What exactly was Caravaggio's black-winged god of love? The insights this masterpiece uncovers about the rogue genius

The young lad screams while his head is forcefully gripped, a massive thumb digging into his face as his father's mighty hand grasps him by the throat. This moment from The Sacrifice of Isaac visits the Uffizi Gallery, creating unease through Caravaggio's chilling portrayal of the suffering child from the scriptural narrative. The painting seems as if Abraham, instructed by God to sacrifice his son, could snap his spinal column with a single turn. However the father's chosen approach involves the metallic grey blade he holds in his remaining hand, ready to slit Isaac's throat. One certain element stands out – whomever modeled as Isaac for this breathtaking piece displayed extraordinary expressive ability. Within exists not just dread, shock and pleading in his darkened gaze but also profound sorrow that a guardian could betray him so utterly.

He took a well-known scriptural story and transformed it so fresh and raw that its terrors appeared to happen directly in view of you

Standing in front of the painting, observers recognize this as a real face, an precise depiction of a adolescent model, because the same boy – identifiable by his disheveled locks and nearly dark pupils – features in two other works by Caravaggio. In each instance, that richly emotional visage commands the composition. In John the Baptist, he gazes playfully from the darkness while embracing a ram. In Amor Vincit Omnia, he grins with a toughness learned on Rome's alleys, his black feathery wings demonic, a naked child creating chaos in a affluent dwelling.

Amor Vincit Omnia, currently displayed at a London museum, constitutes one of the most embarrassing masterpieces ever painted. Observers feel completely disoriented looking at it. Cupid, whose darts fill people with often agonizing longing, is portrayed as a extremely tangible, brightly lit unclothed figure, standing over overturned items that comprise stringed instruments, a music score, plate armour and an builder's ruler. This heap of possessions echoes, intentionally, the geometric and construction gear strewn across the ground in Albrecht Dürer's engraving Melancholy – except in this case, the gloomy mess is caused by this smirking deity and the mayhem he can unleash.

"Love looks not with the eyes, but with the soul, / And therefore is feathered Love painted sightless," wrote Shakespeare, shortly prior to this painting was produced around 1601. But Caravaggio's Cupid is not blind. He gazes directly at you. That countenance – sardonic and ruddy-cheeked, looking with bold assurance as he poses naked – is the same one that screams in terror in Abraham's Test.

As the Italian master created his multiple images of the identical unusual-appearing youth in the Eternal City at the dawn of the 17th century, he was the highly acclaimed religious artist in a city enflamed by Catholic revival. Abraham's Offering demonstrates why he was sought to decorate sanctuaries: he could adopt a scriptural story that had been depicted many times previously and render it so new, so raw and visceral that the terror seemed to be occurring immediately before the spectator.

However there was a different side to Caravaggio, evident as quickly as he arrived in Rome in the cold season that ended the sixteenth century, as a artist in his initial 20s with no mentor or patron in the city, just talent and boldness. Most of the works with which he captured the sacred city's eye were everything but devout. That could be the very first hangs in London's art museum. A youth opens his crimson lips in a scream of pain: while reaching out his dirty digits for a fruit, he has rather been bitten. Boy Bitten By a Lizard is eroticism amid poverty: viewers can see the painter's gloomy room mirrored in the cloudy waters of the glass vase.

The adolescent sports a rose-colored flower in his hair – a symbol of the erotic trade in Renaissance painting. Northern Italian artists such as Titian and Palma Vecchio portrayed prostitutes holding blooms and, in a work lost in the second world war but documented through photographs, the master represented a famous female courtesan, clutching a posy to her chest. The meaning of all these botanical indicators is clear: sex for sale.

How are we to make of Caravaggio's sensual depictions of boys – and of a particular boy in particular? It is a inquiry that has divided his interpreters ever since he achieved widespread recognition in the twentieth century. The complicated historical reality is that the artist was not the homosexual icon that, for instance, the filmmaker put on screen in his twentieth-century movie Caravaggio, nor so entirely pious that, as some artistic historians improbably assert, his Youth Holding Fruit is in fact a likeness of Christ.

His initial works do offer overt sexual suggestions, or even offers. It's as if the painter, then a destitute youthful artist, identified with the city's sex workers, offering himself to survive. In the Florentine gallery, with this idea in consideration, observers might look to another initial work, the 1596 masterpiece the god of wine, in which the god of wine stares coolly at the spectator as he starts to undo the black ribbon of his robe.

A few years after Bacchus, what could have driven the artist to paint Victorious Cupid for the art collector Vincenzo Giustiniani, when he was at last becoming almost respectable with prestigious church commissions? This profane pagan deity revives the sexual provocations of his early paintings but in a increasingly powerful, unsettling way. Half a century later, its secret seemed obvious: it was a portrait of the painter's lover. A English traveller viewed Victorious Cupid in about the mid-seventeenth century and was informed its figure has "the body & face of [Caravaggio's|his] owne youth or assistant that laid with him". The identity of this adolescent was Cecco.

The artist had been dead for about 40 annums when this story was recorded.