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A young lad cries out as his head is firmly held, a large thumb digging into his cheek as his father's powerful hand holds him by the neck. That moment from The Sacrifice of Isaac visits the Uffizi Gallery, evoking distress through Caravaggio's harrowing rendition of the tormented child from the scriptural account. The painting seems as if Abraham, instructed by the Divine to kill his offspring, could snap his neck with a single turn. However the father's chosen approach involves the silvery steel knife he grips in his remaining hand, ready to slit Isaac's throat. One certain aspect remains – whoever posed as Isaac for this astonishing piece demonstrated extraordinary expressive skill. There exists not only fear, shock and begging in his darkened eyes but also profound grief that a guardian could abandon him so completely.

He took a familiar biblical story and made it so fresh and raw that its horrors seemed to unfold directly in front of you

Standing in front of the artwork, observers identify this as a real face, an accurate depiction of a adolescent model, because the same boy – recognizable by his tousled hair and nearly dark eyes – features in several additional paintings by Caravaggio. In each case, that highly expressive visage commands the scene. In Youth With a Ram, he peers playfully from the shadows while holding a ram. In Victorious Cupid, he smirks with a hardness learned on the city's streets, his dark feathery appendages demonic, a naked child running chaos in a well-to-do dwelling.

Amor Vincit Omnia, currently exhibited at a London gallery, constitutes one of the most embarrassing artworks ever painted. Viewers feel completely unsettled gazing at it. The god of love, whose arrows fill people with frequently agonizing longing, is portrayed as a very tangible, vividly lit nude figure, straddling overturned items that include musical instruments, a musical score, metal armour and an builder's T-square. This heap of items echoes, intentionally, the geometric and architectural gear scattered across the floor in Albrecht Dürer's engraving Melancholy – save in this case, the gloomy disorder is caused by this smirking Cupid and the turmoil he can release.

"Love looks not with the vision, but with the mind, / And therefore is feathered Cupid depicted sightless," penned Shakespeare, shortly before this work was produced around the early 1600s. But the painter's Cupid is not blind. He gazes directly at the observer. That face – sardonic and rosy-cheeked, looking with bold assurance as he poses unclothed – is the same one that shrieks in fear in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio painted his three images of the same unusual-looking youth in Rome at the dawn of the 17th century, he was the highly celebrated sacred artist in a metropolis enflamed by Catholic revival. Abraham's Offering reveals why he was sought to adorn churches: he could take a biblical story that had been portrayed many times before and make it so new, so unfiltered and visceral that the horror seemed to be happening immediately before you.

Yet there was another side to Caravaggio, apparent as soon as he came in Rome in the winter that concluded the sixteenth century, as a artist in his initial 20s with no teacher or supporter in the city, only skill and audacity. Most of the works with which he captured the sacred metropolis's eye were everything but devout. That could be the very earliest resides in London's art museum. A youth parts his red lips in a yell of agony: while reaching out his dirty fingers for a fruit, he has instead been attacked. Youth Bitten by a Reptile is eroticism amid squalor: viewers can see Caravaggio's dismal room reflected in the murky liquid of the glass vase.

The adolescent wears a pink blossom in his coiffure – a emblem of the sex trade in early modern painting. Northern Italian artists such as Titian and Palma Vecchio depicted courtesans holding blooms and, in a work destroyed in the second world war but documented through images, Caravaggio represented a famous woman prostitute, clutching a posy to her chest. The message of all these botanical indicators is obvious: sex for sale.

What are we to interpret of the artist's sensual portrayals of youths – and of one boy in specific? It is a inquiry that has split his interpreters since he gained widespread recognition in the twentieth century. The complex historical reality is that the artist was not the homosexual icon that, for example, the filmmaker presented on screen in his 1986 movie about the artist, nor so completely devout that, as some art scholars improbably assert, his Youth Holding Fruit is actually a likeness of Christ.

His early works do offer overt erotic implications, or including offers. It's as if the painter, then a destitute young artist, identified with the city's prostitutes, offering himself to survive. In the Florentine gallery, with this thought in consideration, observers might turn to another initial work, the sixteenth-century masterwork the god of wine, in which the deity of wine stares calmly at you as he starts to undo the black sash of his garment.

A few annums following Bacchus, what could have driven the artist to paint Amor Vincit Omnia for the art patron the nobleman, when he was finally growing nearly respectable with prestigious church projects? This profane pagan deity resurrects the erotic provocations of his initial works but in a increasingly powerful, uneasy manner. Fifty years afterwards, its secret seemed clear: it was a portrait of Caravaggio's companion. A English visitor saw the painting 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 name of this adolescent was Cecco.

The painter had been deceased for about forty annums when this account was documented.