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The youthful boy screams while his skull is firmly gripped, a large thumb pressing into his face as his father's powerful hand grasps him by the throat. This moment from The Sacrifice of Isaac visits the Florentine museum, creating distress through Caravaggio's chilling portrayal of the suffering youth from the scriptural narrative. It seems as if Abraham, commanded by God to sacrifice his son, could break his neck with a solitary twist. However Abraham's preferred method involves the silvery grey blade he grips in his remaining hand, ready to cut the boy's throat. One certain element stands out – whomever posed as Isaac for this breathtaking piece demonstrated remarkable expressive skill. Within exists not only fear, surprise and begging in his shadowed eyes but additionally deep grief that a guardian could abandon him so completely.

He took a well-known scriptural tale and transformed it so vibrant and raw that its horrors appeared to unfold right in front of you

Viewing before the painting, viewers identify this as a real face, an accurate record of a young subject, because the same boy – identifiable by his tousled hair and nearly dark pupils – appears in several additional works by the master. In each case, that highly emotional face dominates the composition. In Youth With a Ram, he gazes mischievously from the shadows while embracing a ram. In Amor Vincit Omnia, he smirks with a hardness acquired on the city's streets, his dark plumed appendages demonic, a unclothed child creating chaos in a affluent dwelling.

Amor Vincit Omnia, presently exhibited at a British museum, constitutes one of the most embarrassing artworks ever created. Observers feel completely unsettled looking at it. Cupid, whose arrows inspire people with often agonizing desire, is shown as a extremely tangible, brightly lit nude form, straddling overturned items that comprise stringed devices, a musical score, plate armour and an architect's T-square. This pile of items echoes, intentionally, the mathematical and architectural gear scattered across the floor in Albrecht Dürer's print Melancholy – except in this case, the melancholic mess is created by this grinning Cupid and the mayhem he can unleash.

"Love looks not with the eyes, but with the mind, / And thus is feathered Cupid depicted blind," wrote Shakespeare, shortly prior to this painting was produced around 1601. But the painter's god is not unseeing. He gazes directly at you. That countenance – sardonic and ruddy-faced, looking with brazen confidence as he poses unclothed – is the same one that screams in terror in The Sacrifice of Isaac.

As the Italian master created his multiple portrayals of the identical unusual-looking youth in the Eternal City at the dawn of the seventeenth century, he was the highly acclaimed religious painter in a metropolis enflamed by Catholic revival. The Sacrifice of Isaac demonstrates why he was commissioned to decorate sanctuaries: he could adopt a biblical story that had been depicted numerous times previously and render it so new, so unfiltered and visceral that the horror seemed to be happening directly in front of you.

However there was another aspect to Caravaggio, evident as quickly as he came in the capital in the winter that ended 1592, as a painter in his initial twenties with no teacher or supporter in the city, only talent and boldness. The majority of the works with which he captured the holy city's eye were anything but devout. What may be the absolute first hangs in London's art museum. A young man parts his red lips in a yell of agony: while reaching out his filthy digits for a fruit, he has rather been attacked. Youth Bitten by a Reptile is sensuality amid squalor: viewers can see the painter's gloomy chamber mirrored in the murky waters of the glass vase.

The boy wears a pink blossom in his hair – a symbol of the sex commerce in Renaissance painting. Northern Italian painters such as Tiziano and Jacopo Palma portrayed prostitutes grasping flowers and, in a painting lost in the second world war but known through images, Caravaggio portrayed a famous female courtesan, clutching a bouquet to her chest. The message of all these botanical signifiers is obvious: intimacy for purchase.

What are we to interpret of the artist's erotic depictions of youths – and of a particular boy in specific? It is a inquiry that has divided his commentators since he achieved mega-fame in the 1980s. The complex historical reality is that the artist was not the homosexual icon that, for example, the filmmaker presented on screen in his twentieth-century film about the artist, nor so entirely devout that, as certain artistic historians improbably assert, his Youth Holding Fruit is actually a portrait of Jesus.

His early paintings indeed make overt sexual implications, or even offers. It's as if the painter, then a destitute youthful creator, identified with the city's prostitutes, offering himself to live. In the Florentine gallery, with this idea in mind, viewers might turn to an additional initial work, the sixteenth-century masterpiece the god of wine, in which the deity of alcohol stares coolly at the spectator as he begins to untie the black ribbon of his garment.

A few annums following Bacchus, what could have motivated the artist to create Victorious Cupid for the artistic collector Vincenzo Giustiniani, when he was finally becoming almost respectable with important church commissions? This unholy non-Christian deity resurrects the sexual challenges of his early works but in a more intense, uneasy way. Half a century afterwards, its secret seemed clear: it was a portrait of Caravaggio's lover. A British traveller saw Victorious Cupid in about 1649 and was informed its subject has "the body & face of [Caravaggio's|his] owne youth or assistant that laid with him". The identity of this boy was Cecco.

The artist had been dead for about forty years when this story was recorded.