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A young lad screams as his head is firmly held, a massive digit pressing into his face as his father's powerful palm grasps him by the throat. This scene from The Sacrifice of Isaac visits the Uffizi Gallery, creating unease through Caravaggio's harrowing rendition of the suffering youth from the biblical account. The painting appears as if Abraham, commanded by God to sacrifice his son, could snap his spinal column with a single turn. Yet the father's chosen method involves the metallic steel knife he holds in his other palm, ready to cut the boy's neck. One definite element stands out – whomever posed as Isaac for this astonishing work displayed remarkable expressive ability. Within exists not only dread, shock and pleading in his darkened gaze but also deep grief that a guardian could betray him so completely.

He adopted a well-known biblical story and made it so fresh and raw that its terrors seemed to unfold right in front of you

Standing in front of the painting, viewers recognize this as a actual countenance, an precise depiction of a adolescent model, because the identical youth – identifiable by his disheveled locks and nearly black eyes – appears in two other paintings by Caravaggio. In each case, that highly emotional face commands the scene. In John the Baptist, he gazes mischievously from the darkness while embracing a ram. In Amor Vincit Omnia, he smirks with a toughness learned on Rome's streets, his black plumed appendages sinister, a unclothed child creating chaos in a well-to-do residence.

Victorious Cupid, presently displayed at a London museum, constitutes one of the most embarrassing artworks ever created. Viewers feel totally unsettled gazing at it. Cupid, whose darts inspire people with often agonizing desire, is portrayed as a extremely tangible, brightly lit unclothed figure, straddling overturned items that include musical devices, a musical manuscript, plate armour and an architect's ruler. This heap of items echoes, deliberately, the geometric and architectural equipment scattered across the floor in Albrecht Dürer's engraving Melancholy – except here, the melancholic mess is caused by this grinning Cupid and the turmoil he can release.

"Love looks not with the vision, but with the soul, / And thus is winged Love depicted blind," wrote Shakespeare, shortly before this work was created around the early 1600s. But the painter's Cupid is not unseeing. He gazes directly at the observer. That countenance – sardonic and rosy-cheeked, looking with bold confidence as he poses naked – is the identical one that screams in fear in Abraham's Test.

When Michelangelo Merisi da Caravaggio created his multiple portrayals of the same distinctive-looking kid in Rome at the dawn of the 17th century, he was the highly celebrated sacred artist in a city enflamed by religious renewal. The Sacrifice of Isaac reveals why he was sought to decorate sanctuaries: he could adopt a scriptural narrative that had been depicted many times previously and render it so new, so raw and visceral that the terror appeared to be occurring directly before the spectator.

Yet there existed another side to the artist, apparent as quickly as he came in the capital in the winter that concluded the sixteenth century, as a artist in his initial twenties with no teacher or patron in the urban center, just skill and audacity. Most of the paintings with which he captured the sacred city's attention were everything but devout. What could be the very first resides in the UK's art museum. A young man opens his red mouth in a yell of agony: while stretching out his dirty digits for a fruit, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid poverty: viewers can see Caravaggio's dismal chamber mirrored in the cloudy waters of the transparent container.

The boy wears a pink flower in his hair – a emblem of the sex trade in early modern art. Venetian artists such as Tiziano and Jacopo Palma depicted prostitutes holding flowers and, in a work destroyed in the second world war but documented through images, the master represented a renowned woman courtesan, holding a bouquet to her chest. The message of all these botanical signifiers is clear: sex for sale.

What are we to make of Caravaggio's erotic portrayals of youths – and of a particular boy in particular? It is a inquiry that has split his commentators since he gained widespread recognition in the 1980s. The complex past truth is that the painter was neither the queer hero that, for instance, Derek Jarman put on film in his 1986 film Caravaggio, nor so entirely devout that, as some artistic scholars unbelievably claim, his Youth Holding Fruit is actually a portrait of Jesus.

His early works do make overt erotic suggestions, or even offers. It's as if the painter, then a destitute young artist, aligned with the city's sex workers, offering himself to live. In the Florentine gallery, with this idea in mind, observers might look to another early creation, the 1596 masterwork the god of wine, in which the deity of wine stares coolly at you as he begins to undo the black sash of his garment.

A several annums following Bacchus, what could have driven Caravaggio to paint Victorious Cupid for the art collector Vincenzo Giustiniani, when he was finally growing nearly established with prestigious ecclesiastical projects? This unholy pagan god resurrects the erotic challenges of his early paintings but in a more powerful, uneasy manner. Half a century later, its hidden meaning seemed clear: it was a representation of Caravaggio's companion. A British visitor viewed the painting in about 1649 and was told its figure has "the physique and countenance of [Caravaggio's|his] owne youth or servant that slept with him". The identity of this boy was Cecco.

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