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The young boy cries out as his head is forcefully held, a massive thumb digging into his cheek as his father's mighty hand holds him by the neck. That moment from The Sacrifice of Isaac appears in the Florentine museum, evoking unease through Caravaggio's harrowing portrayal of the suffering child from the biblical narrative. The painting appears as if the patriarch, commanded by God to kill his offspring, could snap his neck with a solitary twist. However the father's chosen approach involves the silvery grey blade he grips in his other palm, prepared to cut Isaac's throat. One definite element stands out – whoever modeled as the sacrifice for this astonishing piece displayed extraordinary acting skill. There exists not just fear, shock and begging in his darkened eyes but additionally profound sorrow that a guardian could abandon him so utterly.

He adopted a familiar biblical tale and transformed it so fresh and raw that its horrors appeared to unfold right in front of you

Viewing in front of the painting, observers recognize this as a actual face, an accurate depiction of a young subject, because the same youth – identifiable by his disheveled hair and almost dark pupils – features in several additional paintings by the master. In each instance, that richly expressive visage dominates the composition. In Youth With a Ram, he gazes mischievously from the darkness while embracing a ram. In Amor Vincit Omnia, he smirks with a toughness acquired on Rome's alleys, his black feathery appendages sinister, a unclothed adolescent running riot in a well-to-do residence.

Victorious Cupid, currently exhibited at a London gallery, represents one of the most discomfiting masterpieces ever painted. Observers feel totally unsettled looking at it. The god of love, whose arrows fill people with frequently painful desire, is portrayed as a very real, brightly illuminated unclothed figure, standing over overturned items that include stringed instruments, a musical score, metal armor and an builder's T-square. This heap of possessions echoes, deliberately, the mathematical and architectural equipment strewn across the floor in the German master's print Melancholy – save in this case, the gloomy mess is created by this smirking deity and the turmoil he can unleash.

"Affection looks not with the eyes, but with the mind, / And therefore is winged Love depicted sightless," wrote Shakespeare, just before this work was produced around the early 1600s. But Caravaggio's Cupid is not blind. He stares directly at you. That face – ironic and rosy-cheeked, looking with brazen confidence as he poses naked – is the same one that screams in fear in The Sacrifice of Isaac.

As the Italian master created his three images of the identical unusual-appearing youth in Rome at the dawn of the seventeenth century, he was the most acclaimed religious painter in a city enflamed by Catholic renewal. The Sacrifice of Isaac reveals why he was sought to adorn sanctuaries: he could adopt a biblical narrative that had been depicted many times before and render it so fresh, so unfiltered and physical that the horror seemed to be happening immediately in front of the spectator.

Yet there was a different side to the artist, apparent as quickly as he came in Rome in the winter that ended 1592, as a artist in his early twenties with no mentor or supporter in the city, only skill and boldness. Most of the paintings with which he captured the sacred metropolis's eye were everything but devout. What may be the absolute first resides in London's art museum. A young man opens his crimson 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 eroticism amid squalor: viewers can see the painter's gloomy chamber reflected in the cloudy liquid of the glass container.

The boy sports a pink flower in his hair – a symbol of the erotic commerce in Renaissance painting. Northern Italian artists such as Tiziano and Jacopo Palma depicted courtesans holding flowers and, in a work lost in the WWII but known through images, the master represented a famous female courtesan, holding a bouquet to her bosom. The message of all these botanical signifiers is clear: intimacy for sale.

What are we to make of Caravaggio's sensual portrayals of youths – and of one adolescent in specific? It is a question that has divided his interpreters ever since he gained mega-fame in the 1980s. The complicated past reality is that the painter was neither the queer icon that, for instance, the filmmaker put on film in his twentieth-century movie Caravaggio, nor so completely pious that, as some art scholars improbably claim, his Boy With a Basket of Fruit is in fact a likeness of Christ.

His early works do offer overt sexual suggestions, or even offers. It's as if Caravaggio, then a destitute youthful creator, aligned with the city's prostitutes, offering himself to survive. In the Uffizi, with this thought in consideration, observers might look to another early creation, the sixteenth-century masterwork Bacchus, in which the deity of alcohol stares coolly at you as he begins to undo the black sash of his robe.

A few annums following Bacchus, what could have motivated Caravaggio to paint Amor Vincit Omnia for the artistic collector Vincenzo Giustiniani, when he was finally growing nearly respectable with important church projects? This profane pagan deity resurrects the sexual challenges of his early works but in a increasingly powerful, uneasy manner. Fifty years afterwards, its hidden meaning seemed clear: it was a representation of the painter's lover. A British traveller saw the painting in about 1649 and was informed its figure has "the physique and countenance of [Caravaggio's|his] own boy or servant that slept with him". The identity of this adolescent was Cecco.

The artist had been deceased for about forty annums when this account was documented.