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A youthful lad cries out as his skull is firmly held, a large digit digging into his face as his father's mighty palm holds him by the throat. That scene from Abraham's Sacrifice visits the Uffizi Gallery, creating distress through Caravaggio's chilling portrayal of the tormented youth from the scriptural narrative. The painting appears as if the patriarch, instructed by God to kill his son, could snap his spinal column with a solitary twist. Yet the father's chosen approach involves the silvery steel blade he grips in his remaining palm, ready to slit Isaac's neck. One certain element stands out – whoever modeled as Isaac for this astonishing work demonstrated remarkable acting skill. Within exists not just dread, surprise and begging in his shadowed gaze but additionally profound grief that a guardian could betray him so utterly.

The artist adopted a familiar scriptural story and transformed it so fresh and visceral that its horrors appeared to unfold right in view of the viewer

Viewing before the painting, viewers identify this as a actual countenance, an accurate record of a adolescent model, because the same youth – recognizable by his tousled hair and almost dark pupils – appears in two additional paintings by Caravaggio. In each instance, that richly expressive face dominates the composition. In John the Baptist, he gazes mischievously from the darkness while holding a ram. In Amor Vincit Omnia, he smirks with a hardness learned on the city's alleys, his black plumed appendages sinister, a unclothed child running chaos in a well-to-do dwelling.

Victorious Cupid, currently exhibited at a British gallery, represents one of the most discomfiting artworks ever created. Observers feel completely disoriented gazing at it. The god of love, whose arrows inspire people with often agonizing desire, is portrayed as a extremely tangible, brightly illuminated nude figure, straddling toppled-over objects that comprise stringed instruments, a music score, plate armour and an builder's T-square. This heap of items echoes, intentionally, the mathematical and construction gear strewn across the floor in the German master's print Melencolia I – save in this case, the melancholic disorder is caused by this smirking deity and the mayhem he can unleash.

"Affection sees not with the eyes, but with the mind, / And therefore is winged Love depicted sightless," penned Shakespeare, just prior to this painting was produced around 1601. But Caravaggio's Cupid is not unseeing. He stares straight at you. That countenance – sardonic and ruddy-faced, staring with brazen assurance as he struts unclothed – is the same one that screams in terror in The Sacrifice of Isaac.

As the Italian master created his multiple portrayals of the same distinctive-appearing youth in Rome at the start of the 17th century, he was the most acclaimed religious artist in a metropolis ignited by Catholic revival. Abraham's Offering reveals why he was commissioned to adorn sanctuaries: he could adopt a biblical story that had been portrayed numerous occasions previously and make it so new, so unfiltered and physical that the horror appeared to be occurring immediately before you.

However there was a different side to the artist, evident as soon as he came in Rome in the winter that ended the sixteenth century, as a artist in his early twenties with no teacher or supporter in the urban center, just skill and audacity. The majority of the works with which he captured the sacred city's eye were everything but holy. What could be the absolute earliest resides in London's National Gallery. A youth parts his crimson mouth in a scream of agony: while stretching out his filthy digits for a fruit, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid squalor: observers can see the painter's gloomy room mirrored in the murky waters of the glass container.

The adolescent sports a pink blossom in his hair – a symbol of the erotic trade in early modern painting. Northern Italian painters such as Tiziano and Palma Vecchio portrayed courtesans holding flowers and, in a work destroyed in the WWII but documented through images, Caravaggio represented a renowned woman prostitute, clutching a posy to her chest. The message of all these botanical indicators is clear: intimacy for purchase.

How are we to interpret of Caravaggio's erotic portrayals of youths – and of one adolescent in particular? It is a question that has divided his commentators ever since he gained widespread recognition in the 1980s. The complicated historical reality is that the artist was not the queer icon that, for instance, Derek Jarman presented on screen in his twentieth-century film about the artist, nor so entirely pious that, as certain artistic scholars unbelievably assert, his Youth Holding Fruit is in fact a portrait of Christ.

His early works indeed make overt erotic suggestions, or even offers. It's as if Caravaggio, then a penniless youthful artist, aligned with Rome's prostitutes, offering himself to survive. In the Uffizi, with this idea in consideration, observers might look to another initial work, the sixteenth-century masterpiece the god of wine, in which the god of wine stares coolly at the spectator as he starts to undo the black ribbon of his garment.

A several annums following the wine deity, what could have motivated the artist to paint Victorious Cupid for the artistic patron the nobleman, when he was at last growing almost respectable with prestigious church projects? This unholy pagan deity resurrects the sexual challenges of his initial paintings but in a more intense, unsettling way. Fifty years afterwards, its secret seemed obvious: it was a representation of Caravaggio's lover. A British traveller saw the painting in about the mid-seventeenth century and was told its subject has "the body & face of [Caravaggio's|his] own boy or servant that slept with him". The name of this adolescent was Francesco.

The painter had been dead for about 40 years when this story was documented.