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A youthful boy screams while his skull is firmly gripped, a large thumb pressing into his cheek as his father's powerful palm holds him by the neck. This scene from The Sacrifice of Isaac appears in the Florentine museum, evoking unease through the artist's harrowing portrayal of the suffering youth from the scriptural account. It seems as if Abraham, commanded by God to sacrifice his offspring, could break his neck with a solitary turn. However the father's chosen method involves the silvery grey blade he grips in his other palm, prepared to cut the boy's throat. One certain element stands out – whomever posed as the sacrifice for this breathtaking work displayed remarkable acting skill. Within exists not just dread, shock and pleading in his shadowed eyes but also profound sorrow that a protector could betray him so completely.

He adopted a familiar biblical story and made it so fresh and visceral that its horrors appeared to unfold directly in front of you

Viewing in front of the painting, viewers identify this as a actual countenance, an accurate depiction of a adolescent model, because the same boy – recognizable by his disheveled locks and nearly black pupils – features in two additional works by the master. In each instance, that highly emotional visage commands the scene. In Youth With a Ram, he peers playfully from the shadows while holding a ram. In Amor Vincit Omnia, he grins with a hardness learned on Rome's streets, his black plumed appendages demonic, a naked child running riot in a affluent dwelling.

Victorious Cupid, presently displayed at a London gallery, represents one of the most embarrassing masterpieces ever painted. Observers feel completely unsettled gazing at it. Cupid, whose arrows inspire people with frequently painful longing, is portrayed as a very tangible, vividly illuminated unclothed figure, standing over toppled-over items that include musical devices, a musical manuscript, plate armour and an builder's T-square. This pile of items resembles, deliberately, the mathematical and architectural gear scattered across the ground in Albrecht Dürer's print Melencolia I – save in this case, the melancholic mess is caused by this smirking Cupid and the turmoil he can release.

"Love sees not with the eyes, but with the mind, / And therefore is feathered Love depicted sightless," penned Shakespeare, just before this work was produced around the early 1600s. But Caravaggio's Cupid is not blind. He gazes straight at you. That countenance – ironic and ruddy-faced, looking with brazen confidence as he struts unclothed – is the identical one that shrieks in fear in Abraham's Test.

When Michelangelo Merisi da Caravaggio painted his three portrayals of the same unusual-appearing youth in Rome at the start of the seventeenth century, he was the most celebrated religious artist in a city ignited by Catholic revival. Abraham's Offering reveals why he was sought to adorn sanctuaries: he could take a scriptural narrative that had been depicted many times previously and make it so new, so unfiltered and physical that the terror appeared to be occurring immediately before you.

Yet there was a different side to the artist, evident as soon as he arrived in the capital in the winter that ended the sixteenth century, as a painter in his initial twenties with no mentor or patron in the urban center, just skill and audacity. Most of the paintings with which he caught the sacred metropolis's eye were everything but holy. What could be the absolute first resides in London's art museum. A youth parts his red lips in a yell of agony: while reaching out his filthy fingers for a fruit, he has instead been bitten. Youth Bitten by a Reptile is sensuality amid squalor: observers can discern the painter's gloomy chamber mirrored in the cloudy liquid of the transparent container.

The adolescent sports a rose-colored flower in his hair – a symbol of the sex commerce in Renaissance painting. Venetian artists such as Titian and Palma Vecchio portrayed courtesans holding blooms and, in a work lost in the second world war but documented through photographs, Caravaggio represented a famous female courtesan, holding a posy to her chest. The message of all these botanical indicators is obvious: sex for sale.

How are we to interpret of the artist's sensual portrayals of boys – and of one adolescent in specific? It is a inquiry that has divided his commentators ever since he achieved widespread recognition in the twentieth century. The complicated past reality is that the artist was neither the homosexual icon that, for instance, the filmmaker presented on film in his twentieth-century film Caravaggio, nor so entirely pious that, as certain art historians unbelievably claim, his Youth Holding Fruit is actually a portrait of Jesus.

His early paintings indeed make overt sexual implications, or including propositions. It's as if Caravaggio, then a destitute youthful artist, identified with Rome's sex workers, offering himself to live. In the Uffizi, with this thought in consideration, viewers might turn to an additional early creation, the sixteenth-century masterwork Bacchus, in which the deity of alcohol gazes coolly at you as he starts to untie the dark ribbon of his garment.

A several years following Bacchus, what could have motivated the artist to paint Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was at last growing almost established with important ecclesiastical projects? This unholy non-Christian god resurrects the sexual provocations of his initial paintings but in a increasingly powerful, unsettling way. Fifty years afterwards, its hidden meaning seemed clear: it was a portrait of Caravaggio's lover. A British visitor saw the painting in about the mid-seventeenth century and was informed its subject has "the physique and countenance of [Caravaggio's|his] owne boy or assistant that slept with him". The identity of this adolescent was Francesco.

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