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A youthful boy screams while his skull is firmly held, a large thumb pressing into his face as his parent's powerful hand holds him by the neck. That scene from The Sacrifice of Isaac appears in the Uffizi Gallery, creating distress through Caravaggio's harrowing portrayal of the tormented youth from the scriptural narrative. It seems as if the patriarch, instructed by the Divine to kill his offspring, could snap his neck with a single twist. Yet the father's chosen method involves the metallic steel knife he grips in his remaining palm, ready to cut the boy's throat. One certain element stands out – whoever posed as the sacrifice for this astonishing work demonstrated extraordinary expressive ability. There exists not just fear, shock and pleading in his shadowed gaze but additionally deep grief that a protector could betray him so completely.

The artist adopted a familiar biblical story and transformed it so vibrant and raw that its horrors seemed to unfold right in front of you

Standing in front of the artwork, observers identify this as a actual face, an accurate depiction of a adolescent subject, because the same boy – identifiable by his disheveled locks and almost dark pupils – appears in two additional paintings by Caravaggio. In every instance, that richly emotional face commands the scene. In Youth With a Ram, he gazes mischievously from the shadows while holding a ram. In Victorious Cupid, he smirks with a hardness acquired on the city's streets, his dark plumed wings sinister, a unclothed adolescent running riot in a well-to-do dwelling.

Victorious Cupid, presently exhibited at a British gallery, represents one of the most discomfiting artworks ever created. Observers feel totally disoriented looking at it. Cupid, whose darts fill people with frequently agonizing desire, is portrayed as a extremely real, vividly illuminated unclothed form, standing over toppled-over items that include musical devices, a musical score, plate armor and an architect's T-square. This pile of items echoes, deliberately, the mathematical and architectural equipment strewn across the ground in Albrecht Dürer's engraving Melancholy – except here, the melancholic disorder is created by this grinning deity and the turmoil he can release.

"Affection sees not with the vision, but with the mind, / And thus is feathered Cupid depicted sightless," penned the Bard, shortly prior to this painting was produced around 1601. But the painter's Cupid is not unseeing. He gazes directly at you. That countenance – ironic and ruddy-cheeked, staring with bold assurance as he struts naked – is the identical one that shrieks in terror in Abraham's Test.

When Michelangelo Merisi da Caravaggio painted his three portrayals of the same unusual-appearing kid in the Eternal City at the start of the seventeenth century, he was the highly celebrated sacred artist in a metropolis enflamed by religious revival. Abraham's Offering reveals why he was sought to adorn sanctuaries: he could adopt a biblical narrative that had been depicted numerous occasions before and render it so fresh, so unfiltered and visceral that the terror appeared to be happening immediately in front of the spectator.

Yet there existed a different side to Caravaggio, apparent as quickly as he came in Rome in the winter that ended 1592, as a artist in his initial 20s with no mentor or supporter in the urban center, only skill and audacity. Most of the works with which he caught the sacred city's eye were anything but devout. What could be the absolute first resides in London's art museum. A young man opens his red mouth in a scream of agony: while stretching out his dirty fingers for a cherry, he has instead been bitten. Boy Bitten By a Lizard is eroticism amid squalor: viewers can see Caravaggio's gloomy chamber mirrored in the murky waters of the transparent container.

The boy wears a pink blossom in his coiffure – a emblem of the sex trade in Renaissance painting. Northern Italian painters such as Tiziano and Palma Vecchio portrayed courtesans grasping blooms and, in a painting destroyed in the second world war but known through images, Caravaggio represented a renowned woman courtesan, clutching a posy to her bosom. The meaning of all these floral indicators is clear: intimacy for purchase.

What are we to interpret of Caravaggio's erotic depictions of boys – and of a particular boy in particular? It is a inquiry that has split his interpreters since he achieved widespread recognition in the 1980s. The complicated past truth is that the artist was not the homosexual icon that, for example, Derek Jarman presented on film in his 1986 film Caravaggio, nor so entirely pious that, as certain art scholars unbelievably assert, his Boy With a Basket of Fruit is actually a portrait of Christ.

His early paintings do make explicit sexual suggestions, or even propositions. It's as if the painter, then a penniless young artist, identified with the city's sex workers, offering himself to survive. In the Uffizi, with this thought in mind, observers might look to another initial work, the 1596 masterpiece Bacchus, in which the god of wine stares coolly at the spectator as he begins to untie the black ribbon of his robe.

A few annums following the wine deity, what could have motivated the artist to paint Victorious Cupid for the art collector the nobleman, when he was finally growing nearly respectable with prestigious church projects? This unholy pagan god resurrects the erotic provocations of his early works but in a more powerful, uneasy manner. Half a century later, its secret seemed clear: it was a representation of the painter's lover. A British traveller saw Victorious Cupid in about 1649 and was informed its figure has "the physique and countenance of [Caravaggio's|his] owne youth or servant that laid with him". The identity of this adolescent was Francesco.

The artist had been dead for about forty years when this story was documented.