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A youthful lad cries out while his head is forcefully gripped, a massive thumb digging into his cheek as his father's mighty palm holds him by the neck. That moment from The Sacrifice of Isaac visits the Florentine museum, creating distress through Caravaggio's chilling rendition of the tormented youth from the scriptural narrative. It appears as if the patriarch, commanded by the Divine to kill his offspring, could break his neck with a single turn. However the father's chosen approach involves the silvery steel knife he holds in his other palm, ready to cut the boy's throat. A definite element remains – whomever posed as Isaac for this breathtaking piece displayed remarkable expressive skill. Within exists not just fear, surprise and begging in his darkened gaze but also deep grief that a guardian could abandon him so completely.

The artist took a familiar scriptural tale and transformed it so fresh and visceral that its horrors seemed to unfold directly in view of the viewer

Standing in front of the painting, viewers recognize this as a real face, an accurate depiction of a adolescent subject, because the identical boy – identifiable by his tousled locks and nearly dark eyes – appears in two other paintings by the master. In every instance, that richly expressive face commands the composition. In Youth With a Ram, he gazes playfully from the darkness while holding a lamb. In Victorious Cupid, he smirks with a toughness acquired on Rome's streets, his dark feathery appendages demonic, a naked adolescent running riot in a well-to-do residence.

Amor Vincit Omnia, presently exhibited at a London museum, constitutes one of the most embarrassing artworks ever painted. Observers feel totally unsettled gazing at it. Cupid, whose darts fill people with frequently agonizing longing, is shown as a extremely tangible, vividly illuminated nude form, standing over overturned items that include musical instruments, a musical manuscript, metal armor and an builder's T-square. This pile of items resembles, intentionally, the mathematical and architectural gear scattered across the ground in Albrecht Dürer's engraving Melencolia I – except here, the gloomy mess is created by this smirking deity and the turmoil he can unleash.

"Love looks not with the eyes, but with the soul, / And therefore is feathered Cupid painted sightless," wrote Shakespeare, just before this work was produced around 1601. But Caravaggio's god is not blind. He gazes straight at you. That countenance – sardonic and rosy-faced, staring with brazen confidence as he struts unclothed – is the same one that screams in terror in The Sacrifice of Isaac.

When the Italian master created his multiple portrayals of the same unusual-appearing kid in the Eternal City at the dawn of the 17th century, he was the most celebrated sacred painter in a metropolis ignited by religious revival. The Sacrifice of Isaac demonstrates why he was sought to decorate sanctuaries: he could adopt a scriptural story that had been depicted numerous times before and render it so fresh, so raw and visceral that the horror seemed to be occurring immediately in front of the spectator.

However there existed a different side to Caravaggio, evident as quickly as he came in the capital in the winter that concluded the sixteenth century, as a painter in his early twenties with no mentor or patron in the city, only talent and audacity. Most of the works with which he caught the holy metropolis's attention were everything but devout. That may be the absolute earliest hangs in the UK's art museum. A youth parts his crimson mouth in a scream of agony: while stretching out his dirty fingers for a cherry, he has rather been bitten. Youth Bitten by a Reptile is sensuality amid squalor: viewers can discern the painter's dismal chamber reflected in the cloudy waters of the transparent container.

The adolescent sports a rose-colored flower in his coiffure – a emblem of the sex trade in Renaissance painting. Venetian painters such as Tiziano and Palma Vecchio portrayed prostitutes grasping blooms and, in a painting lost in the second world war but known through photographs, the master portrayed a renowned female prostitute, holding a posy to her bosom. The meaning of all these botanical signifiers is obvious: sex for purchase.

What are we to make of the artist's erotic portrayals of boys – and of one adolescent in specific? It is a inquiry that has divided his interpreters since he gained widespread recognition in the 1980s. The complex past truth is that the artist was not the queer icon that, for example, the filmmaker put on film in his 1986 movie about the artist, nor so entirely pious that, as certain art scholars unbelievably claim, his Boy With a Basket of Fruit is actually a likeness of Christ.

His initial works do make overt erotic implications, or including offers. It's as if Caravaggio, then a penniless youthful artist, aligned with the city's prostitutes, selling himself to survive. In the Florentine gallery, with this idea in mind, observers might turn to another initial creation, the sixteenth-century masterpiece Bacchus, in which the deity of alcohol stares coolly at the spectator as he begins to undo the dark sash of his robe.

A few annums after Bacchus, what could have motivated Caravaggio to create Victorious Cupid for the art patron Vincenzo Giustiniani, when he was at last growing almost respectable with important church projects? This unholy pagan god revives the erotic provocations of his initial works but in a more powerful, unsettling way. Half a century later, its hidden meaning seemed obvious: it was a representation of Caravaggio's companion. A English visitor viewed Victorious Cupid in about 1649 and was informed its subject has "the physique and countenance of [Caravaggio's|his] own boy or assistant that laid with him". The name of this boy was Francesco.

The artist had been dead for about forty annums when this story was documented.