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A youthful lad screams while his skull is forcefully held, a large digit digging into his face as his father's mighty hand grasps him by the throat. This scene from The Sacrifice of Isaac visits the Florentine museum, evoking distress through the artist's harrowing rendition of the tormented child from the scriptural narrative. It seems as if the patriarch, commanded by God to sacrifice his offspring, could snap his spinal column with a solitary twist. However Abraham's chosen method involves the metallic steel knife he grips in his other hand, prepared to slit Isaac's neck. A definite element stands out – whomever modeled as Isaac for this breathtaking work demonstrated extraordinary expressive ability. Within exists not just fear, surprise and pleading in his darkened gaze but also profound grief that a guardian could abandon him so utterly.

He adopted a familiar scriptural story and transformed it so vibrant and visceral that its horrors seemed to happen right in front of you

Standing before the artwork, viewers identify this as a actual countenance, an precise record of a adolescent model, because the same boy – recognizable by his disheveled locks and almost black eyes – appears in several additional paintings by Caravaggio. In each case, that richly expressive face dominates the composition. In John the Baptist, he gazes playfully from the shadows while holding a lamb. In Victorious Cupid, he smirks with a hardness learned on the city's streets, his dark plumed appendages demonic, a naked adolescent creating riot in a well-to-do residence.

Amor Vincit Omnia, presently exhibited at a British museum, constitutes one of the most embarrassing masterpieces ever painted. Observers feel totally disoriented gazing at it. The god of love, whose darts fill people with often painful longing, is portrayed as a extremely tangible, brightly lit unclothed form, straddling overturned items that include musical devices, a musical manuscript, metal armour and an builder's T-square. This pile of items resembles, intentionally, the mathematical and construction equipment strewn across the ground in Albrecht Dürer's print Melancholy – except here, the gloomy mess is caused by this smirking deity and the mayhem he can unleash.

"Love sees not with the eyes, but with the soul, / And thus is winged Love depicted blind," wrote the Bard, shortly before this painting was produced around 1601. But the painter's Cupid is not unseeing. He stares straight at the observer. That countenance – ironic and ruddy-faced, staring with bold confidence as he poses unclothed – is the same one that shrieks in terror in Abraham's Test.

As the Italian master created his three images of the same unusual-looking youth in the Eternal City at the dawn of the seventeenth century, he was the most celebrated sacred painter in a metropolis ignited by Catholic renewal. The Sacrifice of Isaac reveals why he was commissioned to decorate churches: he could adopt a biblical story that had been depicted many occasions previously and make it so new, so unfiltered and physical that the terror seemed to be occurring immediately before the spectator.

Yet there was a different side to the artist, apparent as soon as he arrived in Rome in the cold season that concluded 1592, as a painter in his early twenties with no teacher or patron in the city, just skill and boldness. Most of the works with which he captured the holy metropolis's eye were anything but devout. What could be the very earliest hangs in London's National Gallery. A young man parts his crimson lips in a scream of pain: while stretching out his dirty fingers for a fruit, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid squalor: viewers can see the painter's dismal room reflected in the cloudy liquid of the transparent container.

The boy sports a rose-colored flower in his hair – a emblem of the sex trade in Renaissance painting. Northern Italian artists such as Tiziano and Jacopo Palma depicted courtesans grasping blooms and, in a painting destroyed in the WWII but known through photographs, Caravaggio represented a famous female courtesan, holding a bouquet to her bosom. The message of all these botanical signifiers is obvious: sex for purchase.

What are we to make of the artist's sensual depictions of boys – and of one adolescent in specific? It is a question that has divided his commentators ever since he gained widespread recognition in the twentieth century. The complicated past truth is that the artist was neither the homosexual hero that, for example, the filmmaker presented on screen in his 1986 movie about the artist, nor so completely pious that, as some art historians unbelievably claim, his Youth Holding Fruit is in fact a likeness of Christ.

His initial paintings do make overt sexual implications, or even propositions. It's as if the painter, then a penniless youthful creator, identified with the city's prostitutes, offering himself to survive. In the Florentine gallery, with this idea in mind, viewers might look to another early creation, the 1596 masterwork Bacchus, in which the deity of alcohol gazes calmly at the spectator as he starts to untie the dark ribbon of his robe.

A several years following the wine deity, what could have driven the artist to create Victorious Cupid for the artistic patron the nobleman, when he was at last growing nearly respectable with important church commissions? This unholy pagan deity resurrects the erotic provocations of his initial paintings but in a increasingly intense, unsettling way. Fifty years afterwards, its secret seemed clear: it was a representation of the painter's lover. A British visitor saw the painting in about 1649 and was told its subject has "the physique and countenance of [Caravaggio's|his] owne youth or servant that laid with him". The identity of this boy was Francesco.

The artist had been deceased for about forty annums when this account was recorded.