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The youthful boy screams while his head is forcefully gripped, a large digit pressing into his cheek as his father's mighty palm grasps him by the neck. That moment from The Sacrifice of Isaac visits the Uffizi Gallery, creating unease through Caravaggio's harrowing rendition of the tormented child from the scriptural account. It appears as if Abraham, instructed by the Divine to sacrifice his offspring, could break his spinal column with a single twist. Yet the father's chosen method involves the silvery steel blade he holds in his remaining hand, prepared to slit the boy's neck. A definite aspect stands out – whomever modeled as Isaac for this breathtaking piece displayed extraordinary acting ability. There exists not only dread, surprise and begging in his shadowed eyes but additionally profound sorrow that a guardian could abandon him so completely.

He took a well-known biblical tale and made it so fresh and raw that its horrors seemed to unfold directly in view of the viewer

Standing before the artwork, observers identify this as a real countenance, an accurate depiction of a adolescent subject, because the same youth – recognizable by his tousled locks and almost black pupils – features in two additional paintings by Caravaggio. In each case, that highly emotional visage dominates the scene. In Youth With a Ram, he peers playfully from the darkness while holding a ram. In Amor Vincit Omnia, he smirks with a hardness acquired on the city's alleys, his dark feathery appendages demonic, a unclothed child running riot in a affluent dwelling.

Amor Vincit Omnia, presently displayed at a London museum, represents one of the most discomfiting artworks ever painted. Observers feel totally disoriented gazing at it. Cupid, whose darts inspire people with frequently painful desire, is shown as a very real, vividly illuminated unclothed form, standing over toppled-over items that comprise stringed devices, a music manuscript, plate armor and an architect's T-square. This heap of possessions resembles, intentionally, the geometric and construction equipment scattered across the floor in the German master's engraving Melencolia I – except here, the gloomy disorder is created by this smirking Cupid and the turmoil he can release.

"Love looks not with the eyes, but with the mind, / And thus is winged Cupid depicted sightless," wrote Shakespeare, shortly before this painting was produced around the early 1600s. But the painter's god is not unseeing. He stares directly at you. That countenance – ironic and ruddy-faced, staring with bold confidence as he struts unclothed – is the identical one that screams in terror in Abraham's Test.

As Michelangelo Merisi da Caravaggio created his three portrayals of the identical distinctive-appearing kid in Rome at the dawn of the seventeenth century, he was the highly celebrated sacred painter in a city enflamed by religious renewal. Abraham's Offering reveals why he was sought to adorn churches: he could adopt a scriptural story that had been depicted numerous occasions previously and make it so fresh, so raw and physical that the terror appeared to be occurring directly before the spectator.

However there existed another side to the artist, apparent as quickly as he came in Rome in the cold season that ended 1592, as a artist in his early 20s with no mentor or supporter in the city, just skill and boldness. The majority of the paintings with which he caught the holy city's eye were everything but holy. That could be the absolute first hangs in the UK's National Gallery. A young man opens his crimson mouth in a yell of agony: while reaching out his dirty digits for a fruit, he has rather been bitten. Boy Bitten By a Lizard is eroticism amid squalor: viewers can see Caravaggio's gloomy room reflected in the murky liquid of the transparent container.

The boy sports a pink flower in his hair – a emblem of the erotic trade in early modern art. Northern Italian painters such as Tiziano and Palma Vecchio portrayed prostitutes grasping flowers and, in a work destroyed in the WWII but known through photographs, Caravaggio portrayed a renowned woman courtesan, clutching a bouquet to her bosom. The meaning of all these botanical indicators is clear: intimacy for purchase.

What are we to make of Caravaggio's erotic depictions of boys – and of a particular adolescent in particular? It is a question that has divided his interpreters ever since he achieved mega-fame in the twentieth century. The complex historical truth is that the artist was neither the queer icon that, for instance, the filmmaker presented on screen in his twentieth-century film about the artist, nor so completely devout that, as some artistic historians unbelievably claim, his Youth Holding Fruit is in fact a portrait of Christ.

His early works indeed make overt erotic suggestions, or even propositions. It's as if the painter, then a destitute youthful artist, aligned with the city's sex workers, offering himself to survive. In the Florentine gallery, with this idea in consideration, observers might look to an additional early creation, the 1596 masterpiece Bacchus, in which the deity of alcohol gazes calmly at you as he starts to untie the black sash of his robe.

A few annums after the wine deity, what could have motivated the artist to create Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was finally becoming almost respectable with important church projects? This profane pagan god revives the sexual provocations of his early works but in a more powerful, unsettling manner. Half a century later, its secret seemed clear: it was a representation of the painter's lover. A English visitor viewed the painting in about 1649 and was told its figure has "the physique and countenance of [Caravaggio's|his] own boy or assistant that slept with him". The identity of this adolescent was Cecco.

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