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A youthful lad cries out as his head is firmly held, a large thumb pressing into his cheek as his parent's powerful palm holds him by the neck. This moment from Abraham's Sacrifice appears in the Uffizi Gallery, creating distress through the artist's harrowing rendition of the tormented child from the biblical narrative. The painting seems as if the patriarch, commanded by the Divine to kill his son, could snap his spinal column with a solitary turn. Yet the father's chosen approach involves the silvery steel blade he grips in his remaining palm, prepared to cut the boy's neck. A certain element remains – whoever posed as Isaac for this astonishing work demonstrated remarkable acting skill. There exists not just fear, shock and pleading in his darkened gaze but also profound grief that a guardian could betray him so completely.

The artist adopted a well-known scriptural tale and made it so fresh and visceral that its horrors seemed to happen right in front of the viewer

Viewing before the painting, viewers recognize this as a real countenance, an accurate record of a adolescent subject, because the same youth – recognizable by his tousled hair and almost black eyes – features in two additional paintings by Caravaggio. In every case, that highly expressive face commands the composition. In Youth With a Ram, he gazes mischievously from the shadows while embracing a lamb. In Victorious Cupid, he grins with a hardness acquired on Rome's alleys, his black feathery wings demonic, a naked adolescent running chaos in a affluent dwelling.

Victorious Cupid, presently displayed at a British gallery, constitutes one of the most discomfiting masterpieces ever painted. Observers feel totally disoriented gazing at it. Cupid, whose darts fill people with often painful longing, is shown as a extremely real, vividly lit nude figure, standing over toppled-over items that comprise musical devices, a musical manuscript, metal armor and an builder's T-square. This heap of items echoes, intentionally, the mathematical and construction gear strewn across the ground in Albrecht Dürer's engraving Melancholy – save here, the melancholic mess is created by this smirking Cupid and the turmoil he can release.

"Affection looks not with the eyes, but with the mind, / And thus is winged Love painted sightless," penned Shakespeare, just before this painting was created around the early 1600s. But Caravaggio's Cupid is not unseeing. He gazes straight at you. That countenance – sardonic and ruddy-faced, staring with brazen confidence as he struts naked – is the same one that shrieks in fear in Abraham's Test.

When Michelangelo Merisi da Caravaggio painted his multiple portrayals of the same distinctive-appearing youth in Rome at the start of the 17th century, he was the most celebrated sacred artist in a metropolis enflamed by religious renewal. Abraham's Offering reveals why he was sought to adorn sanctuaries: he could take a scriptural narrative that had been depicted numerous times previously and make it so new, so unfiltered and visceral that the terror appeared to be occurring immediately in front of you.

However there existed a different aspect to Caravaggio, apparent as quickly as he arrived in Rome in the winter that concluded 1592, as a artist in his initial twenties with no mentor or patron in the urban center, only skill and boldness. The majority of the paintings with which he caught the holy city's eye were anything but holy. That could be the absolute first hangs in London's National Gallery. A young man parts his crimson mouth in a yell of agony: while stretching out his filthy fingers for a fruit, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid squalor: observers can discern Caravaggio's dismal chamber mirrored in the cloudy waters of the glass container.

The adolescent sports a pink flower in his hair – a symbol of the erotic trade in early modern painting. Venetian painters such as Titian and Palma Vecchio depicted prostitutes holding blooms and, in a work lost in the WWII but known through images, the master represented a famous female prostitute, holding a bouquet to her chest. The message of all these botanical signifiers is obvious: sex for sale.

What are we to make of the artist's sensual portrayals of boys – and of one adolescent in particular? It is a inquiry that has split his interpreters ever since he gained widespread recognition in the twentieth century. The complicated past reality is that the artist was neither the homosexual icon that, for instance, Derek Jarman presented on screen in his 1986 movie Caravaggio, nor so completely devout that, as some artistic historians improbably assert, his Boy With a Basket of Fruit is in fact a portrait of Christ.

His early paintings do offer overt sexual implications, or even offers. It's as if the painter, then a penniless youthful creator, identified with the city's prostitutes, offering himself to live. In the Florentine gallery, with this idea in mind, observers might look to an additional initial creation, the 1596 masterwork Bacchus, in which the deity of alcohol stares coolly at you as he starts to undo the dark sash of his robe.

A few annums after Bacchus, what could have motivated Caravaggio to create Victorious Cupid for the artistic collector Vincenzo Giustiniani, when he was at last growing nearly respectable with prestigious ecclesiastical projects? This unholy non-Christian god revives the sexual challenges of his initial paintings but in a more powerful, uneasy manner. Fifty years later, its hidden meaning seemed clear: it was a representation of the painter's lover. A British visitor saw the painting in about 1649 and was told its subject has "the physique and countenance of [Caravaggio's|his] own youth or assistant that laid with him". The identity of this boy was Francesco.

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