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A young lad cries out while his head is firmly gripped, a large thumb pressing into his face as his parent's powerful hand holds him by the neck. This scene from Abraham's Sacrifice visits the Uffizi Gallery, evoking unease through the artist's chilling portrayal of the suffering youth from the biblical account. The painting seems as if Abraham, instructed by God to sacrifice his son, could snap his spinal column with a solitary twist. Yet Abraham's preferred approach involves the silvery steel blade he holds in his other palm, ready to slit the boy's neck. One definite element remains – whoever modeled as Isaac for this breathtaking piece demonstrated remarkable expressive skill. Within exists not only dread, shock and pleading in his shadowed gaze but also deep grief that a guardian could abandon him so completely.

The artist adopted a well-known scriptural story and made it so fresh and visceral that its horrors appeared to happen right in front of you

Standing before the painting, viewers identify this as a real countenance, an accurate record of a adolescent model, because the identical youth – identifiable by his tousled locks and nearly dark eyes – features in several other paintings by the master. In each instance, that richly expressive face dominates the composition. In John the Baptist, he peers playfully from the darkness while holding a lamb. In Amor Vincit Omnia, he grins with a hardness learned on the city's alleys, his dark plumed appendages demonic, a unclothed adolescent running riot in a affluent residence.

Victorious Cupid, presently displayed at a London museum, represents one of the most discomfiting artworks ever painted. Viewers feel totally disoriented looking at it. The god of love, whose darts inspire people with often agonizing longing, is shown as a very real, vividly illuminated unclothed form, standing over toppled-over objects that comprise musical devices, a music score, metal armor and an builder's ruler. This pile of items echoes, intentionally, the geometric and architectural gear strewn across the ground in Albrecht Dürer's engraving Melencolia I – except in this case, the melancholic mess is caused by this grinning deity and the turmoil he can unleash.

"Love looks not with the eyes, but with the soul, / And therefore is winged Love depicted blind," penned Shakespeare, shortly prior to this work was produced around 1601. But Caravaggio's Cupid is not blind. He gazes straight at the observer. That face – ironic and rosy-faced, looking with bold confidence as he struts unclothed – is the same one that shrieks in fear in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio painted his multiple images of the same unusual-appearing kid in the Eternal City at the start of the 17th century, he was the most celebrated religious artist in a city ignited by Catholic revival. Abraham's Offering demonstrates why he was commissioned to decorate sanctuaries: he could adopt a scriptural story that had been depicted many times previously and make it so fresh, so unfiltered and physical that the terror appeared to be occurring immediately in front of the spectator.

However there existed a different aspect to Caravaggio, evident as quickly as he arrived in Rome in the winter that ended 1592, as a artist in his early twenties with no teacher or patron in the city, only skill and boldness. Most of the works with which he captured the holy metropolis's attention were anything but devout. That could be the absolute first hangs in London's art museum. A young man parts his red mouth in a yell of pain: while reaching out his dirty digits for a fruit, he has instead been bitten. Boy Bitten By a Lizard is eroticism amid squalor: viewers can see the painter's gloomy room reflected in the cloudy liquid of the glass vase.

The adolescent wears a pink flower in his coiffure – a symbol of the erotic trade in early modern art. Venetian painters such as Tiziano and Palma Vecchio portrayed courtesans holding flowers and, in a work lost in the second world war but known through images, Caravaggio represented a renowned woman courtesan, clutching a posy to her chest. The meaning of all these botanical indicators is obvious: intimacy for purchase.

How are we to make of the artist's erotic portrayals of boys – and of one adolescent in particular? It is a inquiry that has divided his interpreters ever since he gained widespread recognition in the twentieth century. The complicated historical reality is that the artist was neither the homosexual icon that, for instance, the filmmaker put on screen in his 1986 movie about the artist, nor so entirely pious that, as some art scholars unbelievably claim, his Youth Holding Fruit is actually a portrait of Jesus.

His initial paintings do make explicit erotic suggestions, or even offers. It's as if the painter, then a penniless young artist, aligned with the city's prostitutes, offering himself to live. In the Florentine gallery, with this idea in consideration, observers might look to an additional initial work, the sixteenth-century masterwork Bacchus, in which the god of alcohol stares coolly at you as he begins to undo the dark ribbon of his garment.

A several years following the wine deity, what could have driven the artist to paint Victorious Cupid for the artistic patron the nobleman, when he was at last growing almost respectable with important ecclesiastical commissions? This profane non-Christian deity resurrects the sexual challenges of his initial paintings but in a increasingly intense, unsettling way. Fifty years later, its secret seemed clear: it was a representation of the painter's companion. A English visitor saw the painting in about the mid-seventeenth century and was told its figure has "the body & face of [Caravaggio's|his] owne youth or assistant that laid with him". The name of this boy was Cecco.

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