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A youthful boy screams while his skull is forcefully gripped, a massive thumb digging into his face as his father's mighty hand grasps him by the throat. This scene from Abraham's Sacrifice visits the Uffizi Gallery, evoking distress through Caravaggio's harrowing portrayal of the suffering child from the biblical narrative. The painting seems as if Abraham, commanded by God to sacrifice his offspring, could snap his spinal column with a single twist. However the father's preferred approach involves the silvery grey knife he grips in his other palm, prepared to cut Isaac's neck. One certain element stands out – whoever modeled as Isaac for this astonishing piece demonstrated remarkable expressive ability. There exists not only fear, surprise and pleading in his shadowed eyes but also profound grief that a guardian could betray him so completely.

He took a familiar scriptural story and made it so fresh and visceral that its terrors seemed to happen right in front of you

Viewing in front of the painting, observers identify this as a actual face, an precise depiction of a young model, because the identical youth – identifiable by his tousled locks and almost dark eyes – appears in several additional paintings by the master. In every instance, that richly emotional visage dominates the scene. In John the Baptist, he peers mischievously from the darkness while holding a ram. In Victorious Cupid, he grins with a toughness learned on Rome's alleys, his black plumed wings demonic, a naked adolescent running chaos in a affluent residence.

Amor Vincit Omnia, currently exhibited at a London gallery, constitutes one of the most discomfiting artworks ever created. Viewers feel totally disoriented looking at it. The god of love, whose darts fill people with frequently painful longing, is portrayed as a very real, brightly lit nude figure, standing over overturned items that comprise musical devices, a music manuscript, metal armor and an builder's ruler. This heap of possessions echoes, intentionally, the mathematical and architectural gear strewn across the floor in Albrecht Dürer's engraving Melancholy – except here, the gloomy mess is caused by this smirking Cupid and the turmoil he can unleash.

"Affection looks not with the vision, but with the soul, / And therefore is winged Love depicted sightless," wrote the Bard, just prior to this painting was created around 1601. But the painter's god is not unseeing. He gazes directly at you. That countenance – sardonic and rosy-faced, looking with brazen confidence as he poses unclothed – is the same one that screams in fear in Abraham's Test.

As Michelangelo Merisi da Caravaggio painted his three portrayals of the same distinctive-looking kid in Rome at the dawn of the seventeenth century, he was the highly celebrated religious painter in a metropolis enflamed by religious revival. The Sacrifice of Isaac reveals why he was commissioned to decorate churches: he could take a scriptural story that had been portrayed many times previously and render it so new, so raw and physical that the horror appeared to be happening directly before you.

Yet there existed a different aspect to the artist, evident as soon as he arrived in Rome in the cold season that concluded 1592, as a painter in his early 20s with no teacher or supporter in the urban center, just skill and audacity. The majority of the paintings with which he captured the holy metropolis's attention were everything but holy. What could be the absolute earliest resides in the UK's art museum. A youth parts his red mouth in a scream of agony: while stretching out his dirty fingers for a fruit, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid poverty: viewers can see Caravaggio's dismal room reflected in the murky waters of the glass container.

The boy wears a pink flower in his hair – a emblem of the erotic trade in Renaissance painting. Northern Italian painters such as Titian and Jacopo Palma depicted prostitutes holding flowers and, in a work destroyed in the second world war but known through photographs, Caravaggio represented a famous woman prostitute, holding a bouquet to her chest. The message of all these floral signifiers is obvious: sex for purchase.

What are we to make of Caravaggio's erotic depictions of youths – and of a particular adolescent in specific? It is a inquiry that has split his commentators ever since he achieved mega-fame in the 1980s. The complex past truth is that the artist was neither the queer hero that, for instance, the filmmaker put on screen in his 1986 film Caravaggio, nor so entirely devout that, as some art historians improbably claim, his Youth Holding Fruit is in fact a likeness of Jesus.

His early paintings do offer overt erotic suggestions, or even propositions. It's as if the painter, then a destitute youthful creator, identified with the city's prostitutes, selling himself to live. In the Florentine gallery, with this thought in consideration, observers might look to an additional initial work, the 1596 masterwork Bacchus, in which the deity of alcohol stares coolly at you as he begins to undo the dark sash of his garment.

A few annums after the wine deity, what could have driven the artist to create Victorious Cupid for the artistic patron the nobleman, when he was finally growing almost established with prestigious church commissions? This unholy pagan god resurrects the erotic challenges of his early works but in a more intense, uneasy way. Fifty years later, its hidden meaning seemed clear: it was a representation of Caravaggio's companion. A English visitor viewed the painting in about 1649 and was informed its figure has "the body & face of [Caravaggio's|his] owne youth or servant that laid with him". The identity of this adolescent was Cecco.

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