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A youthful lad screams while his skull is forcefully held, a large thumb pressing into his cheek as his parent's powerful hand holds him by the neck. This moment from The Sacrifice of Isaac visits the Uffizi Gallery, evoking unease through the artist's chilling rendition of the tormented youth from the biblical account. It appears as if Abraham, instructed by the Divine to kill his son, could snap his spinal column with a solitary turn. Yet Abraham's preferred method involves the silvery steel blade he grips in his remaining palm, ready to cut Isaac's neck. One certain element remains – whomever posed as Isaac for this astonishing piece displayed extraordinary expressive skill. There exists not just fear, surprise and begging in his darkened gaze but also profound grief that a guardian could betray him so utterly.

The artist took a familiar biblical tale and made it so vibrant and raw that its horrors appeared to unfold right in front of the viewer

Viewing before the artwork, viewers recognize this as a actual face, an accurate record of a adolescent model, because the same boy – recognizable by his disheveled hair and almost black pupils – features in two other paintings by the master. In every instance, that highly emotional visage commands the scene. In Youth With a Ram, he peers mischievously from the darkness while holding a ram. In Victorious Cupid, he smirks with a hardness acquired on the city's alleys, his dark plumed appendages demonic, a naked child creating chaos in a affluent dwelling.

Amor Vincit Omnia, presently displayed at a London museum, represents one of the most embarrassing artworks ever painted. Viewers feel totally unsettled looking at it. Cupid, whose arrows fill people with frequently agonizing desire, is portrayed as a extremely tangible, brightly lit nude figure, straddling overturned items that include stringed instruments, a musical manuscript, plate armour and an architect's T-square. This pile of possessions resembles, deliberately, the geometric and construction equipment strewn across the ground in Albrecht Dürer's engraving Melancholy – except in this case, the gloomy mess is created by this smirking deity and the turmoil he can release.

"Love looks not with the vision, but with the soul, / And therefore is winged Love painted sightless," wrote the Bard, shortly before this work was created around 1601. But Caravaggio's god is not unseeing. He stares straight at the observer. That countenance – ironic and rosy-faced, staring with brazen confidence as he struts naked – is the same one that screams in fear in The Sacrifice of Isaac.

As the Italian master created his three portrayals of the identical unusual-appearing kid in the Eternal City at the dawn of the 17th century, he was the highly acclaimed sacred artist in a city enflamed by religious renewal. The Sacrifice of Isaac demonstrates why he was commissioned to adorn churches: he could take a scriptural narrative that had been depicted many times before and make it so fresh, so raw and visceral that the horror appeared to be happening immediately before you.

However there existed a different aspect to the artist, evident as quickly as he arrived in the capital in the cold season that ended the sixteenth century, as a painter in his initial 20s with no mentor or supporter in the urban center, just skill and audacity. Most of the works with which he caught the holy metropolis's eye were anything but holy. What could be the absolute earliest hangs in the UK's art museum. A young man parts his crimson lips in a yell of agony: while stretching out his filthy fingers for a fruit, he has rather been attacked. Youth Bitten by a Reptile is eroticism amid poverty: observers can see Caravaggio's gloomy chamber mirrored in the cloudy waters of the glass container.

The boy sports a pink flower in his coiffure – a symbol of the sex trade in Renaissance painting. Venetian painters such as Tiziano and Palma Vecchio depicted courtesans holding flowers and, in a painting destroyed in the second world war but known through photographs, Caravaggio represented a renowned woman prostitute, clutching a posy to her bosom. The meaning of all these botanical signifiers is obvious: intimacy for sale.

How are we to make of the artist's sensual portrayals of boys – and of a particular adolescent in particular? It is a inquiry that has split his interpreters since he achieved mega-fame in the 1980s. The complicated past truth is that the painter was neither the homosexual icon that, for instance, the filmmaker put on screen in his twentieth-century movie about the artist, nor so entirely devout that, as certain artistic scholars unbelievably assert, his Boy With a Basket of Fruit is actually a likeness of Christ.

His early works indeed offer explicit sexual implications, or including offers. It's as if Caravaggio, then a destitute youthful artist, identified with the city's prostitutes, selling himself to live. In the Uffizi, with this idea in consideration, observers might look to an additional early creation, the 1596 masterwork Bacchus, in which the deity of wine stares calmly at the spectator as he starts to untie the black ribbon of his garment.

A several annums following Bacchus, what could have driven the artist to paint Amor Vincit Omnia for the art patron Vincenzo Giustiniani, when he was finally becoming almost established with prestigious ecclesiastical projects? This profane pagan deity revives the erotic provocations of his initial paintings but in a increasingly intense, uneasy way. Half a century afterwards, its secret seemed obvious: it was a representation of the painter's companion. A British traveller viewed Victorious Cupid in about 1649 and was told its figure has "the body & face of [Caravaggio's|his] owne boy or assistant that laid with him". The identity of this adolescent was Francesco.

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