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The young lad screams while his skull is firmly held, a large thumb digging into his cheek as his father's mighty hand holds him by the throat. This moment from The Sacrifice of Isaac visits the Uffizi Gallery, creating unease through Caravaggio's harrowing portrayal of the suffering child from the biblical narrative. The painting appears as if Abraham, instructed by the Divine to kill his son, could snap his spinal column with a solitary turn. However Abraham's chosen method involves the silvery grey blade he holds in his remaining hand, prepared to cut the boy's neck. A certain aspect stands out – whomever posed as the sacrifice for this astonishing piece displayed remarkable acting ability. There exists not just fear, surprise and begging in his shadowed eyes but also deep grief that a guardian could abandon him so utterly.

He took a well-known scriptural story and transformed it so fresh and raw that its terrors seemed to unfold right in view of you

Standing before the painting, viewers recognize this as a actual face, an precise record of a adolescent subject, because the same boy – identifiable by his disheveled locks and nearly black eyes – appears in two additional works by the master. In each case, that highly expressive face dominates the composition. In Youth With a Ram, he peers mischievously from the darkness while holding a lamb. In Victorious Cupid, he smirks with a hardness acquired on Rome's alleys, his dark feathery wings demonic, a naked adolescent creating chaos in a well-to-do dwelling.

Amor Vincit Omnia, presently displayed at a London gallery, represents one of the most discomfiting masterpieces ever painted. Viewers feel completely unsettled looking at it. The god of love, whose arrows fill people with often painful longing, is shown as a extremely tangible, vividly illuminated nude form, standing over overturned objects that include musical devices, a musical score, metal armor and an architect's ruler. This heap of items echoes, deliberately, the mathematical and architectural gear scattered across the ground in the German master's engraving Melencolia I – save here, the melancholic mess is caused by this smirking Cupid and the mayhem he can release.

"Affection looks not with the eyes, but with the soul, / And therefore is feathered Love painted sightless," wrote the Bard, shortly prior to this work was created around the early 1600s. But Caravaggio's Cupid is not blind. He gazes directly at you. That countenance – ironic and rosy-faced, staring with brazen assurance as he poses naked – is the same one that shrieks in terror in Abraham's Test.

As the Italian master painted his three portrayals of the same unusual-looking youth in the Eternal City at the start of the 17th century, he was the highly celebrated religious painter in a city ignited by Catholic revival. Abraham's Offering demonstrates why he was commissioned to adorn churches: he could take a biblical narrative that had been depicted many occasions previously and render it so new, so unfiltered and visceral that the horror appeared to be occurring immediately before the spectator.

However there existed a different side to Caravaggio, apparent as soon as he came in Rome in the winter that concluded 1592, as a artist in his early 20s with no teacher or supporter in the city, only talent and audacity. Most of the paintings with which he captured the sacred metropolis's eye were everything but holy. That could be the absolute earliest hangs in London's art museum. A young man opens his red lips in a yell of agony: while reaching out his filthy digits for a fruit, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid squalor: viewers can see the painter's dismal chamber mirrored in the murky waters of the glass vase.

The adolescent wears a pink flower in his coiffure – a symbol of the erotic commerce in early modern painting. Venetian artists such as Titian and Jacopo Palma depicted courtesans holding blooms and, in a painting destroyed in the WWII but known through images, the master represented a renowned female courtesan, holding a posy to her chest. The message of all these floral signifiers is clear: intimacy for purchase.

How are we to make of Caravaggio's sensual depictions of youths – and of a particular adolescent in specific? It is a inquiry that has divided his commentators since he achieved mega-fame in the twentieth century. The complex historical reality is that the painter was neither the queer icon that, for example, Derek Jarman put on screen in his twentieth-century movie Caravaggio, nor so entirely devout that, as certain artistic scholars unbelievably claim, his Youth Holding Fruit is in fact a portrait of Jesus.

His early works do offer explicit erotic implications, or even propositions. It's as if the painter, then a destitute young artist, identified with the city's sex workers, selling himself to survive. In the Uffizi, with this idea in mind, viewers might turn to another initial work, the sixteenth-century masterwork the god of wine, in which the god of wine gazes calmly at the spectator as he begins to undo the black sash of his robe.

A several annums following the wine deity, what could have motivated the artist to create Victorious Cupid for the artistic collector Vincenzo Giustiniani, when he was finally becoming nearly respectable with important ecclesiastical projects? This unholy pagan god revives the sexual provocations of his initial works but in a more powerful, unsettling manner. Half a century afterwards, its secret seemed clear: it was a representation of Caravaggio's lover. A English visitor saw the painting in about the mid-seventeenth century and was told its subject has "the physique and countenance of [Caravaggio's|his] owne boy or servant that laid with him". The name of this adolescent was Francesco.

The painter had been deceased for about 40 years when this account was documented.