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The young boy screams while his head is firmly held, a massive thumb pressing into his face as his parent's powerful palm holds him by the neck. This moment from Abraham's Sacrifice visits the Uffizi Gallery, evoking distress through the artist's chilling rendition of the suffering youth from the biblical narrative. The painting seems as if Abraham, commanded by God to kill his son, could snap his neck with a single twist. However the father's chosen approach involves the silvery grey blade he holds in his remaining palm, ready to slit Isaac's neck. A definite element remains – whomever posed as Isaac for this astonishing work demonstrated extraordinary expressive skill. There exists not just fear, shock and begging in his darkened eyes but additionally profound grief that a protector could abandon him so utterly.

The artist took a familiar scriptural story and transformed it so fresh and visceral that its horrors appeared to unfold directly in view of you

Viewing before the artwork, observers identify this as a actual face, an precise depiction of a adolescent subject, because the identical boy – identifiable by his disheveled hair and almost black pupils – features in two other works by the master. In every instance, that highly expressive face commands the composition. In Youth With a Ram, he gazes playfully from the shadows while embracing a lamb. In Victorious Cupid, he smirks with a toughness learned on the city's streets, his dark plumed appendages demonic, a naked adolescent running chaos in a affluent dwelling.

Amor Vincit Omnia, currently exhibited at a London gallery, constitutes one of the most discomfiting artworks ever painted. Viewers feel completely disoriented gazing at it. The god of love, whose darts fill people with often agonizing longing, is portrayed as a very real, brightly illuminated unclothed form, straddling overturned objects that include musical instruments, a music manuscript, metal armour and an architect's ruler. This heap of items resembles, intentionally, the mathematical and architectural gear scattered across the ground in the German master's engraving Melancholy – save here, the gloomy mess is caused by this smirking Cupid and the turmoil he can unleash.

"Love looks not with the vision, but with the mind, / And thus is winged Cupid depicted sightless," wrote Shakespeare, just before this work was created around the early 1600s. But the painter's Cupid is not unseeing. He stares straight at the observer. That face – sardonic and rosy-cheeked, looking with bold confidence as he struts naked – is the identical one that screams in terror in Abraham's Test.

When the Italian master created his three portrayals of the same unusual-appearing youth in Rome at the dawn of the 17th century, he was the most celebrated religious painter in a city ignited by Catholic revival. The Sacrifice of Isaac demonstrates why he was sought to adorn sanctuaries: he could adopt a biblical narrative that had been depicted numerous occasions before and render it so fresh, so unfiltered and visceral that the terror appeared to be happening immediately in front of the spectator.

However there existed a different aspect to Caravaggio, apparent as soon as he arrived in the capital in the cold season that ended the sixteenth century, as a painter in his initial twenties with no teacher or patron in the city, only talent and audacity. The majority of the works with which he caught the holy metropolis's attention were anything but holy. What could be the very first resides in the UK's National Gallery. A young man parts his red lips in a scream of pain: while stretching out his dirty digits for a fruit, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid squalor: observers can discern the painter's dismal chamber reflected in the cloudy waters of the transparent container.

The adolescent wears a rose-colored flower in his coiffure – a emblem of the erotic commerce in Renaissance painting. Northern Italian painters such as Tiziano and Jacopo Palma portrayed courtesans grasping flowers and, in a work destroyed in the second world war but documented through photographs, the master represented a famous woman courtesan, clutching a bouquet to her chest. The meaning of all these botanical indicators is clear: sex for sale.

What are we to interpret of Caravaggio's sensual portrayals of boys – and of one adolescent in specific? It is a question that has divided his commentators since he gained mega-fame in the 1980s. The complex historical truth is that the painter was not the homosexual icon that, for instance, Derek Jarman presented on film in his 1986 film Caravaggio, nor so entirely pious that, as some art scholars improbably assert, his Youth Holding Fruit is in fact a portrait of Jesus.

His early works indeed offer overt erotic implications, or even offers. It's as if Caravaggio, then a penniless youthful artist, identified with the city's sex workers, selling himself to survive. In the Uffizi, with this idea in mind, observers might turn to an additional early creation, the sixteenth-century masterwork Bacchus, in which the god of wine stares calmly at you as he begins to undo the dark ribbon of his garment.

A few years following Bacchus, what could have driven Caravaggio to create Victorious Cupid for the art collector Vincenzo Giustiniani, when he was at last growing almost respectable with prestigious church projects? This profane non-Christian deity resurrects the sexual provocations of his early paintings but in a more powerful, uneasy manner. Half a century later, its hidden meaning seemed obvious: it was a portrait of Caravaggio's lover. A English traveller saw Victorious Cupid in about 1649 and was told its subject has "the physique and countenance of [Caravaggio's|his] own youth or assistant that laid with him". The name of this boy was Cecco.

The painter had been dead for about 40 annums when this story was recorded.