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The youthful lad cries out as his skull is forcefully gripped, a large digit digging into his face as his parent's mighty palm holds him by the neck. That moment from The Sacrifice of Isaac visits the Uffizi Gallery, creating distress through the artist's chilling portrayal of the suffering child from the biblical account. It seems as if Abraham, instructed by God to sacrifice his son, could snap his neck with a solitary twist. Yet the father's chosen method involves the metallic steel blade he grips in his other hand, ready to slit Isaac's throat. A definite element stands out – whoever posed as the sacrifice for this breathtaking piece demonstrated remarkable expressive skill. There exists not only dread, shock and pleading in his darkened gaze but also profound sorrow that a guardian could betray him so completely.

The artist adopted a well-known biblical tale and made it so fresh and visceral that its terrors appeared to unfold right in view of the viewer

Viewing before the painting, viewers identify this as a actual face, an accurate depiction of a young subject, because the same youth – recognizable by his tousled hair and almost black pupils – appears in several other paintings by Caravaggio. In each instance, that highly expressive face dominates the scene. In John the Baptist, he peers mischievously from the darkness while holding a lamb. In Amor Vincit Omnia, he grins with a hardness acquired on the city's alleys, his black plumed wings demonic, a naked child running chaos in a affluent residence.

Amor Vincit Omnia, currently displayed at a British museum, represents one of the most discomfiting masterpieces ever painted. Observers feel completely unsettled gazing at it. Cupid, whose arrows fill people with often painful longing, is shown as a very real, brightly lit unclothed figure, standing over overturned items that comprise stringed instruments, a musical score, plate armor and an builder's T-square. This pile of items echoes, deliberately, the geometric and architectural equipment strewn across the ground in Albrecht Dürer's print Melencolia I – except here, the melancholic disorder is created by this smirking deity and the turmoil he can release.

"Love looks not with the vision, but with the soul, / And thus is feathered Cupid painted blind," wrote Shakespeare, just prior to this work was created around 1601. But Caravaggio's god is not blind. He gazes straight at the observer. That face – ironic and rosy-cheeked, looking with brazen assurance as he struts naked – is the identical one that screams in fear in Abraham's Test.

When Michelangelo Merisi da Caravaggio created his multiple images of the same unusual-appearing kid in Rome at the dawn of the seventeenth century, he was the most acclaimed sacred artist in a metropolis ignited by Catholic renewal. The Sacrifice of Isaac reveals why he was commissioned to decorate sanctuaries: he could adopt a biblical story that had been portrayed many occasions before and render it so new, so unfiltered and visceral that the terror appeared to be happening immediately in front of you.

However there was another side to Caravaggio, apparent as quickly as he arrived in Rome in the cold season that concluded the sixteenth century, as a artist in his early 20s with no mentor or patron in the urban center, only skill and boldness. Most of the paintings with which he caught the holy city's eye were anything but devout. What may be the absolute earliest resides in London's art museum. A youth parts his crimson mouth in a yell of pain: while reaching out his dirty fingers for a cherry, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid squalor: viewers can see Caravaggio's dismal chamber reflected in the cloudy waters of the transparent container.

The adolescent wears a pink blossom in his hair – a symbol of the erotic trade in early modern art. Venetian artists such as Titian and Palma Vecchio portrayed courtesans grasping blooms and, in a work destroyed in the WWII but known through photographs, the master portrayed a renowned woman prostitute, clutching a posy to her bosom. The message of all these botanical signifiers is obvious: sex for purchase.

What are we to interpret of Caravaggio's erotic portrayals of youths – and of one adolescent in specific? It is a inquiry that has divided his interpreters ever since he achieved widespread recognition in the 1980s. The complex historical truth is that the artist was not the homosexual hero that, for example, Derek Jarman presented on screen in his twentieth-century film Caravaggio, nor so completely devout that, as some artistic historians improbably claim, his Boy With a Basket of Fruit is in fact a likeness of Christ.

His early works do offer overt erotic suggestions, or even offers. It's as if Caravaggio, then a penniless young creator, aligned with the city's sex workers, offering himself to live. In the Florentine gallery, with this thought in mind, viewers might look to an additional early work, the 1596 masterwork the god of wine, in which the deity of alcohol stares calmly at the spectator as he begins to undo the black sash of his garment.

A several years following the wine deity, what could have motivated the artist to paint Victorious Cupid for the art collector Vincenzo Giustiniani, when he was finally growing almost established with important church projects? This unholy non-Christian deity resurrects the erotic challenges of his initial paintings but in a increasingly intense, uneasy manner. Half a century afterwards, its secret seemed obvious: it was a portrait of Caravaggio's companion. A English traveller viewed Victorious Cupid in about 1649 and was informed its figure has "the physique and countenance 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 annums when this story was documented.