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A youthful boy screams as his skull is firmly held, a large thumb digging into his face as his father's mighty palm holds him by the neck. That scene from Abraham's Sacrifice visits the Uffizi Gallery, creating unease through the artist's chilling portrayal of the suffering child from the biblical narrative. The painting seems as if Abraham, commanded by the Divine to sacrifice his son, could break his neck with a solitary twist. However Abraham's chosen method involves the silvery steel knife he grips in his other palm, ready to slit the boy's throat. A certain element stands out – whoever posed as Isaac for this breathtaking piece demonstrated extraordinary acting ability. There exists not just fear, surprise and begging in his shadowed gaze but also profound grief that a guardian could betray him so utterly.

The artist took a familiar biblical tale and made it so vibrant and visceral that its terrors appeared to happen directly in view of the viewer

Viewing in front of the artwork, viewers identify this as a actual countenance, an accurate record of a adolescent model, because the identical boy – identifiable by his tousled hair and almost dark pupils – features in two additional works by the master. In each case, that highly expressive face commands the scene. In John the Baptist, he gazes mischievously from the shadows while embracing a ram. In Victorious Cupid, he grins with a hardness learned on the city's streets, his dark plumed appendages sinister, a naked adolescent running riot in a well-to-do dwelling.

Victorious Cupid, presently displayed at a British gallery, constitutes one of the most discomfiting artworks ever painted. Observers feel completely unsettled gazing at it. The god of love, whose darts inspire people with frequently painful longing, is shown as a very tangible, vividly illuminated nude form, straddling overturned items that include musical devices, a musical score, metal armour and an architect's T-square. This pile of items echoes, deliberately, the mathematical and architectural gear scattered across the ground in Albrecht Dürer's engraving Melancholy – except here, the gloomy disorder is caused by this grinning Cupid and the mayhem he can unleash.

"Love looks not with the vision, but with the mind, / And therefore is feathered Cupid painted blind," wrote the Bard, just prior to this work was created around 1601. But the painter's god is not unseeing. He stares directly at you. That face – sardonic and ruddy-faced, looking with brazen assurance as he struts unclothed – is the identical one that shrieks in fear in Abraham's Test.

As the Italian master painted his three images of the same distinctive-looking youth in Rome at the dawn of the 17th century, he was the highly acclaimed religious painter in a metropolis ignited by Catholic renewal. Abraham's Offering reveals why he was sought to decorate churches: he could take a scriptural story that had been depicted many times before and make it so new, so unfiltered and physical that the horror appeared to be happening directly before you.

However there was a different 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 early twenties with no teacher or patron in the city, just skill and boldness. The majority of the works with which he caught the sacred metropolis's eye were anything but devout. What could be the very first hangs in London's National Gallery. A youth opens his red mouth in a scream of pain: while reaching out his dirty fingers for a cherry, he has rather been bitten. Boy Bitten By a Lizard is eroticism amid poverty: viewers can discern Caravaggio's dismal room mirrored in the murky waters of the transparent vase.

The boy wears a rose-colored flower in his coiffure – a emblem of the erotic trade in early modern art. Northern Italian artists such as Titian and Jacopo Palma portrayed prostitutes grasping flowers and, in a work lost in the second world war but known through photographs, the master represented a famous female courtesan, holding a bouquet to her bosom. The meaning of all these botanical indicators is obvious: intimacy for purchase.

What are we to interpret of Caravaggio's sensual portrayals of youths – and of one adolescent in particular? It is a inquiry that has split his interpreters ever since he achieved widespread recognition in the twentieth century. The complex past reality is that the artist was not the queer icon that, for instance, the filmmaker put on screen in his twentieth-century film Caravaggio, nor so entirely devout that, as some artistic scholars unbelievably assert, his Youth Holding Fruit is actually a likeness of Christ.

His early works indeed make explicit erotic suggestions, or including offers. It's as if Caravaggio, then a destitute young creator, identified with Rome's prostitutes, offering himself to survive. In the Uffizi, with this idea in mind, viewers might turn to another early creation, the sixteenth-century masterpiece Bacchus, in which the god of wine stares calmly at you as he starts to untie the black sash of his garment.

A few annums after the wine deity, what could have driven Caravaggio to create Victorious Cupid for the artistic collector Vincenzo Giustiniani, when he was finally growing nearly established with prestigious ecclesiastical projects? This profane pagan god revives the sexual challenges of his early paintings but in a more intense, uneasy manner. Fifty years afterwards, its hidden meaning seemed clear: it was a representation of the painter's companion. A English traveller viewed the painting in about 1649 and was told its figure has "the physique and countenance of [Caravaggio's|his] own youth or assistant that laid with him". The name of this adolescent was Cecco.

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