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The young boy screams while his head is firmly gripped, a massive digit pressing into his face as his parent's powerful palm holds him by the throat. That scene from The Sacrifice of Isaac appears in the Uffizi Gallery, creating distress through Caravaggio's chilling rendition of the tormented child from the biblical narrative. The painting seems as if Abraham, commanded by God to sacrifice his son, could break his neck with a single twist. However Abraham's preferred method involves the metallic grey knife he holds in his other hand, ready to slit Isaac's neck. One definite element remains – whoever modeled as the sacrifice for this astonishing piece displayed remarkable expressive skill. There exists not just fear, surprise and pleading in his darkened gaze but additionally profound sorrow that a guardian could betray him so utterly.

The artist adopted a well-known scriptural story and made it so vibrant and visceral that its terrors appeared to unfold right in view of the viewer

Viewing in front of the painting, observers identify this as a actual countenance, an accurate record of a adolescent model, because the same boy – identifiable by his tousled hair and almost dark eyes – features in several additional paintings by the master. In every case, that richly emotional visage commands the scene. In John the Baptist, he gazes playfully from the darkness while holding a lamb. In Victorious Cupid, he smirks with a toughness learned on Rome's alleys, his dark plumed appendages demonic, a naked child running riot in a affluent residence.

Amor Vincit Omnia, presently exhibited at a London museum, constitutes one of the most discomfiting masterpieces ever painted. Observers feel totally disoriented looking at it. Cupid, whose darts fill people with often agonizing longing, is shown as a very tangible, vividly lit nude form, straddling toppled-over items that comprise stringed instruments, a musical manuscript, plate armour and an builder's T-square. This heap of possessions echoes, deliberately, the mathematical and construction equipment scattered across the ground in Albrecht Dürer's print Melencolia I – save in this case, the melancholic disorder is created by this grinning Cupid and the turmoil he can unleash.

"Affection looks not with the vision, but with the soul, / And therefore is feathered Love painted sightless," wrote the Bard, just before this painting was produced around 1601. But the painter's god is not blind. He stares straight at you. That countenance – sardonic and ruddy-faced, staring with brazen confidence as he struts naked – is the identical one that shrieks in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio created his multiple portrayals of the identical distinctive-looking youth in the Eternal City at the dawn of the 17th century, he was the most celebrated religious artist in a city ignited by Catholic revival. Abraham's Offering reveals why he was commissioned to decorate churches: he could adopt a biblical story that had been depicted numerous occasions before and make it so new, so raw and visceral that the terror seemed to be happening immediately in front of the spectator.

However there was a different aspect to Caravaggio, evident as quickly as he came in Rome in the cold season that ended the sixteenth century, as a artist in his early 20s with no mentor or patron in the urban center, only skill and audacity. Most of the paintings with which he captured the sacred metropolis's eye were anything but devout. That could be the very first hangs in London's National Gallery. A young man opens his red mouth in a yell of agony: while reaching out his filthy fingers for a cherry, he has instead been attacked. Boy Bitten By a Lizard is eroticism amid squalor: observers can see the painter's dismal room mirrored in the murky waters of the transparent container.

The adolescent wears a pink flower in his coiffure – a symbol of the sex commerce in early modern painting. Venetian painters such as Tiziano and Palma Vecchio depicted prostitutes holding blooms and, in a painting lost in the WWII but documented through photographs, Caravaggio portrayed a renowned woman courtesan, holding a bouquet to her chest. The meaning of all these botanical signifiers is clear: intimacy for purchase.

How are we to make of Caravaggio's sensual depictions of boys – and of a particular boy in specific? It is a question that has split his commentators ever since he achieved mega-fame in the twentieth century. The complicated past truth is that the artist was not the queer hero that, for instance, Derek Jarman presented on film in his 1986 movie about the artist, nor so entirely devout that, as some art scholars improbably assert, his Youth Holding Fruit is in fact a likeness of Jesus.

His initial paintings do offer overt sexual suggestions, or even propositions. It's as if Caravaggio, then a destitute young artist, aligned with the city's prostitutes, selling himself to live. In the Florentine gallery, with this idea in mind, observers might turn to another early creation, the 1596 masterpiece Bacchus, in which the deity of alcohol gazes coolly at you as he begins to undo the dark sash of his garment.

A several annums following the wine deity, what could have driven the artist to create Victorious Cupid for the art collector the nobleman, when he was finally growing almost respectable with important ecclesiastical projects? This profane pagan deity revives the sexual provocations of his early paintings but in a more powerful, uneasy manner. Fifty years later, its hidden meaning seemed clear: it was a representation of Caravaggio's lover. A British visitor viewed the painting in about 1649 and was informed its subject has "the body & face of [Caravaggio's|his] owne youth or servant that laid with him". The identity of this boy was Cecco.

The artist had been deceased for about forty annums when this account was documented.