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The young lad cries out while his skull is forcefully gripped, a large thumb pressing into his cheek as his parent's powerful hand holds him by the neck. This moment from The Sacrifice of Isaac visits the Uffizi Gallery, evoking unease through Caravaggio's chilling rendition of the tormented youth from the biblical narrative. It appears as if Abraham, commanded by the Divine to sacrifice his offspring, could break his neck with a single twist. However Abraham's chosen approach involves the metallic grey knife he holds in his other hand, prepared to slit Isaac's neck. A certain aspect remains – whoever posed as Isaac for this breathtaking work displayed remarkable expressive ability. There exists not only dread, surprise and pleading in his darkened gaze but also profound sorrow that a protector could abandon him so utterly.

He took a familiar scriptural tale and transformed it so vibrant and raw that its horrors seemed to unfold right in view of you

Viewing before the artwork, viewers recognize this as a real countenance, an accurate depiction of a young model, because the same youth – identifiable by his disheveled hair and nearly black pupils – features in several other paintings by the master. In every case, that highly expressive visage dominates the scene. In Youth With a Ram, he gazes playfully from the darkness while holding a lamb. In Victorious Cupid, he grins with a toughness learned on the city's streets, his dark feathery wings demonic, a naked child running chaos in a well-to-do dwelling.

Victorious Cupid, presently displayed at a London gallery, constitutes one of the most embarrassing artworks ever painted. Observers feel totally disoriented gazing at it. Cupid, whose darts fill people with often painful desire, is shown as a extremely real, vividly lit nude form, straddling overturned items that include musical instruments, a music manuscript, metal armour and an builder's T-square. This pile of items echoes, deliberately, the mathematical and construction equipment strewn across the ground in Albrecht Dürer's engraving Melencolia I – save in this case, the gloomy disorder is caused by this smirking deity and the turmoil he can unleash.

"Love looks not with the vision, but with the soul, / And therefore is feathered Love depicted blind," wrote Shakespeare, just prior to this painting was produced around the early 1600s. But the painter's Cupid is not unseeing. He stares straight at the observer. That countenance – ironic and ruddy-cheeked, staring with bold confidence as he poses unclothed – is the identical one that screams in fear in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio painted his multiple portrayals of the same unusual-appearing youth in the Eternal City at the dawn of the seventeenth century, he was the highly celebrated religious artist in a city ignited by religious revival. Abraham's Offering reveals why he was sought to decorate sanctuaries: he could take a scriptural story that had been depicted numerous times before and render it so fresh, so unfiltered and visceral that the terror appeared to be happening immediately before you.

Yet there was another side to the artist, evident as soon as he arrived in Rome in the cold season that ended 1592, as a painter in his early twenties with no teacher or patron in the city, just talent and boldness. Most of the paintings with which he captured the holy metropolis's attention were everything but devout. What may be the absolute first hangs in London's art museum. A youth parts his red mouth in a scream of pain: while stretching out his filthy fingers for a cherry, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid poverty: viewers can discern the painter's gloomy room reflected in the murky waters of the glass container.

The boy sports a pink blossom in his hair – a symbol of the erotic trade in Renaissance art. Northern Italian artists such as Titian and Jacopo Palma depicted courtesans grasping blooms and, in a work lost in the WWII but known through images, the master represented a famous woman courtesan, holding a bouquet to her bosom. The meaning of all these floral indicators is clear: sex for purchase.

How are we to interpret of the artist's sensual portrayals of youths – and of a particular boy in specific? It is a inquiry that has split his interpreters since he achieved widespread recognition in the twentieth century. The complicated past truth is that the artist was neither the queer icon that, for example, Derek Jarman put on screen in his 1986 movie Caravaggio, nor so completely pious that, as some art historians unbelievably assert, his Youth Holding Fruit is actually a portrait of Jesus.

His early works indeed offer explicit erotic implications, or including propositions. It's as if the painter, then a penniless youthful creator, identified with the city's prostitutes, selling himself to survive. In the Uffizi, with this thought in mind, observers might look to another early creation, the sixteenth-century masterpiece Bacchus, in which the god of alcohol stares coolly at you as he begins to undo the dark ribbon of his robe.

A several annums after Bacchus, what could have motivated Caravaggio to create Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was at last growing almost established with prestigious ecclesiastical commissions? This unholy non-Christian deity resurrects the erotic challenges of his initial paintings but in a increasingly powerful, uneasy manner. Half a century later, its secret seemed clear: it was a portrait of Caravaggio's companion. A British visitor viewed Victorious Cupid in about the mid-seventeenth century and was told its subject has "the physique and countenance of [Caravaggio's|his] owne boy or assistant that laid with him". The identity of this boy was Francesco.

The painter had been deceased for about 40 annums when this story was recorded.