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A young boy cries out while his head is firmly gripped, a large thumb digging into his cheek as his father's powerful palm grasps him by the throat. That scene from The Sacrifice of Isaac visits the Florentine museum, creating unease through the artist's harrowing rendition of the tormented youth from the biblical narrative. It appears as if the patriarch, instructed by God to sacrifice his offspring, could break his neck with a single turn. Yet Abraham's chosen method involves the metallic grey knife he grips in his other palm, ready to cut Isaac's neck. One certain element remains – whomever posed as Isaac for this astonishing work displayed extraordinary expressive skill. Within exists not just dread, surprise and begging in his darkened eyes but also deep grief that a guardian could betray him so utterly.

The artist took a well-known biblical tale and transformed it so fresh and raw that its horrors appeared to unfold right in view of the viewer

Viewing before the artwork, observers identify this as a real countenance, an precise depiction of a young model, because the identical youth – recognizable by his tousled hair and nearly dark pupils – features in several additional paintings by the master. In each instance, that highly emotional face commands the scene. In John the Baptist, he gazes playfully from the shadows while embracing a ram. In Victorious Cupid, he grins with a hardness acquired on the city's alleys, his black feathery appendages sinister, a unclothed adolescent creating riot in a well-to-do residence.

Victorious Cupid, currently displayed at a British gallery, represents one of the most discomfiting masterpieces ever created. Observers feel completely unsettled gazing at it. The god of love, whose arrows inspire people with often painful desire, is portrayed as a very tangible, brightly illuminated nude form, standing over toppled-over objects that include stringed devices, a music manuscript, metal armor and an builder's T-square. This heap of items resembles, intentionally, the mathematical and architectural gear scattered across the ground in Albrecht Dürer's engraving Melancholy – except in this case, the gloomy disorder is created by this smirking Cupid and the turmoil he can unleash.

"Affection looks not with the vision, but with the mind, / And thus is winged Cupid painted sightless," penned Shakespeare, just prior to this work was created around the early 1600s. But the painter's god is not blind. He stares straight at the observer. That face – ironic and ruddy-cheeked, looking with bold confidence as he struts naked – is the identical one that shrieks in terror in Abraham's Test.

When Michelangelo Merisi da Caravaggio painted his multiple images of the same unusual-looking kid in Rome at the start of the 17th century, he was the most celebrated religious artist in a metropolis enflamed by religious revival. The Sacrifice of Isaac demonstrates why he was sought to decorate churches: he could adopt a scriptural story that had been portrayed many times before and make it so fresh, so unfiltered and visceral that the horror seemed to be happening immediately in front of you.

However there existed another aspect to the artist, apparent as quickly as he arrived in Rome in the winter that ended 1592, as a artist in his initial twenties with no mentor or supporter in the urban center, only talent and boldness. The majority of the paintings with which he captured the holy city's eye were anything but holy. That may be the absolute earliest hangs in the UK's National Gallery. A youth opens his red lips in a yell of agony: while reaching out his filthy fingers for a cherry, he has rather been attacked. Boy Bitten By a Lizard is sensuality amid poverty: observers can discern Caravaggio's gloomy room mirrored in the cloudy liquid of the transparent container.

The adolescent wears a pink flower in his coiffure – a symbol of the erotic trade in Renaissance painting. Northern Italian artists such as Titian and Palma Vecchio portrayed courtesans grasping flowers and, in a work destroyed in the WWII but known through photographs, Caravaggio portrayed a famous female prostitute, clutching a bouquet to her chest. The message of all these botanical signifiers is clear: sex for purchase.

How are we to make of Caravaggio's sensual depictions of youths – and of a particular boy in specific? It is a inquiry that has split his commentators ever since he gained mega-fame in the twentieth century. The complex historical truth is that the artist was not the queer icon that, for instance, Derek Jarman presented on screen in his twentieth-century film Caravaggio, nor so completely pious that, as some art historians unbelievably assert, his Youth Holding Fruit is in fact a portrait of Christ.

His early paintings indeed offer overt sexual implications, or including propositions. It's as if Caravaggio, then a destitute young creator, aligned with the city's prostitutes, offering himself to survive. In the Florentine gallery, with this thought in consideration, observers might turn to an additional early work, the sixteenth-century masterpiece Bacchus, in which the god of alcohol stares coolly at you as he starts to untie the dark ribbon of his garment.

A several annums after Bacchus, what could have driven the artist to paint Amor Vincit Omnia for the art patron the nobleman, when he was finally growing nearly respectable with important church projects? This profane non-Christian deity resurrects the sexual challenges of his initial works but in a increasingly intense, unsettling way. Fifty years afterwards, its hidden meaning seemed clear: it was a representation of the painter's lover. A English traveller viewed the painting in about 1649 and was told its figure has "the body & face of [Caravaggio's|his] owne youth or assistant that laid with him". The identity of this boy was Cecco.

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