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A young lad cries out as his skull is firmly held, a massive digit digging into his cheek as his parent's mighty hand holds him by the neck. That moment from Abraham's Sacrifice appears in the Uffizi Gallery, evoking distress through the artist's harrowing portrayal of the suffering youth from the biblical narrative. The painting appears as if Abraham, instructed by the Divine to kill his son, could snap his spinal column with a solitary twist. Yet the father's preferred method involves the silvery steel blade he holds in his other hand, prepared to slit Isaac's throat. One definite aspect remains – whomever posed as Isaac for this astonishing work displayed remarkable expressive ability. Within exists not just fear, shock and pleading in his shadowed eyes but also deep sorrow that a protector could abandon him so utterly.

The artist adopted a well-known biblical tale and transformed it so fresh and visceral that its horrors seemed to unfold directly in front of the viewer

Standing before the painting, observers recognize this as a real face, an accurate record of a adolescent model, because the same youth – recognizable by his tousled locks and nearly dark pupils – appears in several other works by Caravaggio. In every case, that richly emotional visage dominates the scene. In John the Baptist, he peers mischievously from the darkness while holding a lamb. In Victorious Cupid, he grins with a toughness acquired on Rome's alleys, his black plumed wings sinister, a unclothed child running chaos in a affluent residence.

Amor Vincit Omnia, currently exhibited at a British museum, represents one of the most embarrassing masterpieces ever created. Observers feel totally unsettled gazing at it. Cupid, whose darts fill people with often painful longing, is shown as a very real, vividly lit nude figure, standing over toppled-over items that include stringed devices, a music score, metal armor and an builder's T-square. This pile of items resembles, deliberately, the geometric and construction gear strewn across the ground in Albrecht Dürer's engraving Melencolia I – save here, the gloomy mess is created by this grinning Cupid and the mayhem he can unleash.

"Affection sees not with the vision, but with the mind, / And therefore is winged Love painted blind," penned the Bard, shortly prior to this work was produced around 1601. But the painter's god is not blind. He gazes directly at the observer. That countenance – ironic and rosy-faced, looking with bold assurance as he struts naked – is the same one that screams in terror in Abraham's Test.

When Michelangelo Merisi da Caravaggio painted his three images of the same unusual-appearing kid in the Eternal City at the start of the seventeenth century, he was the highly acclaimed sacred artist in a city ignited by religious revival. Abraham's Offering demonstrates why he was commissioned to adorn churches: he could adopt a scriptural narrative that had been portrayed numerous occasions previously and make it so fresh, so raw and visceral that the terror seemed to be occurring immediately in front of the spectator.

Yet 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 twenties with no teacher or supporter in the urban center, only skill and boldness. The majority of the paintings with which he captured the sacred city's eye were anything but devout. That could be the very first resides in the UK's National Gallery. A youth opens his crimson mouth in a yell of pain: while reaching out his filthy digits for a fruit, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid squalor: viewers can discern Caravaggio's dismal room reflected in the cloudy waters of the transparent vase.

The adolescent sports a pink blossom in his coiffure – a symbol of the sex commerce in early modern art. Northern Italian artists such as Titian and Jacopo Palma portrayed courtesans holding blooms and, in a work lost in the WWII but known through photographs, Caravaggio portrayed a famous woman courtesan, holding a bouquet to her bosom. The meaning of all these floral signifiers is clear: sex for purchase.

What are we to interpret of the artist's sensual depictions of youths – and of a particular boy in particular? It is a question that has split his commentators since he gained widespread recognition in the twentieth century. The complex historical truth is that the painter was not the homosexual icon that, for example, the filmmaker put on screen in his 1986 movie about the artist, nor so entirely pious that, as certain artistic historians unbelievably assert, his Youth Holding Fruit is in fact a portrait of Christ.

His initial works do offer overt erotic implications, or even offers. It's as if the painter, then a penniless young artist, aligned with the city's sex workers, offering himself to survive. In the Florentine gallery, with this idea in mind, observers might look to another initial creation, the sixteenth-century masterwork Bacchus, in which the god of alcohol stares calmly at you as he starts to untie the dark ribbon of his robe.

A several annums after the wine deity, what could have motivated Caravaggio to create Amor Vincit Omnia for the art collector 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 early paintings but in a increasingly intense, unsettling manner. Fifty years afterwards, its secret seemed obvious: it was a representation of Caravaggio's companion. A British visitor viewed the painting in about the mid-seventeenth century and was told its subject has "the body & face of [Caravaggio's|his] owne youth or servant that slept with him". The name of this adolescent was Cecco.

The artist had been dead for about forty annums when this account was recorded.