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A youthful lad cries out while his skull is forcefully gripped, a large thumb digging into his cheek as his father's mighty palm holds him by the neck. This moment from The Sacrifice of Isaac appears in the Florentine museum, evoking unease through Caravaggio's chilling portrayal of the tormented child from the biblical account. It appears as if Abraham, commanded by the Divine to kill his offspring, could snap his spinal column with a single twist. Yet the father's preferred method involves the silvery grey blade he holds in his remaining hand, ready to cut Isaac's throat. One certain element stands out – whoever posed as the sacrifice for this breathtaking piece displayed remarkable expressive ability. There exists not only fear, surprise and begging in his darkened gaze but also profound sorrow that a protector could abandon him so completely.

The artist adopted a familiar biblical story and transformed it so fresh and raw that its horrors appeared to unfold directly in front of you

Standing before the artwork, observers recognize this as a real countenance, an accurate record of a adolescent subject, because the identical boy – identifiable by his disheveled hair and nearly black pupils – features in several other works by Caravaggio. In each instance, that highly expressive visage dominates the scene. In John the Baptist, he gazes playfully from the shadows while holding a lamb. In Amor Vincit Omnia, he grins with a toughness learned on the city's streets, his dark feathery appendages sinister, a unclothed adolescent running riot in a affluent dwelling.

Amor Vincit Omnia, presently exhibited at a London gallery, represents one of the most discomfiting artworks ever created. Viewers feel totally disoriented looking at it. Cupid, whose arrows fill people with frequently agonizing longing, is shown as a extremely tangible, brightly illuminated nude figure, straddling overturned items that comprise musical devices, a music manuscript, plate armor and an builder's ruler. This pile of possessions echoes, intentionally, the mathematical and construction gear scattered across the ground in Albrecht Dürer's engraving Melancholy – except here, the melancholic mess is created by this grinning deity and the mayhem he can release.

"Love looks not with the vision, but with the soul, / And therefore is feathered Cupid painted blind," penned Shakespeare, shortly prior to this work was created around 1601. But Caravaggio's god is not blind. He stares directly at you. That countenance – sardonic and ruddy-cheeked, looking with brazen confidence as he poses unclothed – is the identical one that screams in fear in Abraham's Test.

When the Italian master created his three portrayals of the same distinctive-looking youth in the Eternal City at the start of the seventeenth century, he was the most celebrated sacred artist in a city enflamed by Catholic renewal. Abraham's Offering demonstrates why he was sought to decorate churches: he could take a scriptural story that had been depicted numerous occasions before and make it so fresh, so raw and visceral that the horror seemed to be occurring directly in front of you.

Yet there was another aspect to Caravaggio, apparent as soon as he arrived in Rome in the winter that concluded 1592, as a artist in his initial twenties with no mentor or patron in the city, just skill and audacity. Most of the works with which he caught the sacred city's attention were anything but holy. That could be the absolute earliest hangs in London's National Gallery. A young man parts his red lips in a scream of pain: while reaching out his filthy fingers for a cherry, he has instead been attacked. Youth Bitten by a Reptile is sensuality amid poverty: viewers can discern Caravaggio's dismal chamber reflected in the cloudy liquid of the transparent container.

The adolescent wears a rose-colored blossom in his coiffure – a symbol of the sex commerce in early modern painting. Northern Italian artists such as Titian and Palma Vecchio portrayed prostitutes holding flowers and, in a painting destroyed in the second world war but documented through images, Caravaggio portrayed a renowned female prostitute, clutching a posy to her chest. The meaning of all these floral signifiers is obvious: sex for purchase.

What are we to interpret of the artist's erotic portrayals of youths – and of one adolescent in particular? It is a question that has split his interpreters since he gained mega-fame in the twentieth century. The complex past reality is that the artist was neither the homosexual icon that, for example, Derek Jarman presented on film in his 1986 movie about the artist, nor so completely devout that, as some artistic scholars unbelievably assert, his Youth Holding Fruit is actually a portrait of Christ.

His initial paintings indeed offer explicit erotic implications, or even offers. It's as if the painter, then a penniless youthful creator, aligned with the city's prostitutes, offering himself to live. In the Florentine gallery, with this idea in consideration, observers might look to another initial creation, the 1596 masterpiece the god of wine, in which the god of alcohol gazes calmly at you as he begins to untie the dark ribbon of his garment.

A several annums after Bacchus, what could have driven the artist to create Victorious Cupid for the artistic patron the nobleman, when he was at last becoming almost respectable with important church commissions? This unholy non-Christian god resurrects the sexual challenges of his early works but in a more powerful, unsettling manner. Half a century later, its secret seemed clear: it was a portrait of Caravaggio's lover. A British traveller viewed Victorious Cupid in about 1649 and was told its subject has "the body & face of [Caravaggio's|his] own boy or assistant that slept with him". The name of this adolescent was Francesco.

The painter had been dead for about forty annums when this account was recorded.