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The youthful boy screams as his head is forcefully gripped, a large thumb pressing into his face as his father's mighty palm grasps him by the throat. That scene from The Sacrifice of Isaac visits the Florentine museum, creating distress through the artist's harrowing portrayal of the suffering youth from the scriptural account. It seems as if the patriarch, commanded by God to sacrifice his offspring, could snap his neck with a solitary twist. Yet the father's chosen approach involves the metallic steel knife he holds in his other hand, ready to slit the boy's neck. A definite aspect stands out – whomever posed as Isaac for this astonishing work displayed remarkable acting skill. There exists not only fear, shock and pleading in his darkened gaze but additionally deep grief that a protector could abandon him so completely.

He took a familiar scriptural tale and transformed it so fresh and visceral that its terrors seemed to unfold directly in view of you

Standing before the artwork, viewers recognize this as a real countenance, an accurate depiction of a young subject, because the identical youth – recognizable by his tousled locks and nearly dark eyes – appears in two other paintings by Caravaggio. In each instance, that highly expressive face commands the scene. In Youth With a Ram, he gazes mischievously from the shadows while holding a lamb. In Amor Vincit Omnia, he smirks with a toughness acquired on Rome's streets, his dark plumed wings demonic, a unclothed adolescent running chaos in a affluent dwelling.

Amor Vincit Omnia, currently displayed at a British museum, represents one of the most discomfiting artworks ever painted. Viewers feel totally disoriented looking at it. Cupid, whose arrows inspire people with frequently painful desire, is portrayed as a extremely real, brightly illuminated nude figure, straddling overturned objects that comprise musical instruments, a music score, metal armor and an architect's ruler. This pile of possessions resembles, intentionally, the mathematical and construction equipment scattered across the floor in Albrecht Dürer's engraving Melencolia I – except here, the gloomy mess is caused by this grinning Cupid and the mayhem he can unleash.

"Affection looks not with the eyes, but with the mind, / And thus is winged Love painted sightless," wrote Shakespeare, just prior to this painting was produced around 1601. But Caravaggio's Cupid is not unseeing. He stares directly at you. That countenance – ironic and rosy-faced, looking with brazen assurance as he poses naked – is the same one that shrieks in terror in The Sacrifice of Isaac.

As the Italian master created his three images of the identical distinctive-looking youth in Rome at the start of the 17th century, he was the highly celebrated sacred painter in a city enflamed by Catholic revival. The Sacrifice of Isaac reveals why he was commissioned to adorn sanctuaries: he could adopt a biblical story that had been portrayed numerous times previously and make it so fresh, so raw and physical that the terror seemed to be occurring directly before the spectator.

However there existed another side to Caravaggio, evident as quickly as he arrived in Rome in the cold season that ended 1592, as a painter in his initial 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 eye were anything but devout. What could be the absolute earliest resides in the UK's art museum. A youth parts his crimson mouth in a scream of pain: while stretching out his filthy fingers for a cherry, he has rather been attacked. Youth Bitten by a Reptile is eroticism amid squalor: observers can discern Caravaggio's gloomy chamber reflected in the cloudy liquid of the glass vase.

The boy sports a pink blossom in his coiffure – a symbol of the erotic trade in early modern painting. Northern Italian artists such as Titian and Palma Vecchio portrayed prostitutes holding flowers and, in a work destroyed in the WWII but documented through photographs, the master portrayed a renowned woman prostitute, clutching a bouquet to her chest. The meaning of all these botanical signifiers is clear: sex for purchase.

How are we to interpret of Caravaggio's erotic portrayals of boys – and of one boy in particular? It is a inquiry that has split his commentators since he gained mega-fame in the 1980s. The complex past truth is that the painter was not the queer hero that, for instance, the filmmaker presented on screen in his 1986 film about the artist, nor so entirely pious that, as some artistic scholars unbelievably assert, his Boy With a Basket of Fruit is actually a likeness of Jesus.

His initial paintings do make explicit sexual suggestions, or even propositions. It's as if the painter, then a destitute young artist, identified with Rome's prostitutes, selling himself to survive. In the Florentine gallery, with this idea in mind, viewers might look to an additional early creation, the 1596 masterwork the god of wine, in which the god of alcohol stares calmly at you as he starts to untie the dark ribbon of his garment.

A few years after the wine deity, what could have driven Caravaggio to paint Amor Vincit Omnia for the artistic collector Vincenzo Giustiniani, when he was at last growing nearly established with prestigious ecclesiastical projects? This profane pagan deity revives the erotic challenges of his early paintings but in a increasingly intense, unsettling manner. Fifty years later, its secret seemed clear: it was a portrait of Caravaggio's lover. A British visitor viewed the painting in about the mid-seventeenth century and was informed its subject has "the physique and countenance of [Caravaggio's|his] own youth or servant that slept with him". The name of this boy was Cecco.

The painter had been dead for about 40 annums when this story was recorded.