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The young boy cries out as his head is forcefully gripped, a large digit digging into his face as his parent's mighty hand holds him by the throat. This scene from Abraham's Sacrifice visits the Uffizi Gallery, creating distress through the artist's chilling portrayal of the suffering youth from the scriptural account. The painting appears as if Abraham, commanded by the Divine to sacrifice his offspring, could break his spinal column with a solitary twist. However the father's preferred approach involves the silvery steel knife he holds in his other palm, ready to cut Isaac's neck. A definite aspect remains – whomever modeled as the sacrifice for this astonishing piece displayed extraordinary expressive ability. Within exists not only fear, shock and begging in his shadowed gaze but also profound sorrow that a protector could abandon him so utterly.

The artist adopted a familiar scriptural story and made it so fresh and raw that its terrors appeared to happen right in view of the viewer

Viewing in front of the artwork, observers identify this as a real countenance, an accurate record of a adolescent model, because the identical youth – identifiable by his tousled hair and nearly dark eyes – features in several additional works by Caravaggio. In every instance, that highly emotional visage commands the scene. In Youth With a Ram, he peers mischievously from the darkness while embracing a ram. In Victorious Cupid, he grins with a toughness learned on the city's alleys, his black feathery wings sinister, a naked child running riot in a affluent residence.

Victorious Cupid, presently exhibited at a British museum, represents one of the most discomfiting masterpieces ever painted. Observers feel totally disoriented looking at it. Cupid, whose arrows fill people with often painful longing, is shown as a very real, vividly lit unclothed form, standing over overturned objects that include musical devices, a music score, metal armor and an architect's T-square. This heap of possessions resembles, intentionally, the geometric and construction gear strewn across the floor in the German master's engraving Melencolia I – except here, the gloomy disorder is created by this grinning Cupid and the turmoil he can release.

"Affection looks not with the vision, but with the mind, / And therefore is winged Cupid depicted blind," penned the Bard, shortly before this painting was produced around the early 1600s. But Caravaggio's god is not blind. He gazes directly at the observer. That face – sardonic and ruddy-faced, looking with brazen assurance as he struts unclothed – is the identical one that shrieks in terror in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio created his three images of the identical unusual-looking youth in the Eternal City at the start of the seventeenth century, he was the most acclaimed religious painter in a city enflamed by religious revival. Abraham's Offering reveals why he was sought to decorate sanctuaries: he could take a biblical story that had been depicted numerous times before and make it so fresh, so raw and physical that the horror seemed to be happening immediately before the spectator.

Yet there existed a different aspect to Caravaggio, apparent as soon as he came in Rome in the winter that ended the sixteenth century, as a artist in his initial 20s with no mentor or patron in the city, only skill and audacity. The majority of the works with which he caught the sacred city's attention were anything but holy. What could be the absolute earliest hangs in the UK's National Gallery. A youth parts his crimson lips in a scream of pain: while reaching out his dirty digits for a cherry, he has instead been attacked. Youth Bitten by a Reptile is sensuality amid poverty: viewers can see the painter's dismal room mirrored in the murky waters of the transparent container.

The boy wears a pink flower in his coiffure – a symbol of the sex commerce in Renaissance painting. Venetian artists such as Titian and Jacopo Palma depicted prostitutes grasping flowers and, in a painting lost in the second world war but known through images, Caravaggio represented a famous female courtesan, holding a bouquet to her bosom. The meaning of all these botanical signifiers is clear: sex for sale.

How are we to interpret of the artist's erotic portrayals of boys – and of one adolescent in particular? It is a question that has divided his interpreters since he achieved widespread recognition in the twentieth century. The complicated past truth is that the artist was not the queer icon that, for example, the filmmaker put on screen in his 1986 film about the artist, nor so completely devout that, as some artistic historians unbelievably claim, his Boy With a Basket of Fruit is in fact a portrait of Jesus.

His early paintings do offer explicit sexual suggestions, or including propositions. It's as if the painter, then a penniless young artist, aligned with the city's prostitutes, offering himself to survive. In the Uffizi, with this thought in consideration, viewers might look to an additional initial work, the 1596 masterpiece the god of wine, in which the god of wine gazes calmly at the spectator as he starts to untie the black sash of his garment.

A few annums after Bacchus, what could have motivated Caravaggio to create Victorious Cupid for the artistic patron Vincenzo Giustiniani, when he was finally becoming almost respectable with prestigious ecclesiastical projects? This profane non-Christian god revives the sexual challenges of his initial paintings but in a more intense, uneasy manner. Half a century later, its secret seemed obvious: it was a portrait of Caravaggio's lover. A British traveller viewed the painting in about the mid-seventeenth century and was told its figure has "the physique and countenance of [Caravaggio's|his] own youth or assistant that slept with him". The identity of this boy was Cecco.

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