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A young lad screams as his head is firmly gripped, a large digit pressing into his cheek as his father's mighty palm holds him by the neck. That scene from The Sacrifice of Isaac visits the Florentine museum, creating unease through Caravaggio's chilling portrayal of the suffering youth from the biblical narrative. It seems as if the patriarch, commanded by the Divine to sacrifice his offspring, could break his neck with a solitary turn. Yet the father's chosen approach involves the metallic grey knife he holds in his other palm, prepared to cut the boy's throat. A definite aspect stands out – whoever posed as Isaac for this astonishing work demonstrated remarkable expressive ability. There exists not only dread, shock and begging in his shadowed gaze but also deep sorrow that a guardian could abandon him so utterly.

He took a familiar scriptural story and transformed it so fresh and raw that its terrors appeared to unfold directly in view of the viewer

Standing in front of the artwork, viewers identify this as a actual face, an precise depiction of a adolescent model, because the same youth – identifiable by his tousled hair and almost dark eyes – features in several other works by the master. In each case, that richly expressive face commands the scene. In Youth With a Ram, he gazes mischievously from the darkness while embracing a ram. In Amor Vincit Omnia, he smirks with a toughness acquired on the city's alleys, his black feathery appendages sinister, a naked adolescent running riot in a well-to-do dwelling.

Victorious Cupid, presently displayed at a British museum, constitutes one of the most embarrassing masterpieces ever painted. Observers feel totally disoriented looking at it. The god of love, whose darts inspire people with frequently agonizing longing, is portrayed as a very real, brightly lit nude figure, standing over toppled-over objects that comprise musical instruments, a music score, metal armour and an builder's T-square. This heap of items resembles, deliberately, the geometric and architectural equipment strewn across the ground in Albrecht Dürer's print Melancholy – save here, the melancholic disorder is caused by this smirking deity and the turmoil he can release.

"Affection sees not with the vision, but with the soul, / And thus is feathered Cupid depicted sightless," penned the Bard, shortly before this painting was created around 1601. But Caravaggio's god is not unseeing. He gazes directly at you. That countenance – sardonic and ruddy-faced, staring with bold confidence as he struts unclothed – is the identical one that screams in terror in Abraham's Test.

As the Italian master painted his three images of the identical distinctive-looking youth in the Eternal City at the start of the 17th century, he was the highly acclaimed religious artist in a city enflamed by Catholic renewal. Abraham's Offering reveals why he was sought to decorate sanctuaries: he could take a scriptural narrative that had been portrayed numerous times before and make it so fresh, so unfiltered and physical that the horror seemed to be occurring immediately before you.

Yet there was a different aspect to the artist, apparent as quickly as he arrived in Rome in the cold season that ended the sixteenth century, as a painter in his early 20s with no teacher or supporter in the urban center, just talent and audacity. Most of the works with which he captured the sacred city's eye were everything but holy. What may be the absolute first resides in the UK's art museum. A youth opens his crimson mouth in a scream of agony: while reaching out his filthy digits for a cherry, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid squalor: viewers can see Caravaggio's gloomy chamber mirrored in the cloudy liquid of the transparent vase.

The boy sports a rose-colored flower in his coiffure – a emblem of the erotic commerce in early modern painting. Northern Italian artists such as Titian and Jacopo Palma depicted courtesans grasping flowers and, in a painting lost in the WWII but documented through photographs, the master represented a renowned female prostitute, holding a bouquet to her bosom. The meaning of all these botanical indicators is obvious: intimacy for purchase.

How are we to make of the artist's sensual depictions of youths – and of one adolescent in specific? It is a inquiry that has split his commentators ever since he gained widespread recognition in the 1980s. The complex past reality is that the artist was neither the queer hero that, for example, Derek Jarman presented on film in his twentieth-century film Caravaggio, nor so completely devout that, as some artistic historians unbelievably claim, his Boy With a Basket of Fruit is in fact a likeness of Christ.

His early paintings indeed make explicit sexual implications, or including propositions. It's as if Caravaggio, then a destitute youthful creator, identified with the city's sex workers, offering himself to survive. In the Florentine gallery, with this idea in mind, observers might turn to another early creation, the sixteenth-century masterpiece Bacchus, in which the deity of wine stares calmly at the spectator as he starts to untie the black sash of his robe.

A few annums following Bacchus, what could have motivated Caravaggio to paint Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was finally growing nearly established with prestigious church commissions? This profane non-Christian deity resurrects the erotic provocations of his initial works but in a increasingly intense, unsettling way. Fifty years later, its secret seemed obvious: it was a portrait of the painter's companion. A British visitor viewed the painting in about the mid-seventeenth century and was told its figure has "the physique and countenance of [Caravaggio's|his] owne boy or assistant that laid with him". The name of this adolescent was Francesco.

The artist had been dead for about forty years when this account was documented.