What was the black-winged god of love? The secrets that masterpiece reveals about the rebellious artist

The young lad screams as his skull is firmly held, a massive thumb pressing into his face as his father's powerful palm holds him by the throat. That moment from The Sacrifice of Isaac visits the Uffizi Gallery, evoking unease through Caravaggio's chilling portrayal of the suffering youth from the biblical account. It seems as if the patriarch, instructed by the Divine to sacrifice his offspring, could snap his spinal column with a solitary twist. Yet Abraham's chosen approach involves the silvery grey blade he grips in his other palm, prepared to cut the boy's throat. A certain aspect remains – whomever modeled as Isaac for this astonishing work displayed remarkable expressive skill. Within exists not only fear, shock and pleading in his darkened eyes but additionally deep grief that a protector could betray him so completely.

He adopted a familiar scriptural tale and transformed it so vibrant and raw that its horrors seemed to happen right in front of the viewer

Viewing in front of the artwork, viewers recognize this as a real countenance, an accurate depiction of a young model, because the identical boy – identifiable by his disheveled hair and almost dark eyes – features in two other paintings by Caravaggio. In each instance, that richly expressive visage dominates the scene. In John the Baptist, he peers playfully from the darkness while holding a ram. In Victorious Cupid, he smirks with a hardness acquired on the city's alleys, his black plumed appendages demonic, a unclothed adolescent running chaos in a well-to-do dwelling.

Victorious Cupid, currently displayed at a British gallery, constitutes one of the most discomfiting artworks ever created. Viewers feel totally disoriented looking at it. The god of love, whose arrows inspire people with often agonizing desire, is portrayed as a very real, brightly lit nude form, standing over overturned objects that comprise stringed devices, a musical manuscript, metal armour and an builder's ruler. This pile of possessions resembles, intentionally, the mathematical and architectural gear strewn across the floor in Albrecht Dürer's print Melencolia I – except in this case, the gloomy disorder is created by this smirking deity and the turmoil he can release.

"Love sees not with the vision, but with the mind, / And thus is feathered Love painted sightless," wrote Shakespeare, just before this work was produced around the early 1600s. But the painter's god is not unseeing. He gazes straight at the observer. That face – ironic and ruddy-cheeked, looking with brazen confidence as he struts unclothed – is the same one that screams in terror in Abraham's Test.

As Michelangelo Merisi da Caravaggio created his three images of the same unusual-appearing kid in Rome at the dawn of the 17th century, he was the highly acclaimed sacred artist in a metropolis enflamed by religious renewal. The Sacrifice of Isaac reveals why he was commissioned to decorate sanctuaries: he could take a biblical narrative that had been depicted numerous times previously and render it so new, so raw and physical that the horror seemed to be occurring directly before you.

Yet there existed another aspect to the artist, evident as soon as he came in the capital in the winter that concluded 1592, as a artist in his early twenties with no teacher or supporter in the urban center, only talent and boldness. Most of the paintings with which he caught the holy metropolis's eye were everything but holy. That may be the absolute first hangs in the UK's National Gallery. A youth opens his red mouth in a yell of pain: while reaching out his filthy fingers for a fruit, he has rather been attacked. Boy Bitten By a Lizard is sensuality amid poverty: observers can see Caravaggio's gloomy chamber reflected in the cloudy waters of the transparent vase.

The boy sports a rose-colored flower in his hair – a emblem of the sex trade in early modern painting. Venetian artists such as Tiziano and Palma Vecchio depicted prostitutes grasping flowers and, in a painting lost in the second world war but known through images, Caravaggio portrayed a famous female courtesan, clutching a bouquet to her chest. The message of all these botanical signifiers is obvious: sex for sale.

What are we to make of Caravaggio's erotic portrayals of youths – and of a particular boy in specific? It is a inquiry that has divided his interpreters since he achieved widespread recognition in the twentieth century. The complex historical reality is that the artist was not the homosexual icon that, for example, Derek Jarman presented on film in his 1986 movie Caravaggio, nor so entirely devout that, as certain art scholars unbelievably assert, his Boy With a Basket of Fruit is actually a portrait of Jesus.

His early works indeed make overt erotic implications, or even propositions. It's as if Caravaggio, then a destitute youthful artist, identified with the city's sex workers, selling himself to survive. In the Florentine gallery, with this idea in mind, viewers might turn to an additional initial creation, the sixteenth-century masterpiece the god of wine, in which the god of alcohol gazes calmly at the spectator as he starts to undo the dark sash of his robe.

A few annums following the wine deity, what could have driven the artist to paint Amor Vincit Omnia for the artistic collector Vincenzo Giustiniani, when he was at last becoming almost respectable with prestigious ecclesiastical projects? This profane pagan god resurrects the sexual challenges of his early paintings but in a more powerful, unsettling manner. Fifty years later, its hidden meaning seemed clear: it was a portrait of the painter's lover. A British visitor saw the painting in about 1649 and was told its subject has "the physique and countenance 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 forty annums when this account was recorded.