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The youthful boy screams as his skull is forcefully gripped, a large digit digging into his cheek as his father's mighty hand holds him by the neck. That moment from The Sacrifice of Isaac visits the Uffizi Gallery, evoking unease through the artist's harrowing portrayal of the tormented child from the biblical account. The painting appears as if Abraham, commanded by God to sacrifice his son, could break his neck with a single turn. Yet the father's chosen approach involves the metallic grey knife he grips in his other palm, prepared to slit Isaac's throat. One definite aspect remains – whomever posed as the sacrifice for this breathtaking piece displayed remarkable acting skill. There exists not just dread, surprise and pleading in his darkened eyes but additionally profound grief that a protector could betray him so completely.

The artist adopted a familiar scriptural story and made it so vibrant and raw that its horrors seemed to happen directly in front of the viewer

Standing before the painting, viewers identify this as a actual face, an accurate record of a adolescent model, because the identical youth – recognizable by his tousled locks and nearly dark eyes – appears in two additional paintings by Caravaggio. In each instance, that highly emotional visage dominates the composition. In John the Baptist, he peers playfully from the darkness while holding a ram. In Amor Vincit Omnia, he smirks with a hardness learned on the city's alleys, his black plumed wings sinister, a naked adolescent creating chaos in a affluent dwelling.

Amor Vincit Omnia, currently exhibited at a British gallery, constitutes one of the most discomfiting artworks ever painted. Observers feel totally unsettled looking at it. The god of love, whose darts inspire people with often agonizing desire, is portrayed as a extremely tangible, brightly lit unclothed figure, standing over toppled-over items that comprise stringed devices, a music manuscript, metal armour and an builder's T-square. This pile of possessions resembles, deliberately, the mathematical and architectural gear strewn across the floor in Albrecht Dürer's print Melencolia I – except in this case, the melancholic mess is caused by this smirking Cupid and the mayhem he can release.

"Love looks not with the eyes, but with the mind, / And therefore is winged Love painted sightless," wrote the Bard, shortly prior to this painting was produced around 1601. But Caravaggio's god is not unseeing. He gazes straight at the observer. That face – sardonic and ruddy-faced, looking with brazen confidence as he poses unclothed – is the same one that shrieks in terror in The Sacrifice of Isaac.

When the Italian master created his multiple portrayals of the same unusual-appearing youth in the Eternal City at the dawn of the 17th century, he was the most acclaimed sacred painter in a city ignited by Catholic renewal. Abraham's Offering reveals why he was commissioned to decorate churches: he could take a scriptural narrative that had been portrayed many times before and make it so new, so raw and physical that the terror appeared to be happening immediately before you.

However there was a different side to Caravaggio, apparent as quickly as he came in the capital in the winter that concluded the sixteenth century, as a artist in his initial twenties with no mentor or patron in the city, just skill and audacity. The majority of the paintings with which he captured the sacred city's attention were everything but devout. That may be the very earliest hangs in London's National Gallery. A young man parts his red lips in a scream of pain: while reaching out his dirty digits for a fruit, he has instead been bitten. Boy Bitten By a Lizard is sensuality amid squalor: viewers can discern Caravaggio's gloomy room mirrored in the cloudy waters of the transparent container.

The boy wears a pink flower in his hair – a emblem of the erotic trade in Renaissance art. Northern Italian painters such as Titian and Jacopo Palma portrayed prostitutes grasping blooms and, in a work destroyed in the second world war but documented through photographs, Caravaggio represented a famous female courtesan, clutching a bouquet to her chest. The message of all these floral indicators is clear: intimacy for sale.

How are we to make of Caravaggio's erotic depictions of youths – and of one boy in particular? It is a question that has divided his interpreters since he achieved widespread recognition in the 1980s. The complicated past reality is that the artist was neither the queer icon that, for instance, Derek Jarman put on film in his twentieth-century movie Caravaggio, nor so entirely pious that, as certain artistic scholars improbably assert, his Boy With a Basket of Fruit is actually a likeness of Jesus.

His early paintings do offer explicit sexual implications, or even propositions. It's as if the painter, then a penniless youthful artist, aligned with Rome's sex workers, selling himself to live. In the Florentine gallery, with this idea in mind, viewers might look to an additional early creation, the sixteenth-century masterpiece the god of wine, in which the deity of wine stares calmly at the spectator as he starts to untie the black ribbon of his garment.

A few annums after Bacchus, what could have motivated Caravaggio to create Amor Vincit Omnia for the art patron the nobleman, when he was at last becoming nearly established with important ecclesiastical projects? This unholy pagan deity resurrects the erotic provocations of his initial works but in a more intense, unsettling manner. Half a century afterwards, its secret seemed obvious: it was a portrait of the painter's companion. A British traveller viewed the painting in about the mid-seventeenth century and was told its figure 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 recorded.