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A youthful boy screams as his skull is firmly gripped, a large thumb pressing into his cheek as his father's powerful hand grasps him by the throat. This moment from The Sacrifice of Isaac visits the Florentine museum, creating distress through Caravaggio's chilling portrayal of the tormented youth from the biblical narrative. The painting seems as if Abraham, instructed by God to sacrifice his offspring, could snap his neck with a single twist. Yet Abraham's chosen method involves the metallic grey blade he grips in his other hand, prepared to slit Isaac's throat. A certain aspect remains – whoever posed as Isaac for this breathtaking work demonstrated remarkable acting ability. Within exists not only fear, surprise and pleading in his darkened gaze but additionally deep sorrow that a protector could abandon him so completely.

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

Standing before the artwork, viewers identify this as a real countenance, an accurate record of a young model, because the same boy – identifiable by his disheveled locks and nearly black pupils – appears in two additional works by Caravaggio. In each instance, that highly expressive visage commands the scene. In John the Baptist, he peers playfully from the darkness while holding a lamb. In Amor Vincit Omnia, he grins with a hardness acquired on Rome's alleys, his black feathery wings sinister, a naked adolescent creating riot in a well-to-do residence.

Victorious Cupid, currently displayed at a British gallery, constitutes one of the most discomfiting artworks ever painted. Viewers feel totally unsettled gazing at it. Cupid, whose arrows inspire people with often painful desire, is shown as a extremely real, brightly lit unclothed form, standing over toppled-over items that comprise musical instruments, a musical manuscript, plate armor and an builder's ruler. This pile of possessions resembles, deliberately, the geometric and architectural gear scattered across the ground in Albrecht Dürer's print Melencolia I – except in this case, the melancholic mess is caused by this smirking Cupid and the turmoil he can release.

"Affection looks not with the eyes, but with the soul, / And thus is winged Love depicted blind," wrote the Bard, just prior to this work was created around the early 1600s. But the painter's god is not unseeing. He gazes directly at you. That countenance – sardonic and ruddy-cheeked, looking with brazen confidence as he poses naked – is the identical one that shrieks in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio painted his three portrayals of the same distinctive-looking kid in Rome at the start of the 17th century, he was the most acclaimed sacred artist in a city enflamed by Catholic renewal. Abraham's Offering reveals why he was sought to decorate churches: he could take a biblical narrative that had been depicted numerous times before and render it so new, so unfiltered and physical that the horror appeared to be occurring directly in front of the spectator.

Yet there existed another aspect to the artist, apparent as quickly as he arrived in Rome in the winter that concluded the sixteenth century, as a artist in his early twenties with no teacher or supporter in the urban center, only talent and boldness. The majority of the paintings with which he captured the sacred city's attention were anything but devout. That could be the very earliest hangs in London's National Gallery. A young man parts his red lips in a yell of pain: while stretching out his dirty digits for a cherry, he has instead been bitten. Boy Bitten By a Lizard is eroticism amid poverty: viewers can discern Caravaggio's dismal room mirrored in the murky liquid of the glass container.

The adolescent sports a pink flower in his coiffure – a symbol of the sex commerce in Renaissance art. Northern Italian painters such as Titian and Jacopo Palma depicted prostitutes holding blooms and, in a painting lost in the WWII but documented through images, the master represented a famous female courtesan, clutching a posy to her chest. The message of all these botanical signifiers is obvious: intimacy for sale.

How are we to make of Caravaggio's erotic depictions of youths – and of one boy in particular? It is a question that has divided his interpreters since he gained mega-fame in the 1980s. The complicated historical truth is that the artist was not the homosexual icon that, for example, Derek Jarman presented on screen in his twentieth-century movie about the artist, nor so entirely pious that, as certain artistic scholars unbelievably assert, his Boy With a Basket of Fruit is actually a portrait of Christ.

His early paintings indeed offer overt erotic implications, or even propositions. It's as if Caravaggio, then a penniless youthful creator, aligned with the city's sex workers, offering himself to survive. In the Uffizi, with this idea in consideration, viewers might turn to an additional initial creation, the 1596 masterwork Bacchus, in which the deity of alcohol stares coolly at you as he starts to untie the dark sash of his garment.

A few annums after the wine deity, what could have driven Caravaggio to paint Victorious Cupid for the artistic patron the nobleman, when he was finally becoming nearly respectable with important ecclesiastical commissions? This unholy pagan god revives the sexual challenges of his early paintings but in a increasingly powerful, unsettling manner. Half a century later, its secret seemed clear: it was a representation of Caravaggio's lover. A English visitor saw Victorious Cupid in about the mid-seventeenth century and was told its subject has "the physique and countenance of [Caravaggio's|his] owne boy or servant that laid with him". The identity of this boy was Francesco.

The artist had been deceased for about 40 annums when this account was recorded.