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The youthful lad screams as his head is firmly held, a large thumb digging into his cheek as his parent's mighty hand holds him by the throat. This moment from Abraham's Sacrifice appears in the Uffizi Gallery, evoking distress through the artist's chilling rendition of the tormented youth from the biblical narrative. The painting appears as if the patriarch, commanded by God to sacrifice his son, could snap his neck with a solitary turn. However the father's chosen method involves the metallic steel knife he grips in his other palm, prepared to slit the boy's throat. One definite element remains – whoever posed as Isaac for this astonishing piece demonstrated remarkable acting skill. There exists not only dread, shock and begging in his darkened gaze but also profound grief that a guardian could betray him so utterly.

The artist adopted a well-known biblical tale and transformed it so vibrant and visceral that its terrors seemed to happen directly in view of the viewer

Standing before the painting, observers identify this as a actual face, an precise record of a adolescent model, because the identical boy – identifiable by his disheveled locks and almost dark eyes – appears in two other works by Caravaggio. In each case, that highly expressive visage dominates the scene. In Youth With a Ram, he peers mischievously from the shadows while embracing a lamb. In Victorious Cupid, he grins with a toughness acquired on the city's alleys, his black feathery wings demonic, a unclothed adolescent running chaos in a well-to-do dwelling.

Victorious Cupid, currently displayed at a British museum, constitutes one of the most embarrassing masterpieces ever painted. Observers feel totally disoriented gazing at it. The god of love, whose darts fill people with often agonizing desire, is portrayed as a extremely tangible, brightly illuminated unclothed figure, standing over overturned objects that include musical devices, a musical manuscript, metal armour and an builder's T-square. This pile of items echoes, deliberately, the geometric and architectural equipment scattered across the ground in the German master's print Melancholy – except here, the gloomy mess is created by this smirking deity and the mayhem he can unleash.

"Affection sees not with the vision, but with the mind, / And therefore is feathered Cupid depicted blind," wrote Shakespeare, shortly prior to this painting was produced around 1601. But Caravaggio's Cupid is not unseeing. He stares directly at the observer. That face – ironic and ruddy-faced, looking with bold assurance as he poses naked – is the same one that shrieks in terror in The Sacrifice of Isaac.

When the Italian master created his three images of the identical unusual-looking kid in Rome at the dawn of the 17th century, he was the highly acclaimed religious artist in a city enflamed by Catholic revival. The Sacrifice of Isaac reveals why he was sought to adorn churches: he could adopt a scriptural narrative that had been depicted many occasions previously and render it so new, so unfiltered and physical that the terror appeared to be occurring directly before the spectator.

Yet there was another side to the artist, apparent as soon as he came in Rome in the cold season that concluded the sixteenth century, as a painter in his early 20s with no mentor or patron in the urban center, only talent and boldness. Most of the paintings with which he captured the sacred city's attention were anything but holy. What may be the absolute earliest hangs in the UK's art museum. A young man parts his red mouth in a scream of pain: while reaching out his filthy fingers for a fruit, he has rather been bitten. Youth Bitten by a Reptile is eroticism amid poverty: observers can see Caravaggio's dismal chamber reflected in the murky liquid of the glass vase.

The adolescent wears a pink blossom in his coiffure – a emblem of the erotic trade in early modern art. Venetian artists such as Tiziano and Jacopo Palma portrayed prostitutes holding flowers and, in a painting destroyed in the second world war but known through images, Caravaggio represented a famous female prostitute, holding a bouquet to her chest. The meaning of all these floral signifiers is clear: intimacy for sale.

What are we to make of the artist's erotic depictions of youths – and of one boy in specific? It is a question that has divided his interpreters ever since he achieved mega-fame in the 1980s. The complex past reality is that the artist was not the queer hero that, for example, the filmmaker put on screen in his twentieth-century movie Caravaggio, nor so completely pious that, as certain art scholars unbelievably assert, his Boy With a Basket of Fruit is actually a likeness of Christ.

His initial paintings indeed make overt erotic implications, or even offers. It's as if Caravaggio, then a destitute young artist, aligned with the city's prostitutes, offering himself to survive. In the Florentine gallery, with this thought in consideration, observers might look to another early work, the sixteenth-century masterpiece Bacchus, in which the deity of wine stares calmly at the spectator as he starts to undo the dark ribbon of his garment.

A several annums following Bacchus, what could have driven the artist to paint Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was at last becoming nearly established with important ecclesiastical projects? This unholy non-Christian deity revives the erotic provocations of his initial paintings but in a increasingly intense, unsettling way. Fifty years later, its hidden meaning seemed obvious: it was a portrait of Caravaggio's lover. A English traveller viewed the painting in about the mid-seventeenth century and was informed its figure has "the body & face of [Caravaggio's|his] own youth or assistant that slept with him". The identity of this boy was Francesco.

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