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The youthful boy cries out as his skull is firmly gripped, a massive digit digging into his face as his parent's mighty palm grasps him by the neck. That moment from The Sacrifice of Isaac appears in the Florentine museum, evoking distress through Caravaggio's harrowing portrayal of the tormented youth from the scriptural narrative. It seems as if the patriarch, instructed by God to kill his son, could break his spinal column with a single twist. However Abraham's preferred approach involves the metallic grey blade he holds in his other hand, prepared to slit Isaac's throat. One certain aspect remains – whoever modeled as Isaac for this breathtaking work demonstrated remarkable acting ability. There exists not only dread, shock and pleading in his shadowed eyes but additionally deep grief that a guardian could abandon him so completely.

The artist took a familiar biblical story and made it so vibrant and raw that its terrors appeared to unfold right in view of the viewer

Viewing in front of the painting, viewers identify this as a real face, an precise record of a young subject, because the identical boy – identifiable by his tousled locks and nearly black pupils – appears in several other paintings by Caravaggio. In each instance, that richly expressive face commands the composition. In Youth With a Ram, he gazes playfully from the shadows while embracing a lamb. In Amor Vincit Omnia, he smirks with a toughness learned on Rome's streets, his dark feathery wings demonic, a naked adolescent creating chaos in a well-to-do residence.

Amor Vincit Omnia, currently displayed at a London museum, represents one of the most discomfiting masterpieces ever painted. Viewers feel completely unsettled looking at it. The god of love, whose darts fill people with often painful longing, is shown as a very tangible, brightly lit unclothed form, straddling toppled-over objects that include musical instruments, a music score, plate armor and an builder's T-square. This pile of items resembles, deliberately, the mathematical and architectural gear scattered across the floor in the German master's print Melencolia I – save in this case, the gloomy disorder is created by this smirking Cupid and the turmoil he can unleash.

"Affection sees not with the vision, but with the mind, / And thus is feathered Cupid painted sightless," penned Shakespeare, shortly before this work was produced around the early 1600s. But Caravaggio's Cupid is not unseeing. He gazes directly at the observer. That countenance – sardonic and rosy-cheeked, looking with bold assurance as he struts unclothed – is the identical one that screams in terror in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio created his three images of the same distinctive-looking kid in Rome at the dawn of the seventeenth century, he was the highly celebrated religious artist in a metropolis ignited by Catholic renewal. Abraham's Offering demonstrates why he was sought to adorn sanctuaries: he could adopt a scriptural narrative that had been depicted numerous times previously and make it so fresh, so unfiltered and physical that the horror appeared to be occurring immediately in front of the spectator.

Yet there existed another side to Caravaggio, apparent as soon as he came in Rome in the winter that ended the sixteenth century, as a painter in his initial twenties with no teacher or supporter in the city, only talent and boldness. Most of the works with which he caught the sacred city's eye were anything but holy. What could be the absolute earliest resides in the UK's National Gallery. A youth opens his red lips in a yell of agony: while reaching out his dirty digits for a cherry, he has instead been bitten. Youth Bitten by a Reptile is sensuality amid poverty: viewers can see the painter's dismal room mirrored in the cloudy liquid of the transparent vase.

The boy sports a pink flower in his hair – a emblem of the sex trade in early modern art. Northern Italian painters such as Tiziano and Jacopo Palma portrayed courtesans grasping flowers and, in a painting destroyed in the WWII but documented through photographs, the master portrayed a renowned woman prostitute, holding a posy to her bosom. The meaning of all these botanical indicators is obvious: sex for purchase.

What are we to make of the artist's sensual portrayals of youths – and of a particular boy in particular? It is a question that has divided his commentators since he achieved mega-fame in the 1980s. The complicated past truth is that the painter was neither the homosexual icon that, for example, Derek Jarman put on film in his 1986 film Caravaggio, nor so completely pious that, as some artistic scholars unbelievably claim, his Boy With a Basket of Fruit is actually a portrait of Christ.

His early paintings do make overt sexual suggestions, or even offers. It's as if the painter, then a penniless young creator, aligned with the city's prostitutes, offering himself to live. In the Florentine gallery, with this idea in mind, viewers might turn to another early work, the sixteenth-century masterwork Bacchus, in which the god of wine gazes coolly at you as he starts to untie the dark sash of his robe.

A several annums after the wine deity, what could have driven Caravaggio to create Victorious Cupid for the art collector Vincenzo Giustiniani, when he was finally growing nearly established with prestigious church projects? This profane non-Christian god revives the erotic challenges of his initial works but in a more powerful, unsettling manner. Fifty years later, its hidden meaning seemed clear: it was a portrait of Caravaggio's lover. A English traveller viewed the painting in about 1649 and was told its figure 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 deceased for about 40 years when this story was documented.