What exactly was the black-winged deity of love? The insights that masterwork reveals about the rebellious genius

The youthful lad cries out as his head is forcefully gripped, a massive digit pressing into his face as his parent's mighty palm holds him by the throat. This scene from Abraham's Sacrifice appears in the Uffizi Gallery, creating distress through Caravaggio's chilling rendition of the tormented youth from the biblical narrative. The painting appears as if the patriarch, instructed by the Divine to sacrifice his son, could break his spinal column with a single twist. However the father's preferred method involves the silvery steel knife he holds in his remaining palm, ready to slit the boy's throat. A certain aspect remains – whoever modeled as Isaac for this astonishing work displayed extraordinary acting skill. There exists not just dread, surprise and begging in his shadowed gaze but also profound grief that a protector could betray him so utterly.

The artist took a well-known biblical story and made it so vibrant and visceral that its terrors appeared to happen right in view of the viewer

Viewing in front of the painting, viewers identify this as a actual countenance, an precise record of a adolescent subject, because the same boy – recognizable by his tousled hair and almost black eyes – features in two other paintings by the master. In every case, that richly expressive face 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 toughness learned on Rome's streets, his black feathery appendages demonic, a naked child running riot in a affluent residence.

Amor Vincit Omnia, presently exhibited at a British museum, constitutes one of the most embarrassing masterpieces ever created. Observers feel totally disoriented looking at it. The god of love, whose arrows inspire people with frequently agonizing desire, is portrayed as a very tangible, brightly illuminated unclothed figure, standing over overturned items that comprise stringed instruments, a musical score, plate armour and an builder's ruler. This heap of items echoes, intentionally, the geometric and construction gear strewn across the ground in Albrecht Dürer's engraving Melancholy – except in this case, the gloomy disorder is caused by this smirking deity and the turmoil he can unleash.

"Love looks not with the eyes, but with the soul, / And thus is feathered Cupid depicted sightless," wrote the Bard, just before this work was produced around the early 1600s. But the painter's god is not blind. He gazes straight at you. That face – ironic and rosy-cheeked, staring with brazen confidence as he poses naked – is the same one that shrieks in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio painted his three portrayals of the identical unusual-looking youth in the Eternal City at the start of the 17th century, he was the most celebrated religious artist in a city enflamed by religious revival. The Sacrifice of Isaac demonstrates why he was commissioned to adorn sanctuaries: he could adopt a biblical story that had been depicted numerous occasions previously and make it so new, so raw and physical that the horror seemed to be occurring directly before you.

However there was a different side to Caravaggio, evident as quickly as he came in the capital in the winter that concluded 1592, as a artist in his initial 20s with no teacher or supporter in the urban center, only skill and audacity. Most of the works with which he captured the holy metropolis's attention were anything but holy. What could be the very earliest hangs in the UK's National Gallery. A young man opens his crimson mouth in a scream of agony: while reaching out his dirty fingers for a fruit, he has instead been bitten. Youth Bitten by a Reptile is sensuality amid poverty: observers can discern the painter's gloomy room reflected in the cloudy liquid of the transparent vase.

The adolescent wears a pink flower in his coiffure – a emblem of the erotic commerce in Renaissance art. Northern Italian artists such as Titian and Palma Vecchio depicted prostitutes holding blooms and, in a painting lost in the WWII but documented through photographs, the master represented a renowned female prostitute, holding a posy to her bosom. The meaning of all these botanical signifiers is obvious: sex for sale.

How are we to make of Caravaggio's sensual portrayals of youths – and of one adolescent in particular? It is a question that has divided his interpreters ever since he gained mega-fame in the 1980s. The complicated historical reality is that the painter was neither the homosexual icon that, for instance, Derek Jarman presented on film in his twentieth-century movie Caravaggio, nor so completely pious that, as some art scholars improbably claim, his Boy With a Basket of Fruit is actually a likeness of Jesus.

His early works do offer overt erotic implications, or even propositions. It's as if the painter, then a penniless young artist, identified with Rome's prostitutes, selling himself to survive. In the Florentine gallery, with this thought in mind, viewers might look to another early work, the 1596 masterwork the god of wine, in which the god of alcohol gazes coolly at the spectator as he begins to untie the dark sash of his robe.

A several annums following Bacchus, what could have driven the artist to create Victorious Cupid for the art collector Vincenzo Giustiniani, when he was at last becoming almost established with important church projects? This unholy non-Christian god resurrects the sexual challenges of his early works but in a more powerful, uneasy way. Half a century later, its secret seemed obvious: it was a representation of the painter's companion. A English visitor saw Victorious Cupid in about 1649 and was told its subject has "the body & face of [Caravaggio's|his] owne boy or assistant that slept with him". The name of this adolescent was Cecco.

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