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A youthful lad cries out as his skull is forcefully gripped, a massive thumb digging into his face as his parent's powerful palm holds him by the throat. That scene from The Sacrifice of Isaac appears in the Florentine museum, evoking unease through the artist's chilling rendition of the tormented child from the scriptural narrative. The painting appears as if the patriarch, commanded by the Divine to kill his son, could snap his neck with a solitary twist. Yet the father's preferred method involves the metallic grey knife he grips in his remaining palm, ready to cut the boy's throat. A definite aspect remains – whomever posed as the sacrifice for this breathtaking piece displayed remarkable expressive skill. Within exists not only dread, shock and begging in his darkened eyes but also deep sorrow that a protector could betray him so utterly.

The artist took a well-known scriptural story and transformed it so vibrant and raw that its horrors seemed to unfold directly in front of you

Viewing in front of the artwork, observers recognize this as a real face, an accurate depiction of a adolescent model, because the identical youth – identifiable by his tousled hair and almost black eyes – appears in two other paintings by the master. In every case, that richly expressive face dominates the composition. In John the Baptist, he peers mischievously from the darkness while holding a lamb. In Amor Vincit Omnia, he grins with a hardness acquired on Rome's streets, his dark plumed appendages sinister, a naked adolescent running riot in a affluent residence.

Amor Vincit Omnia, currently displayed at a British gallery, represents one of the most embarrassing masterpieces ever created. Viewers feel completely unsettled gazing at it. Cupid, whose darts inspire people with often agonizing longing, is shown as a very real, vividly lit nude form, straddling overturned objects that include stringed devices, a musical manuscript, metal armour and an architect's ruler. This heap of items echoes, deliberately, the mathematical and architectural gear scattered across the ground in Albrecht Dürer's print Melancholy – save here, the melancholic mess is created by this grinning Cupid and the turmoil he can unleash.

"Affection looks not with the eyes, but with the mind, / And therefore is winged Cupid painted blind," penned Shakespeare, shortly before this painting was created around the early 1600s. But Caravaggio's god is not unseeing. He stares directly at you. That face – ironic and rosy-faced, looking with bold confidence as he poses naked – is the identical one that screams in fear in Abraham's Test.

When the Italian master painted his three portrayals of the same unusual-appearing youth in Rome at the start of the 17th century, he was the most acclaimed religious painter in a city enflamed by religious renewal. The Sacrifice of Isaac demonstrates why he was commissioned to decorate churches: he could adopt a scriptural story that had been portrayed numerous times before and make it so fresh, so unfiltered and physical that the horror appeared to be happening directly before the spectator.

Yet there existed another aspect to the artist, apparent as quickly as he came in the capital in the cold season that ended 1592, as a painter in his initial 20s with no mentor or supporter in the city, just skill and audacity. The majority of the works with which he captured the holy city's eye were everything but holy. That may be the very earliest resides in the UK's National Gallery. A young man parts his red mouth in a scream of pain: while stretching out his dirty digits for a fruit, he has instead been bitten. Boy Bitten By a Lizard is sensuality amid squalor: observers can discern Caravaggio's gloomy room reflected in the cloudy waters of the glass vase.

The adolescent wears a pink flower in his hair – a emblem of the erotic commerce in Renaissance painting. Northern Italian painters such as Tiziano and Jacopo Palma depicted courtesans holding flowers and, in a painting lost in the second world war but known through images, Caravaggio represented a renowned woman courtesan, clutching a bouquet to her chest. The message of all these botanical signifiers is obvious: intimacy for sale.

What are we to make of Caravaggio's sensual depictions of boys – and of one boy in specific? It is a inquiry that has divided his interpreters since he achieved widespread recognition in the 1980s. The complex past truth is that the painter was not the homosexual hero that, for instance, the filmmaker presented on film in his twentieth-century movie about the artist, nor so completely pious that, as certain art historians unbelievably assert, his Boy With a Basket of Fruit is actually a likeness of Jesus.

His initial paintings indeed make overt sexual implications, or including offers. It's as if the painter, then a destitute youthful artist, aligned with the city's sex workers, selling himself to live. In the Florentine gallery, with this idea in mind, observers might look to another early creation, the sixteenth-century masterwork the god of wine, in which the god of alcohol gazes calmly at the spectator as he starts to untie the dark ribbon of his robe.

A several years after the wine deity, what could have motivated the artist to paint Amor Vincit Omnia for the artistic collector Vincenzo Giustiniani, when he was at last growing almost respectable with prestigious ecclesiastical projects? This unholy non-Christian deity resurrects the erotic provocations of his initial works but in a increasingly powerful, unsettling way. Half a century afterwards, its hidden meaning seemed obvious: it was a portrait of the painter's lover. A English visitor viewed the painting in about the mid-seventeenth century and was informed its subject has "the physique and countenance of [Caravaggio's|his] own boy or assistant that laid with him". The name of this adolescent was Cecco.

The painter had been dead for about forty annums when this account was documented.