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The youthful boy cries out as his head is forcefully held, a massive digit digging into his face as his father's powerful hand grasps him by the neck. This scene from The Sacrifice of Isaac visits the Florentine museum, evoking distress through the artist's harrowing portrayal of the suffering youth from the biblical account. It appears as if Abraham, instructed by the Divine to sacrifice his offspring, could snap his spinal column with a solitary turn. Yet the father's chosen approach involves the metallic steel blade he holds in his other hand, ready to cut the boy's throat. One definite element remains – whomever posed as Isaac for this astonishing work demonstrated remarkable acting skill. Within exists not only fear, surprise and pleading in his shadowed eyes but also profound sorrow that a protector could betray him so utterly.

The artist adopted a well-known biblical tale and transformed it so fresh and raw that its horrors appeared to unfold directly in view of you

Standing before the painting, viewers recognize this as a actual face, an precise depiction of a young subject, because the same boy – identifiable by his disheveled hair and almost black eyes – features in several other works by Caravaggio. In each case, that highly expressive face commands the scene. In Youth With a Ram, he gazes mischievously from the shadows while embracing a ram. In Amor Vincit Omnia, he smirks with a toughness learned on Rome's alleys, his black plumed appendages sinister, a naked adolescent creating riot in a affluent residence.

Amor Vincit Omnia, currently exhibited at a London museum, represents one of the most embarrassing artworks ever painted. Observers feel totally disoriented gazing at it. The god of love, whose darts inspire people with frequently agonizing desire, is portrayed as a extremely tangible, brightly illuminated nude form, straddling toppled-over items that comprise musical instruments, a musical manuscript, metal armor and an builder's T-square. This pile of possessions echoes, intentionally, the mathematical and construction equipment strewn across the floor in Albrecht Dürer's print Melencolia I – except in this case, the melancholic mess is caused by this grinning Cupid and the turmoil he can unleash.

"Affection sees not with the vision, but with the soul, / And thus is winged Love painted blind," wrote the Bard, shortly prior to this painting was created around the early 1600s. But Caravaggio's Cupid is not blind. He stares straight at the observer. That face – sardonic and ruddy-cheeked, staring with bold confidence as he struts unclothed – is the same one that shrieks in terror in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio created his multiple portrayals of the identical unusual-appearing youth in Rome at the start of the 17th century, he was the highly celebrated religious artist in a city ignited by religious renewal. The Sacrifice of Isaac reveals why he was commissioned to decorate churches: he could adopt a biblical story that had been depicted many times previously and make it so new, so raw and physical that the terror seemed to be occurring immediately before the spectator.

However there was another side to Caravaggio, apparent as quickly as he came in Rome in the cold season that concluded 1592, as a artist in his early twenties with no mentor or patron in the city, just skill and audacity. The majority of the paintings with which he captured the sacred city's eye were everything but holy. That may be the very earliest resides in the UK's National Gallery. A young man parts his red lips in a scream of agony: while stretching out his filthy fingers for a fruit, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid squalor: viewers can see the painter's gloomy chamber reflected in the cloudy liquid of the glass vase.

The adolescent wears a rose-colored blossom in his hair – a emblem of the sex commerce in early modern art. Northern Italian painters such as Titian and Jacopo Palma portrayed prostitutes grasping flowers and, in a work destroyed in the second world war but known through images, Caravaggio portrayed a famous woman prostitute, holding a posy to her chest. The meaning of all these floral indicators is clear: sex for sale.

What are we to make of the artist's erotic portrayals of boys – and of one adolescent in particular? It is a question that has split his interpreters since he gained widespread recognition in the 1980s. The complex past truth is that the painter was not the homosexual icon that, for instance, Derek Jarman presented on screen in his twentieth-century movie about the artist, nor so completely devout that, as certain artistic historians improbably claim, his Youth Holding Fruit is in fact a likeness of Christ.

His initial paintings do make overt sexual suggestions, or including offers. It's as if Caravaggio, then a penniless young artist, aligned with the city's sex workers, selling himself to survive. In the Uffizi, with this idea in consideration, viewers might look to another initial work, the 1596 masterpiece Bacchus, in which the deity of alcohol stares calmly at the spectator as he starts to untie the dark sash of his garment.

A several years following Bacchus, what could have motivated Caravaggio to create Amor Vincit Omnia for the artistic patron the nobleman, when he was finally becoming nearly respectable with important church projects? This profane pagan god revives the sexual challenges of his early paintings but in a more intense, unsettling manner. Fifty years later, its hidden meaning seemed clear: it was a representation of the painter's companion. A British visitor saw the painting in about 1649 and was told its subject has "the physique and countenance of [Caravaggio's|his] own boy or assistant that laid with him". The name of this boy was Francesco.

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