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A young lad cries out as his skull is firmly held, a large digit digging into his cheek as his parent's powerful palm grasps him by the neck. That scene from Abraham's Sacrifice appears in the Uffizi Gallery, creating distress through the artist's chilling portrayal of the tormented youth from the scriptural narrative. The painting appears as if Abraham, instructed by God to sacrifice his son, could break his neck with a single turn. Yet Abraham's preferred approach involves the metallic grey knife he holds in his remaining hand, ready to slit Isaac's throat. A certain aspect remains – whoever modeled as Isaac for this breathtaking work displayed extraordinary expressive skill. There exists not only fear, shock and begging in his darkened eyes but also profound sorrow that a protector could abandon him so utterly.

He took a well-known biblical story and transformed it so fresh and raw that its terrors seemed to happen right in front of you

Viewing before the painting, observers recognize this as a actual face, an precise depiction of a adolescent subject, because the same boy – identifiable by his disheveled locks and almost dark eyes – features in several additional paintings by Caravaggio. In each case, that highly emotional face commands the scene. In Youth With a Ram, he peers mischievously from the shadows while holding a lamb. In Amor Vincit Omnia, he smirks with a hardness acquired on Rome's streets, his black feathery appendages sinister, a unclothed adolescent creating chaos in a well-to-do dwelling.

Victorious Cupid, currently exhibited at a British museum, represents one of the most embarrassing artworks ever created. Viewers feel completely disoriented gazing at it. The god of love, whose arrows inspire people with often agonizing longing, is shown as a very real, vividly lit nude figure, standing over toppled-over items that include musical instruments, a musical score, plate armour and an architect's ruler. This heap of possessions resembles, deliberately, the mathematical and architectural equipment scattered across the ground in Albrecht Dürer's print Melancholy – save here, the gloomy disorder is caused by this smirking deity and the mayhem he can release.

"Affection sees not with the eyes, but with the soul, / And therefore is winged Cupid painted blind," penned the Bard, shortly before this painting was created around the early 1600s. But Caravaggio's god is not blind. He stares straight at you. That countenance – ironic and ruddy-faced, staring with brazen confidence as he poses naked – is the identical one that screams in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio created his multiple portrayals of the identical distinctive-looking kid in the Eternal City at the dawn of the seventeenth century, he was the most acclaimed religious painter in a city ignited by Catholic revival. Abraham's Offering reveals why he was sought to decorate churches: he could adopt a biblical story that had been depicted many occasions before and render it so fresh, so unfiltered and visceral that the horror seemed to be occurring directly before you.

However there was another side to the artist, apparent as quickly as he came in Rome in the cold season that ended the sixteenth century, as a artist in his initial twenties with no mentor or patron in the city, just talent and boldness. Most of the works with which he caught the holy metropolis's attention were everything but devout. What may be the absolute first resides in the UK's National Gallery. A youth opens his crimson mouth in a scream of pain: while reaching out his filthy digits for a fruit, he has instead been attacked. Youth Bitten by a Reptile is eroticism amid poverty: observers can see the painter's dismal room mirrored in the cloudy waters of the glass vase.

The boy wears a pink blossom in his coiffure – a symbol of the sex commerce in early modern art. Northern Italian artists such as Tiziano and Palma Vecchio portrayed prostitutes holding flowers and, in a work lost in the second world war but known through images, the master represented a renowned female courtesan, holding a posy to her bosom. The meaning of all these floral signifiers is clear: sex for sale.

How are we to make of Caravaggio's erotic depictions of youths – and of a particular adolescent in specific? It is a question that has split his commentators ever since he achieved widespread recognition in the twentieth century. The complicated past reality is that the artist was not the homosexual hero that, for instance, the filmmaker put on film in his 1986 film Caravaggio, nor so entirely pious that, as certain art historians improbably assert, his Youth Holding Fruit is in fact a portrait of Jesus.

His early paintings do offer explicit sexual suggestions, or even offers. It's as if the painter, then a penniless youthful creator, aligned with Rome's prostitutes, selling himself to live. In the Uffizi, with this idea in mind, viewers might look to another early creation, the sixteenth-century masterwork the god of wine, in which the god of wine gazes coolly at you as he starts to undo the dark sash of his robe.

A few years following Bacchus, what could have motivated Caravaggio to create Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was at last growing nearly respectable with prestigious church projects? This unholy pagan god resurrects the sexual provocations of his initial works but in a more intense, unsettling way. Half a century later, its secret seemed clear: it was a portrait of the painter's companion. A British visitor saw the painting in about the mid-seventeenth century and was told its figure has "the body & face of [Caravaggio's|his] own youth or assistant that slept with him". The identity of this boy was Cecco.

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