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The young boy screams as his head is firmly held, a large digit pressing into his face as his father's mighty palm grasps him by the neck. This scene from The Sacrifice of Isaac visits the Uffizi Gallery, evoking distress through the artist's chilling rendition of the tormented child from the biblical narrative. The painting seems as if the patriarch, commanded by God to sacrifice his son, could break his neck with a solitary turn. However Abraham's chosen approach involves the metallic steel knife he grips in his other palm, ready to slit Isaac's throat. A certain aspect stands out – whomever posed as Isaac for this breathtaking piece demonstrated extraordinary acting ability. Within exists not only dread, shock and begging in his darkened eyes but additionally profound sorrow that a protector could abandon him so completely.

The artist took a well-known scriptural tale and transformed it so fresh and visceral that its terrors seemed to happen directly in front of the viewer

Viewing in front of the painting, observers identify this as a actual countenance, an accurate record of a adolescent model, because the same youth – recognizable by his tousled hair and nearly dark eyes – appears in several additional paintings by the master. In each instance, that richly expressive visage commands the composition. In Youth With a Ram, he peers mischievously from the darkness while holding a lamb. In Victorious Cupid, he grins with a toughness acquired on the city's streets, his black plumed appendages demonic, a unclothed adolescent creating riot in a affluent dwelling.

Amor Vincit Omnia, currently displayed at a British museum, constitutes one of the most discomfiting masterpieces ever created. Viewers feel completely disoriented looking at it. The god of love, whose darts inspire people with frequently painful longing, is portrayed as a very tangible, brightly lit unclothed form, straddling overturned items that include stringed instruments, a music manuscript, plate armor and an architect's ruler. This pile of items echoes, deliberately, the geometric and architectural equipment strewn across the floor in Albrecht Dürer's engraving Melencolia I – except here, the gloomy disorder is created by this grinning Cupid and the mayhem he can release.

"Affection sees not with the vision, but with the soul, / And therefore is feathered Love depicted blind," wrote Shakespeare, just prior to this work was created around 1601. But Caravaggio's god is not blind. He stares directly at the observer. That face – sardonic and rosy-cheeked, staring with brazen assurance as he poses unclothed – is the identical one that screams in fear in The Sacrifice of Isaac.

When the Italian master created his multiple images of the identical unusual-appearing youth in the Eternal City at the dawn of the 17th century, he was the highly acclaimed sacred painter in a metropolis enflamed by Catholic renewal. The Sacrifice of Isaac demonstrates why he was sought to decorate churches: he could take a scriptural narrative that had been portrayed numerous occasions before and make it so fresh, so unfiltered and visceral that the terror seemed to be occurring directly in front of the spectator.

However there was another aspect to Caravaggio, evident as quickly as he came in the capital in the winter that concluded the sixteenth century, as a painter in his initial 20s with no teacher or patron in the city, only skill and boldness. The majority of the paintings with which he caught the sacred city's attention were everything but devout. What could be the absolute first hangs in the UK's National Gallery. A youth opens his crimson mouth in a scream of agony: while reaching out his filthy fingers for a fruit, he has rather been attacked. Boy Bitten By a Lizard is sensuality amid squalor: observers can discern the painter's dismal chamber mirrored in the cloudy liquid of the glass vase.

The adolescent wears a pink flower in his coiffure – a emblem of the sex trade in Renaissance art. Northern Italian artists such as Titian and Jacopo Palma portrayed courtesans holding blooms and, in a work lost in the second world war but documented through photographs, the master portrayed a renowned female courtesan, clutching a posy to her bosom. The meaning of all these floral indicators is obvious: sex for sale.

How are we to make of Caravaggio's sensual portrayals of boys – and of a particular boy in particular? It is a question that has split his commentators ever since he gained widespread recognition in the twentieth century. The complicated historical truth is that the painter was not the queer hero that, for instance, the filmmaker presented on film in his twentieth-century movie about the artist, nor so entirely devout that, as some artistic historians improbably claim, his Youth Holding Fruit is in fact a portrait of Jesus.

His early works indeed offer overt sexual suggestions, or including offers. It's as if the painter, then a destitute youthful artist, aligned with the city's sex workers, offering himself to live. In the Florentine gallery, with this thought in mind, observers might look to an additional early work, the 1596 masterpiece Bacchus, in which the god of alcohol stares coolly at you as he starts to untie the black ribbon of his garment.

A few annums after the wine deity, what could have driven Caravaggio to create Victorious Cupid for the artistic collector the nobleman, when he was at last becoming almost established with prestigious church projects? This profane non-Christian deity revives the erotic challenges of his initial works but in a increasingly powerful, unsettling way. Half a century afterwards, its secret seemed clear: it was a representation of Caravaggio's lover. A British visitor viewed the painting in about 1649 and was told its figure has "the physique and countenance of [Caravaggio's|his] own youth or assistant that laid with him". The identity of this adolescent was Francesco.

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