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A youthful lad screams as his head is forcefully gripped, a massive digit pressing into his cheek as his parent's powerful palm holds him by the throat. This moment from The Sacrifice of Isaac appears in the Uffizi Gallery, creating unease through the artist's harrowing rendition of the tormented youth from the scriptural account. The painting appears as if Abraham, commanded by the Divine to sacrifice his offspring, could snap his neck with a solitary twist. Yet the father's preferred method involves the metallic grey blade he grips in his other palm, prepared to cut Isaac's throat. A definite element remains – whoever modeled as the sacrifice for this astonishing piece displayed extraordinary expressive ability. There exists not just dread, surprise and begging in his darkened eyes but also deep grief 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 front of you

Viewing in front of the painting, viewers identify this as a real face, an accurate depiction of a young model, because the same boy – identifiable by his tousled locks and almost dark eyes – appears in several other paintings by the master. In every case, that richly expressive visage commands the composition. In John the Baptist, he peers playfully from the shadows while holding a lamb. In Amor Vincit Omnia, he grins with a toughness acquired on Rome's alleys, his black feathery appendages sinister, a unclothed adolescent running riot in a well-to-do residence.

Amor Vincit Omnia, presently exhibited at a London museum, represents one of the most embarrassing artworks ever created. Observers feel totally disoriented looking at it. The god of love, whose arrows inspire people with often agonizing desire, is shown as a extremely real, vividly lit unclothed form, standing over overturned items that comprise musical instruments, a music score, plate armour and an builder's ruler. This heap of items resembles, intentionally, the mathematical and architectural gear strewn across the floor in Albrecht Dürer's print Melancholy – save in this case, the melancholic mess is created by this grinning Cupid and the mayhem he can release.

"Affection looks not with the eyes, but with the mind, / And therefore is winged Love painted sightless," wrote the Bard, shortly before this painting was produced around the early 1600s. But the painter's Cupid is not blind. He stares straight at you. That countenance – sardonic and ruddy-cheeked, staring with brazen assurance as he poses unclothed – is the same one that shrieks in terror in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio painted his three images of the same distinctive-looking kid in Rome at the start of the 17th century, he was the most acclaimed religious painter in a city enflamed by Catholic revival. The Sacrifice of Isaac reveals why he was sought to adorn sanctuaries: he could adopt a biblical narrative that had been depicted numerous times previously and make it so new, so unfiltered and physical that the terror appeared to be happening immediately before you.

Yet there was a different aspect to Caravaggio, apparent as quickly as he came in Rome in the winter that ended 1592, as a painter in his early twenties with no teacher or supporter in the city, just skill and audacity. Most of the paintings with which he captured the holy city's eye were anything but devout. What may be the very earliest resides in London's National Gallery. A young man opens his red lips in a yell of agony: while reaching out his filthy digits for a cherry, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid poverty: viewers can see Caravaggio's dismal room reflected in the murky waters of the glass vase.

The boy sports a rose-colored blossom in his coiffure – a emblem of the erotic commerce in early modern art. Northern Italian artists such as Titian and Jacopo Palma depicted courtesans holding flowers and, in a work lost in the second world war but known through images, the master portrayed a famous female courtesan, clutching a posy to her bosom. The message of all these floral signifiers is clear: sex for purchase.

How are we to interpret of the artist's erotic depictions of youths – and of a particular adolescent in particular? It is a inquiry that has split his commentators since he achieved mega-fame in the twentieth century. The complicated past reality is that the painter was neither the homosexual hero that, for instance, Derek Jarman presented on film in his twentieth-century movie Caravaggio, nor so entirely pious that, as certain artistic scholars improbably claim, his Youth Holding Fruit is actually a portrait of Jesus.

His early works indeed offer explicit erotic implications, or even propositions. It's as if the painter, then a destitute youthful artist, aligned with the city's sex workers, offering himself to survive. In the Florentine gallery, with this idea in mind, viewers might turn to an additional early creation, the 1596 masterpiece Bacchus, in which the god of alcohol stares coolly at you as he begins to undo the black ribbon of his robe.

A few annums after Bacchus, what could have driven Caravaggio to paint Victorious Cupid for the artistic patron Vincenzo Giustiniani, when he was at last growing almost established with important ecclesiastical projects? This profane pagan deity revives the sexual challenges of his initial paintings but in a increasingly intense, uneasy manner. Fifty years afterwards, its hidden meaning seemed clear: it was a portrait of Caravaggio's companion. A English traveller viewed Victorious Cupid in about 1649 and was informed its subject has "the physique and countenance of [Caravaggio's|his] owne youth or assistant that slept with him". The name of this adolescent was Francesco.

The artist had been dead for about 40 annums when this account was documented.