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The youthful boy screams while his skull is firmly held, a massive thumb pressing into his cheek as his father's powerful palm holds him by the neck. This moment from Abraham's Sacrifice visits the Uffizi Gallery, evoking distress through Caravaggio's harrowing portrayal of the suffering youth from the biblical account. It appears as if Abraham, commanded by the Divine to sacrifice his offspring, could break his neck with a single twist. However the father's preferred method involves the silvery steel knife he grips in his remaining hand, ready to slit the boy's throat. One certain element remains – whomever posed as Isaac for this astonishing work demonstrated extraordinary expressive ability. There exists not just fear, surprise and pleading in his shadowed eyes but also profound sorrow that a guardian could betray him so utterly.

The artist adopted a familiar scriptural tale and transformed it so vibrant and raw that its horrors seemed to unfold directly in view of you

Standing before the artwork, observers recognize this as a real face, an precise record of a adolescent subject, because the identical boy – identifiable by his disheveled locks and almost dark pupils – appears in several additional paintings by the master. In every instance, that richly expressive face dominates the composition. In John the Baptist, he gazes mischievously from the shadows while embracing a ram. In Victorious Cupid, he smirks with a toughness acquired on the city's streets, his dark feathery wings sinister, a naked child creating riot in a well-to-do residence.

Amor Vincit Omnia, currently displayed at a London gallery, represents one of the most discomfiting artworks ever created. Observers feel completely unsettled gazing at it. The god of love, whose darts inspire people with often agonizing desire, is shown as a extremely real, vividly illuminated nude figure, straddling toppled-over objects that include musical instruments, a music score, metal armor and an architect's T-square. This heap of items echoes, deliberately, the mathematical and architectural equipment scattered across the ground in the German master's print Melancholy – except here, the gloomy disorder is caused by this grinning deity and the mayhem he can release.

"Love sees not with the eyes, but with the soul, / And therefore is feathered Love depicted sightless," wrote the Bard, just before this work was created around 1601. But the painter's Cupid is not blind. He gazes straight at the observer. That countenance – ironic and rosy-cheeked, staring with bold confidence as he struts naked – is the same one that screams in fear in The Sacrifice of Isaac.

As the Italian master painted his three portrayals of the identical distinctive-looking kid in Rome at the start of the 17th century, he was the highly celebrated religious painter in a city enflamed by religious revival. The Sacrifice of Isaac demonstrates why he was sought to decorate churches: he could take a biblical story that had been portrayed many times previously and make it so fresh, so raw and physical that the horror seemed to be happening directly before the spectator.

However there was another aspect to the artist, apparent as quickly as he arrived in Rome in the winter that ended the sixteenth century, as a artist in his early 20s with no mentor or supporter in the urban center, only skill and audacity. The majority of the paintings with which he captured the sacred metropolis's eye were anything but devout. What could be the absolute first resides in the UK's National Gallery. A young man opens his red mouth in a yell of pain: while reaching out his filthy fingers for a fruit, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid squalor: viewers can see Caravaggio's gloomy room mirrored in the murky liquid of the glass vase.

The adolescent sports a pink blossom in his coiffure – a symbol of the sex commerce in Renaissance art. Venetian painters such as Titian and Palma Vecchio portrayed courtesans grasping flowers and, in a work lost in the second world war but known through photographs, the master portrayed a renowned female prostitute, clutching a posy to her chest. The meaning of all these botanical indicators is clear: sex for purchase.

What are we to interpret of Caravaggio's erotic portrayals of boys – and of a particular adolescent in specific? It is a inquiry that has divided his commentators ever since he gained widespread recognition in the 1980s. The complicated historical truth is that the painter was not the queer icon that, for instance, the filmmaker presented on screen in his twentieth-century movie Caravaggio, nor so completely pious that, as some art historians unbelievably assert, his Boy With a Basket of Fruit is actually a likeness of Christ.

His initial works do offer overt sexual suggestions, or including propositions. It's as if Caravaggio, then a destitute young artist, aligned with the city's prostitutes, selling himself to survive. In the Uffizi, with this thought in consideration, viewers might look to another initial work, the sixteenth-century masterpiece the god of wine, in which the deity of alcohol gazes calmly at you as he starts to undo the dark ribbon of his robe.

A few years after Bacchus, what could have motivated Caravaggio to create Amor Vincit Omnia for the artistic patron the nobleman, when he was at last becoming nearly established with prestigious ecclesiastical commissions? This unholy pagan god revives the sexual challenges of his initial paintings but in a increasingly powerful, unsettling way. Half a century later, its hidden meaning seemed clear: it was a portrait of Caravaggio's companion. A English traveller viewed Victorious Cupid in about 1649 and was told its figure has "the physique and countenance of [Caravaggio's|his] owne boy or servant that slept with him". The identity of this boy was Francesco.

The painter had been deceased for about 40 years when this account was documented.