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The young boy cries out while his head is firmly gripped, a massive digit pressing into his face as his parent's mighty palm holds him by the neck. That scene from The Sacrifice of Isaac visits the Uffizi Gallery, creating unease through the artist's chilling portrayal of the tormented child from the scriptural narrative. The painting seems as if the patriarch, commanded by the Divine to kill his offspring, could break his neck with a solitary twist. Yet Abraham's preferred method involves the metallic steel blade he holds in his remaining palm, prepared to slit Isaac's throat. A definite element remains – whoever posed as Isaac for this astonishing piece demonstrated remarkable expressive skill. There exists not only dread, surprise and begging in his shadowed gaze but also profound sorrow that a protector could abandon him so completely.

He adopted a well-known biblical story and transformed it so fresh and raw that its horrors appeared to unfold right in front of the viewer

Standing before the painting, observers identify this as a actual countenance, an precise depiction of a adolescent subject, because the same youth – recognizable by his tousled hair and almost dark eyes – features in several additional works by Caravaggio. In each case, that highly emotional visage dominates the scene. In John the Baptist, he gazes playfully from the shadows while holding a ram. In Victorious Cupid, he smirks with a toughness acquired on the city's streets, his black plumed appendages sinister, a unclothed adolescent creating riot in a affluent residence.

Victorious Cupid, presently exhibited at a London gallery, represents one of the most embarrassing masterpieces ever created. Viewers feel totally unsettled looking at it. The god of love, whose darts fill people with frequently painful longing, is portrayed as a very tangible, vividly lit nude form, straddling overturned items that comprise stringed instruments, a musical manuscript, metal armour and an architect's ruler. This heap of possessions resembles, intentionally, the mathematical and architectural equipment scattered across the floor in Albrecht Dürer's engraving Melancholy – save here, the gloomy mess is created by this smirking deity and the turmoil he can release.

"Affection sees not with the vision, but with the mind, / And thus is winged Love painted blind," wrote Shakespeare, shortly prior to this painting was created around the early 1600s. But the painter's Cupid is not blind. He gazes straight at the observer. That countenance – ironic and ruddy-faced, looking with brazen assurance as he struts naked – is the same one that screams in fear in Abraham's Test.

As the Italian master created his three images of the identical unusual-looking youth in Rome at the dawn of the seventeenth century, he was the most celebrated religious painter in a metropolis enflamed by religious renewal. The Sacrifice of Isaac demonstrates why he was commissioned to decorate churches: he could take a biblical narrative that had been portrayed numerous times before and make it so new, so unfiltered and physical that the horror appeared to be occurring immediately in front of you.

Yet there was another aspect to Caravaggio, apparent as soon as he arrived in Rome in the winter that ended 1592, as a artist in his initial twenties with no mentor or supporter in the urban center, just talent and boldness. Most of the works with which he captured the holy city's eye were everything but devout. That may be the very first hangs in the UK's art museum. A youth opens his crimson lips in a yell of pain: while stretching out his dirty digits for a cherry, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid poverty: viewers can discern the painter's gloomy room mirrored in the murky liquid of the glass container.

The boy wears a rose-colored flower in his hair – a emblem of the erotic commerce in Renaissance art. Venetian painters such as Titian and Jacopo Palma depicted prostitutes grasping flowers and, in a work destroyed in the second world war but documented through images, Caravaggio represented a famous woman prostitute, holding a bouquet to her chest. The meaning of all these floral signifiers is obvious: intimacy for purchase.

What are we to make of the artist's sensual portrayals of youths – and of one boy in particular? It is a question that has divided his commentators since he achieved mega-fame in the 1980s. The complex historical reality is that the artist was neither the queer icon that, for instance, Derek Jarman put on film in his twentieth-century film Caravaggio, nor so entirely devout that, as some art historians unbelievably claim, his Boy With a Basket of Fruit is actually a likeness of Christ.

His initial paintings do offer explicit sexual suggestions, or including offers. It's as if Caravaggio, then a penniless youthful artist, identified with the city's prostitutes, offering himself to live. In the Uffizi, with this thought in mind, observers might look to another initial creation, the sixteenth-century masterwork Bacchus, in which the god of alcohol gazes coolly at the spectator as he starts to undo the black sash of his garment.

A few years after the wine deity, what could have driven 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 god revives the sexual challenges of his initial works but in a increasingly powerful, unsettling way. Fifty years afterwards, its secret seemed clear: it was a portrait of Caravaggio's companion. A British visitor viewed Victorious Cupid in about the mid-seventeenth century and was informed its figure has "the physique and countenance of [Caravaggio's|his] owne boy or assistant that slept with him". The name of this adolescent was Francesco.

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