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The youthful boy screams while his skull is firmly held, a massive thumb digging into his face as his father's powerful hand grasps him by the throat. That moment from Abraham's Sacrifice visits the Uffizi Gallery, creating unease through Caravaggio's harrowing portrayal of the suffering youth from the biblical narrative. It seems as if the patriarch, instructed by the Divine to sacrifice his offspring, could snap his neck with a solitary turn. However Abraham's preferred method involves the silvery grey knife he grips in his other hand, ready to cut Isaac's throat. One certain aspect remains – whoever posed as the sacrifice for this astonishing work displayed remarkable expressive skill. Within exists not only dread, shock and begging in his darkened gaze but also deep grief that a protector could betray him so completely.

He adopted a well-known biblical story and transformed it so vibrant and visceral that its horrors appeared to happen right in front of the viewer

Viewing in front of the painting, viewers recognize this as a real face, an accurate depiction of a adolescent model, because the identical youth – identifiable by his tousled locks and nearly dark pupils – features in two additional works by Caravaggio. In every instance, that highly expressive visage dominates the scene. In John the Baptist, he gazes playfully from the shadows while holding a lamb. In Amor Vincit Omnia, he grins with a toughness learned on Rome's streets, his black feathery appendages demonic, a unclothed adolescent creating riot in a well-to-do dwelling.

Victorious Cupid, currently exhibited at a London gallery, constitutes one of the most discomfiting masterpieces ever created. Observers feel totally disoriented gazing at it. Cupid, whose darts fill people with frequently painful longing, is portrayed as a extremely real, brightly illuminated unclothed form, straddling toppled-over items that include musical devices, a music manuscript, metal armour and an builder's ruler. This pile of items echoes, deliberately, the mathematical and architectural gear scattered across the ground in Albrecht Dürer's print Melencolia I – save in this case, the gloomy mess is caused by this grinning Cupid and the turmoil he can release.

"Love sees not with the vision, but with the soul, / And therefore is feathered Cupid painted blind," penned the Bard, just before this work was produced around the early 1600s. But the painter's god is not blind. He stares directly at you. That face – ironic and rosy-cheeked, looking with brazen assurance as he struts naked – is the identical one that screams in terror in The Sacrifice of Isaac.

When the Italian master created his three images of the same unusual-looking youth in Rome at the dawn of the 17th century, he was the most acclaimed sacred painter in a city enflamed by Catholic revival. Abraham's Offering reveals why he was commissioned to adorn churches: he could adopt a scriptural narrative that had been portrayed numerous times before and make it so fresh, so raw and physical that the terror appeared to be happening immediately before you.

However there existed another side to the artist, apparent as soon as he came in the capital in the cold season that ended the sixteenth century, as a artist in his initial 20s with no mentor or supporter in the urban center, just talent and boldness. Most of the works with which he caught the sacred metropolis's attention were everything but holy. What may be the absolute first resides in London's National Gallery. A youth opens his red mouth in a scream of pain: while reaching out his filthy digits for a fruit, he has instead been attacked. Youth Bitten by a Reptile is eroticism amid poverty: viewers can discern Caravaggio's dismal chamber reflected in the cloudy liquid of the glass vase.

The adolescent wears a pink flower in his hair – a emblem of the sex trade in early modern art. Venetian painters such as Titian and Jacopo Palma portrayed prostitutes grasping blooms and, in a work lost in the second world war but known through images, the master represented a famous female prostitute, clutching a bouquet to her bosom. The message of all these floral signifiers is clear: sex for sale.

How are we to make of the artist's erotic depictions of youths – and of a particular boy in particular? It is a question that has split his commentators since he achieved mega-fame in the 1980s. The complicated past truth is that the painter was not the homosexual icon that, for example, Derek Jarman presented on film in his twentieth-century film about the artist, nor so completely devout that, as certain artistic historians unbelievably assert, his Boy With a Basket of Fruit is in fact a portrait of Jesus.

His early works do make overt erotic suggestions, or including propositions. It's as if the painter, then a destitute youthful artist, aligned with the city's prostitutes, selling himself to live. In the Uffizi, with this thought in mind, viewers might look to an additional initial work, the 1596 masterwork Bacchus, in which the deity of alcohol stares coolly at the spectator as he starts to undo the black ribbon of his garment.

A several annums following Bacchus, what could have driven Caravaggio to create Amor Vincit Omnia for the artistic collector the nobleman, when he was finally becoming nearly established with important ecclesiastical projects? This profane pagan deity revives the sexual challenges of his early works but in a more powerful, uneasy way. Fifty years later, its secret seemed obvious: it was a representation of Caravaggio's companion. A English visitor saw the painting in about 1649 and was told its figure has "the body & face of [Caravaggio's|his] own youth or servant that laid with him". The identity of this boy was Cecco.

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