What exactly was the dark-feathered god of love? What insights that masterwork reveals about the rebellious genius

A youthful lad cries out as his skull is firmly gripped, a large digit pressing into his face as his parent's mighty palm holds him by the throat. This moment from The Sacrifice of Isaac appears in the Uffizi Gallery, evoking distress through the artist's harrowing portrayal of the suffering child from the biblical account. The painting seems as if Abraham, commanded by God to kill his offspring, could break his neck with a single twist. However the father's preferred approach involves the metallic steel blade he grips in his remaining hand, ready to slit the boy's neck. A definite element stands out – whomever modeled as Isaac for this breathtaking work displayed remarkable expressive ability. There exists not just fear, surprise and pleading in his shadowed gaze but also profound sorrow that a protector could abandon him so completely.

The artist took a familiar biblical story and made it so fresh and visceral that its terrors seemed to happen directly in front of you

Standing in front of the painting, observers recognize this as a actual countenance, an accurate depiction of a adolescent model, because the same boy – identifiable by his disheveled hair and nearly black pupils – appears in several additional works by Caravaggio. In each case, that highly expressive visage dominates the scene. In Youth With a Ram, he gazes mischievously from the darkness while holding a lamb. In Amor Vincit Omnia, he smirks with a toughness acquired on Rome's alleys, his black plumed appendages demonic, a unclothed adolescent creating riot in a well-to-do residence.

Amor Vincit Omnia, currently displayed at a British gallery, constitutes one of the most embarrassing masterpieces ever painted. Viewers feel completely unsettled looking at it. Cupid, whose arrows fill people with often painful longing, is portrayed as a very tangible, brightly illuminated nude form, standing over toppled-over objects that include stringed devices, a musical manuscript, plate armor and an architect's T-square. This heap of items echoes, intentionally, the geometric and construction equipment scattered across the ground in Albrecht Dürer's print Melencolia I – save in this case, the gloomy mess is caused by this smirking deity and the mayhem he can release.

"Affection looks not with the vision, but with the soul, / And therefore is winged Cupid depicted blind," wrote the Bard, shortly before this work was created around the early 1600s. But Caravaggio's god is not unseeing. He gazes directly at you. That countenance – sardonic and ruddy-cheeked, staring with bold assurance as he poses naked – is the identical one that screams in fear in Abraham's Test.

When the Italian master painted his multiple images of the identical distinctive-appearing youth in the Eternal City at the start of the seventeenth century, he was the highly celebrated religious artist in a city ignited by religious revival. The Sacrifice of Isaac reveals why he was commissioned to adorn churches: he could take a scriptural narrative that had been depicted numerous occasions before and render it so fresh, so raw and visceral that the terror seemed to be happening immediately before you.

However there was another aspect to the artist, evident as soon as he arrived in Rome in the cold season that concluded the sixteenth century, as a artist in his initial 20s with no teacher or patron in the city, only talent and boldness. The majority of the paintings with which he captured the sacred metropolis's eye were everything but devout. What may be the very earliest hangs in London's National Gallery. A youth opens his red lips in a scream of pain: while stretching out his dirty fingers for a cherry, he has rather been attacked. Youth Bitten by a Reptile is eroticism amid poverty: observers can see the painter's gloomy chamber reflected in the murky waters of the transparent container.

The adolescent sports a rose-colored flower in his hair – a symbol of the erotic trade in early modern painting. Northern Italian artists such as Tiziano and Jacopo Palma portrayed courtesans grasping flowers and, in a work lost in the second world war but known through images, Caravaggio represented a famous female courtesan, holding a posy to her bosom. The meaning of all these botanical signifiers is obvious: sex for purchase.

How are we to make of Caravaggio's sensual 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 1980s. The complicated historical reality is that the artist was neither the queer hero that, for instance, Derek Jarman presented on screen in his twentieth-century movie about the artist, nor so completely devout that, as some art scholars unbelievably assert, his Boy With a Basket of Fruit is in fact a likeness of Christ.

His initial paintings do make explicit sexual implications, or including propositions. It's as if Caravaggio, then a destitute youthful artist, aligned with Rome's sex workers, offering himself to survive. In the Uffizi, with this thought in mind, observers might turn to an additional initial work, the 1596 masterpiece Bacchus, in which the deity of alcohol stares coolly at the spectator as he starts to untie the dark ribbon of his garment.

A several years after the wine deity, what could have motivated Caravaggio to paint Victorious Cupid for the art patron Vincenzo Giustiniani, when he was finally becoming almost respectable with important ecclesiastical commissions? This unholy non-Christian deity revives the erotic provocations of his early paintings but in a increasingly powerful, uneasy manner. Half a century later, its secret seemed obvious: it was a portrait of Caravaggio's companion. A British visitor viewed the painting in about 1649 and was told its subject has "the physique and countenance of [Caravaggio's|his] own youth or assistant that laid with him". The identity of this adolescent was Francesco.

The artist had been deceased for about forty years when this account was recorded.