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The youthful lad cries out as his head is firmly held, a massive digit pressing into his cheek as his father's powerful palm grasps him by the neck. This moment from The Sacrifice of Isaac appears in the Uffizi Gallery, creating distress through Caravaggio's harrowing portrayal of the suffering child from the biblical account. The painting seems as if the patriarch, instructed by the Divine to kill his offspring, could snap his neck with a solitary turn. Yet the father's preferred approach involves the metallic grey knife he grips in his remaining palm, ready to cut Isaac's neck. A definite element stands out – whomever posed as Isaac for this breathtaking piece demonstrated extraordinary expressive ability. There exists not just dread, surprise and pleading in his shadowed gaze but additionally deep sorrow that a guardian could abandon him so utterly.

The artist adopted a familiar biblical story and transformed it so fresh and visceral that its terrors appeared to unfold directly in front of you

Viewing before the painting, observers recognize this as a real countenance, an accurate depiction of a adolescent subject, because the identical youth – identifiable by his disheveled hair and almost dark eyes – appears in two additional works by the master. In every case, that highly expressive visage commands the composition. In John the Baptist, he gazes playfully from the darkness while holding a lamb. In Amor Vincit Omnia, he grins with a hardness learned on the city's streets, his dark feathery wings demonic, a naked adolescent creating riot in a affluent dwelling.

Victorious Cupid, currently displayed at a London gallery, represents one of the most embarrassing masterpieces ever created. Observers feel completely disoriented looking at it. The god of love, whose arrows inspire people with frequently agonizing longing, is shown as a extremely real, vividly lit unclothed figure, standing over overturned items that include musical devices, a music manuscript, metal armour and an architect's ruler. This pile of items echoes, intentionally, the geometric and construction equipment strewn across the ground in Albrecht Dürer's engraving Melencolia I – save here, the melancholic disorder is created by this grinning deity and the mayhem he can release.

"Affection looks not with the eyes, but with the soul, / And thus is feathered Love depicted blind," wrote Shakespeare, shortly before this work was produced around the early 1600s. But the painter's Cupid is not blind. He gazes directly at you. That face – sardonic and rosy-cheeked, looking with brazen assurance as he poses unclothed – is the identical one that screams in fear in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio created his multiple portrayals of the identical unusual-looking kid in Rome at the start of the 17th century, he was the most celebrated religious painter in a metropolis enflamed by Catholic renewal. The Sacrifice of Isaac demonstrates why he was commissioned to decorate churches: he could take a biblical narrative that had been portrayed numerous occasions before and render it so fresh, so raw and visceral that the terror appeared to be occurring directly before the spectator.

However there was another side to Caravaggio, evident as quickly as he arrived in the capital in the cold season that concluded 1592, as a painter in his initial 20s with no mentor or patron in the city, only talent and boldness. Most of the works with which he captured the sacred metropolis's attention were everything but devout. That may be the absolute first resides in the UK's art museum. A youth parts his crimson mouth in a scream of agony: while stretching out his dirty digits for a cherry, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid squalor: observers can discern Caravaggio's gloomy room reflected in the cloudy waters of the glass vase.

The boy sports a rose-colored flower in his hair – a symbol of the erotic trade in Renaissance art. Venetian artists such as Titian and Palma Vecchio depicted prostitutes holding blooms and, in a painting destroyed in the second world war but known through images, the master portrayed a famous woman prostitute, clutching a bouquet to her bosom. The message of all these floral indicators is clear: intimacy for sale.

How are we to interpret of Caravaggio's erotic portrayals of youths – and of a particular boy in particular? It is a inquiry that has split his interpreters since he achieved widespread recognition in the 1980s. The complicated past truth is that the painter was not the queer hero that, for example, Derek Jarman presented on screen in his twentieth-century movie about the artist, nor so completely devout that, as some art scholars improbably claim, his Youth Holding Fruit is actually a likeness of Christ.

His early paintings do offer overt sexual suggestions, or even propositions. It's as if the painter, then a penniless young creator, identified with Rome's prostitutes, selling himself to survive. In the Uffizi, with this thought in mind, observers might look to another early work, the 1596 masterwork Bacchus, in which the deity of wine gazes calmly at you as he begins to undo the black ribbon of his robe.

A several annums following the wine deity, what could have motivated the artist to create Amor Vincit Omnia for the art patron Vincenzo Giustiniani, when he was at last growing nearly established with important ecclesiastical commissions? This unholy pagan god resurrects the erotic provocations of his initial paintings but in a more intense, uneasy way. Fifty years afterwards, its hidden meaning seemed clear: it was a representation of the painter's lover. A English visitor saw the painting in about 1649 and was told its figure has "the physique and countenance of [Caravaggio's|his] owne boy or servant that laid with him". The identity of this boy was Francesco.

The artist had been dead for about 40 years when this account was documented.