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A young boy screams while his skull is forcefully held, a large thumb digging into his cheek as his parent's powerful palm grasps him by the throat. This moment from The Sacrifice of Isaac visits the Florentine museum, creating unease through the artist's chilling portrayal of the suffering child from the biblical account. The painting seems as if the patriarch, instructed by the Divine to sacrifice his offspring, could break his neck with a solitary turn. Yet the father's chosen approach involves the metallic grey blade he grips in his remaining hand, prepared to cut Isaac's neck. One definite aspect stands out – whoever posed as Isaac for this astonishing work displayed remarkable acting skill. Within exists not only dread, surprise and pleading in his darkened eyes but also deep grief that a guardian could abandon him so completely.

He took a well-known scriptural tale and transformed it so vibrant and raw that its terrors appeared to unfold right in view of you

Standing before the artwork, viewers identify this as a real countenance, an accurate record of a young subject, because the identical boy – recognizable by his disheveled locks and almost black eyes – features in several other works by Caravaggio. In every instance, that highly expressive visage commands the composition. In John the Baptist, he gazes mischievously from the shadows while holding a ram. In Victorious Cupid, he smirks with a toughness learned on Rome's streets, his black feathery wings demonic, a unclothed child creating riot in a affluent dwelling.

Victorious Cupid, currently displayed at a London museum, represents one of the most discomfiting artworks ever created. Viewers feel completely disoriented looking at it. Cupid, whose darts fill people with frequently agonizing longing, is shown as a extremely real, brightly illuminated nude figure, standing over overturned items that include musical instruments, a musical score, plate armour and an builder's T-square. This heap of items echoes, deliberately, the mathematical and architectural equipment strewn across the ground in the German master's print Melancholy – save in this case, the gloomy mess is created by this grinning Cupid and the turmoil he can release.

"Love looks not with the eyes, but with the mind, / And therefore is winged Cupid depicted sightless," wrote Shakespeare, just prior to this work was produced around 1601. But the painter's god is not unseeing. He gazes straight at the observer. That face – sardonic and ruddy-cheeked, looking with brazen confidence as he poses unclothed – is the identical one that screams in terror in The Sacrifice of Isaac.

When the Italian master created his three images of the identical unusual-appearing youth in Rome at the start of the 17th century, he was the most acclaimed religious artist in a city ignited by Catholic revival. The Sacrifice of Isaac demonstrates why he was sought to adorn churches: he could adopt a scriptural narrative that had been portrayed numerous times previously and make it so new, so raw and visceral that the terror seemed to be happening immediately before you.

However there was another aspect to Caravaggio, evident as soon as he arrived in the capital in the winter that concluded the sixteenth century, as a painter in his initial twenties with no mentor or supporter in the urban center, only skill and audacity. The majority of the paintings with which he captured the holy metropolis's eye were everything but devout. What could be the very first hangs in the UK's National Gallery. A young man parts his red mouth in a yell of agony: while stretching out his filthy fingers for a fruit, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid squalor: viewers can see the painter's gloomy chamber mirrored in the cloudy waters of the glass container.

The adolescent wears a pink blossom in his hair – a emblem of the sex commerce in Renaissance art. Northern Italian artists such as Titian and Palma Vecchio portrayed prostitutes holding blooms and, in a painting lost in the second world war but known through images, the master portrayed a famous woman prostitute, holding a bouquet to her bosom. The message of all these botanical indicators is obvious: intimacy for sale.

How are we to make of Caravaggio's sensual depictions of youths – and of one boy in particular? It is a inquiry that has divided his commentators ever since he gained mega-fame in the 1980s. The complicated past truth is that the artist was neither the homosexual icon that, for instance, the filmmaker presented on film in his 1986 movie about the artist, nor so completely pious that, as certain artistic scholars improbably claim, his Youth Holding Fruit is in fact a portrait of Christ.

His initial paintings do offer explicit sexual implications, or even propositions. It's as if Caravaggio, then a destitute youthful artist, aligned with Rome's prostitutes, offering himself to live. In the Uffizi, with this idea in consideration, observers might look to an additional early work, the 1596 masterpiece the god of wine, in which the deity of alcohol stares coolly at the spectator as he starts to undo the dark ribbon of his garment.

A several years after the wine deity, what could have motivated Caravaggio to paint Amor Vincit Omnia for the artistic patron the nobleman, when he was finally growing nearly respectable with important church commissions? This unholy non-Christian god revives the sexual challenges of his initial paintings but in a increasingly intense, uneasy way. Fifty years later, its secret seemed clear: 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 subject has "the physique and countenance of [Caravaggio's|his] owne youth or servant that laid with him". The identity of this adolescent was Cecco.

The artist had been dead for about 40 annums when this story was documented.