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The young boy cries out while his head is forcefully gripped, a large digit pressing into his face as his father's mighty hand grasps him by the neck. That scene from The Sacrifice of Isaac appears in the Uffizi Gallery, creating unease through the artist's harrowing rendition of the suffering youth from the scriptural narrative. It seems as if the patriarch, commanded by the Divine to sacrifice his son, could snap his spinal column with a solitary turn. Yet the father's preferred method involves the silvery steel knife he holds in his other palm, ready to slit the boy's throat. A certain element remains – whomever posed as the sacrifice for this breathtaking work demonstrated remarkable acting ability. There exists not just fear, surprise and begging in his darkened eyes but additionally deep sorrow that a guardian could betray him so completely.

He took a well-known biblical story and made it so vibrant and visceral that its horrors appeared to unfold directly in view of you

Standing before the artwork, viewers recognize this as a real face, an precise record of a young model, because the same boy – identifiable by his disheveled locks and nearly dark eyes – appears in two additional works by Caravaggio. In every instance, that richly emotional face commands the scene. In Youth With a Ram, he peers playfully from the shadows while holding a lamb. In Amor Vincit Omnia, he smirks with a toughness acquired on Rome's alleys, his black plumed appendages sinister, a unclothed adolescent creating chaos in a affluent dwelling.

Amor Vincit Omnia, currently displayed at a London museum, constitutes one of the most discomfiting masterpieces ever created. Viewers feel totally disoriented looking at it. Cupid, whose arrows inspire people with often agonizing desire, is portrayed as a very real, vividly lit unclothed form, straddling overturned objects that include stringed instruments, a music score, metal armor and an architect's T-square. This pile of items resembles, intentionally, the mathematical and architectural gear scattered across the ground in the German master's print Melancholy – save here, the gloomy disorder is caused by this smirking deity and the turmoil he can unleash.

"Love looks not with the eyes, but with the mind, / And thus is winged Love depicted blind," wrote the Bard, just prior to this painting was created around the early 1600s. But the painter's god is not blind. He gazes directly at you. That countenance – sardonic and rosy-cheeked, staring with bold assurance as he struts naked – is the identical one that screams in fear in Abraham's Test.

When Michelangelo Merisi da Caravaggio painted his three images of the identical distinctive-appearing youth in Rome at the dawn of the seventeenth century, he was the most celebrated sacred painter in a metropolis ignited by Catholic renewal. Abraham's Offering demonstrates why he was sought to decorate churches: he could adopt a scriptural story that had been depicted many occasions previously and make it so new, so raw and visceral that the horror seemed to be occurring immediately before the spectator.

Yet there was another aspect to Caravaggio, evident as soon as he arrived in the capital in the winter that concluded the sixteenth century, as a painter in his initial 20s with no mentor or supporter in the city, only talent and audacity. Most of the works with which he caught the sacred metropolis's attention were anything but holy. What may be the absolute earliest hangs in London's National Gallery. A young man 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 sensuality amid squalor: observers can see Caravaggio's gloomy chamber mirrored in the murky waters of the glass vase.

The adolescent sports a rose-colored blossom in his coiffure – a emblem of the erotic trade in Renaissance art. Northern Italian painters such as Tiziano and Palma Vecchio depicted prostitutes holding flowers and, in a work destroyed in the WWII but documented through images, the master represented a famous female prostitute, clutching a posy to her bosom. The meaning of all these floral indicators is obvious: intimacy for purchase.

How are we to interpret of Caravaggio's sensual portrayals of youths – and of one boy in particular? It is a question that has divided his commentators since he gained widespread recognition in the twentieth century. The complex past truth is that the painter was not the homosexual hero that, for example, Derek Jarman put on screen in his twentieth-century film about the artist, nor so entirely pious that, as some artistic historians unbelievably assert, his Boy With a Basket of Fruit is in fact a portrait of Jesus.

His initial paintings do offer overt erotic implications, or including offers. It's as if the painter, then a destitute young creator, aligned with Rome's prostitutes, offering himself to live. In the Uffizi, with this thought in mind, observers might look to another early work, the sixteenth-century masterpiece Bacchus, in which the god of alcohol stares calmly at the spectator as he starts to undo the black sash of his garment.

A several annums following Bacchus, what could have driven Caravaggio to create Amor Vincit Omnia for the art patron the nobleman, when he was finally growing almost established with prestigious church projects? This profane pagan deity revives the sexual provocations of his early paintings but in a more powerful, unsettling way. Fifty years later, its hidden meaning seemed obvious: it was a portrait of the painter's companion. A British traveller viewed Victorious Cupid in about the mid-seventeenth century and was informed its figure has "the body & face of [Caravaggio's|his] owne boy or servant that laid with him". The identity of this boy was Cecco.

The artist had been dead for about forty annums when this story was documented.