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A youthful lad cries out while his head is forcefully gripped, a massive thumb pressing into his face as his parent's mighty hand grasps him by the neck. That moment 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 account. It appears as if Abraham, instructed by God to kill his son, could snap his spinal column with a solitary twist. However Abraham's preferred approach involves the silvery grey knife he grips in his other palm, ready to slit Isaac's throat. One certain aspect stands out – whoever posed as the sacrifice for this astonishing work displayed remarkable acting skill. Within exists not only fear, shock and begging in his darkened gaze but also profound sorrow that a guardian could betray him so completely.

He adopted a well-known biblical story and transformed it so fresh and visceral that its horrors seemed to happen right in front of the viewer

Standing before the artwork, observers recognize this as a real face, an precise record of a young model, because the same youth – recognizable by his disheveled locks and almost dark eyes – appears in two other paintings by the master. In every instance, that richly emotional face commands the scene. In Youth With a Ram, he gazes playfully from the darkness while embracing a ram. In Amor Vincit Omnia, he grins with a hardness learned on Rome's streets, his black feathery appendages demonic, a unclothed child running chaos in a well-to-do dwelling.

Amor Vincit Omnia, presently displayed at a British museum, represents one of the most embarrassing masterpieces ever created. Observers feel completely unsettled looking at it. The god of love, whose darts fill people with frequently agonizing desire, is portrayed as a extremely real, brightly illuminated nude figure, straddling toppled-over items that include stringed instruments, a music manuscript, plate armour and an builder's ruler. This pile of items echoes, intentionally, the geometric and architectural gear strewn across the floor in Albrecht Dürer's print Melancholy – save in this case, the gloomy disorder is created by this smirking Cupid and the mayhem he can release.

"Affection sees not with the eyes, but with the soul, / And thus is winged Cupid painted sightless," wrote Shakespeare, shortly before this painting was produced around the early 1600s. But Caravaggio's Cupid is not blind. He gazes directly at you. That countenance – sardonic and rosy-cheeked, staring with brazen assurance as he poses unclothed – is the same one that shrieks in terror in Abraham's Test.

As Michelangelo Merisi da Caravaggio created his three portrayals of the identical unusual-looking youth in Rome at the dawn of the seventeenth century, he was the highly celebrated sacred painter in a city enflamed by religious revival. Abraham's Offering reveals why he was sought to decorate churches: he could take a biblical narrative that had been portrayed many times before and render it so new, so raw and physical that the horror seemed to be happening immediately before the spectator.

However there existed a different side to Caravaggio, apparent as quickly as he came in the capital in the cold season that ended 1592, as a painter in his early twenties with no teacher or supporter in the city, only skill and boldness. The majority of the works with which he caught the sacred metropolis's eye were everything but holy. That could be the very first resides in London's art museum. A youth parts his crimson lips in a scream of agony: while stretching out his dirty fingers for a cherry, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid poverty: observers can see Caravaggio's gloomy chamber mirrored in the cloudy liquid of the transparent vase.

The adolescent wears a pink flower in his coiffure – a symbol of the sex trade in early modern painting. Venetian artists such as Titian and Palma Vecchio depicted prostitutes grasping flowers and, in a work destroyed in the second world war but known through images, the master represented a famous female prostitute, clutching a posy to her chest. The message of all these floral signifiers is clear: intimacy for sale.

How are we to interpret of the artist's erotic portrayals of youths – and of a particular boy in particular? It is a inquiry that has divided his interpreters ever since he achieved mega-fame in the twentieth century. The complicated historical truth is that the painter was neither the queer icon that, for instance, the filmmaker put on screen in his 1986 movie Caravaggio, nor so completely devout that, as certain artistic scholars unbelievably assert, his Youth Holding Fruit is actually a likeness of Jesus.

His early paintings indeed offer overt sexual implications, or including offers. It's as if the painter, then a destitute young creator, aligned with the city's prostitutes, offering himself to live. In the Florentine gallery, with this thought in consideration, observers might look to another early creation, the sixteenth-century masterpiece the god of wine, in which the deity of alcohol gazes calmly at you as he begins to undo the black sash of his garment.

A several years following Bacchus, what could have driven the artist to paint Victorious Cupid for the art patron Vincenzo Giustiniani, when he was at last growing nearly respectable with important ecclesiastical projects? This profane pagan deity resurrects the erotic provocations of his early works but in a increasingly intense, unsettling manner. Half a century afterwards, its secret seemed clear: it was a portrait of the painter's lover. A English traveller saw the painting in about 1649 and was told its figure has "the physique and countenance of [Caravaggio's|his] own youth or assistant that slept with him". The identity of this boy was Francesco.

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