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The young boy screams as his skull is firmly held, a massive thumb digging into his face as his father's powerful hand grasps him by the throat. This scene from Abraham's Sacrifice appears in the Florentine museum, evoking unease through Caravaggio's harrowing rendition of the tormented child from the scriptural narrative. It appears as if Abraham, commanded by the Divine to sacrifice his son, could snap his spinal column with a single turn. However the father's chosen method involves the metallic steel blade he grips in his remaining hand, prepared to cut Isaac's neck. A definite aspect stands out – whomever posed as Isaac for this breathtaking piece demonstrated remarkable acting ability. Within exists not only dread, shock and pleading in his darkened eyes but also profound sorrow that a protector could abandon him so utterly.

The artist took a well-known biblical story and made it so fresh and raw that its terrors seemed to happen right in view of the viewer

Standing before the artwork, viewers recognize this as a actual face, an accurate record of a young model, because the identical youth – recognizable by his tousled locks and nearly black eyes – appears in several other paintings by Caravaggio. In each case, that highly emotional visage dominates the scene. In Youth With a Ram, he gazes mischievously from the shadows while embracing a lamb. In Amor Vincit Omnia, he smirks with a hardness acquired on Rome's alleys, his dark plumed appendages demonic, a naked child creating riot in a affluent residence.

Amor Vincit Omnia, currently displayed at a London gallery, represents one of the most discomfiting artworks ever created. Observers feel totally disoriented looking at it. The god of love, whose darts fill people with frequently agonizing desire, is portrayed as a very real, brightly illuminated nude form, standing over overturned objects that include musical devices, a musical manuscript, plate armour and an builder's T-square. This heap of items echoes, deliberately, the mathematical and construction gear strewn across the ground in the German master's print Melencolia I – save here, the melancholic mess is created by this grinning deity and the mayhem he can release.

"Love looks not with the vision, but with the soul, / And thus is winged Cupid depicted blind," penned the Bard, shortly before this work was created around 1601. But the painter's Cupid is not blind. He stares directly at you. That countenance – ironic and ruddy-faced, staring with bold assurance as he poses naked – is the same one that shrieks in terror in The Sacrifice of Isaac.

As the Italian master painted his multiple images of the identical unusual-looking youth in the Eternal City at the start of the seventeenth century, he was the highly acclaimed sacred painter in a metropolis ignited by Catholic renewal. The Sacrifice of Isaac demonstrates why he was commissioned to decorate churches: he could adopt a biblical narrative that had been portrayed many times before and make it so fresh, so unfiltered and physical that the terror appeared to be occurring immediately before you.

However there was another side to the artist, apparent as quickly as he arrived in the capital in the cold season that concluded the sixteenth century, as a painter in his initial twenties with no teacher or supporter in the city, just talent and boldness. Most of the paintings with which he caught the holy metropolis's eye were everything but holy. What may be the very first resides in London's art museum. A young man parts his crimson mouth in a scream of agony: while stretching out his dirty digits for a cherry, he has instead been attacked. Youth Bitten by a Reptile is sensuality amid poverty: observers can see the painter's gloomy chamber mirrored in the murky liquid of the transparent container.

The boy wears a rose-colored flower in his hair – a emblem of the sex commerce in early modern painting. Venetian artists such as Titian and Palma Vecchio depicted courtesans holding blooms and, in a work lost in the second world war but known through photographs, Caravaggio represented a famous woman courtesan, clutching a bouquet to her chest. The meaning of all these floral indicators is clear: sex for purchase.

How are we to make of Caravaggio's sensual depictions of youths – and of a particular boy in particular? It is a question that has divided his commentators since he achieved mega-fame in the twentieth century. The complicated past truth is that the painter was neither the queer icon that, for instance, Derek Jarman presented on film in his twentieth-century film about the artist, nor so entirely pious that, as some artistic scholars unbelievably assert, his Youth Holding Fruit is actually a likeness of Christ.

His early paintings do make overt sexual implications, or including offers. It's as if the painter, then a penniless young creator, aligned with Rome's prostitutes, selling himself to survive. In the Florentine gallery, with this thought in mind, observers might turn to an additional early work, the sixteenth-century masterwork Bacchus, in which the god of wine gazes calmly at you as he begins to untie the dark ribbon of his garment.

A several years after Bacchus, what could have motivated the artist to paint Victorious Cupid for the art collector the nobleman, when he was finally becoming almost respectable with important church commissions? This unholy pagan god resurrects the sexual provocations of his early paintings but in a more intense, uneasy way. Half a century afterwards, its secret seemed obvious: it was a portrait of Caravaggio's lover. A British traveller saw Victorious Cupid in about 1649 and was told its subject has "the body & face of [Caravaggio's|his] own boy or assistant that laid with him". The name of this adolescent was Francesco.

The artist had been dead for about forty annums when this account was recorded.