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A youthful boy cries out as his skull is forcefully gripped, a large thumb pressing into his cheek as his father's powerful hand holds him by the neck. This scene from Abraham's Sacrifice appears in the Uffizi Gallery, creating distress through Caravaggio's harrowing rendition of the suffering child from the biblical account. It seems as if Abraham, commanded by God to sacrifice his offspring, could break his neck with a solitary twist. However Abraham's preferred method involves the silvery steel knife he grips in his other palm, prepared to cut Isaac's neck. A definite aspect stands out – whomever posed as the sacrifice for this astonishing work demonstrated extraordinary acting ability. There exists not only fear, surprise and pleading in his shadowed eyes but also profound sorrow that a guardian could betray him so utterly.

He adopted a well-known biblical story and made it so vibrant and visceral that its terrors seemed to unfold directly in view of you

Viewing in front of the artwork, observers identify this as a actual countenance, an precise record of a adolescent subject, because the identical youth – recognizable by his tousled hair and almost black eyes – features in several other paintings by Caravaggio. In every case, that highly expressive visage dominates the composition. In Youth With a Ram, he peers mischievously from the shadows while embracing a lamb. In Amor Vincit Omnia, he grins with a toughness acquired on the city's alleys, his black plumed wings demonic, a naked adolescent creating riot in a affluent dwelling.

Victorious Cupid, currently exhibited at a British museum, constitutes one of the most discomfiting artworks ever created. Observers feel completely unsettled gazing at it. Cupid, whose arrows fill people with frequently agonizing desire, is portrayed as a very real, vividly illuminated nude form, standing over overturned objects that comprise stringed instruments, a music score, metal armour and an architect's T-square. This pile of items echoes, deliberately, the geometric and architectural equipment strewn across the floor in the German master's engraving Melencolia I – except in this case, the gloomy mess is caused by this smirking Cupid and the turmoil he can release.

"Affection sees not with the eyes, but with the mind, / And therefore is winged Love painted blind," wrote Shakespeare, just prior to this painting was produced around the early 1600s. But Caravaggio's Cupid is not unseeing. He stares straight at the observer. That countenance – sardonic and rosy-cheeked, looking with brazen confidence as he poses unclothed – is the identical one that screams in fear in The Sacrifice of Isaac.

When the Italian master painted his three portrayals of the same unusual-looking kid in Rome at the start of the 17th century, he was the most acclaimed sacred artist in a city ignited by religious renewal. The Sacrifice of Isaac reveals why he was sought to decorate churches: he could adopt a biblical narrative that had been depicted many occasions previously and render it so new, so unfiltered and visceral that the horror appeared to be occurring immediately in front of you.

Yet there was another aspect to the artist, evident as soon as he arrived in Rome in the winter that ended the sixteenth century, as a painter in his early 20s with no mentor or supporter in the urban center, just talent and boldness. The majority of the works with which he caught the sacred metropolis's eye were everything but holy. That may be the absolute first resides in the UK's art museum. A youth parts his red lips in a scream of agony: while stretching out his dirty fingers for a cherry, he has instead been attacked. Boy Bitten By a Lizard is eroticism amid squalor: viewers can discern Caravaggio's dismal room reflected in the cloudy liquid of the glass vase.

The boy sports a rose-colored blossom in his coiffure – a emblem of the erotic commerce in Renaissance painting. Venetian artists such as Titian and Palma Vecchio depicted courtesans grasping flowers and, in a work lost in the second world war but known through images, Caravaggio portrayed a renowned woman prostitute, clutching a posy to her bosom. The meaning of all these floral signifiers is obvious: intimacy for sale.

How are we to interpret of Caravaggio's erotic depictions of boys – and of one boy in specific? It is a question that has divided his commentators since he achieved widespread recognition in the 1980s. The complex past truth is that the painter was neither the homosexual icon that, for instance, the filmmaker presented on film in his twentieth-century film about the artist, nor so completely devout that, as some art scholars improbably assert, his Youth Holding Fruit is in fact a likeness of Jesus.

His early works indeed make explicit sexual suggestions, or including propositions. It's as if the painter, then a penniless young creator, identified with the city's sex workers, selling himself to survive. In the Uffizi, with this thought in mind, observers might look to an additional early work, the sixteenth-century masterwork the god of wine, in which the deity of wine stares coolly at the spectator as he starts to untie the dark sash of his robe.

A several annums after the wine deity, what could have driven Caravaggio to create Amor Vincit Omnia for the art collector Vincenzo Giustiniani, when he was at last becoming almost respectable with prestigious ecclesiastical projects? This profane non-Christian deity revives the sexual provocations of his early works but in a more powerful, unsettling manner. Fifty years afterwards, its hidden meaning seemed clear: it was a portrait of the painter's lover. A British traveller saw the painting in about 1649 and was told its subject has "the physique and countenance of [Caravaggio's|his] own youth or servant that laid with him". The identity of this boy was Cecco.

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