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A youthful boy screams while his skull is firmly gripped, a massive digit digging into his cheek as his father's mighty hand holds him by the throat. That scene from Abraham's Sacrifice appears in the Florentine museum, evoking distress through the artist's chilling rendition of the tormented youth from the scriptural account. The painting seems as if Abraham, instructed by the Divine to kill his son, could snap his neck with a single twist. However Abraham's preferred method involves the silvery steel knife he grips in his other palm, prepared to cut the boy's neck. A definite element stands out – whoever modeled as the sacrifice for this breathtaking work demonstrated extraordinary expressive ability. Within exists not only fear, surprise and pleading in his shadowed gaze but additionally profound grief that a protector could betray him so utterly.

The artist adopted a well-known scriptural story and made it so fresh and raw that its terrors appeared to unfold directly in front of the viewer

Standing before the painting, observers identify this as a actual countenance, an accurate record of a adolescent subject, because the same youth – recognizable by his disheveled hair and nearly black pupils – features in several other paintings by the master. In every case, that highly emotional visage dominates the scene. In Youth With a Ram, he gazes mischievously from the darkness while holding a ram. In Victorious Cupid, he grins with a hardness acquired on the city's alleys, his dark feathery appendages sinister, a unclothed child creating riot in a affluent dwelling.

Amor Vincit Omnia, currently exhibited at a London museum, represents one of the most discomfiting artworks ever painted. Observers feel totally unsettled looking at it. Cupid, whose arrows fill people with frequently agonizing longing, is portrayed as a very tangible, brightly lit unclothed form, standing over overturned objects that include stringed devices, a music manuscript, metal armour and an architect's T-square. This heap of items echoes, deliberately, the geometric and architectural gear scattered across the floor in the German master's engraving Melancholy – except here, the melancholic mess is caused by this grinning deity and the mayhem he can release.

"Love sees not with the vision, but with the soul, / And therefore is winged Love painted sightless," wrote Shakespeare, just prior to this work was created around the early 1600s. But Caravaggio's god is not unseeing. He gazes directly at the observer. That countenance – ironic and rosy-cheeked, looking with bold confidence as he struts naked – is the identical one that shrieks in terror in The Sacrifice of Isaac.

As the Italian master painted his multiple portrayals of the same distinctive-looking kid in Rome at the dawn of the seventeenth century, he was the highly celebrated sacred painter in a metropolis enflamed by religious revival. The Sacrifice of Isaac reveals why he was sought to decorate sanctuaries: he could take a biblical narrative that had been depicted many occasions previously and make it so fresh, so unfiltered and physical that the terror appeared to be happening immediately in front of you.

However there was a different aspect to the artist, apparent as soon as he arrived in the capital in the cold season that ended the sixteenth century, as a painter in his initial 20s with no teacher or patron in the urban center, only talent and audacity. Most of the works with which he caught the holy metropolis's eye were everything but holy. What could be the very earliest resides in the UK's art museum. A youth parts his red lips in a scream of pain: while stretching out his dirty fingers for a cherry, he has instead been attacked. Boy Bitten By a Lizard is eroticism amid squalor: viewers can discern Caravaggio's dismal room mirrored in the cloudy liquid of the glass vase.

The adolescent wears a rose-colored flower in his hair – a emblem of the erotic commerce in early modern art. Northern Italian painters such as Titian and Palma Vecchio portrayed prostitutes holding flowers and, in a painting lost in the WWII but documented through images, Caravaggio portrayed a famous woman courtesan, holding a bouquet to her bosom. The message of all these floral signifiers is obvious: intimacy for sale.

What are we to interpret of Caravaggio's sensual depictions of youths – and of one adolescent in particular? It is a question that has split his commentators since he gained widespread recognition in the 1980s. The complicated past truth is that the painter was neither the homosexual hero that, for example, Derek Jarman put on screen in his twentieth-century film about the artist, nor so completely devout that, as some artistic scholars unbelievably assert, his Youth Holding Fruit is actually a likeness of Christ.

His initial works indeed offer overt sexual implications, or including propositions. It's as if the painter, then a destitute young artist, aligned with the city's prostitutes, selling himself to survive. In the Florentine gallery, with this thought in consideration, observers might look to another early creation, the sixteenth-century masterwork Bacchus, in which the deity of alcohol gazes coolly at the spectator as he begins to undo the black ribbon of his garment.

A few years following Bacchus, what could have motivated Caravaggio to paint Victorious Cupid for the art patron the nobleman, when he was finally becoming nearly established with important church commissions? This profane non-Christian god revives the erotic provocations of his early paintings but in a increasingly intense, uneasy manner. Fifty years afterwards, its hidden meaning seemed clear: it was a portrait of the painter's companion. A English visitor saw the painting in about the mid-seventeenth century and was told its figure has "the physique and countenance of [Caravaggio's|his] owne boy or assistant that slept with him". The identity of this boy was Francesco.

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