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The youthful boy screams while his head is forcefully gripped, a large thumb digging into his cheek as his parent's mighty palm holds him by the throat. This scene from Abraham's Sacrifice visits the Uffizi Gallery, evoking distress through Caravaggio's chilling portrayal of the tormented youth from the biblical account. The painting seems as if the patriarch, commanded by God to kill his offspring, could break his spinal column with a single turn. However Abraham's chosen method involves the silvery steel blade he holds in his remaining palm, ready to slit the boy's neck. A certain element stands out – whomever posed as the sacrifice for this breathtaking piece displayed extraordinary expressive skill. Within exists not just fear, surprise and begging in his darkened eyes but also deep grief that a guardian could abandon him so completely.

He adopted a familiar scriptural story and transformed it so vibrant and raw that its terrors seemed to unfold right in front of you

Viewing before the painting, observers identify this as a actual countenance, an accurate depiction of a young subject, because the same boy – recognizable by his disheveled hair and almost black eyes – features in several additional paintings by Caravaggio. In every instance, that richly expressive visage dominates the scene. In Youth With a Ram, he peers mischievously from the darkness while embracing a ram. In Victorious Cupid, he grins with a toughness learned on the city's streets, his dark plumed appendages demonic, a naked adolescent creating chaos in a affluent residence.

Amor Vincit Omnia, presently exhibited at a London museum, constitutes one of the most embarrassing artworks ever painted. Viewers feel totally unsettled looking at it. Cupid, whose darts inspire people with often agonizing desire, is shown as a extremely real, brightly lit unclothed form, standing over overturned objects that include musical devices, a music score, plate armor and an architect's T-square. This heap of items echoes, deliberately, the mathematical and architectural gear strewn across the ground in the German master's engraving Melencolia I – except here, the gloomy disorder is created by this smirking deity and the mayhem he can unleash.

"Affection looks not with the eyes, but with the soul, / And thus is winged Cupid depicted sightless," penned the Bard, shortly prior to this work was created around 1601. But the painter's god is not blind. He gazes straight at the observer. That face – sardonic and rosy-faced, looking with bold assurance as he struts unclothed – is the same one that shrieks in fear in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio painted his three portrayals of the same distinctive-appearing youth in the Eternal City at the start of the seventeenth century, he was the most celebrated religious painter in a metropolis ignited by Catholic revival. The Sacrifice of Isaac demonstrates why he was commissioned to adorn sanctuaries: he could adopt a scriptural narrative that had been depicted many times previously and make it so fresh, so raw and visceral that the horror seemed to be happening directly before the spectator.

However there was a different side to Caravaggio, evident as soon as he arrived in Rome in the winter that concluded the sixteenth century, as a artist in his initial twenties with no teacher or supporter in the city, only talent and boldness. The majority of the works with which he caught the holy city's eye were everything but devout. That may be the very earliest hangs in the UK's National Gallery. A youth parts his crimson lips in a scream of agony: while stretching out his filthy digits for a fruit, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid squalor: viewers can discern Caravaggio's gloomy room reflected in the cloudy liquid of the transparent container.

The adolescent wears a pink blossom in his hair – a symbol of the erotic trade in Renaissance art. Venetian artists such as Titian and Jacopo Palma depicted courtesans holding blooms and, in a work lost in the second world war but known through images, Caravaggio portrayed a renowned female prostitute, clutching a posy to her chest. The message of all these floral indicators is obvious: intimacy for sale.

How are we to make of Caravaggio's erotic portrayals of boys – and of a particular adolescent in particular? It is a question that has split his commentators ever since he achieved mega-fame in the twentieth century. The complicated past reality is that the painter was neither the homosexual icon that, for example, Derek Jarman put on screen in his twentieth-century film about the artist, nor so entirely devout that, as some artistic scholars improbably claim, his Boy With a Basket of Fruit is in fact a portrait of Christ.

His initial works do make overt sexual suggestions, or even offers. It's as if the painter, then a penniless youthful creator, aligned with Rome's sex workers, selling himself to survive. In the Florentine gallery, with this idea in mind, observers might look to another early work, the 1596 masterpiece the god of wine, in which the god of wine stares coolly at the spectator as he begins to untie the black sash of his robe.

A several annums following Bacchus, what could have motivated the artist to create Victorious Cupid for the artistic patron the nobleman, when he was finally growing almost established with important ecclesiastical commissions? This unholy non-Christian deity resurrects the sexual provocations of his early paintings but in a increasingly powerful, uneasy way. Fifty years afterwards, its hidden meaning seemed obvious: it was a representation of the painter's companion. A English traveller saw Victorious Cupid in about the mid-seventeenth century and was told its subject has "the physique and countenance of [Caravaggio's|his] owne boy or assistant that slept with him". The identity of this adolescent was Cecco.

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