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The youthful lad screams while his skull is forcefully gripped, a massive thumb digging into his cheek as his parent's powerful palm holds him by the throat. That moment from Abraham's Sacrifice appears in the Uffizi Gallery, creating unease through Caravaggio's harrowing portrayal of the tormented child from the scriptural account. It seems as if the patriarch, commanded by God to sacrifice his son, could snap his spinal column with a single turn. However Abraham's chosen method involves the metallic grey blade he grips in his remaining hand, ready to cut Isaac's throat. One definite element remains – whomever posed as Isaac for this breathtaking piece displayed remarkable acting skill. Within exists not just dread, shock and pleading in his shadowed eyes but additionally profound sorrow that a guardian could abandon him so completely.

He adopted a familiar biblical story and transformed it so vibrant and visceral that its horrors seemed to happen directly in front of the viewer

Viewing in front of the artwork, viewers identify this as a actual face, an precise depiction of a young subject, because the identical youth – recognizable by his disheveled hair and nearly black eyes – features in several other paintings by Caravaggio. In each case, that richly expressive visage commands the composition. In John the Baptist, he gazes mischievously from the darkness while holding a lamb. In Victorious Cupid, he grins with a toughness acquired on Rome's streets, his black feathery appendages demonic, a naked child running riot in a affluent residence.

Amor Vincit Omnia, currently displayed at a British gallery, constitutes one of the most discomfiting artworks ever painted. Viewers feel completely unsettled looking at it. The god of love, whose arrows fill people with often painful longing, is portrayed as a extremely real, brightly lit unclothed figure, straddling toppled-over items that include stringed instruments, a music manuscript, metal armour and an builder's ruler. This pile of items resembles, intentionally, the geometric and construction equipment strewn across the ground in Albrecht Dürer's engraving Melencolia I – except in this case, the gloomy mess is created by this smirking deity and the mayhem he can release.

"Affection looks not with the vision, but with the mind, / And thus is winged Love depicted blind," wrote the Bard, just prior to this painting was produced around 1601. But Caravaggio's Cupid is not unseeing. He gazes directly at the observer. That face – sardonic and rosy-faced, looking with bold assurance as he struts naked – is the same one that shrieks in terror in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio painted his three portrayals of the identical distinctive-looking youth in Rome at the start of the 17th century, he was the highly acclaimed sacred artist in a metropolis ignited by Catholic revival. The Sacrifice of Isaac demonstrates why he was sought to adorn churches: he could adopt a biblical narrative that had been depicted numerous times previously and make it so new, so raw and physical that the horror seemed to be happening directly before the spectator.

Yet there existed another aspect to Caravaggio, evident as soon as he came in the capital in the winter that ended the sixteenth century, as a painter in his early twenties with no mentor or patron in the urban center, only talent and boldness. Most of the paintings with which he captured the holy metropolis's attention were everything but devout. That may be the very earliest hangs in London's National Gallery. A young man opens his red mouth in a scream of pain: while reaching out his dirty digits for a fruit, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid poverty: viewers can see Caravaggio's gloomy chamber reflected in the cloudy liquid of the glass vase.

The boy wears a rose-colored blossom in his coiffure – a symbol of the sex trade in Renaissance art. Venetian painters such as Titian and Jacopo Palma portrayed prostitutes holding blooms and, in a work destroyed in the second world war but known through photographs, Caravaggio portrayed a renowned woman prostitute, holding a posy to her bosom. The meaning of all these floral indicators is obvious: sex for sale.

What are we to interpret of the artist's sensual portrayals of boys – and of one boy in particular? It is a inquiry that has split his interpreters ever since he achieved mega-fame in the twentieth century. The complex historical reality is that the artist was neither the homosexual icon that, for instance, Derek Jarman put on screen in his 1986 film about the artist, nor so completely pious that, as certain artistic scholars improbably claim, his Boy With a Basket of Fruit is in fact a likeness of Christ.

His early paintings indeed offer overt sexual suggestions, or including offers. It's as if Caravaggio, then a destitute youthful creator, identified with the city's prostitutes, offering himself to live. In the Uffizi, with this thought in mind, viewers might turn to an additional initial creation, the sixteenth-century masterwork the god of wine, in which the deity of alcohol gazes coolly at the spectator as he starts to untie the dark sash of his robe.

A few annums following Bacchus, what could have driven Caravaggio to create Amor Vincit Omnia for the art patron Vincenzo Giustiniani, when he was at last becoming nearly respectable with prestigious ecclesiastical projects? This unholy pagan god revives the erotic challenges of his initial paintings but in a increasingly intense, unsettling way. Half a century later, its hidden meaning seemed clear: it was a portrait of Caravaggio's companion. A British traveller viewed Victorious Cupid in about the mid-seventeenth century and was told its subject has "the body & face of [Caravaggio's|his] owne boy or assistant that laid with him". The identity of this boy was Cecco.

The artist had been dead for about 40 years when this story was documented.