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A youthful lad cries out while his skull is firmly gripped, a massive digit pressing into his face as his parent's mighty palm grasps him by the neck. This scene from Abraham's Sacrifice visits the Florentine museum, evoking unease through the artist's harrowing rendition of the suffering child from the scriptural account. It seems as if the patriarch, instructed by the Divine to kill his son, could break his neck with a single turn. However the father's preferred method involves the silvery grey blade he holds in his remaining hand, prepared to slit Isaac's neck. A definite aspect remains – whoever modeled as Isaac for this breathtaking work displayed extraordinary acting ability. There exists not only dread, shock and pleading in his darkened eyes but also profound grief that a protector could betray him so utterly.

He adopted a familiar biblical tale and transformed it so vibrant and raw that its horrors appeared to happen right in view of you

Viewing in front of the artwork, viewers identify this as a real countenance, an precise record of a adolescent subject, because the same boy – recognizable by his tousled locks and almost dark eyes – appears in two other paintings by the master. In every instance, that highly expressive visage dominates the composition. In John the Baptist, he gazes mischievously from the shadows while holding a ram. In Amor Vincit Omnia, he grins with a toughness learned on the city's streets, his black feathery appendages sinister, a naked adolescent creating chaos in a well-to-do dwelling.

Amor Vincit Omnia, currently displayed at a British gallery, constitutes one of the most discomfiting masterpieces ever created. Observers feel totally unsettled looking at it. The god of love, whose arrows inspire people with often painful desire, is portrayed as a extremely tangible, vividly lit nude figure, straddling toppled-over items that comprise stringed devices, a music score, metal armor and an builder's T-square. This pile of items resembles, deliberately, the mathematical and construction gear strewn across the ground in Albrecht Dürer's print Melancholy – save here, the gloomy disorder is caused by this grinning deity and the turmoil he can unleash.

"Love sees not with the vision, but with the mind, / And thus is winged Cupid depicted sightless," wrote Shakespeare, shortly prior to this painting was created around 1601. But Caravaggio's Cupid is not blind. He stares directly at the observer. That face – sardonic and ruddy-faced, staring with bold assurance as he poses naked – is the same one that shrieks in terror in Abraham's Test.

When the Italian master painted his three images of the same distinctive-appearing youth in Rome at the dawn of the 17th century, he was the most acclaimed sacred artist in a city ignited by Catholic revival. The Sacrifice of Isaac reveals why he was sought to adorn sanctuaries: he could take a biblical story that had been depicted numerous times before and render it so new, so raw and physical that the terror appeared to be occurring immediately before you.

Yet there was another side to the artist, evident as quickly as he came in the capital in the cold season that ended 1592, as a painter in his early 20s with no mentor or patron in the city, only skill and audacity. The majority of the works with which he captured the holy city's attention were anything but holy. What may be the very first resides in London's National Gallery. A youth opens his red mouth in a scream of agony: while stretching out his filthy fingers for a fruit, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid squalor: viewers can discern the painter's gloomy chamber reflected in the cloudy liquid of the transparent vase.

The adolescent sports a pink flower in his coiffure – a emblem of the sex trade in Renaissance painting. Northern Italian painters such as Titian and Palma Vecchio depicted prostitutes holding flowers and, in a work destroyed in the second world war but known through images, Caravaggio portrayed a famous female prostitute, clutching a bouquet to her bosom. The meaning of all these floral indicators is obvious: intimacy for purchase.

How are we to interpret of Caravaggio's sensual depictions of youths – and of a particular boy in particular? It is a inquiry that has divided his commentators since he achieved mega-fame in the twentieth century. The complex historical truth is that the artist was not the queer icon that, for example, the filmmaker presented on film in his twentieth-century film about the artist, nor so entirely pious that, as some art historians unbelievably assert, his Youth Holding Fruit is actually a portrait of Christ.

His early works do make overt erotic implications, or including propositions. It's as if Caravaggio, then a penniless youthful creator, aligned with the city's sex workers, offering himself to live. In the Florentine gallery, with this idea in mind, viewers might turn to another early creation, the sixteenth-century masterpiece the god of wine, in which the god of alcohol stares coolly at the spectator as he begins to untie the black sash of his garment.

A few annums following the wine deity, what could have driven the artist to create Amor Vincit Omnia for the art collector Vincenzo Giustiniani, when he was at last becoming nearly established with important church projects? This profane non-Christian deity revives the sexual provocations of his early paintings but in a more intense, uneasy way. Fifty years later, its secret seemed clear: it was a representation of the painter's companion. A British traveller saw the painting in about the mid-seventeenth century and was told its subject has "the physique and countenance of [Caravaggio's|his] own youth or servant that laid with him". The name of this adolescent was Cecco.

The painter had been deceased for about 40 annums when this account was documented.