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A youthful lad screams as his skull is firmly gripped, a massive thumb pressing into his face as his parent's powerful hand grasps him by the neck. This scene from The Sacrifice of Isaac appears in the Florentine museum, creating unease through Caravaggio's harrowing rendition of the tormented youth from the scriptural narrative. It seems as if Abraham, instructed by God to sacrifice his offspring, could snap his spinal column with a solitary twist. Yet Abraham's chosen approach involves the silvery steel blade he holds in his remaining hand, ready to cut the boy's throat. One definite element remains – whomever posed as Isaac for this astonishing piece demonstrated remarkable expressive skill. There exists not just dread, shock and begging in his darkened gaze but additionally deep grief that a guardian could abandon him so completely.

He took a familiar biblical story and transformed it so fresh and raw that its terrors appeared to happen right in view of you

Standing before the painting, viewers identify this as a actual countenance, an accurate depiction of a young subject, because the same youth – identifiable by his disheveled hair and nearly black pupils – features in several other paintings by Caravaggio. In every instance, that richly expressive visage commands the scene. In Youth With a Ram, he gazes mischievously from the darkness while holding a lamb. In Amor Vincit Omnia, he smirks with a toughness learned on Rome's streets, his black feathery appendages demonic, a unclothed adolescent running riot in a affluent residence.

Victorious Cupid, currently exhibited at a British gallery, represents one of the most embarrassing masterpieces ever painted. Observers feel completely disoriented gazing at it. Cupid, whose arrows fill people with often agonizing longing, is shown as a very tangible, vividly illuminated nude figure, standing over overturned objects that include musical devices, a musical score, metal armour and an builder's ruler. This pile of possessions echoes, deliberately, the geometric and architectural equipment scattered across the floor in the German master's print Melencolia I – except in this case, the gloomy mess is created by this smirking deity and the turmoil he can release.

"Affection sees not with the eyes, but with the mind, / And thus is winged Cupid painted blind," wrote Shakespeare, just prior to this painting was created around 1601. But the painter's god is not blind. He gazes straight at you. That countenance – ironic and ruddy-faced, staring with bold assurance as he poses unclothed – is the same one that shrieks in fear in Abraham's Test.

When Michelangelo Merisi da Caravaggio created his three portrayals of the same distinctive-appearing kid in the Eternal City at the start of the seventeenth century, he was the most acclaimed sacred painter in a metropolis enflamed by religious renewal. Abraham's Offering reveals why he was sought to adorn churches: he could take a biblical story that had been depicted numerous times previously and render it so fresh, so raw and visceral that the horror appeared to be occurring immediately before you.

However there was a different aspect to the artist, evident as soon as he arrived in the capital in the winter that ended the sixteenth century, as a artist in his early twenties with no mentor or patron in the urban center, just talent and boldness. The majority of the works with which he caught the sacred city's eye were everything but holy. That could be the very earliest resides in London's National Gallery. A young man parts his crimson mouth in a yell of pain: while reaching out his filthy fingers for a cherry, he has instead been attacked. Youth Bitten by a Reptile is eroticism amid squalor: viewers can discern Caravaggio's gloomy room reflected in the cloudy waters of the transparent vase.

The adolescent sports a rose-colored blossom in his coiffure – a symbol of the sex trade in early modern painting. Northern Italian artists such as Tiziano and Jacopo Palma portrayed prostitutes holding blooms and, in a work lost in the second world war but known through photographs, Caravaggio represented a famous woman prostitute, holding a posy to her bosom. The meaning of all these botanical indicators is obvious: intimacy for purchase.

What are we to make of Caravaggio's sensual depictions of youths – and of one adolescent in specific? It is a inquiry that has divided his interpreters since he achieved widespread recognition in the twentieth century. The complicated historical truth is that the artist was not the queer hero that, for example, Derek Jarman put on screen in his 1986 film Caravaggio, nor so entirely devout that, as certain art scholars improbably claim, his Boy With a Basket of Fruit is actually a portrait of Christ.

His initial paintings indeed offer overt erotic suggestions, or even offers. It's as if the painter, then a destitute youthful artist, aligned with Rome's prostitutes, selling himself to live. In the Uffizi, with this idea in mind, observers might turn to an additional initial creation, the 1596 masterwork Bacchus, in which the deity of alcohol gazes calmly at you as he begins to untie the dark ribbon of his garment.

A few annums following the wine deity, what could have driven the artist to create Victorious Cupid for the artistic collector the nobleman, when he was finally becoming almost established with important church projects? This profane non-Christian deity revives the erotic provocations of his initial works but in a increasingly intense, uneasy way. Half a century afterwards, its secret seemed clear: it was a representation of Caravaggio's lover. A British traveller viewed the painting in about the mid-seventeenth century and was told its figure has "the physique and countenance of [Caravaggio's|his] owne boy or servant that laid with him". The identity of this adolescent was Francesco.

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