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The youthful lad cries out while his skull is firmly held, a massive digit digging into his face as his parent's mighty palm holds him by the neck. This moment from The Sacrifice of Isaac appears in the Uffizi Gallery, evoking unease through Caravaggio's chilling rendition of the suffering youth from the scriptural narrative. The painting appears as if Abraham, instructed by the Divine to sacrifice his son, could snap his spinal column with a single twist. Yet Abraham's preferred method involves the silvery grey blade he grips in his remaining palm, ready to slit the boy's throat. One certain aspect remains – whomever posed as the sacrifice for this breathtaking work displayed extraordinary expressive ability. There exists not just dread, shock and pleading in his darkened eyes but also deep sorrow that a guardian could abandon him so completely.

The artist adopted a familiar biblical story and transformed it so fresh and raw that its horrors appeared to unfold directly in front of you

Standing before the artwork, viewers recognize this as a actual countenance, an accurate depiction of a adolescent subject, because the identical boy – recognizable by his disheveled locks and almost black pupils – features in several additional paintings by the master. In each case, that highly emotional face commands the composition. In Youth With a Ram, he gazes playfully from the darkness while embracing a lamb. In Amor Vincit Omnia, he grins with a hardness acquired on the city's alleys, his black feathery appendages demonic, a naked child creating riot in a well-to-do residence.

Amor Vincit Omnia, presently displayed at a London museum, constitutes one of the most embarrassing masterpieces ever created. Viewers feel completely disoriented looking at it. The god of love, whose darts fill people with often painful desire, is portrayed as a extremely real, vividly lit unclothed form, straddling overturned objects that comprise musical instruments, a music manuscript, plate armour and an builder's ruler. This pile of possessions resembles, deliberately, the mathematical and construction gear scattered across the floor in the German master's engraving Melancholy – save in this case, the melancholic mess is caused by this smirking Cupid and the mayhem he can unleash.

"Love sees not with the eyes, but with the soul, / And thus is feathered Love depicted sightless," penned Shakespeare, just prior to this work was produced around the early 1600s. But the painter's god is not blind. He gazes straight at the observer. That countenance – ironic and ruddy-cheeked, looking with bold confidence as he poses naked – is the same one that shrieks in terror in Abraham's Test.

When Michelangelo Merisi da Caravaggio painted his three portrayals of the same distinctive-appearing kid in the Eternal City at the dawn of the 17th century, he was the most acclaimed sacred painter in a city enflamed by religious renewal. Abraham's Offering demonstrates why he was commissioned to adorn churches: he could adopt a scriptural narrative that had been depicted many times before and make it so new, so unfiltered and visceral that the terror seemed to be occurring immediately before you.

However there existed a different aspect to the artist, evident as soon as he came in Rome in the cold season that ended the sixteenth century, as a painter in his early twenties with no mentor or patron in the city, just skill and audacity. The majority of the paintings with which he caught the holy metropolis's attention were anything but devout. What could be the very earliest resides in the UK's National Gallery. A young man opens his red mouth in a scream of pain: while reaching out his filthy digits for a fruit, he has instead been attacked. Youth Bitten by a Reptile is eroticism amid squalor: observers can discern Caravaggio's dismal chamber reflected in the murky waters of the glass vase.

The boy wears a pink blossom in his coiffure – a emblem of the erotic trade in early modern painting. Venetian painters such as Titian and Jacopo Palma portrayed courtesans holding flowers and, in a painting destroyed in the second world war but known through photographs, Caravaggio represented a famous woman courtesan, clutching a posy to her chest. The message of all these floral signifiers is clear: sex for sale.

How are we to interpret of Caravaggio's erotic portrayals of youths – and of a particular adolescent in specific? It is a inquiry that has split his commentators ever since he gained widespread recognition in the twentieth century. The complicated past reality is that the painter was neither the queer icon that, for instance, Derek Jarman put on screen in his twentieth-century movie Caravaggio, nor so completely pious that, as some artistic scholars unbelievably claim, his Boy With a Basket of Fruit is in fact a portrait of Christ.

His early works do offer explicit erotic suggestions, or even offers. It's as if the painter, then a penniless young artist, identified with Rome's prostitutes, offering himself to survive. In the Florentine gallery, with this thought in mind, observers might turn to another early creation, the sixteenth-century masterwork Bacchus, in which the god of alcohol gazes calmly at you as he begins to undo the dark sash of his robe.

A several years following the wine deity, what could have motivated Caravaggio to paint Amor Vincit Omnia for the art patron the nobleman, when he was at last becoming nearly respectable with prestigious ecclesiastical commissions? This profane non-Christian god resurrects the erotic provocations of his early works but in a increasingly powerful, unsettling manner. Half a century afterwards, its hidden meaning seemed obvious: it was a representation of Caravaggio's lover. A British traveller saw Victorious Cupid in about the mid-seventeenth century and was told its subject has "the physique and countenance of [Caravaggio's|his] owne youth or assistant that slept with him". The name of this boy was Cecco.

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