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A youthful lad cries out as his head is firmly held, a massive digit pressing into his cheek as his father's powerful hand grasps him by the throat. That scene from The Sacrifice of Isaac appears in the Florentine museum, evoking unease through the artist's chilling portrayal of the tormented child from the biblical narrative. The painting appears as if the patriarch, commanded by God to kill his son, could snap his spinal column with a solitary turn. Yet Abraham's preferred approach involves the silvery grey knife he grips in his other palm, ready to cut the boy's throat. One certain element remains – whomever posed as Isaac for this breathtaking piece displayed remarkable acting ability. Within exists not only dread, surprise and begging in his darkened eyes but also deep grief that a guardian could betray him so utterly.

The artist took a familiar biblical story and made it so fresh and raw that its horrors seemed to unfold right in view of you

Viewing before the artwork, observers recognize this as a actual face, an accurate depiction of a adolescent model, because the identical boy – identifiable by his disheveled hair and nearly dark eyes – features in two other paintings by Caravaggio. In each case, that richly expressive face commands the composition. In John the Baptist, he gazes mischievously from the darkness while holding a lamb. In Victorious Cupid, he grins with a toughness learned on Rome's streets, his dark feathery wings demonic, a unclothed child creating chaos in a well-to-do residence.

Victorious Cupid, currently displayed at a British museum, constitutes one of the most embarrassing artworks ever created. Observers feel totally disoriented gazing at it. The god of love, whose darts inspire people with often agonizing desire, is shown as a extremely tangible, brightly illuminated nude form, straddling overturned objects that comprise musical devices, a musical score, plate armor and an architect's T-square. This heap of items resembles, intentionally, the geometric and architectural equipment strewn across the floor in the German master's engraving Melencolia I – save here, the gloomy disorder is created by this grinning Cupid and the turmoil he can release.

"Affection sees not with the vision, but with the mind, / And thus is feathered Cupid depicted blind," penned Shakespeare, just before this painting was produced around the early 1600s. But the painter's Cupid is not unseeing. He gazes directly at the observer. That countenance – sardonic and rosy-cheeked, looking with bold assurance as he poses unclothed – is the same one that shrieks in terror in Abraham's Test.

As the Italian master painted his multiple portrayals of the same distinctive-appearing youth in Rome at the dawn of the 17th century, he was the highly acclaimed religious painter in a city ignited by Catholic revival. The Sacrifice of Isaac reveals why he was sought to adorn sanctuaries: he could take a scriptural story that had been depicted many times previously and render it so fresh, so unfiltered and visceral that the horror appeared to be happening immediately in front of you.

Yet there existed a different side to Caravaggio, apparent as quickly as he arrived in Rome in the cold season that concluded 1592, as a painter in his early 20s with no teacher or patron in the city, only skill and boldness. Most of the works with which he caught the holy city's eye were everything but devout. That may be the absolute first resides in the UK's art museum. A youth opens his red mouth in a scream of pain: while stretching out his dirty digits for a cherry, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid poverty: viewers can discern the painter's dismal chamber mirrored in the murky waters of the transparent vase.

The adolescent wears a rose-colored flower in his hair – a emblem of the erotic commerce in early modern painting. Northern Italian painters such as Titian and Jacopo Palma depicted courtesans grasping blooms and, in a painting destroyed in the WWII but known through photographs, Caravaggio portrayed a famous female prostitute, clutching a posy to her bosom. The message of all these botanical signifiers is clear: sex for purchase.

How are we to interpret of the artist's sensual depictions of youths – and of a particular adolescent in particular? It is a question that has divided his commentators ever since he gained widespread recognition in the 1980s. The complicated historical truth is that the artist was neither the queer hero that, for instance, Derek Jarman put on screen in his 1986 film about the artist, nor so completely pious that, as certain artistic historians improbably assert, his Youth Holding Fruit is actually a likeness of Christ.

His early paintings indeed offer overt sexual implications, or even propositions. It's as if Caravaggio, then a destitute youthful creator, aligned with the city's prostitutes, offering himself to survive. In the Florentine gallery, with this idea in mind, observers might turn to another initial work, the 1596 masterpiece the god of wine, in which the deity of wine gazes coolly at the spectator as he begins to undo the black sash of his garment.

A few annums after the wine deity, what could have driven the artist to create Amor Vincit Omnia for the art collector Vincenzo Giustiniani, when he was at last growing almost respectable with prestigious ecclesiastical projects? This profane pagan god resurrects the sexual challenges of his initial works but in a increasingly intense, unsettling manner. Half a century afterwards, its secret seemed clear: it was a portrait of Caravaggio's companion. A English visitor viewed Victorious Cupid in about 1649 and was told its figure has "the body & face of [Caravaggio's|his] own youth or servant that slept with him". The identity of this boy was Francesco.

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