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The young boy cries out as his skull is forcefully held, a massive thumb pressing into his face as his parent's powerful hand holds him by the throat. This moment from Abraham's Sacrifice appears in the Uffizi Gallery, evoking distress through Caravaggio's harrowing rendition of the suffering child from the biblical account. It seems as if Abraham, instructed by God to kill his son, could snap his neck with a single twist. Yet Abraham's preferred approach involves the metallic grey blade he holds in his remaining hand, ready to cut Isaac's neck. A definite element stands out – whomever modeled as the sacrifice for this astonishing piece demonstrated extraordinary expressive ability. Within exists not only fear, surprise and pleading in his shadowed eyes but also profound sorrow that a protector could betray him so completely.

He adopted a familiar biblical story and made it so vibrant and raw that its horrors seemed to happen directly in view of you

Standing before the artwork, viewers recognize this as a real countenance, an precise depiction of a adolescent model, because the same boy – recognizable by his disheveled hair and almost dark pupils – features in several other paintings by Caravaggio. In every instance, that richly emotional face dominates the composition. In Youth With a Ram, he gazes playfully from the shadows while holding a lamb. In Victorious Cupid, he smirks with a toughness acquired on the city's streets, his black feathery wings demonic, a unclothed adolescent creating riot in a affluent residence.

Amor Vincit Omnia, presently exhibited at a London gallery, represents one of the most discomfiting artworks ever created. Viewers feel completely unsettled gazing at it. Cupid, whose arrows fill people with often painful longing, is portrayed as a extremely tangible, vividly lit nude figure, standing over overturned objects that include musical instruments, a musical manuscript, plate armor and an builder's T-square. This heap of items resembles, intentionally, the mathematical and architectural equipment strewn across the ground in Albrecht Dürer's engraving Melencolia I – except in this case, the gloomy disorder is caused by this smirking Cupid and the mayhem he can release.

"Love looks not with the vision, but with the soul, / And therefore is winged Cupid depicted blind," wrote Shakespeare, shortly prior to this work was produced around the early 1600s. But Caravaggio's god is not blind. He stares straight at you. That face – sardonic and ruddy-faced, staring with brazen confidence as he struts naked – is the identical one that screams in fear in The Sacrifice of Isaac.

As the Italian master created his three portrayals of the same unusual-looking youth in the Eternal City at the start of the seventeenth century, he was the most celebrated religious artist in a city enflamed by Catholic revival. Abraham's Offering demonstrates why he was commissioned to adorn churches: he could adopt a biblical story that had been portrayed many occasions previously and render it so new, so unfiltered and visceral that the terror appeared to be occurring directly in front of the spectator.

Yet there was a different side to the artist, apparent as soon as he came in Rome in the winter that concluded the sixteenth century, as a artist in his early 20s with no mentor or supporter in the urban center, just skill and boldness. Most of the works with which he captured the holy city's eye were anything but devout. That may be the absolute first resides in the UK's art museum. A youth parts his red mouth in a scream of agony: while reaching out his filthy digits for a fruit, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid squalor: observers can discern Caravaggio's dismal chamber reflected in the cloudy liquid of the transparent container.

The adolescent wears a pink flower in his hair – a symbol of the erotic trade in early modern painting. Venetian artists such as Titian and Jacopo Palma portrayed courtesans grasping flowers and, in a work lost in the WWII but documented through photographs, Caravaggio portrayed a famous woman prostitute, clutching a bouquet to her chest. The meaning of all these floral signifiers is clear: intimacy for sale.

What are we to make of Caravaggio's erotic portrayals of boys – and of a particular boy in specific? It is a question that has split his commentators ever since he gained mega-fame in the 1980s. The complicated past truth is that the painter was not the queer icon that, for instance, the filmmaker put on film in his 1986 film about the artist, nor so entirely devout that, as some artistic historians unbelievably claim, his Boy With a Basket of Fruit is actually a portrait of Jesus.

His early paintings indeed make explicit erotic suggestions, or even offers. It's as if Caravaggio, then a destitute young creator, identified with the city's prostitutes, selling himself to live. In the Uffizi, with this idea in consideration, viewers might look to an additional early creation, the 1596 masterwork the god of wine, in which the deity of alcohol gazes coolly at you as he starts to undo the dark sash of his garment.

A few years following Bacchus, what could have driven the artist to create Amor Vincit Omnia for the art patron the nobleman, when he was at last growing almost established with important ecclesiastical projects? This profane pagan god resurrects the erotic challenges of his early paintings but in a increasingly intense, uneasy way. Half a century later, its secret seemed obvious: it was a portrait of Caravaggio's lover. A English traveller viewed Victorious Cupid in about 1649 and was informed its figure has "the body & face of [Caravaggio's|his] own youth or assistant that laid with him". The name of this boy was Francesco.

The artist had been dead for about 40 years when this account was documented.