What exactly was Caravaggio's dark-feathered deity of love? The insights this masterwork reveals about the rebellious genius

A youthful boy cries out while his skull is forcefully gripped, a massive digit pressing into his cheek as his parent's mighty hand grasps him by the throat. This moment from Abraham's Sacrifice appears in the Uffizi Gallery, evoking distress through Caravaggio's chilling portrayal of the suffering youth from the biblical narrative. It seems as if Abraham, instructed by the Divine to kill his offspring, could snap his spinal column with a solitary twist. However the father's chosen method involves the metallic grey blade he grips in his other hand, prepared to cut Isaac's throat. A definite element remains – whomever posed as the sacrifice for this astonishing piece demonstrated remarkable acting ability. There exists not just fear, shock and begging in his shadowed gaze but additionally profound grief that a guardian could abandon him so utterly.

He adopted a well-known biblical story and made it so vibrant and raw that its horrors seemed to happen directly in view of you

Viewing before the painting, observers recognize this as a real face, an accurate record of a adolescent model, because the identical youth – recognizable by his tousled locks and nearly dark eyes – features in several other paintings by Caravaggio. In each instance, that richly expressive visage dominates the scene. In John the Baptist, he gazes mischievously from the darkness while holding a ram. In Amor Vincit Omnia, he grins with a toughness acquired on Rome's streets, his black feathery wings demonic, a unclothed child running chaos in a affluent dwelling.

Victorious Cupid, presently exhibited at a London gallery, constitutes one of the most discomfiting artworks ever created. Viewers feel totally unsettled gazing at it. Cupid, whose darts fill people with frequently painful longing, is portrayed as a extremely tangible, vividly lit nude form, standing over overturned items that comprise musical devices, a music score, plate armour and an architect's ruler. This heap of possessions echoes, deliberately, the mathematical and architectural equipment scattered across the floor in Albrecht Dürer's print Melencolia I – save here, the gloomy disorder is caused by this grinning Cupid and the mayhem he can release.

"Love looks not with the eyes, but with the soul, / And thus is feathered Cupid depicted blind," wrote the Bard, just prior to this work was created around the early 1600s. But the painter's god is not unseeing. He gazes straight at you. That countenance – ironic and ruddy-cheeked, looking with bold confidence as he poses unclothed – is the same one that screams in terror in Abraham's Test.

When the Italian master painted his multiple portrayals of the identical distinctive-appearing kid in Rome at the start of the 17th century, he was the most celebrated religious painter in a metropolis enflamed by Catholic renewal. Abraham's Offering reveals why he was commissioned to adorn sanctuaries: he could adopt a biblical story that had been depicted many occasions before and render it so new, so raw and physical that the terror appeared to be happening immediately before the spectator.

However there was another aspect to the artist, apparent as soon as he came in the capital in the winter that concluded the sixteenth century, as a painter in his initial 20s with no mentor or supporter in the city, only skill and audacity. Most of the paintings with which he captured the sacred metropolis's attention were everything but holy. What may be the very first hangs in the UK's National Gallery. A young man parts his red mouth in a scream of agony: while stretching out his filthy digits for a fruit, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid squalor: observers can discern Caravaggio's gloomy chamber mirrored in the murky liquid of the transparent container.

The adolescent wears a pink blossom in his hair – a symbol of the sex trade in Renaissance painting. Venetian artists such as Tiziano and Jacopo Palma portrayed courtesans grasping blooms and, in a painting destroyed in the second world war but known through photographs, Caravaggio portrayed a famous woman prostitute, holding a posy to her bosom. The meaning of all these botanical indicators is obvious: sex for purchase.

How are we to interpret of the artist's erotic portrayals of boys – and of one boy in specific? It is a question that has divided his interpreters since he achieved mega-fame in the 1980s. The complicated historical truth is that the painter was not the queer hero that, for example, Derek Jarman put on screen in his twentieth-century movie Caravaggio, nor so completely devout that, as some artistic historians unbelievably claim, his Youth Holding Fruit is in fact a likeness of Jesus.

His early works indeed make explicit sexual implications, or even offers. It's as if Caravaggio, then a destitute youthful creator, aligned with the city's prostitutes, selling himself to survive. In the Uffizi, with this thought in consideration, observers might turn to an additional early work, the sixteenth-century masterpiece the god of wine, in which the god of wine stares calmly at you as he starts to untie the black ribbon of his garment.

A several annums after Bacchus, what could have driven the artist to paint Amor Vincit Omnia for the artistic collector Vincenzo Giustiniani, when he was at last becoming almost established with important church projects? This profane non-Christian god resurrects the sexual challenges of his early paintings but in a more intense, uneasy manner. Half a century later, its secret seemed clear: it was a portrait of Caravaggio's companion. A British traveller saw Victorious Cupid in about 1649 and was told its subject has "the physique and countenance of [Caravaggio's|his] owne youth or assistant that laid with him". The name of this adolescent was Francesco.

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