a destitute youthful artist, aligned with the city's sex workers, selling himself to survive. In the Uffizi, with this idea in mind, observers might look to an additional initial creation, the 1596 masterwork the god of wine, in which the deity of wine gazes calmly at you as he begins to undo the dark ribbon of his garment.

A few annums following the wine deity, what could have driven the artist to create Amor Vincit Omnia for the art patron the nobleman, when he was at last becoming nearly respectable with prestigious ecclesiastical projects? This unholy non-Christian deity revives the erotic challenges of his initial works but in a increasingly powerful, uneasy manner. Fifty years later, its secret seemed obvious: it was a representation of Caravaggio's lover. A British traveller viewed Victorious Cupid in about the mid-seventeenth century and was told its figure has "the physique and countenance of [Caravaggio's|his] own youth or assistant that slept with him". The name of this boy was Francesco.

The artist had been dead for about 40 years when this account was documented.