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A youthful lad screams while his skull is firmly gripped, a massive digit digging into his cheek as his parent's powerful hand grasps him by the neck. This scene from The Sacrifice of Isaac appears in the Uffizi Gallery, creating unease through Caravaggio's harrowing rendition of the tormented youth from the scriptural account. It seems as if the patriarch, instructed by the Divine to kill his son, could break his spinal column with a single twist. However Abraham's preferred method involves the silvery steel blade he holds in his other hand, prepared to cut Isaac's throat. One definite aspect remains – whoever modeled as Isaac for this astonishing piece demonstrated remarkable acting skill. Within exists not only dread, surprise and begging in his darkened gaze but also profound grief that a guardian could betray him so completely.

The artist took a well-known biblical tale and made it so vibrant and visceral that its horrors appeared to happen right in front of you

Viewing in front of the painting, viewers identify this as a actual face, an precise depiction of a adolescent subject, because the identical boy – recognizable by his tousled locks and nearly dark pupils – appears in two additional paintings by the master. In each case, that richly expressive face dominates the scene. In John the Baptist, he peers playfully from the shadows while embracing a ram. In Victorious Cupid, he grins with a hardness learned on the city's streets, his black plumed appendages demonic, a unclothed child running riot in a well-to-do dwelling.

Amor Vincit Omnia, presently displayed at a British museum, represents one of the most embarrassing masterpieces ever painted. Observers feel completely unsettled gazing at it. The god of love, whose darts fill people with often agonizing desire, is portrayed as a extremely tangible, brightly illuminated nude form, standing over toppled-over objects that include musical devices, a music manuscript, metal armour and an builder's ruler. This pile of possessions echoes, deliberately, the mathematical and architectural equipment strewn across the floor in Albrecht Dürer's engraving Melencolia I – save in this case, the melancholic mess is caused by this grinning Cupid and the mayhem he can release.

"Love sees not with the eyes, but with the soul, / And therefore is winged Love depicted sightless," penned Shakespeare, just prior to this work was created around the early 1600s. But the painter's god is not blind. He stares straight at the observer. That face – sardonic and rosy-cheeked, looking with bold confidence as he struts naked – is the identical one that shrieks in fear in Abraham's Test.

As Michelangelo Merisi da Caravaggio painted his multiple images of the same unusual-looking youth in Rome at the start of the 17th century, he was the most celebrated religious painter in a metropolis ignited by Catholic revival. The Sacrifice of Isaac demonstrates why he was commissioned to adorn sanctuaries: he could take a scriptural narrative that had been depicted numerous times previously and render it so fresh, so unfiltered and visceral that the horror appeared to be happening immediately before you.

Yet there was another side to Caravaggio, apparent as soon as he came in the capital in the cold season that ended 1592, as a painter in his early 20s with no mentor or patron in the urban center, just skill and boldness. Most of the works with which he caught the holy metropolis's attention were everything but holy. That may be the very earliest resides in London's art museum. A young man parts his crimson lips in a scream of pain: while stretching out his filthy digits for a cherry, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid poverty: observers can discern the painter's gloomy room reflected in the cloudy liquid of the transparent vase.

The adolescent sports a pink blossom in his hair – a emblem of the sex trade in early modern painting. Venetian painters such as Titian and Jacopo Palma depicted prostitutes grasping blooms and, in a work destroyed in the second world war but known through photographs, Caravaggio portrayed a famous woman courtesan, holding a posy to her bosom. The meaning of all these floral signifiers is obvious: intimacy for purchase.

What are we to make of Caravaggio's sensual portrayals of youths – and of one adolescent in particular? It is a inquiry that has split his interpreters since he gained mega-fame in the twentieth century. The complex past truth is that the painter was neither the queer hero that, for instance, the filmmaker put on film in his 1986 movie about the artist, nor so completely pious that, as certain art scholars improbably claim, his Boy With a Basket of Fruit is in fact a likeness of Christ.

His early works indeed offer overt sexual implications, or including offers. It's as if the painter, then a penniless young creator, aligned with the city's prostitutes, offering himself to survive. In the Florentine gallery, with this idea in consideration, viewers might look to another initial work, the 1596 masterwork Bacchus, in which the god of alcohol gazes coolly at you as he begins to undo the dark sash of his robe.

A few annums following the wine deity, what could have driven Caravaggio to create Victorious Cupid for the art collector Vincenzo Giustiniani, when he was at last growing nearly established with important church commissions? This profane pagan god resurrects the sexual challenges of his early works but in a increasingly intense, uneasy way. Half a century later, its hidden meaning seemed obvious: it was a representation of the painter's lover. A British visitor saw the painting in about the mid-seventeenth century and was informed its figure has "the body & face of [Caravaggio's|his] own boy or servant that laid with him". The name of this boy was Francesco.

The artist had been dead for about 40 years when this account was documented.