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A youthful boy screams as his head is forcefully gripped, a massive digit digging into his cheek as his father's mighty hand holds him by the neck. This moment from The Sacrifice of Isaac visits the Uffizi Gallery, evoking unease through Caravaggio's chilling rendition of the tormented youth from the scriptural narrative. The painting appears as if Abraham, commanded by God to sacrifice his son, could snap his spinal column with a single twist. However the father's preferred method involves the silvery steel blade he holds in his other hand, prepared to cut the boy's throat. One definite element remains – whoever modeled as Isaac for this breathtaking work demonstrated remarkable acting skill. Within exists not only dread, shock and begging in his darkened gaze but also deep sorrow that a guardian could betray him so completely.

The artist took a well-known scriptural story and transformed it so vibrant and raw that its horrors appeared to happen directly in view of the viewer

Viewing in front of the painting, viewers recognize this as a real countenance, an accurate depiction of a adolescent subject, because the same youth – identifiable by his tousled locks and almost black pupils – features in several other paintings by Caravaggio. In every instance, that richly emotional visage commands the scene. In John the Baptist, he gazes mischievously from the shadows while embracing a ram. In Victorious Cupid, he smirks with a hardness acquired on Rome's alleys, his black plumed wings demonic, a naked adolescent creating chaos in a affluent dwelling.

Amor Vincit Omnia, presently exhibited at a London gallery, constitutes one of the most discomfiting masterpieces ever created. Viewers feel completely unsettled gazing at it. Cupid, whose arrows fill people with often painful longing, is portrayed as a extremely tangible, vividly illuminated unclothed figure, standing over toppled-over items that include musical devices, a music manuscript, plate armor and an architect's ruler. This pile of possessions resembles, deliberately, the geometric and architectural equipment scattered across the floor in Albrecht Dürer's engraving Melencolia I – save in this case, the gloomy mess is caused by this grinning deity and the turmoil he can release.

"Affection looks not with the eyes, but with the mind, / And therefore is feathered Cupid depicted sightless," penned the Bard, shortly before this work was created around the early 1600s. But Caravaggio's god is not unseeing. He stares directly at the observer. That face – sardonic and rosy-cheeked, looking with brazen assurance as he struts unclothed – is the identical one that shrieks in fear in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio created his multiple portrayals of the identical unusual-looking kid in Rome at the start of the 17th century, he was the highly acclaimed sacred painter in a city enflamed by Catholic revival. Abraham's Offering demonstrates why he was sought to adorn sanctuaries: he could take a biblical story that had been depicted many occasions previously and render it so fresh, so unfiltered and physical that the horror appeared to be happening immediately before the spectator.

However there was another side to the artist, apparent as quickly as he came in Rome in the cold season that concluded 1592, as a painter in his initial 20s with no mentor or patron in the urban center, just skill and boldness. The majority of the paintings with which he captured the holy metropolis's attention were anything but holy. What may be the absolute first hangs in the UK's National Gallery. A youth opens his red lips in a yell of pain: while reaching out his filthy fingers for a cherry, he has rather been attacked. Youth Bitten by a Reptile is sensuality amid poverty: viewers can discern the painter's gloomy chamber reflected in the cloudy liquid of the glass container.

The adolescent wears a pink flower in his hair – a emblem of the sex trade in Renaissance painting. Northern Italian painters such as Tiziano and Jacopo Palma depicted prostitutes grasping blooms and, in a work lost in the second world war but known through images, Caravaggio portrayed a famous female prostitute, clutching a bouquet to her chest. The meaning of all these botanical signifiers is obvious: sex for purchase.

What are we to interpret of Caravaggio's sensual portrayals of youths – and of a particular adolescent in particular? It is a inquiry that has divided his commentators ever since he gained widespread recognition in the twentieth century. The complex historical truth is that the painter was not the queer hero that, for example, Derek Jarman presented on screen in his twentieth-century film Caravaggio, nor so completely devout that, as certain artistic scholars unbelievably claim, his Youth Holding Fruit is in fact a likeness of Christ.

His early paintings indeed offer explicit erotic suggestions, or including propositions. It's as if Caravaggio, then a penniless young creator, identified with the city's sex workers, offering himself to survive. In the Florentine gallery, with this thought in consideration, observers might look to an additional initial creation, the 1596 masterpiece the god of wine, in which the deity of alcohol stares calmly at the spectator as he begins to undo the dark sash of his robe.

A several years after the wine deity, what could have motivated the artist to paint Amor Vincit Omnia for the art collector Vincenzo Giustiniani, when he was finally becoming nearly established with prestigious ecclesiastical commissions? This profane non-Christian god resurrects the sexual provocations of his initial works but in a more powerful, uneasy manner. Fifty years later, its secret seemed clear: it was a portrait of Caravaggio's lover. A British traveller saw Victorious Cupid in about the mid-seventeenth century and was informed its figure has "the body & face of [Caravaggio's|his] owne boy or assistant that slept with him". The identity of this adolescent was Cecco.

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