What exactly was the dark-feathered god of desire? What insights this masterpiece reveals about the rogue artist

A youthful boy cries out while his head is forcefully held, a large thumb digging into his cheek as his father's mighty hand grasps him by the neck. That moment from Abraham's Sacrifice visits the Uffizi Gallery, evoking unease through Caravaggio's chilling rendition of the tormented youth from the biblical account. It appears as if Abraham, instructed by God to sacrifice his son, could snap his spinal column with a solitary twist. Yet the father's preferred method involves the silvery steel knife he holds in his other hand, ready to cut Isaac's neck. A certain aspect remains – whoever posed as the sacrifice for this astonishing work displayed remarkable acting ability. Within exists not just fear, surprise and pleading in his darkened gaze but additionally profound grief that a protector could betray him so utterly.

He took a well-known scriptural tale and transformed it so vibrant and raw that its terrors seemed to unfold directly in front of you

Viewing in front of the painting, viewers recognize this as a actual countenance, an precise record of a adolescent model, because the same boy – identifiable by his disheveled hair and almost dark eyes – features in several additional works by Caravaggio. In every case, that highly expressive visage commands the scene. In Youth With a Ram, he peers playfully from the shadows while embracing a ram. In Amor Vincit Omnia, he smirks with a hardness acquired on Rome's streets, his black feathery appendages demonic, a naked adolescent creating chaos in a well-to-do residence.

Victorious Cupid, currently displayed at a London gallery, constitutes one of the most discomfiting artworks ever painted. Viewers feel completely unsettled looking at it. The god of love, whose darts inspire people with often painful longing, is shown as a very tangible, vividly illuminated unclothed form, straddling toppled-over items that include stringed devices, a musical manuscript, plate armour and an builder's ruler. This pile of possessions echoes, intentionally, the mathematical and construction gear strewn across the floor in Albrecht Dürer's print Melencolia I – save in this case, the gloomy disorder is created by this smirking deity and the turmoil he can unleash.

"Affection sees not with the eyes, but with the soul, / And thus is winged Cupid depicted blind," wrote the Bard, shortly before this work was produced around the early 1600s. But Caravaggio's god is not unseeing. He stares directly at you. That face – sardonic and rosy-cheeked, staring with bold assurance as he poses unclothed – is the same one that screams in fear in The Sacrifice of Isaac.

As the Italian master painted his multiple portrayals of the identical distinctive-appearing kid in the Eternal City at the start of the seventeenth century, he was the most acclaimed sacred artist in a city enflamed by religious renewal. The Sacrifice of Isaac reveals why he was commissioned to adorn churches: he could adopt a scriptural narrative that had been portrayed many occasions previously and make it so new, so raw and physical that the terror seemed to be happening immediately before you.

However there was a different aspect to the artist, apparent as quickly as he arrived in the capital in the winter that ended 1592, as a artist in his early 20s with no mentor or patron in the city, only skill and audacity. The majority of the works with which he caught the holy metropolis's attention were everything but holy. That may be the very first hangs in the UK's National Gallery. A young man parts his crimson lips in a scream of pain: while stretching out his filthy digits for a cherry, he has instead been attacked. Youth Bitten by a Reptile is sensuality amid poverty: observers can see the painter's dismal room mirrored in the cloudy liquid of the glass vase.

The boy sports a pink blossom in his hair – a emblem of the sex trade in Renaissance art. Venetian painters such as Titian and Jacopo Palma portrayed prostitutes grasping blooms and, in a painting destroyed in the second world war but documented through photographs, the master portrayed a famous woman courtesan, holding a posy to her chest. The message of all these botanical signifiers is obvious: sex for purchase.

How are we to interpret of the artist's sensual depictions of boys – and of one adolescent in specific? It is a inquiry that has split his commentators since he achieved widespread recognition in the twentieth century. The complex past truth is that the artist was neither the queer icon that, for example, Derek Jarman presented on screen in his twentieth-century movie about the artist, nor so entirely devout that, as certain artistic scholars improbably assert, his Youth Holding Fruit is actually a portrait of Christ.

His early paintings indeed offer overt sexual implications, or including propositions. It's as if the painter, then a penniless young artist, identified with Rome's prostitutes, offering himself to survive. In the Uffizi, with this thought in mind, observers might look to an additional early work, the 1596 masterpiece the god of wine, in which the deity of alcohol gazes calmly at the spectator as he starts to untie the black ribbon of his garment.

A several years following the wine deity, what could have motivated the artist to create Amor Vincit Omnia for the art patron the nobleman, when he was finally becoming almost established with important church projects? This profane pagan deity resurrects the sexual challenges of his early paintings but in a more intense, unsettling manner. Half a century afterwards, its secret seemed clear: it was a portrait of the painter's companion. A English visitor viewed Victorious Cupid in about 1649 and was told its figure has "the body & face of [Caravaggio's|his] owne boy or servant that laid with him". The identity of this boy was Cecco.

The painter had been deceased for about forty years when this account was documented.