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The youthful boy cries out as his head is firmly held, a massive thumb digging into his face as his parent's mighty hand holds him by the neck. This moment from The Sacrifice of Isaac appears in the Florentine museum, creating unease through Caravaggio's chilling rendition of the suffering child from the scriptural account. The painting seems as if the patriarch, instructed by God to sacrifice his son, could break his neck with a single twist. Yet Abraham's preferred method involves the silvery steel blade he grips in his other hand, prepared to slit the boy's neck. A definite element stands out – whomever posed as Isaac for this astonishing piece demonstrated extraordinary expressive ability. Within exists not just dread, surprise and begging in his darkened eyes but also deep grief that a protector could betray him so utterly.

The artist took a familiar biblical tale and transformed it so fresh and raw that its terrors appeared to unfold right in front of the viewer

Viewing before the painting, observers identify this as a actual countenance, an precise depiction of a adolescent subject, because the identical boy – recognizable by his tousled hair and nearly dark eyes – features in two additional works by the master. In each case, that richly expressive visage commands the scene. In Youth With a Ram, he peers playfully from the darkness while embracing a ram. In Amor Vincit Omnia, he smirks with a hardness acquired on the city's streets, his black plumed wings sinister, a unclothed child running riot in a affluent residence.

Victorious Cupid, presently displayed at a London museum, constitutes one of the most discomfiting masterpieces ever created. Viewers feel totally disoriented gazing at it. Cupid, whose darts inspire people with frequently agonizing desire, is portrayed as a extremely tangible, brightly lit nude figure, standing over overturned items that include musical instruments, a music score, plate armour and an architect's T-square. This pile of items echoes, deliberately, the geometric and construction gear strewn across the floor in Albrecht Dürer's engraving Melancholy – except in this case, the gloomy disorder is caused by this grinning Cupid and the turmoil he can release.

"Affection looks not with the vision, but with the mind, / And thus is winged Cupid painted blind," penned Shakespeare, just before this painting was produced around the early 1600s. But the painter's god is not blind. He gazes straight at you. That face – ironic and rosy-faced, looking with brazen confidence as he poses naked – is the same one that shrieks in terror in Abraham's Test.

As the Italian master painted his three images of the same unusual-appearing kid in Rome at the dawn of the 17th century, he was the highly celebrated sacred painter in a city ignited by Catholic revival. Abraham's Offering demonstrates why he was sought to decorate churches: he could take a scriptural narrative that had been portrayed many times before and render it so fresh, so raw and visceral that the horror appeared to be occurring directly before you.

However there was a different aspect to the artist, evident as soon as he arrived in Rome in the cold season that ended the sixteenth century, as a painter in his initial 20s with no teacher or supporter in the urban center, only skill and boldness. The majority of the works with which he captured the sacred metropolis's attention were everything but devout. What could be the very first resides in the UK's art museum. A young man parts his red lips in a scream of agony: while stretching out his filthy digits for a cherry, he has rather been bitten. Boy Bitten By a Lizard is eroticism amid poverty: viewers can see Caravaggio's gloomy chamber reflected in the murky waters of the transparent container.

The adolescent sports a pink blossom in his coiffure – a emblem of the sex trade in Renaissance art. Northern Italian artists such as Tiziano and Jacopo Palma portrayed courtesans grasping flowers and, in a work lost in the second world war but known through photographs, Caravaggio portrayed a famous female courtesan, holding a posy to her bosom. The message of all these floral indicators is obvious: intimacy for purchase.

What are we to make of Caravaggio's erotic portrayals of youths – and of a particular boy in specific? It is a question that has split his commentators since he achieved widespread recognition in the 1980s. The complex historical reality is that the artist was neither the homosexual icon that, for example, Derek Jarman presented on screen in his 1986 film Caravaggio, nor so completely pious that, as some art scholars unbelievably assert, his Youth Holding Fruit is in fact a likeness of Jesus.

His initial paintings indeed offer overt erotic suggestions, or even offers. It's as if Caravaggio, then a penniless young artist, aligned with Rome's sex workers, selling himself to survive. In the Uffizi, with this idea in mind, viewers might look to an additional early work, the sixteenth-century masterwork the god of wine, in which the deity of wine gazes calmly at the spectator as he begins to untie the dark sash of his garment.

A several years after Bacchus, what could have driven Caravaggio to paint Amor Vincit Omnia for the art collector the nobleman, when he was finally growing almost respectable with important ecclesiastical commissions? This profane pagan god resurrects the erotic challenges of his initial paintings but in a increasingly powerful, uneasy manner. Fifty years afterwards, its hidden meaning seemed obvious: it was a portrait of the painter's companion. A English traveller viewed the painting in about the mid-seventeenth century and was informed its subject has "the body & face of [Caravaggio's|his] own youth or assistant that laid with him". The name of this adolescent was Cecco.

The artist had been dead for about 40 annums when this account was documented.