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The young lad cries out while his skull is forcefully gripped, a large thumb digging into his face as his father's mighty hand holds him by the neck. That moment from Abraham's Sacrifice appears in the Uffizi Gallery, evoking unease through Caravaggio's chilling rendition of the suffering youth from the biblical account. The painting appears as if the patriarch, commanded by the Divine to kill his son, could break his neck with a solitary twist. Yet Abraham's preferred approach involves the silvery grey knife he grips in his remaining hand, prepared to slit the boy's neck. One definite aspect stands out – whoever modeled as the sacrifice for this breathtaking work demonstrated remarkable acting skill. There exists not only fear, shock and begging in his shadowed eyes but additionally deep grief that a protector could abandon him so utterly.

The artist adopted a familiar biblical story and made it so fresh and raw that its terrors appeared to happen directly in view of the viewer

Viewing before the painting, observers identify this as a real face, an accurate depiction of a young subject, because the same youth – recognizable by his tousled hair and nearly black eyes – appears in two other paintings by Caravaggio. In every case, that highly expressive visage dominates the scene. In Youth With a Ram, he gazes mischievously from the darkness while holding a ram. In Amor Vincit Omnia, he grins with a hardness acquired on the city's streets, his black feathery wings demonic, a naked child running chaos in a well-to-do residence.

Amor Vincit Omnia, presently exhibited at a London museum, constitutes one of the most discomfiting artworks ever painted. Viewers feel totally unsettled gazing at it. Cupid, whose darts fill people with often painful longing, is shown as a very real, brightly illuminated unclothed form, standing over toppled-over items that comprise musical instruments, a musical manuscript, plate armor and an architect's T-square. This pile of possessions echoes, deliberately, the geometric and construction equipment scattered across the ground in the German master's engraving Melencolia I – save in this case, the melancholic mess is caused by this grinning deity and the mayhem he can unleash.

"Love looks not with the eyes, but with the soul, / And therefore is winged Love painted blind," penned the Bard, just prior to this painting was produced around the early 1600s. But Caravaggio's Cupid is not unseeing. He stares straight at you. That face – ironic and rosy-faced, staring with brazen confidence as he struts naked – is the identical one that screams in fear in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio painted his three images of the same distinctive-looking youth in Rome at the start of the seventeenth century, he was the highly celebrated religious painter in a city ignited by Catholic renewal. The Sacrifice of Isaac demonstrates why he was sought to adorn sanctuaries: he could adopt a biblical story that had been depicted many occasions before and make it so fresh, so unfiltered and visceral that the terror appeared to be occurring directly in front of you.

However there existed another aspect to Caravaggio, apparent as quickly as he came in the capital in the winter that concluded 1592, as a painter in his early 20s with no teacher or supporter in the city, only skill and audacity. The majority of the works with which he caught the sacred city's eye were everything but devout. What may be the absolute earliest hangs in the UK's National Gallery. A youth parts his crimson mouth in a scream of pain: while reaching out his dirty fingers for a fruit, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid poverty: viewers can see the painter's dismal room mirrored in the murky waters of the transparent container.

The adolescent wears a pink blossom in his hair – a emblem of the sex trade in Renaissance art. Venetian painters such as Titian and Jacopo Palma portrayed courtesans holding blooms and, in a painting lost in the second world war but documented through photographs, the master portrayed a famous female courtesan, clutching a posy to her chest. The meaning of all these floral signifiers is clear: sex for sale.

How are we to interpret of the artist's sensual portrayals of youths – and of one boy in particular? It is a inquiry that has split his interpreters ever since he gained mega-fame in the 1980s. The complicated historical reality is that the artist was neither the homosexual icon that, for instance, Derek Jarman put on film in his twentieth-century movie about the artist, nor so entirely devout that, as some art historians unbelievably claim, his Youth Holding Fruit is in fact a portrait of Christ.

His initial paintings indeed offer overt sexual implications, or even offers. It's as if the painter, then a destitute youthful creator, aligned with the city's prostitutes, selling himself to survive. In the Uffizi, with this thought in mind, viewers might look to another initial work, the sixteenth-century masterwork Bacchus, in which the god of wine stares calmly at you as he starts to untie the dark sash of his garment.

A several annums after Bacchus, what could have motivated Caravaggio to paint Amor Vincit Omnia for the artistic collector Vincenzo Giustiniani, when he was finally becoming almost established with prestigious church projects? This unholy pagan god resurrects the erotic provocations of his initial works but in a more powerful, unsettling way. Fifty years later, its secret seemed clear: it was a portrait of Caravaggio's lover. A British visitor saw Victorious Cupid in about the mid-seventeenth century and was told its subject has "the body & face of [Caravaggio's|his] own boy or assistant that laid with him". The name of this boy was Francesco.

The artist had been deceased for about forty annums when this story was documented.