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A youthful boy screams while his head is firmly held, a massive thumb digging into his face as his parent's mighty hand grasps him by the neck. This moment from The Sacrifice of Isaac appears in the Florentine museum, evoking distress through the artist's chilling portrayal of the suffering youth from the scriptural narrative. The painting seems as if Abraham, instructed by the Divine to kill his son, could snap his neck with a solitary turn. However the father's chosen method involves the metallic grey knife he grips in his remaining palm, prepared to slit the boy's neck. One definite aspect remains – whomever modeled as the sacrifice for this breathtaking work displayed remarkable expressive ability. There exists not only fear, surprise and begging in his darkened eyes but additionally deep sorrow that a guardian could abandon him so completely.

He took a well-known biblical tale and transformed it so vibrant and raw that its horrors seemed to unfold right in front of you

Viewing before the artwork, viewers identify this as a actual countenance, an accurate record of a adolescent subject, because the identical youth – recognizable by his tousled locks and almost black eyes – features in two additional works by Caravaggio. In every case, that richly expressive visage dominates the composition. In Youth With a Ram, he gazes mischievously from the shadows while holding a lamb. In Victorious Cupid, he smirks with a toughness acquired on Rome's streets, his black plumed wings sinister, a naked child running riot in a well-to-do dwelling.

Amor Vincit Omnia, presently displayed at a British gallery, constitutes one of the most embarrassing masterpieces ever created. Observers feel totally unsettled looking at it. Cupid, whose darts inspire people with frequently painful longing, is shown as a extremely tangible, vividly lit nude form, standing over overturned items that comprise musical devices, a musical score, metal armour and an builder's T-square. This pile of items resembles, deliberately, the geometric and architectural equipment scattered across the ground in the German master's print Melancholy – save here, the gloomy disorder is created by this grinning Cupid and the mayhem he can unleash.

"Affection sees not with the eyes, but with the mind, / And therefore is feathered Love depicted sightless," wrote Shakespeare, shortly before this work was produced around 1601. But the painter's god is not unseeing. He gazes straight at the observer. That face – ironic and ruddy-cheeked, staring with bold assurance as he struts naked – is the same one that shrieks in terror in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio created his three images of the same distinctive-appearing youth in the Eternal City at the dawn of the 17th century, he was the most acclaimed sacred artist in a city ignited by religious revival. The Sacrifice of Isaac reveals why he was commissioned to adorn sanctuaries: he could adopt a scriptural narrative that had been depicted many occasions previously and render it so new, so raw and physical that the horror seemed to be occurring directly before the spectator.

However there was another aspect to Caravaggio, evident as soon as he arrived in the capital in the winter that ended the sixteenth century, as a painter in his initial 20s with no mentor or patron in the city, only talent and audacity. Most of the works with which he caught the holy city's eye were anything but holy. What could be the absolute first resides in London's art museum. A young man opens his red mouth in a scream of pain: while reaching out his dirty digits for a fruit, he has instead been attacked. Youth Bitten by a Reptile is sensuality amid poverty: observers can discern the painter's gloomy room reflected in the murky waters of the glass container.

The adolescent sports a rose-colored blossom in his coiffure – a emblem of the sex trade in early modern painting. Venetian painters such as Titian and Jacopo Palma depicted courtesans grasping flowers and, in a work destroyed in the second world war but documented through images, the master represented a renowned female prostitute, clutching a posy to her bosom. The meaning of all these floral indicators is obvious: sex for purchase.

How are we to make of Caravaggio's erotic depictions of boys – and of a particular adolescent in specific? It is a question that has split his interpreters ever since he achieved mega-fame in the twentieth century. The complex historical reality is that the artist was neither the homosexual icon that, for example, Derek Jarman presented on film in his twentieth-century film about the artist, nor so entirely pious that, as some art historians improbably claim, his Youth Holding Fruit is in fact a likeness of Jesus.

His early paintings indeed make explicit sexual implications, or including offers. It's as if Caravaggio, then a destitute young creator, identified with Rome's sex workers, offering himself to survive. In the Florentine gallery, with this idea in mind, viewers might turn to another initial creation, the sixteenth-century masterpiece Bacchus, in which the god of alcohol stares calmly at the spectator as he begins to undo the dark ribbon of his robe.

A several annums following Bacchus, what could have driven the artist to paint Victorious Cupid for the art collector the nobleman, when he was at last becoming nearly respectable with important church commissions? This profane pagan deity resurrects the erotic challenges of his initial paintings but in a more intense, uneasy way. Half a century afterwards, its secret seemed clear: it was a portrait of the painter's lover. A British traveller viewed Victorious Cupid in about the mid-seventeenth century and was informed its subject has "the body & face of [Caravaggio's|his] owne youth or assistant that slept with him". The name of this adolescent was Francesco.

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