What was the black-winged god of desire? The insights this masterpiece reveals about the rebellious genius

The young boy screams as his skull is forcefully gripped, a large digit digging into his face as his parent's mighty hand holds him by the neck. This scene from The Sacrifice of Isaac appears in the Uffizi Gallery, evoking distress through the artist's harrowing rendition of the suffering youth from the scriptural account. It appears as if Abraham, commanded by God to kill his son, could snap his neck with a single twist. However Abraham's chosen method involves the metallic steel blade he grips in his other hand, prepared to slit Isaac's neck. One definite element stands out – whomever modeled as the sacrifice for this astonishing work demonstrated extraordinary acting ability. There exists not just fear, shock and begging in his shadowed eyes but also profound grief that a protector could abandon him so utterly.

The artist adopted a well-known biblical tale and made it so vibrant and visceral that its horrors seemed to unfold right in view of the viewer

Viewing in front of the painting, viewers identify this as a actual face, an accurate record of a adolescent subject, because the same youth – recognizable by his tousled hair and almost dark eyes – appears in several other works by Caravaggio. In every case, that highly emotional visage dominates the scene. In Youth With a Ram, he peers mischievously from the shadows while embracing a ram. In Victorious Cupid, he smirks with a hardness learned on Rome's alleys, his dark plumed wings sinister, a unclothed child running chaos in a affluent residence.

Amor Vincit Omnia, presently exhibited at a London gallery, constitutes one of the most embarrassing artworks ever painted. Viewers feel completely unsettled looking at it. The god of love, whose arrows fill people with often agonizing longing, is portrayed as a extremely real, brightly lit nude form, straddling toppled-over items that include musical devices, a musical manuscript, metal armour and an architect's ruler. This heap of items resembles, intentionally, the mathematical and construction equipment strewn across the ground in Albrecht Dürer's engraving Melencolia I – save in this case, the melancholic disorder is created by this grinning deity and the mayhem he can unleash.

"Love looks not with the vision, but with the mind, / And thus is feathered Cupid painted blind," wrote the Bard, just prior to this painting was produced around the early 1600s. But Caravaggio's god is not blind. He gazes directly at the observer. That countenance – ironic and ruddy-faced, staring with brazen assurance as he struts unclothed – is the same one that shrieks in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio painted his three portrayals of the same unusual-looking kid in the Eternal City at the start of the 17th century, he was the highly acclaimed religious painter in a metropolis enflamed by religious revival. The Sacrifice of Isaac reveals why he was sought to adorn sanctuaries: he could take a biblical story that had been depicted numerous times before and make it so fresh, so unfiltered and physical that the terror seemed to be happening directly before you.

However there was another aspect to Caravaggio, apparent as quickly as he came in Rome in the winter that ended the sixteenth century, as a painter in his early 20s with no mentor or supporter in the urban center, just talent and audacity. Most of the works with which he captured the sacred metropolis's eye were everything but devout. What could be the absolute first resides in the UK's art museum. A youth parts his crimson lips in a scream of pain: while reaching out his dirty fingers for a cherry, he has instead been bitten. Youth Bitten by a Reptile is sensuality amid squalor: viewers can see Caravaggio's dismal chamber reflected in the murky waters of the transparent container.

The adolescent wears a rose-colored flower in his hair – a emblem of the erotic commerce in early modern art. Venetian artists such as Titian and Palma Vecchio portrayed courtesans grasping blooms and, in a work destroyed in the WWII but known through images, Caravaggio portrayed a renowned woman courtesan, clutching a posy to her chest. The meaning of all these botanical signifiers is clear: intimacy for sale.

What are we to make of Caravaggio's erotic portrayals of youths – and of a particular boy in specific? It is a inquiry that has split his interpreters ever since he achieved widespread recognition in the 1980s. The complicated historical truth is that the painter was neither the queer hero that, for instance, the filmmaker put on screen in his 1986 movie about the artist, nor so entirely devout that, as some artistic historians improbably claim, his Youth Holding Fruit is in fact a likeness of Christ.

His initial paintings do make overt erotic suggestions, or even offers. It's as if the painter, then a penniless young creator, aligned with Rome's prostitutes, selling himself to live. In the Uffizi, with this idea in consideration, observers might look to an additional initial creation, the sixteenth-century masterwork the god of wine, in which the deity of alcohol stares coolly at the spectator as he starts to undo the dark ribbon of his garment.

A several years following Bacchus, what could have motivated the artist to paint Amor Vincit Omnia for the artistic collector the nobleman, when he was finally becoming almost respectable with prestigious church projects? This unholy non-Christian god resurrects the sexual challenges of his initial paintings but in a increasingly intense, uneasy way. Half a century later, its secret seemed obvious: it was a portrait of Caravaggio's lover. A British visitor viewed the painting in about 1649 and was informed its subject has "the body & face of [Caravaggio's|his] own youth or assistant that slept with him". The name of this boy was Cecco.

The artist had been dead for about forty annums when this story was documented.