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A youthful boy screams while his head is forcefully held, a large thumb pressing into his cheek as his father's mighty palm grasps him by the throat. This moment from Abraham's Sacrifice visits the Uffizi Gallery, creating distress through the artist's harrowing rendition of the suffering youth from the biblical narrative. The painting appears as if the patriarch, commanded by the Divine to sacrifice his son, could snap his neck with a single twist. Yet the father's preferred method involves the metallic steel blade he grips in his other palm, ready to cut Isaac's throat. One certain aspect stands out – whoever posed as the sacrifice for this astonishing piece displayed remarkable acting ability. Within exists not only dread, shock and pleading in his darkened gaze but also profound sorrow that a protector could abandon him so utterly.

The artist adopted a well-known scriptural story and made it so fresh and raw that its horrors appeared to happen right in front of you

Viewing in front of the artwork, viewers identify this as a actual countenance, an precise depiction of a young model, because the same boy – identifiable by his disheveled locks and almost black eyes – features in several additional paintings by the master. In every instance, that highly emotional visage commands the composition. In John the Baptist, he gazes playfully from the shadows while holding a lamb. In Victorious Cupid, he smirks with a toughness acquired on the city's streets, his black plumed wings sinister, a unclothed child creating riot in a well-to-do dwelling.

Amor Vincit Omnia, presently displayed at a London gallery, represents one of the most discomfiting masterpieces ever painted. Observers feel completely disoriented looking at it. The god of love, whose arrows fill people with often agonizing longing, is portrayed as a extremely real, brightly illuminated nude form, straddling overturned items that comprise musical instruments, a music score, metal armour and an architect's ruler. This heap of possessions echoes, intentionally, the mathematical and architectural equipment strewn across the floor in the German master's engraving Melencolia I – save here, the melancholic disorder is caused by this smirking deity and the mayhem he can release.

"Love sees not with the vision, but with the soul, / And thus is feathered Cupid depicted sightless," penned Shakespeare, just 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 assurance as he struts unclothed – is the same one that shrieks in fear in Abraham's Test.

When the Italian master created his multiple images of the identical distinctive-appearing youth in Rome at the start of the 17th century, he was the highly acclaimed religious artist in a city enflamed by religious revival. The Sacrifice of Isaac demonstrates why he was sought to adorn sanctuaries: he could take a scriptural narrative that had been depicted numerous times before and make it so fresh, so raw and physical that the terror appeared to be happening directly in front of you.

Yet there existed another side to Caravaggio, apparent as quickly as he arrived in the capital in the cold season that ended 1592, as a artist in his initial 20s with no teacher or supporter in the city, only skill and boldness. Most of the works with which he captured the holy city's eye were anything but holy. What could be the absolute earliest resides in the UK's art museum. A youth parts his red mouth in a yell of pain: while stretching out his dirty fingers for a cherry, he has instead been attacked. Youth Bitten by a Reptile is sensuality amid squalor: viewers can discern Caravaggio's gloomy chamber mirrored in the cloudy liquid of the transparent vase.

The adolescent sports a pink flower in his coiffure – a symbol of the sex commerce in early modern art. Northern Italian artists such as Tiziano and Palma Vecchio portrayed courtesans grasping flowers and, in a painting lost in the second world war but documented through images, Caravaggio portrayed a renowned female courtesan, clutching a bouquet to her chest. The message of all these botanical indicators is clear: sex for purchase.

What are we to make of the artist's sensual depictions of boys – and of one boy in particular? It is a inquiry that has divided his commentators ever since he achieved widespread recognition in the 1980s. The complex historical reality is that the artist was not the homosexual hero that, for instance, Derek Jarman presented on screen in his twentieth-century movie Caravaggio, nor so entirely pious that, as certain artistic historians improbably claim, his Boy With a Basket of Fruit is in fact a portrait of Christ.

His initial works do make overt sexual suggestions, or even offers. It's as if the painter, then a destitute youthful creator, aligned with the city's prostitutes, selling himself to live. In the Florentine gallery, with this thought in consideration, viewers might turn to another early creation, the sixteenth-century masterpiece Bacchus, in which the god of alcohol stares coolly at the spectator as he begins to undo the black sash of his robe.

A several years following the wine deity, what could have driven the artist to create Amor Vincit Omnia for the art patron the nobleman, when he was finally growing almost respectable with prestigious ecclesiastical commissions? This unholy pagan god resurrects the sexual challenges of his initial paintings but in a more powerful, uneasy way. Fifty years later, its hidden meaning seemed obvious: it was a representation of Caravaggio's companion. A English traveller saw the painting in about the mid-seventeenth century and was told its figure has "the body & face of [Caravaggio's|his] own youth or assistant that slept with him". The name of this adolescent was Cecco.

The painter had been deceased for about forty years when this story was documented.