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A young boy cries out while his skull is forcefully gripped, a large digit pressing into his cheek as his parent's powerful hand holds him by the throat. This scene from The Sacrifice of Isaac appears in the Uffizi Gallery, evoking distress through the artist's chilling rendition of the tormented child from the biblical account. The painting seems as if the patriarch, commanded by God to sacrifice his offspring, could snap his neck with a solitary twist. However Abraham's preferred approach involves the silvery grey blade he holds in his other palm, prepared to cut Isaac's neck. A certain element remains – whomever modeled as Isaac for this astonishing work displayed extraordinary expressive skill. Within exists not only dread, shock and pleading in his shadowed gaze but also deep sorrow that a guardian could abandon him so completely.

The artist took a familiar biblical tale and transformed it so fresh and raw that its horrors seemed to unfold directly in front of you

Viewing in front of the artwork, viewers recognize this as a real countenance, an accurate record of a adolescent subject, because the identical youth – recognizable by his disheveled hair and almost black pupils – features in several additional paintings by Caravaggio. In each case, that richly expressive face commands the composition. In Youth With a Ram, he peers playfully from the darkness while embracing a ram. In Amor Vincit Omnia, he grins with a toughness learned on the city's streets, his black plumed appendages demonic, a unclothed child creating riot in a well-to-do residence.

Victorious Cupid, presently displayed at a British museum, constitutes one of the most embarrassing masterpieces ever created. Viewers feel totally unsettled looking at it. The god of love, whose darts fill people with frequently agonizing desire, is shown as a very tangible, vividly lit nude form, straddling overturned objects that include stringed instruments, a music manuscript, metal armour and an architect's ruler. This pile of items echoes, deliberately, the mathematical and architectural equipment scattered across the floor in Albrecht Dürer's print Melancholy – except here, the gloomy mess is caused by this smirking deity and the mayhem he can release.

"Affection looks not with the eyes, but with the mind, / And therefore is feathered Cupid depicted sightless," wrote Shakespeare, shortly before this work was produced around the early 1600s. But the painter's god is not unseeing. He stares directly at you. That countenance – ironic and rosy-faced, looking 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 unusual-appearing kid in the Eternal City at the dawn of the 17th century, he was the most acclaimed sacred painter in a city ignited by Catholic revival. Abraham's Offering reveals why he was commissioned to adorn churches: he could take a scriptural story that had been portrayed many times previously and make it so new, so raw and physical that the terror seemed to be happening immediately in front of the spectator.

However there existed a different aspect to the artist, apparent as quickly as he arrived in the capital in the winter that ended 1592, as a painter in his initial 20s with no mentor or supporter in the urban center, just talent and audacity. Most of the works with which he captured the holy metropolis's attention were everything but devout. What could be the absolute first hangs in London's art museum. A youth parts his red mouth in a yell of agony: while stretching out his dirty fingers for a cherry, he has rather been attacked. Youth Bitten by a Reptile is eroticism amid poverty: viewers can see Caravaggio's gloomy chamber reflected in the cloudy waters of the glass vase.

The boy sports a pink flower in his hair – a symbol of the sex commerce in early modern art. Venetian artists such as Tiziano and Palma Vecchio portrayed courtesans grasping blooms and, in a work destroyed in the WWII but known through images, Caravaggio portrayed a famous female courtesan, clutching a posy to her chest. The meaning of all these botanical indicators is clear: intimacy for sale.

What are we to make of the artist's erotic portrayals of youths – and of one adolescent in specific? It is a question that has split his interpreters ever since he gained widespread recognition in the twentieth century. The complicated historical reality is that the painter was not the queer hero that, for instance, Derek Jarman put on screen in his twentieth-century film about the artist, nor so entirely pious that, as some artistic historians improbably claim, his Youth Holding Fruit is actually a portrait of Jesus.

His initial paintings indeed make overt sexual suggestions, or including offers. It's as if the painter, then a destitute youthful artist, identified with Rome's sex workers, selling himself to live. In the Florentine gallery, with this idea in consideration, viewers might look to another initial work, the sixteenth-century masterpiece the god of wine, in which the god of wine stares coolly at you as he starts to undo the black sash of his robe.

A few annums following the wine deity, what could have motivated the artist to create Victorious Cupid for the artistic collector the nobleman, when he was finally growing almost established with important church commissions? This unholy pagan god revives the erotic provocations of his initial works but in a increasingly powerful, unsettling manner. Half a century afterwards, its hidden meaning seemed clear: it was a representation of the painter's companion. A English traveller viewed Victorious Cupid in about the mid-seventeenth century and was told its figure has "the physique and countenance of [Caravaggio's|his] own youth or servant that slept with him". The name of this adolescent was Francesco.

The painter had been deceased for about 40 years when this story was recorded.