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A young boy cries out as his skull is firmly gripped, a large thumb pressing into his cheek as his parent's mighty palm holds him by the throat. That moment from The Sacrifice of Isaac visits the Florentine museum, evoking unease through Caravaggio's chilling portrayal of the suffering youth from the biblical narrative. It appears as if the patriarch, commanded by God to sacrifice his son, could break his spinal column with a solitary turn. Yet the father's chosen approach involves the silvery steel knife he grips in his other palm, prepared to cut Isaac's neck. A definite aspect remains – whomever modeled as Isaac for this astonishing work demonstrated remarkable expressive ability. Within exists not only dread, shock and pleading in his shadowed eyes but also profound grief that a protector could betray 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 view of you

Viewing in front of the painting, observers recognize this as a actual face, an precise record of a adolescent subject, because the identical boy – identifiable by his tousled hair and nearly dark pupils – features in two additional works by Caravaggio. In every instance, that highly expressive visage dominates the composition. In Youth With a Ram, he peers mischievously from the darkness while holding a lamb. In Amor Vincit Omnia, he smirks with a toughness learned on Rome's streets, his dark feathery appendages sinister, a naked child running chaos in a well-to-do dwelling.

Victorious Cupid, currently displayed at a British museum, constitutes one of the most discomfiting masterpieces ever created. Observers feel completely unsettled looking at it. Cupid, whose darts fill people with frequently painful longing, is shown as a extremely real, brightly illuminated nude form, standing over toppled-over items that comprise musical instruments, a music score, metal armor and an architect's ruler. This heap of items echoes, intentionally, the geometric and construction equipment scattered across the ground in Albrecht Dürer's print Melancholy – except in this case, the melancholic disorder is created by this grinning deity and the mayhem he can release.

"Love looks not with the vision, but with the mind, / And thus is feathered Love painted sightless," wrote Shakespeare, just before this work was created around 1601. But the painter's Cupid is not blind. He gazes straight at the observer. That countenance – ironic and rosy-cheeked, staring with brazen confidence as he poses naked – is the identical one that shrieks in terror in Abraham's Test.

As the Italian master created his multiple portrayals of the same unusual-appearing kid in Rome at the dawn of the 17th century, he was the most celebrated sacred painter in a city ignited by religious renewal. The Sacrifice of Isaac demonstrates why he was sought to adorn sanctuaries: he could take a scriptural story that had been portrayed numerous times before and render it so fresh, so raw and visceral that the horror seemed to be occurring directly in front of you.

However there existed a different side to Caravaggio, evident as soon as he arrived in the capital in the winter that concluded 1592, as a painter in his initial 20s with no mentor or patron in the city, only talent and audacity. The majority of the paintings with which he caught the holy city's eye were anything but holy. What could be the absolute earliest hangs in the UK's National Gallery. A youth opens his red mouth in a yell of agony: while stretching out his filthy digits for a fruit, he has rather been attacked. Youth Bitten by a Reptile is eroticism amid poverty: observers can see the painter's gloomy room reflected in the murky waters of the transparent vase.

The boy wears a rose-colored flower in his hair – a symbol of the sex trade in Renaissance art. Northern Italian painters such as Tiziano and Palma Vecchio portrayed prostitutes grasping blooms and, in a work lost in the WWII but known through images, Caravaggio represented a famous woman prostitute, clutching a posy to her bosom. The meaning of all these botanical signifiers is clear: sex for sale.

How are we to interpret of Caravaggio's erotic depictions of boys – and of one boy in specific? It is a question that has split his interpreters since he achieved mega-fame in the twentieth century. The complicated past reality is that the painter was neither the queer hero that, for example, the filmmaker presented on screen in his twentieth-century film about the artist, nor so completely devout that, as certain artistic historians unbelievably assert, his Youth Holding Fruit is in fact a likeness of Christ.

His initial works indeed offer explicit sexual implications, or even offers. It's as if Caravaggio, then a destitute young creator, identified with Rome's prostitutes, offering himself to live. In the Uffizi, with this thought in mind, viewers might look to another initial work, the sixteenth-century masterpiece Bacchus, in which the deity of alcohol gazes calmly at the spectator as he starts to untie the black ribbon of his garment.

A several annums after Bacchus, what could have motivated Caravaggio to paint Victorious Cupid for the art patron Vincenzo Giustiniani, when he was finally becoming almost established with important church projects? This unholy pagan god revives the sexual challenges of his early works but in a more intense, uneasy manner. Half a century afterwards, its secret seemed clear: it was a representation of Caravaggio's companion. A English traveller viewed Victorious Cupid in about the mid-seventeenth century and was told its figure has "the physique and countenance of [Caravaggio's|his] owne youth or assistant that laid with him". The name of this adolescent was Francesco.

The painter had been dead for about 40 years when this story was documented.