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A young lad cries out as his skull is firmly gripped, a massive digit digging into his face as his father's powerful palm grasps him by the neck. That moment from Abraham's Sacrifice visits the Uffizi Gallery, evoking unease through the artist's chilling rendition of the tormented youth from the scriptural narrative. The painting seems as if Abraham, commanded by the Divine to sacrifice his offspring, could snap his neck with a single turn. Yet the father's chosen approach involves the metallic grey knife he holds in his other palm, ready to slit Isaac's throat. One definite aspect stands out – whomever posed as Isaac for this breathtaking piece demonstrated extraordinary acting ability. Within exists not just fear, shock and begging in his darkened eyes but also profound sorrow that a protector could betray him so utterly.

He adopted a familiar scriptural story and made it so vibrant and raw that its horrors seemed to happen directly in front of you

Viewing 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 hair and almost dark eyes – features in several other paintings by the master. In each instance, that richly expressive face commands the scene. In John the Baptist, he gazes mischievously from the darkness while embracing a ram. In Victorious Cupid, he grins with a toughness acquired on Rome's alleys, his black feathery appendages sinister, a naked adolescent running riot in a well-to-do dwelling.

Amor Vincit Omnia, presently displayed at a London gallery, represents one of the most discomfiting artworks ever created. Observers feel totally unsettled looking at it. Cupid, whose arrows fill people with frequently agonizing longing, is shown as a very real, brightly illuminated nude form, straddling toppled-over objects that include stringed devices, a music score, metal armour and an architect's T-square. This pile of possessions resembles, intentionally, the mathematical and construction gear strewn across the ground in Albrecht Dürer's print Melancholy – except here, the melancholic disorder is caused by this smirking deity and the mayhem he can release.

"Love looks not with the vision, but with the mind, / And thus is winged Cupid depicted blind," wrote the Bard, shortly prior to this work was created around 1601. But the painter's Cupid is not blind. He gazes directly at the observer. That countenance – ironic and rosy-cheeked, staring with brazen confidence as he poses unclothed – is the identical one that shrieks in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio created his three images of the identical unusual-appearing kid in Rome at the dawn of the 17th century, he was the highly acclaimed religious artist in a metropolis ignited by religious renewal. Abraham's Offering reveals why he was commissioned to adorn churches: he could adopt a scriptural narrative that had been depicted many times previously and render it so fresh, so raw and visceral that the terror seemed to be happening immediately before you.

However there was a different side to the artist, evident as quickly as he arrived in the capital in the cold season that ended 1592, as a painter in his initial 20s with no mentor or patron in the urban center, just skill and audacity. The majority of the paintings with which he captured the holy city's eye were anything but devout. What may be the very earliest resides in the UK's art museum. A youth parts his red mouth in a yell of pain: while reaching out his dirty digits for a fruit, he has rather been attacked. Boy Bitten By a Lizard is sensuality amid poverty: observers can see the painter's gloomy room mirrored in the murky liquid of the transparent vase.

The adolescent wears a pink blossom in his coiffure – a emblem of the erotic trade in early modern painting. Northern Italian painters such as Tiziano and Jacopo Palma depicted courtesans holding flowers and, in a painting lost in the WWII but documented through images, Caravaggio represented a famous woman prostitute, holding a posy to her bosom. The message of all these floral signifiers is obvious: sex for purchase.

How are we to make of the artist's erotic depictions of boys – and of one adolescent in specific? It is a inquiry that has divided his interpreters ever since he gained widespread recognition in the 1980s. The complex past truth is that the painter was neither the homosexual icon that, for example, Derek Jarman put on film in his twentieth-century movie about the artist, nor so entirely devout that, as some artistic historians unbelievably assert, his Youth Holding Fruit is in fact a likeness of Christ.

His initial paintings do offer overt sexual implications, or including offers. It's as if Caravaggio, then a penniless youthful artist, identified with Rome's sex workers, offering himself to live. In the Uffizi, with this thought in mind, observers might turn to another early work, the 1596 masterwork Bacchus, in which the god of alcohol gazes coolly at the spectator as he starts to undo the dark ribbon of his robe.

A several annums following Bacchus, what could have driven Caravaggio to create Victorious Cupid for the artistic collector Vincenzo Giustiniani, when he was finally growing almost respectable with important church projects? This unholy pagan god revives the sexual challenges of his initial paintings but in a increasingly powerful, unsettling way. Fifty years afterwards, its hidden meaning seemed clear: it was a representation of the painter's companion. A English traveller viewed Victorious Cupid in about the mid-seventeenth century and was told its figure has "the physique and countenance of [Caravaggio's|his] owne youth or assistant that slept with him". The identity of this boy was Francesco.

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