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The young lad screams while his head is firmly gripped, a large thumb digging into his cheek as his father's powerful palm grasps him by the neck. That moment from Abraham's Sacrifice visits the Florentine museum, evoking distress through the artist's harrowing portrayal of the suffering youth from the biblical account. The painting seems as if the patriarch, instructed by the Divine to sacrifice his offspring, could break his spinal column with a solitary turn. Yet Abraham's preferred method involves the silvery grey knife he grips in his remaining palm, prepared to slit Isaac's neck. One certain aspect remains – whomever posed as Isaac for this breathtaking piece demonstrated extraordinary expressive skill. Within exists not only fear, shock and begging in his shadowed gaze but also profound grief that a guardian could betray him so utterly.

He adopted a well-known biblical tale and transformed it so fresh and raw that its terrors seemed to unfold right in front of you

Viewing in front of the painting, viewers identify this as a actual countenance, an precise record of a adolescent model, because the same boy – identifiable by his tousled hair and almost black eyes – features in two other works by Caravaggio. In every case, that highly expressive face commands the scene. In Youth With a Ram, he gazes playfully from the darkness while holding a lamb. In Amor Vincit Omnia, he smirks with a toughness learned on Rome's alleys, his dark feathery appendages sinister, a unclothed adolescent creating riot in a affluent dwelling.

Victorious Cupid, presently exhibited at a London museum, represents one of the most discomfiting artworks ever created. Viewers feel totally unsettled gazing at it. The god of love, whose arrows fill people with often agonizing longing, is portrayed as a extremely real, vividly illuminated nude figure, straddling overturned objects that comprise stringed devices, a musical score, plate armour and an builder's T-square. This heap of possessions echoes, deliberately, the geometric and construction equipment scattered across the floor in the German master's engraving Melencolia I – except in this case, the gloomy disorder is created by this grinning deity and the mayhem he can release.

"Affection looks not with the eyes, but with the soul, / And therefore is feathered Cupid painted blind," wrote the Bard, shortly before this work was created around the early 1600s. But Caravaggio's god is not blind. He gazes straight at you. That face – sardonic and rosy-cheeked, looking with brazen assurance as he struts unclothed – is the identical one that screams in fear in Abraham's Test.

When Michelangelo Merisi da Caravaggio created his three images of the identical distinctive-looking youth in Rome at the dawn of the seventeenth century, he was the highly celebrated religious painter in a metropolis enflamed by religious revival. Abraham's Offering demonstrates why he was sought to adorn sanctuaries: he could take a biblical narrative that had been portrayed many occasions before and make it so fresh, so unfiltered and visceral that the terror appeared to be happening directly before you.

However there existed another aspect to the artist, apparent as soon as he arrived in the capital in the winter that ended 1592, as a painter in his early 20s with no mentor or supporter in the city, only skill and audacity. Most of the works with which he captured the sacred city's attention were anything but holy. What may be the absolute earliest resides in the UK's art museum. A young man opens his crimson mouth in a yell of agony: while reaching out his dirty fingers for a cherry, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid poverty: observers can see Caravaggio's gloomy room mirrored in the murky waters of the glass container.

The adolescent wears a pink flower in his coiffure – a symbol of the sex commerce in early modern painting. Northern Italian artists such as Titian and Jacopo Palma portrayed prostitutes holding flowers and, in a work destroyed in the WWII but documented through photographs, the master portrayed a renowned woman courtesan, clutching a bouquet to her chest. The message of all these floral signifiers is obvious: sex for purchase.

How are we to interpret of the artist's erotic depictions of boys – and of a particular adolescent in particular? It is a question that has split his commentators ever since he achieved mega-fame in the twentieth century. The complicated historical reality is that the painter was not the homosexual icon that, for instance, the filmmaker presented on film in his twentieth-century film Caravaggio, nor so completely pious that, as some artistic scholars improbably assert, his Youth Holding Fruit is in fact a likeness of Jesus.

His early works do offer explicit erotic suggestions, or including propositions. It's as if Caravaggio, then a destitute young creator, aligned with Rome's sex workers, selling himself to live. In the Uffizi, with this thought in consideration, observers might turn to another initial creation, the sixteenth-century masterwork the god of wine, in which the god of alcohol stares coolly at the spectator as he starts to undo the dark sash of his robe.

A several annums after Bacchus, what could have driven Caravaggio to paint Victorious Cupid for the art collector Vincenzo Giustiniani, when he was finally becoming almost established with important ecclesiastical projects? This unholy non-Christian deity revives the sexual challenges of his initial works but in a more powerful, uneasy manner. Half a century afterwards, its hidden meaning seemed clear: it was a portrait of the painter's lover. A British traveller viewed the painting in about 1649 and was told its subject has "the physique and countenance of [Caravaggio's|his] owne boy or servant that laid with him". The name of this boy was Francesco.

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