Who exactly was Caravaggio's black-winged deity of desire? What insights this masterpiece uncovers about the rebellious artist

The youthful lad screams as his skull is forcefully held, a massive thumb pressing into his cheek as his parent's powerful hand holds him by the neck. That moment from The Sacrifice of Isaac appears in the Florentine museum, evoking unease through Caravaggio's harrowing portrayal of the tormented youth from the biblical account. It appears as if Abraham, instructed by the Divine to sacrifice his son, could break his neck with a solitary turn. Yet Abraham's preferred method involves the metallic steel knife he grips in his remaining palm, prepared to cut the boy's throat. A certain aspect stands out – whoever modeled as the sacrifice for this breathtaking piece demonstrated extraordinary expressive skill. Within exists not just dread, shock and pleading in his darkened gaze but also profound grief that a protector could abandon him so completely.

He took a well-known scriptural story and made it so vibrant and visceral that its terrors appeared to happen directly in front of you

Viewing before the painting, observers identify this as a real face, an accurate depiction of a adolescent subject, because the identical boy – recognizable by his disheveled locks and almost black pupils – features in two additional works by Caravaggio. In every case, that richly expressive visage dominates the composition. In John the Baptist, he peers playfully from the shadows while embracing a lamb. In Amor Vincit Omnia, he smirks with a hardness acquired on Rome's alleys, his black feathery appendages sinister, a unclothed child creating chaos in a well-to-do residence.

Victorious Cupid, currently displayed at a London gallery, constitutes one of the most embarrassing artworks ever created. Viewers feel completely disoriented looking at it. Cupid, whose darts inspire people with often agonizing longing, is shown as a extremely tangible, vividly illuminated unclothed figure, straddling toppled-over items that include stringed devices, a musical manuscript, metal armour and an builder's ruler. This pile of possessions resembles, intentionally, the mathematical and architectural gear scattered across the ground in the German master's print Melancholy – save here, the gloomy mess is created by this smirking Cupid and the mayhem he can release.

"Love sees not with the eyes, but with the mind, / And thus is winged Love depicted blind," wrote the Bard, just prior to this painting was produced around the early 1600s. But the painter's god is not blind. He gazes straight at you. That countenance – ironic and ruddy-faced, staring with brazen assurance as he poses naked – is the same one that shrieks in terror in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio created his three portrayals of the identical unusual-looking kid in Rome at the dawn of the seventeenth century, he was the most celebrated sacred artist in a metropolis ignited by religious renewal. The Sacrifice of Isaac reveals why he was sought to adorn sanctuaries: he could adopt a scriptural narrative that had been depicted many occasions previously and render it so fresh, so unfiltered and physical that the terror seemed to be happening directly before the spectator.

Yet there was another aspect to Caravaggio, apparent as soon as he arrived in the capital in the winter that ended the sixteenth century, as a artist in his initial twenties with no teacher or supporter in the city, only talent and boldness. The majority of the works with which he captured the sacred metropolis's attention were anything but devout. That could be the very first hangs in London's National Gallery. A young man opens his crimson lips in a scream of agony: while stretching out his dirty digits for a cherry, he has instead been bitten. Boy Bitten By a Lizard is eroticism amid poverty: viewers can discern Caravaggio's gloomy room mirrored in the cloudy liquid of the glass container.

The boy wears a rose-colored flower in his hair – a emblem of the sex trade in early modern art. Northern Italian painters such as Titian and Jacopo Palma depicted prostitutes grasping flowers and, in a work lost in the second world war but documented through photographs, the master represented a famous woman courtesan, clutching a posy to her chest. The meaning of all these botanical signifiers is clear: intimacy for purchase.

How are we to make of the artist's sensual depictions of boys – and of one adolescent in particular? It is a inquiry that has split his commentators since he achieved mega-fame in the 1980s. The complex historical truth is that the painter was not the queer icon that, for instance, Derek Jarman presented on film in his twentieth-century movie about the artist, nor so entirely pious that, as some artistic scholars improbably assert, his Youth Holding Fruit is in fact a portrait of Jesus.

His early paintings do make overt erotic implications, or even offers. It's as if the painter, then a destitute young artist, identified with the city's prostitutes, offering himself to survive. In the Uffizi, with this idea in mind, observers might look to another early creation, the sixteenth-century masterpiece the god of wine, in which the deity of wine stares calmly at you as he begins to untie the dark ribbon of his garment.

A few years after Bacchus, what could have motivated the artist to paint Victorious Cupid for the art collector Vincenzo Giustiniani, when he was finally becoming almost respectable with important church commissions? This unholy non-Christian deity revives the sexual provocations of his early works but in a increasingly intense, unsettling manner. Half a century afterwards, its hidden meaning seemed clear: it was a representation of the painter's companion. A English traveller saw the painting in about the mid-seventeenth century and was informed its figure has "the body & face of [Caravaggio's|his] owne boy or assistant that laid with him". The identity of this boy was Francesco.

The artist had been dead for about 40 annums when this story was recorded.