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A young lad screams as his head is firmly held, a massive digit digging into his cheek as his parent's mighty palm holds him by the throat. This scene from Abraham's Sacrifice visits the Uffizi Gallery, creating unease through the artist's harrowing rendition of the suffering youth from the biblical narrative. It seems as if the patriarch, commanded by the Divine to kill his son, could break his spinal column with a solitary twist. Yet the father's preferred approach involves the silvery grey knife he grips in his other hand, prepared to slit the boy's throat. A definite aspect stands out – whomever posed as Isaac for this breathtaking work displayed extraordinary expressive ability. Within exists not only fear, shock and begging in his darkened gaze but also deep sorrow that a guardian could abandon him so completely.

He adopted a well-known scriptural tale and made it so vibrant and visceral that its terrors appeared to unfold directly in front of the viewer

Viewing before the artwork, observers recognize this as a real face, an precise record of a young model, because the same youth – recognizable by his tousled hair and almost black pupils – features in several other paintings by Caravaggio. In each case, that highly expressive visage dominates the composition. In John the Baptist, he gazes playfully from the darkness while holding a lamb. In Amor Vincit Omnia, he grins with a hardness learned on Rome's streets, his dark plumed wings sinister, a unclothed child running chaos in a affluent dwelling.

Amor Vincit Omnia, currently displayed at a London gallery, represents one of the most embarrassing artworks ever created. Viewers feel totally disoriented looking at it. The god of love, whose arrows fill people with frequently painful longing, is shown as a very real, brightly lit unclothed form, standing over toppled-over items that comprise musical instruments, a musical manuscript, plate armor and an builder's ruler. This heap of possessions resembles, intentionally, the geometric and construction gear strewn across the ground in the German master's engraving Melencolia I – except in this case, the melancholic disorder is created by this grinning deity and the mayhem he can release.

"Love sees not with the eyes, but with the soul, / And therefore is winged Cupid depicted blind," wrote the Bard, just before this work was produced around 1601. But the painter's Cupid is not blind. He stares directly at you. That countenance – sardonic and rosy-faced, staring with brazen assurance as he poses naked – is the same one that screams in terror in Abraham's Test.

As Michelangelo Merisi da Caravaggio created his three images of the identical unusual-looking kid in Rome at the start of the 17th century, he was the most acclaimed sacred artist in a metropolis ignited by religious renewal. The Sacrifice of Isaac demonstrates why he was sought to adorn churches: he could take a scriptural story that had been portrayed numerous occasions before and make it so fresh, so raw and visceral that the terror seemed to be happening directly in front of the spectator.

Yet there was another aspect to the artist, evident as quickly as he came in the capital in the winter that concluded 1592, as a painter in his initial 20s with no teacher or supporter in the urban center, only talent and boldness. Most of the works with which he captured the sacred city's eye were anything but holy. What could be the very first hangs in the UK's National Gallery. A young man parts his red lips in a scream of agony: while reaching out his filthy fingers for a fruit, he has rather been attacked. Boy Bitten By a Lizard is sensuality amid squalor: observers can see Caravaggio's gloomy room reflected in the cloudy waters of the glass vase.

The boy wears a pink blossom in his coiffure – a emblem of the erotic trade in Renaissance painting. Venetian artists such as Titian and Jacopo Palma depicted courtesans holding flowers and, in a work lost in the second world war but documented through photographs, Caravaggio represented a renowned female courtesan, clutching a bouquet to her bosom. The meaning of all these botanical signifiers is obvious: sex for sale.

How are we to interpret of Caravaggio's sensual depictions of youths – and of one adolescent in specific? It is a question that has split his commentators ever since he achieved widespread recognition in the twentieth century. The complicated past truth is that the artist was neither the queer icon that, for instance, the filmmaker presented on screen in his 1986 movie about the artist, nor so completely devout that, as some artistic historians improbably claim, his Boy With a Basket of Fruit is actually a portrait of Christ.

His initial paintings do make explicit erotic suggestions, or even propositions. It's as if the painter, then a destitute youthful creator, identified with Rome's prostitutes, selling himself to survive. In the Uffizi, with this thought in mind, viewers might look to another early work, the sixteenth-century masterwork the god of wine, in which the god of alcohol gazes coolly at the spectator as he begins to undo the black sash of his robe.

A several annums following Bacchus, what could have driven the artist to create Victorious Cupid for the artistic patron Vincenzo Giustiniani, when he was at last becoming nearly respectable with important ecclesiastical projects? This profane non-Christian deity resurrects the sexual challenges of his early works but in a more powerful, unsettling manner. Half a century later, its secret seemed clear: it was a representation of Caravaggio's lover. A British visitor viewed Victorious Cupid in about the mid-seventeenth century and was told its subject has "the body & face of [Caravaggio's|his] owne boy or assistant that laid with him". The name of this adolescent was Cecco.

The artist had been dead for about forty years when this account was documented.