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The young lad cries out while his skull is forcefully held, a massive thumb digging into his cheek as his father's powerful hand grasps him by the throat. This moment from Abraham's Sacrifice appears in the Uffizi Gallery, evoking distress through Caravaggio's harrowing rendition of the tormented youth from the scriptural account. It seems as if the patriarch, commanded by God to kill his offspring, could snap his spinal column with a solitary turn. However Abraham's preferred method involves the silvery grey knife he grips in his other hand, ready to slit the boy's neck. One certain aspect stands out – whoever posed as the sacrifice for this astonishing work displayed remarkable acting skill. Within exists not just dread, shock and pleading in his shadowed gaze but additionally deep grief that a guardian could abandon him so completely.

He adopted a familiar biblical story and transformed it so fresh and visceral that its horrors seemed to happen right in front of you

Standing in front of the painting, observers recognize this as a real face, an accurate record of a adolescent subject, because the same boy – recognizable by his tousled locks and nearly black pupils – appears in several additional works by the master. In every case, that richly expressive visage commands the scene. In John the Baptist, he gazes playfully from the shadows while embracing a ram. In Victorious Cupid, he grins with a hardness learned on Rome's alleys, his black plumed wings sinister, a unclothed child creating riot in a affluent dwelling.

Victorious Cupid, presently exhibited at a British gallery, constitutes one of the most embarrassing artworks ever created. Observers feel totally unsettled gazing at it. Cupid, whose darts fill people with frequently painful desire, is portrayed as a very tangible, brightly illuminated nude figure, straddling overturned objects that comprise stringed devices, a music score, plate armour and an builder's T-square. This pile of possessions resembles, intentionally, the mathematical and construction gear scattered across the floor in the German master's print Melancholy – except in this case, the melancholic disorder is caused by this smirking deity and the mayhem he can unleash.

"Affection sees not with the vision, but with the soul, / And thus is feathered Cupid depicted blind," penned Shakespeare, shortly before this painting was produced around 1601. But Caravaggio's Cupid is not unseeing. He stares directly at the observer. That countenance – sardonic and rosy-cheeked, looking with brazen assurance as he poses unclothed – is the identical one that shrieks in terror in Abraham's Test.

When the Italian master painted his three images of the identical unusual-looking youth in the Eternal City at the dawn of the 17th century, he was the most celebrated religious painter in a metropolis enflamed by Catholic revival. Abraham's Offering reveals why he was sought to adorn churches: he could take a scriptural narrative that had been depicted numerous times previously and render it so new, so unfiltered and physical that the horror seemed to be occurring immediately before you.

Yet there was another aspect to the artist, apparent as quickly as he arrived in Rome in the winter that concluded the sixteenth century, as a painter in his initial twenties with no teacher or patron in the urban center, just talent and audacity. The majority of the paintings with which he caught the holy city's attention were everything but devout. That may be the very earliest resides in London's art museum. A youth opens his crimson mouth in a yell of agony: while stretching out his dirty digits for a fruit, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid poverty: observers can discern the painter's gloomy room reflected in the cloudy liquid of the glass vase.

The boy wears a pink flower in his hair – a symbol of the erotic trade in Renaissance art. Northern Italian painters such as Titian and Palma Vecchio depicted courtesans grasping flowers and, in a painting lost in the WWII but known through photographs, Caravaggio portrayed a renowned female prostitute, clutching a posy to her bosom. The message of all these botanical indicators is clear: sex for sale.

How are we to interpret of the artist's sensual portrayals of boys – and of one boy in particular? It is a inquiry that has split his commentators ever since he achieved mega-fame in the 1980s. The complicated historical reality is that the painter was not the queer hero that, for instance, Derek Jarman presented on screen in his twentieth-century film Caravaggio, nor so entirely pious that, as certain art scholars improbably claim, his Youth Holding Fruit is in fact a likeness of Christ.

His initial works indeed make explicit sexual implications, or even offers. It's as if the painter, then a penniless youthful artist, identified with the city's prostitutes, selling himself to survive. In the Uffizi, with this idea in mind, viewers might turn to another initial work, the sixteenth-century masterpiece the god of wine, in which the god of wine gazes coolly at the spectator as he begins to undo the dark sash of his garment.

A few years after Bacchus, what could have motivated the artist to create Amor Vincit Omnia for the art collector Vincenzo Giustiniani, when he was at last becoming almost respectable with important church projects? This profane non-Christian deity resurrects the sexual challenges of his early paintings but in a increasingly powerful, uneasy manner. Half a century afterwards, its hidden meaning seemed obvious: it was a representation of Caravaggio's companion. A English traveller viewed Victorious Cupid in about 1649 and was told its subject has "the physique and countenance of [Caravaggio's|his] own boy or assistant that slept with him". The name of this adolescent was Francesco.

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