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A young lad screams while his skull is firmly held, a massive digit digging into his cheek as his parent's powerful palm holds him by the neck. That moment from Abraham's Sacrifice visits the Uffizi Gallery, evoking unease through Caravaggio's chilling rendition of the suffering child from the scriptural account. The painting appears as if the patriarch, instructed by the Divine to kill his son, could break his neck with a solitary twist. However the father's chosen approach involves the silvery steel knife he holds in his other hand, ready to slit the boy's throat. One certain element remains – whomever posed as Isaac for this astonishing piece displayed extraordinary expressive ability. There exists not just dread, surprise and begging in his darkened eyes but also deep sorrow that a protector could betray him so completely.

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

Standing in front of the painting, observers identify this as a actual face, an accurate depiction of a young model, because the identical boy – recognizable by his disheveled locks and almost black pupils – features in two additional works by the master. In each instance, that richly expressive face dominates the scene. In John the Baptist, he gazes mischievously from the darkness while embracing a lamb. In Amor Vincit Omnia, he smirks with a hardness learned on the city's streets, his dark plumed wings sinister, a naked child creating chaos in a affluent residence.

Amor Vincit Omnia, presently displayed at a British museum, represents one of the most discomfiting artworks ever created. Viewers feel totally disoriented looking at it. The god of love, whose arrows inspire people with frequently painful longing, is portrayed as a very tangible, brightly illuminated nude form, straddling overturned objects that include musical devices, a musical score, plate armour and an architect's T-square. This heap of items resembles, intentionally, the geometric and architectural equipment scattered across the floor in Albrecht Dürer's engraving Melencolia I – except here, the melancholic disorder is created by this grinning deity and the turmoil he can release.

"Affection looks not with the vision, but with the soul, / And thus is feathered Love painted sightless," penned the Bard, just before this painting was produced around the early 1600s. But Caravaggio's Cupid is not unseeing. He gazes straight at you. That face – sardonic and rosy-faced, looking with bold assurance as he poses naked – is the same one that screams in terror in The Sacrifice of Isaac.

As the Italian master painted his three portrayals of the identical distinctive-looking youth in Rome at the start of the 17th century, he was the highly acclaimed religious artist in a metropolis ignited by religious revival. The Sacrifice of Isaac reveals why he was sought to decorate sanctuaries: he could take a biblical narrative that had been portrayed many occasions previously and make it so fresh, so raw and visceral that the horror seemed to be happening immediately in front of you.

Yet there existed a different side to the artist, evident as quickly as he arrived in the capital in the cold season that concluded the sixteenth century, as a painter in his initial 20s with no mentor or supporter in the city, only skill and audacity. Most of the paintings with which he captured the sacred city's attention were everything but devout. That could be the very earliest hangs in the UK's art museum. A youth parts his crimson mouth in a yell of pain: while stretching out his filthy digits for a fruit, he has instead been attacked. Boy Bitten By a Lizard is eroticism amid poverty: observers can discern Caravaggio's dismal chamber reflected in the cloudy liquid of the glass container.

The boy wears 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 portrayed prostitutes grasping blooms and, in a work lost in the second world war but documented through images, Caravaggio portrayed a famous woman courtesan, clutching a posy to her bosom. The meaning of all these botanical indicators is obvious: intimacy for sale.

What are we to make of Caravaggio's sensual portrayals of boys – and of a particular adolescent in particular? It is a question that has split his commentators since he achieved mega-fame in the twentieth century. The complicated historical reality is that the painter was not the homosexual hero that, for instance, the filmmaker presented on screen in his twentieth-century movie about the artist, nor so completely devout that, as some artistic scholars improbably assert, his Youth Holding Fruit is actually a portrait of Christ.

His initial works indeed offer explicit erotic implications, or even propositions. It's as if the painter, then a destitute young creator, identified with the city's sex workers, selling himself to survive. In the Florentine gallery, with this thought in mind, observers might turn to an additional early work, the 1596 masterwork the god of wine, in which the deity of wine gazes calmly at the spectator as he begins to undo the black ribbon of his robe.

A several years after Bacchus, what could have driven Caravaggio to create Amor Vincit Omnia for the artistic collector Vincenzo Giustiniani, when he was finally growing almost respectable with prestigious ecclesiastical commissions? This unholy non-Christian god revives the sexual provocations of his early works but in a more intense, unsettling manner. Half a century afterwards, its hidden meaning seemed obvious: it was a portrait of Caravaggio's lover. A British traveller saw the painting in about the mid-seventeenth century and was informed its figure has "the physique and countenance of [Caravaggio's|his] own boy or assistant that slept with him". The name of this boy was Cecco.

The artist had been deceased for about forty years when this account was recorded.