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A young boy cries out while his skull is firmly held, a large thumb digging into his face as his father's mighty palm holds him by the throat. This scene from The Sacrifice of Isaac visits the Uffizi Gallery, creating unease through Caravaggio's harrowing rendition of the tormented child from the biblical narrative. It seems as if Abraham, commanded by the Divine to kill his son, could snap his spinal column with a solitary turn. Yet Abraham's preferred approach involves the metallic steel knife he holds in his other palm, ready to slit Isaac's neck. One certain aspect remains – whoever posed as the sacrifice for this breathtaking piece demonstrated remarkable expressive ability. There exists not only dread, shock and begging in his shadowed eyes but also deep grief that a guardian could abandon him so completely.

He adopted a well-known scriptural story and made it so vibrant and raw that its terrors appeared to happen right in view of you

Viewing in front of the artwork, observers recognize this as a actual face, an accurate depiction of a adolescent subject, because the same boy – recognizable by his disheveled hair and almost dark pupils – features in several other works by Caravaggio. In each case, that highly expressive face dominates the scene. In Youth With a Ram, he peers mischievously from the darkness while holding a ram. In Amor Vincit Omnia, he grins with a hardness acquired on Rome's alleys, his dark feathery appendages sinister, a naked adolescent creating chaos in a well-to-do residence.

Amor Vincit Omnia, presently 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 frequently painful desire, is shown as a extremely tangible, vividly lit unclothed form, straddling overturned objects that include stringed instruments, a music manuscript, metal armour and an architect's T-square. This heap of possessions resembles, intentionally, the mathematical and architectural gear scattered across the ground in Albrecht Dürer's engraving Melencolia I – save here, the gloomy disorder is caused by this grinning Cupid and the turmoil he can unleash.

"Affection looks not with the eyes, but with the mind, / And thus is feathered Love depicted sightless," wrote the Bard, just before this work was produced around the early 1600s. But the painter's Cupid is not unseeing. He gazes directly at you. That countenance – sardonic and ruddy-cheeked, looking with bold assurance as he poses unclothed – is the same one that shrieks in terror in Abraham's Test.

When Michelangelo Merisi da Caravaggio painted his three images of the identical unusual-appearing kid in Rome at the dawn of the seventeenth century, he was the most acclaimed sacred artist in a city ignited by Catholic revival. The Sacrifice of Isaac demonstrates why he was commissioned to decorate churches: he could take a scriptural narrative that had been portrayed numerous occasions previously and make it so new, so unfiltered and visceral that the terror seemed to be happening immediately before you.

Yet there was another side to Caravaggio, apparent as soon as he came in Rome in the cold season that concluded 1592, as a painter in his early 20s with no teacher or supporter in the urban center, only talent and boldness. Most of the paintings with which he caught the sacred city's attention were everything but holy. That could be the absolute earliest hangs in London's art museum. A youth parts his red lips in a yell of agony: while reaching out his filthy fingers for a cherry, he has instead been attacked. Youth Bitten by a Reptile is eroticism amid poverty: viewers can discern the painter's dismal chamber mirrored in the cloudy waters of the glass container.

The boy wears a pink flower in his coiffure – a symbol of the sex trade in Renaissance art. Northern Italian artists such as Titian and Jacopo Palma portrayed courtesans grasping flowers and, in a painting lost in the WWII but documented through images, Caravaggio represented a famous woman prostitute, clutching a posy to her bosom. The meaning of all these floral signifiers is clear: intimacy for purchase.

What are we to make of Caravaggio's erotic portrayals of boys – and of a particular adolescent in particular? It is a question that has divided his commentators ever since he achieved widespread recognition in the twentieth century. The complex past reality is that the artist was neither the queer hero that, for example, Derek Jarman put on screen in his twentieth-century movie Caravaggio, nor so entirely devout that, as certain artistic scholars improbably claim, his Boy With a Basket of Fruit is actually a portrait of Jesus.

His initial works indeed offer overt erotic suggestions, or even offers. It's as if the painter, then a destitute young creator, identified with Rome's prostitutes, offering himself to survive. In the Uffizi, with this thought in consideration, viewers might turn to an additional initial work, the 1596 masterwork Bacchus, in which the deity of wine stares calmly at the spectator as he starts to undo the black sash of his garment.

A few years after Bacchus, what could have driven Caravaggio to paint Victorious Cupid for the artistic collector the nobleman, when he was finally growing almost respectable with prestigious ecclesiastical commissions? This unholy pagan god revives the erotic challenges of his early works but in a increasingly intense, uneasy way. Half a century later, its secret seemed obvious: it was a portrait of Caravaggio's lover. A English traveller saw Victorious Cupid in about the mid-seventeenth century and was informed its subject has "the physique and countenance of [Caravaggio's|his] owne youth or assistant that slept with him". The name of this adolescent was Cecco.

The painter had been deceased for about forty years when this story was recorded.