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The young boy cries out while his skull is forcefully gripped, a large digit pressing into his face as his father's powerful palm holds him by the neck. This scene from Abraham's Sacrifice appears in the Florentine museum, evoking distress through Caravaggio's harrowing rendition of the suffering child from the biblical narrative. It seems as if Abraham, commanded by the Divine to sacrifice his offspring, could break his spinal column with a single twist. However Abraham's chosen approach involves the metallic steel knife he holds in his remaining hand, ready to cut Isaac's neck. A certain aspect stands out – whoever posed as Isaac for this astonishing work demonstrated remarkable acting ability. Within exists not only fear, shock and begging in his shadowed eyes but also profound grief that a guardian could betray him so utterly.

The artist adopted a well-known scriptural tale and made it so vibrant and raw that its horrors appeared to happen directly in front of the viewer

Viewing in front of the artwork, observers identify this as a real face, an accurate record of a adolescent subject, because the same youth – recognizable by his disheveled locks and nearly black eyes – features in two other works by the master. In every case, that richly expressive face dominates the composition. In John the Baptist, he gazes playfully from the shadows while embracing a ram. In Victorious Cupid, he smirks with a toughness acquired on the city's streets, his dark feathery wings demonic, a naked adolescent running chaos in a affluent residence.

Victorious Cupid, currently exhibited at a British gallery, constitutes one of the most discomfiting masterpieces ever painted. Viewers feel totally disoriented gazing at it. Cupid, whose darts inspire people with often painful longing, is shown as a very tangible, brightly illuminated nude figure, standing over toppled-over objects that comprise stringed devices, a music manuscript, plate armor and an builder's ruler. This pile of possessions echoes, deliberately, the mathematical and architectural equipment scattered across the ground in Albrecht Dürer's print Melancholy – save in this case, the melancholic disorder is caused by this smirking deity and the turmoil he can release.

"Love sees not with the eyes, but with the soul, / And thus is winged Love painted blind," wrote the Bard, shortly prior to this painting was produced around the early 1600s. But the painter's god is not blind. He stares directly at the observer. That countenance – sardonic and rosy-cheeked, staring with bold assurance as he struts unclothed – is the identical one that screams in fear in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio painted his three images of the same distinctive-appearing youth in Rome at the dawn of the seventeenth century, he was the most celebrated religious artist in a metropolis enflamed by religious revival. The Sacrifice of Isaac demonstrates why he was commissioned to adorn sanctuaries: he could adopt a biblical story that had been portrayed numerous occasions before and make it so new, so raw and physical that the horror seemed to be happening directly before you.

However there existed a different side to Caravaggio, evident as soon as he came in Rome in the cold season that concluded the sixteenth century, as a artist in his early twenties with no teacher or supporter in the city, only skill and boldness. The majority of the works with which he caught the holy metropolis's attention were anything but devout. What may be the absolute first resides in the UK's art museum. A youth opens his red lips in a scream of agony: while reaching out his filthy fingers for a fruit, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid poverty: viewers can see the painter's dismal room mirrored in the cloudy waters of the glass vase.

The boy wears a rose-colored flower in his coiffure – a symbol of the sex trade in early modern art. Northern Italian painters such as Tiziano and Palma Vecchio depicted prostitutes holding flowers and, in a work destroyed in the second world war but known through images, the master portrayed a famous female prostitute, holding a bouquet to her chest. The meaning of all these botanical indicators is obvious: intimacy for purchase.

How are we to interpret of Caravaggio's sensual depictions of youths – and of one adolescent in particular? It is a question that has divided his commentators since he gained widespread recognition in the twentieth century. The complicated past truth is that the painter was neither the homosexual icon that, for example, Derek Jarman put on film in his twentieth-century movie Caravaggio, nor so completely devout that, as certain art historians improbably claim, his Youth Holding Fruit is actually a portrait of Christ.

His initial paintings indeed make overt sexual implications, or even propositions. It's as if Caravaggio, then a penniless young creator, identified with Rome's sex workers, selling himself to live. In the Florentine gallery, with this idea in mind, viewers might look to an additional initial work, the sixteenth-century masterwork Bacchus, in which the deity of wine gazes calmly at the spectator as he starts to untie the dark ribbon of his garment.

A several years following the wine deity, what could have driven the artist to paint Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was finally becoming nearly respectable with prestigious ecclesiastical commissions? This unholy pagan god resurrects the erotic provocations of his early paintings but in a increasingly intense, uneasy way. Half a century afterwards, its secret seemed obvious: it was a portrait of Caravaggio's companion. A English visitor viewed Victorious Cupid in about 1649 and was told its subject has "the body & face of [Caravaggio's|his] own youth or servant that slept with him". The name of this boy was Francesco.

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