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A young boy screams as his skull is firmly held, a massive thumb pressing into his face as his father's mighty hand grasps him by the neck. This moment from Abraham's Sacrifice visits the Florentine museum, evoking unease through Caravaggio's chilling rendition of the suffering child from the biblical account. The painting appears as if the patriarch, instructed by God to kill his son, could break his neck with a solitary turn. However the father's preferred method involves the metallic grey blade he grips in his remaining hand, ready to cut Isaac's throat. A certain element stands out – whomever posed as the sacrifice for this astonishing piece displayed extraordinary expressive skill. There exists not just dread, shock and begging in his darkened gaze but additionally deep sorrow that a protector could betray him so utterly.

The artist took a familiar scriptural story and transformed it so fresh and raw that its terrors seemed to unfold directly in view of you

Standing before the painting, observers recognize this as a actual countenance, an precise depiction of a adolescent model, because the identical boy – identifiable by his tousled locks and almost dark eyes – features in several other works by the master. In each instance, that richly expressive visage commands the composition. In John the Baptist, he peers mischievously from the shadows while embracing a lamb. In Amor Vincit Omnia, he smirks with a toughness learned on Rome's alleys, his dark feathery appendages sinister, a naked child creating chaos in a well-to-do residence.

Amor Vincit Omnia, presently displayed at a London gallery, constitutes one of the most discomfiting masterpieces ever painted. Observers feel totally disoriented looking at it. The god of love, whose arrows inspire people with frequently painful longing, is portrayed as a very tangible, brightly lit nude form, standing over toppled-over objects that include stringed devices, a musical score, metal armour and an architect's ruler. This heap of possessions resembles, intentionally, the geometric and architectural equipment scattered across the ground in the German master's print Melancholy – except in this case, the melancholic mess is caused by this grinning Cupid and the turmoil he can unleash.

"Love looks not with the vision, but with the soul, / And thus is feathered Cupid painted blind," penned the Bard, just before this work was created around the early 1600s. But Caravaggio's god is not unseeing. He stares directly at the observer. That countenance – sardonic and rosy-faced, looking with bold confidence as he struts naked – is the same one that shrieks in terror in The Sacrifice of Isaac.

When the Italian master painted his multiple portrayals of the identical unusual-looking youth in Rome at the dawn of the 17th century, he was the highly celebrated religious painter in a metropolis enflamed by Catholic renewal. Abraham's Offering reveals why he was commissioned to decorate churches: he could adopt a scriptural narrative that had been depicted many occasions before and render it so fresh, so raw and physical that the terror seemed to be happening directly before you.

However there was a different side to Caravaggio, evident as quickly as he arrived in the capital in the winter that concluded the sixteenth century, as a painter in his initial twenties with no mentor or supporter in the city, only talent and audacity. The majority of the works with which he captured the holy metropolis's eye were everything but holy. That could be the absolute earliest resides in the UK's National Gallery. A youth opens his crimson lips in a yell of pain: while stretching out his dirty fingers for a cherry, he has rather been attacked. Youth Bitten by a Reptile is sensuality amid squalor: viewers can see the painter's dismal chamber mirrored in the cloudy liquid of the transparent vase.

The boy wears a rose-colored flower in his hair – a emblem of the sex commerce in Renaissance art. Venetian artists such as Titian and Palma Vecchio depicted courtesans holding blooms and, in a painting destroyed in the WWII but documented through images, Caravaggio portrayed a renowned woman courtesan, clutching a bouquet to her bosom. The message of all these floral signifiers is clear: sex for sale.

What are we to make of Caravaggio's erotic portrayals of boys – and of a particular boy in particular? It is a inquiry that has split his interpreters since he achieved mega-fame in the 1980s. The complex past reality is that the artist was not the queer hero that, for example, the filmmaker put on screen in his twentieth-century film about the artist, nor so completely pious that, as some artistic historians improbably claim, his Youth Holding Fruit is in fact a likeness of Christ.

His initial paintings do offer overt erotic suggestions, or even propositions. It's as if the painter, then a penniless young artist, aligned with the city's sex workers, selling himself to live. In the Uffizi, with this idea in consideration, observers might turn to an additional early work, the sixteenth-century masterwork Bacchus, in which the god of alcohol stares calmly at the spectator as he begins to untie the black ribbon of his garment.

A several annums after the wine deity, what could have motivated Caravaggio to create Victorious Cupid for the artistic patron Vincenzo Giustiniani, when he was finally growing nearly respectable with important church projects? This profane pagan deity revives the sexual provocations of his initial paintings but in a increasingly powerful, uneasy manner. Fifty years afterwards, its secret seemed obvious: it was a portrait of the painter's companion. A British visitor viewed Victorious Cupid in about the mid-seventeenth century and was told its figure has "the body & face of [Caravaggio's|his] owne youth or assistant that slept with him". The identity of this boy was Cecco.

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