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A young lad cries out while his head is forcefully held, a large thumb pressing into his face as his parent's mighty palm grasps him by the throat. This scene from The Sacrifice of Isaac visits the Uffizi Gallery, creating unease through Caravaggio's harrowing portrayal of the tormented youth from the biblical account. It appears as if Abraham, instructed by the Divine to sacrifice his son, could break his spinal column with a single twist. Yet Abraham's preferred method involves the silvery steel blade he grips in his remaining hand, ready to slit the boy's neck. One certain element remains – whoever posed as Isaac for this breathtaking piece displayed remarkable acting ability. There exists not only fear, shock and begging in his darkened eyes but also profound sorrow that a guardian could abandon him so completely.

The artist adopted a well-known biblical tale and made it so fresh and visceral that its horrors seemed to happen directly in front of you

Standing in front of the painting, observers identify this as a actual countenance, an precise depiction of a young subject, because the identical boy – recognizable by his disheveled locks and almost black eyes – appears in two additional paintings by the master. In every case, that highly expressive visage commands the scene. In Youth With a Ram, he gazes playfully from the shadows while holding a ram. In Victorious Cupid, he grins with a hardness acquired on Rome's alleys, his dark plumed appendages demonic, a naked child running riot in a well-to-do dwelling.

Victorious Cupid, currently displayed at a British museum, constitutes one of the most embarrassing artworks ever painted. Viewers feel completely disoriented gazing at it. The god of love, whose arrows inspire people with frequently painful longing, is shown as a very tangible, brightly illuminated unclothed figure, straddling overturned items that include stringed devices, a musical score, metal armour and an builder's T-square. This heap of items resembles, deliberately, the mathematical and construction equipment strewn across the ground in Albrecht Dürer's print Melencolia I – save here, the melancholic disorder is caused by this smirking deity and the mayhem he can unleash.

"Love sees not with the vision, but with the soul, / And thus is feathered Cupid painted blind," wrote Shakespeare, shortly prior to this work was created around the early 1600s. But Caravaggio's Cupid is not blind. He stares directly at you. That face – sardonic and rosy-cheeked, looking with bold confidence as he struts naked – is the identical one that shrieks in fear in Abraham's Test.

As Michelangelo Merisi da Caravaggio painted his three portrayals of the same unusual-looking youth in Rome at the dawn of the 17th century, he was the most acclaimed religious painter in a metropolis ignited by religious renewal. The Sacrifice of Isaac reveals why he was sought to adorn churches: he could take a scriptural story that had been portrayed many occasions before and render it so fresh, so unfiltered and visceral that the terror seemed to be occurring immediately before you.

Yet there was a different side to the artist, apparent as soon as he came in Rome in the winter that concluded the sixteenth century, as a artist in his early 20s with no teacher or patron in the city, only talent and audacity. The majority of the paintings with which he captured the sacred city's eye were anything but devout. What could be the absolute first resides in London's National Gallery. A young man opens his crimson lips in a scream of pain: while reaching out his dirty digits for a cherry, he has instead been bitten. Boy Bitten By a Lizard is sensuality amid squalor: observers can see the painter's gloomy chamber mirrored in the murky liquid of the transparent vase.

The adolescent wears a pink blossom in his coiffure – a emblem of the sex commerce in Renaissance painting. Venetian artists such as Tiziano and Jacopo Palma depicted prostitutes grasping flowers and, in a painting destroyed in the WWII but documented through images, Caravaggio portrayed a renowned female courtesan, clutching a bouquet to her chest. The meaning of all these botanical signifiers is obvious: intimacy for purchase.

What are we to make of Caravaggio's sensual depictions of boys – and of one adolescent in particular? It is a question that has split his commentators ever since he achieved widespread recognition in the 1980s. The complicated historical truth is that the painter was not the homosexual hero that, for example, Derek Jarman presented on film in his 1986 film Caravaggio, nor so entirely pious that, as some artistic historians improbably claim, his Boy With a Basket of Fruit is in fact a likeness of Christ.

His early paintings do make overt sexual suggestions, or including propositions. It's as if the painter, then a penniless young creator, identified with the city's sex workers, offering himself to live. In the Uffizi, with this thought in mind, viewers might turn to another initial work, the 1596 masterwork the god of wine, in which the god of wine gazes coolly at the spectator as he starts to undo the black ribbon of his robe.

A several years after the wine deity, what could have driven Caravaggio to create Victorious Cupid for the art collector the nobleman, when he was finally growing nearly respectable with prestigious church projects? This unholy non-Christian god resurrects the erotic provocations of his initial works but in a more powerful, unsettling way. Fifty years afterwards, its hidden meaning seemed obvious: it was a portrait of the painter's lover. A British visitor viewed the painting in about the mid-seventeenth century and was told its figure has "the physique and countenance of [Caravaggio's|his] owne youth or assistant that laid with him". The name of this adolescent was Francesco.

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