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The youthful lad screams while his skull is forcefully held, a massive thumb digging into his face as his parent's powerful palm grasps him by the neck. That moment from Abraham's Sacrifice visits the Florentine museum, evoking unease through Caravaggio's harrowing portrayal of the tormented youth from the biblical account. It appears as if the patriarch, instructed by the Divine to sacrifice his offspring, could snap his neck with a single turn. Yet the father's preferred method involves the silvery steel blade he holds in his remaining hand, ready to slit Isaac's throat. A definite aspect stands out – whoever posed as Isaac for this breathtaking piece displayed extraordinary acting skill. There exists not just dread, shock and begging in his shadowed gaze but also profound sorrow that a guardian could abandon him so utterly.

The artist adopted a well-known scriptural tale and made it so fresh and raw that its horrors appeared to unfold right in view of you

Viewing before the artwork, observers recognize this as a actual face, an accurate depiction of a adolescent model, because the identical youth – identifiable by his disheveled hair and almost black pupils – features in several other works by Caravaggio. In every case, that richly expressive face commands the composition. In Youth With a Ram, he peers mischievously from the shadows while holding a ram. In Amor Vincit Omnia, he grins with a hardness acquired on Rome's alleys, his dark feathery appendages demonic, a unclothed adolescent creating riot in a well-to-do dwelling.

Victorious Cupid, currently displayed at a British gallery, constitutes one of the most discomfiting artworks ever painted. Observers feel completely unsettled gazing at it. The god of love, whose arrows inspire people with frequently agonizing longing, is portrayed as a very real, vividly lit unclothed form, straddling overturned items that comprise musical devices, a musical score, metal armor and an architect's ruler. This heap of possessions resembles, deliberately, the mathematical and construction equipment strewn across the floor in the German master's engraving Melencolia I – except in this case, the melancholic mess is caused by this smirking Cupid and the turmoil he can release.

"Affection looks not with the eyes, but with the mind, / And therefore is feathered Love painted sightless," penned Shakespeare, shortly before this painting was produced around 1601. But Caravaggio's god is not blind. He gazes straight at you. That face – sardonic and rosy-faced, looking with bold assurance as he poses naked – is the identical one that shrieks in fear in Abraham's Test.

As Michelangelo Merisi da Caravaggio created his three images of the same unusual-appearing youth in the Eternal City at the start of the seventeenth century, he was the most acclaimed sacred painter in a metropolis enflamed by religious renewal. Abraham's Offering reveals why he was commissioned to adorn churches: he could take a biblical story that had been portrayed many times before and make it so new, so unfiltered and visceral that the terror seemed to be occurring directly in front of you.

However there was a different side to Caravaggio, apparent as soon as he arrived in the capital in the cold season that ended 1592, as a painter in his initial twenties with no teacher or patron in the city, just talent and audacity. The majority of the works with which he captured the sacred city's eye were everything but devout. What could be the very first resides in London's National Gallery. A young man parts his crimson mouth in a scream of agony: while reaching out his dirty digits for a cherry, he has rather been bitten. Youth Bitten by a Reptile is sensuality amid squalor: viewers can see Caravaggio's gloomy room reflected in the murky waters of the transparent vase.

The boy sports a rose-colored blossom in his coiffure – a emblem of the erotic trade in Renaissance art. Venetian painters such as Tiziano and Palma Vecchio portrayed courtesans holding blooms and, in a painting destroyed in the second world war but known through images, the master represented a famous woman courtesan, holding a bouquet to her chest. The message of all these botanical signifiers is obvious: sex for purchase.

How are we to make of the artist's erotic portrayals of boys – and of a particular boy in specific? It is a question that has split his commentators since he gained mega-fame in the 1980s. The complex past truth is that the painter was not the queer icon that, for instance, Derek Jarman put on film in his 1986 film Caravaggio, nor so completely pious that, as certain art scholars improbably claim, his Youth Holding Fruit is in fact a portrait of Jesus.

His early works indeed make explicit erotic implications, or including offers. It's as if Caravaggio, then a destitute youthful creator, aligned with Rome's sex workers, selling himself to survive. In the Uffizi, with this idea in consideration, observers might turn to an additional initial creation, the sixteenth-century masterpiece Bacchus, in which the deity of wine stares coolly at you as he starts to undo the dark ribbon of his garment.

A few annums after the wine deity, what could have motivated the artist to paint Amor Vincit Omnia for the artistic patron the nobleman, when he was at last becoming nearly respectable with prestigious church projects? This unholy pagan god revives the erotic provocations of his early paintings but in a increasingly intense, unsettling way. Half a century afterwards, its secret seemed obvious: it was a representation of the painter's companion. A English visitor viewed the painting in about the mid-seventeenth century and was informed its figure has "the physique and countenance of [Caravaggio's|his] own youth or servant that slept with him". The name of this boy was Francesco.

The artist had been deceased for about 40 annums when this account was documented.