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The young boy cries out while his skull is firmly held, a large thumb digging into his face as his father's mighty palm grasps him by the throat. That moment from The Sacrifice of Isaac appears in the Uffizi Gallery, evoking unease through the artist's chilling rendition of the tormented child from the scriptural narrative. It seems as if the patriarch, commanded by the Divine to kill his son, could break his spinal column with a single turn. Yet Abraham's chosen method involves the silvery grey blade he grips in his other hand, prepared to cut the boy's neck. A certain element remains – whomever modeled as Isaac for this astonishing piece demonstrated remarkable acting skill. There exists not just fear, shock and begging in his shadowed gaze but also deep grief that a guardian could abandon him so completely.

The artist adopted a familiar biblical story and made it so vibrant and visceral that its horrors appeared to unfold directly in view of you

Viewing before the artwork, viewers identify this as a real face, an accurate record of a adolescent subject, because the identical youth – recognizable by his tousled locks and nearly black pupils – appears in two other paintings by the master. In every instance, that richly emotional visage dominates the composition. In John the Baptist, he gazes playfully from the darkness while holding a lamb. In Victorious Cupid, he smirks with a hardness learned on Rome's streets, his black feathery appendages demonic, a naked adolescent running riot in a affluent dwelling.

Victorious Cupid, currently displayed at a London museum, represents one of the most discomfiting masterpieces ever created. Observers feel totally disoriented looking at it. Cupid, whose arrows fill people with often painful longing, is shown as a extremely tangible, brightly illuminated unclothed figure, standing over overturned items that comprise musical instruments, a music manuscript, plate armour and an builder's ruler. This heap of possessions echoes, intentionally, the geometric and construction gear scattered across the ground in Albrecht Dürer's engraving Melancholy – except in this case, the gloomy mess is caused by this grinning Cupid and the mayhem he can release.

"Affection looks not with the vision, but with the soul, / And therefore is feathered Love painted sightless," wrote Shakespeare, just prior to this painting was created around the early 1600s. But Caravaggio's god is not blind. He gazes directly at you. That countenance – ironic and ruddy-faced, looking with brazen confidence as he struts unclothed – is the identical one that screams in fear in Abraham's Test.

When Michelangelo Merisi da Caravaggio created his multiple images of the identical unusual-looking kid in the Eternal City at the start of the seventeenth century, he was the highly celebrated religious painter in a city ignited by religious revival. Abraham's Offering reveals why he was sought to decorate sanctuaries: he could adopt a biblical narrative that had been portrayed numerous occasions before and make it so new, so raw and physical that the terror seemed to be occurring directly before the spectator.

However there was a different aspect to Caravaggio, apparent as soon as he came in the capital in the winter that ended the sixteenth century, as a painter in his initial twenties with no mentor or supporter in the city, just skill and boldness. Most of the works with which he captured the holy city's eye were anything but holy. That could be the absolute first resides in the UK's art museum. A youth opens his red lips in a scream of agony: while reaching out his dirty fingers for a cherry, he has rather been bitten. Youth Bitten by a Reptile is eroticism amid poverty: observers can discern the painter's dismal chamber reflected in the cloudy waters of the glass vase.

The boy sports a pink flower in his hair – a symbol of the erotic commerce in Renaissance painting. Venetian painters such as Tiziano and Palma Vecchio depicted courtesans holding blooms and, in a work lost in the second world war but documented through images, Caravaggio represented a famous female courtesan, holding a bouquet to her chest. The meaning of all these floral signifiers is clear: sex for purchase.

How are we to make of Caravaggio's sensual depictions of youths – and of a particular boy in particular? It is a question that has divided his commentators since he gained widespread recognition in the twentieth century. The complicated past reality is that the painter was not the queer icon that, for example, Derek Jarman presented on screen in his twentieth-century film Caravaggio, nor so completely pious that, as certain artistic historians improbably claim, his Boy With a Basket of Fruit is in fact a likeness of Jesus.

His early paintings indeed make overt sexual implications, or even propositions. It's as if the painter, then a penniless young creator, aligned with Rome's sex workers, offering himself to survive. In the Florentine gallery, with this thought in mind, viewers might look to an additional initial creation, the sixteenth-century masterpiece the god of wine, in which the god of alcohol stares coolly at the spectator as he starts to undo the black sash of his garment.

A several annums after the wine deity, what could have motivated the artist to create Victorious Cupid for the artistic patron the nobleman, when he was at last growing almost respectable with prestigious ecclesiastical commissions? This profane pagan god resurrects the erotic provocations of his initial paintings but in a more powerful, unsettling way. Half a century later, its hidden meaning seemed clear: it was a portrait of Caravaggio's companion. A English traveller saw Victorious Cupid in about 1649 and was informed its subject has "the body & face of [Caravaggio's|his] own youth or assistant that slept with him". The identity of this boy was Francesco.

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