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A young boy cries out as his head is forcefully held, a large thumb pressing into his face as his parent's powerful hand grasps him by the throat. This scene from The Sacrifice of Isaac visits the Uffizi Gallery, creating unease through Caravaggio's chilling portrayal of the tormented child from the biblical account. The painting seems as if the patriarch, instructed by God to sacrifice his offspring, could snap his neck with a solitary twist. However the father's chosen method involves the silvery steel blade he holds in his remaining palm, ready to slit Isaac's neck. One definite element stands out – whomever modeled as the sacrifice for this astonishing work displayed extraordinary expressive ability. Within exists not only dread, surprise and begging in his darkened gaze but additionally deep sorrow that a guardian could abandon him so completely.

He took a familiar biblical tale and made it so fresh and visceral that its horrors appeared to happen directly in view of the viewer

Viewing before the artwork, viewers identify this as a actual countenance, an precise record of a adolescent model, because the identical boy – identifiable by his tousled locks and almost black pupils – features in two other paintings by Caravaggio. In every case, that richly expressive face dominates the scene. In Youth With a Ram, he peers playfully from the darkness while embracing a lamb. In Victorious Cupid, he grins with a hardness acquired on Rome's alleys, his dark feathery appendages sinister, a naked child running chaos in a affluent residence.

Victorious Cupid, currently exhibited at a London gallery, constitutes one of the most embarrassing masterpieces ever created. Observers feel completely unsettled looking at it. The god of love, whose arrows fill people with frequently painful longing, is shown as a very tangible, vividly lit nude figure, standing over toppled-over items that include musical instruments, a musical manuscript, plate armour and an builder's T-square. This heap of possessions echoes, intentionally, the mathematical and architectural equipment scattered across the floor in Albrecht Dürer's engraving Melancholy – except here, the gloomy disorder is created by this grinning deity and the turmoil he can unleash.

"Love sees not with the eyes, but with the mind, / And therefore is winged Love painted sightless," wrote Shakespeare, just before this painting was produced around the early 1600s. But the painter's Cupid is not unseeing. He stares directly at you. That countenance – sardonic and rosy-cheeked, staring with bold assurance as he poses unclothed – is the identical one that screams in fear in The Sacrifice of Isaac.

As the Italian master created his multiple images of the same distinctive-appearing youth in the Eternal City at the start of the 17th century, he was the most celebrated sacred painter in a city enflamed by religious revival. Abraham's Offering reveals why he was commissioned to adorn sanctuaries: he could take a scriptural story that had been portrayed many occasions previously and render it so new, so raw and physical that the terror appeared to be occurring immediately before the spectator.

However there was another aspect to Caravaggio, evident as soon as he arrived in the capital in the cold season that ended 1592, as a artist in his initial twenties with no teacher or patron in the city, only skill and audacity. The majority of the works with which he captured the holy metropolis's eye were anything but holy. That may be the absolute first resides in London's art museum. A young man parts his red lips in a yell of agony: while stretching out his filthy fingers for a cherry, he has rather been attacked. Boy Bitten By a Lizard is sensuality amid poverty: viewers can discern Caravaggio's dismal chamber mirrored in the murky liquid of the glass container.

The adolescent wears a pink blossom in his coiffure – a emblem of the erotic commerce in Renaissance art. Venetian painters such as Tiziano and Jacopo Palma portrayed prostitutes holding flowers and, in a work lost in the second world war but documented through images, Caravaggio portrayed a renowned female prostitute, clutching a posy to her bosom. The message of all these floral indicators is obvious: sex for purchase.

What are we to interpret of the artist's sensual portrayals of youths – and of a particular adolescent in particular? It is a question that has divided his interpreters ever since he achieved widespread recognition in the twentieth century. The complex past truth is that the painter was neither the queer icon that, for example, Derek Jarman put on film in his twentieth-century film about the artist, nor so entirely pious that, as some art scholars improbably assert, his Boy With a Basket of Fruit is actually a portrait of Jesus.

His early paintings indeed make explicit sexual suggestions, or even offers. It's as if Caravaggio, then a destitute young creator, aligned with Rome's sex workers, selling himself to survive. In the Florentine gallery, with this thought in mind, observers might look to an additional initial creation, the sixteenth-century masterpiece Bacchus, in which the god of wine stares calmly at you as he begins to undo the black sash of his robe.

A few years after the wine deity, what could have driven the artist to create Amor Vincit Omnia for the art collector Vincenzo Giustiniani, when he was at last becoming almost established with prestigious ecclesiastical projects? This unholy pagan god resurrects the sexual provocations of his initial works but in a increasingly powerful, uneasy manner. Fifty years afterwards, its hidden meaning seemed clear: it was a representation of the painter's companion. A English traveller viewed Victorious Cupid in about the mid-seventeenth century and was informed its figure has "the physique and countenance of [Caravaggio's|his] owne youth or servant that slept with him". The name of this adolescent was Cecco.

The artist had been dead for about forty annums when this account was recorded.