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The youthful boy cries out as his head is forcefully gripped, a large digit pressing into his cheek as his father's powerful hand holds him by the throat. This scene from The Sacrifice of Isaac appears in the Florentine museum, evoking distress through the artist's chilling rendition of the tormented child from the scriptural narrative. The painting seems as if Abraham, commanded by the Divine to sacrifice his offspring, could snap his neck with a single twist. However the father's preferred approach involves the metallic grey knife he grips in his other palm, prepared to cut Isaac's neck. A definite element remains – whoever posed as the sacrifice for this astonishing piece displayed remarkable acting ability. There exists not only dread, shock and begging in his darkened eyes but additionally deep grief that a protector could abandon him so completely.

He adopted a well-known biblical story and transformed it so vibrant and visceral that its terrors appeared to unfold right in front of the viewer

Viewing before the artwork, observers identify this as a real countenance, an accurate record of a young model, because the same boy – identifiable by his disheveled hair and nearly dark eyes – appears in several additional works by the master. In every case, that highly emotional visage commands the composition. In John the Baptist, he gazes mischievously from the darkness while holding a ram. In Victorious Cupid, he grins with a toughness learned on Rome's alleys, his dark feathery appendages demonic, a unclothed child creating riot in a affluent residence.

Victorious Cupid, currently exhibited at a London gallery, constitutes one of the most discomfiting masterpieces ever created. Viewers feel totally unsettled gazing at it. The god of love, whose darts inspire people with often agonizing desire, is portrayed as a extremely real, brightly illuminated unclothed figure, standing over overturned objects that include stringed instruments, a music manuscript, metal armour and an builder's ruler. This pile of possessions resembles, intentionally, the mathematical and architectural equipment strewn across the ground in Albrecht Dürer's print Melencolia I – save in this case, the melancholic mess is caused by this grinning deity and the mayhem he can unleash.

"Affection looks not with the eyes, but with the mind, / And therefore is winged Cupid painted sightless," wrote Shakespeare, just before this work was produced around 1601. But Caravaggio's Cupid is not unseeing. He stares directly at the observer. That countenance – sardonic and rosy-cheeked, staring with brazen assurance as he poses naked – is the same one that shrieks in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio painted his three images of the same distinctive-looking kid in Rome at the dawn of the 17th century, he was the most celebrated sacred painter in a metropolis ignited by religious renewal. The Sacrifice of Isaac demonstrates why he was commissioned to decorate sanctuaries: he could adopt a scriptural story that had been depicted numerous times previously and render it so new, so raw and physical that the terror seemed to be happening directly in front of you.

Yet there existed a different aspect to Caravaggio, apparent as quickly as he came in Rome in the cold season that concluded the sixteenth century, as a painter in his initial twenties with no teacher or patron in the city, just talent and audacity. The majority of the paintings with which he caught the holy city's eye were everything but holy. What could be the very earliest hangs in London's National Gallery. A young man opens his crimson mouth in a scream of agony: while stretching out his dirty digits for a fruit, he has rather been attacked. Youth Bitten by a Reptile is eroticism amid squalor: viewers can discern the painter's dismal room reflected in the cloudy waters of the transparent vase.

The adolescent wears a pink blossom in his hair – a symbol of the sex trade in Renaissance painting. Venetian artists such as Tiziano and Palma Vecchio portrayed courtesans grasping blooms and, in a work lost in the WWII but documented through images, the master represented a renowned female prostitute, clutching a bouquet to her chest. The message of all these botanical indicators is clear: intimacy for purchase.

What are we to interpret of Caravaggio's erotic portrayals of boys – and of a particular adolescent in particular? It is a question that has divided his commentators ever since he gained mega-fame in the 1980s. The complex past truth is that the painter was neither the queer icon that, for instance, Derek Jarman put on film in his twentieth-century film about the artist, nor so completely pious that, as certain artistic historians unbelievably assert, his Youth Holding Fruit is in fact a portrait of Jesus.

His initial paintings do make overt sexual implications, or including propositions. It's as if the painter, then a destitute young creator, identified with Rome's sex workers, offering himself to live. In the Florentine gallery, with this idea in mind, viewers might look to an additional early creation, the sixteenth-century masterwork the god of wine, in which the deity of wine stares coolly at the spectator as he starts to undo the black sash of his robe.

A several annums following Bacchus, what could have driven the artist to paint Victorious Cupid for the art patron the nobleman, when he was at last growing nearly established with important church projects? This unholy pagan god revives the erotic challenges of his initial paintings but in a increasingly intense, uneasy manner. Fifty years later, its hidden meaning seemed clear: it was a representation of Caravaggio's lover. A British traveller viewed the painting in about 1649 and was informed its figure has "the physique and countenance of [Caravaggio's|his] own boy or servant that laid with him". The name of this boy was Francesco.

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