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A youthful boy screams while his head is firmly held, a massive thumb pressing into his cheek as his father's powerful hand holds him by the throat. This scene from The Sacrifice of Isaac appears in the Uffizi Gallery, creating distress through the artist's harrowing portrayal of the suffering youth from the biblical account. It appears as if the patriarch, instructed by God to kill his offspring, could snap his spinal column with a single turn. Yet the father's preferred method involves the silvery grey knife he grips in his remaining palm, prepared to cut the boy's neck. One certain element remains – whomever modeled as Isaac for this breathtaking piece displayed remarkable acting skill. There exists not only dread, shock and begging in his shadowed eyes but additionally deep grief that a guardian could betray him so completely.

The artist took a well-known scriptural story and transformed it so vibrant and raw that its horrors seemed to unfold directly in view of you

Viewing before the painting, viewers identify this as a actual face, an accurate record of a young model, because the same youth – identifiable by his tousled locks and almost dark eyes – features in two additional paintings by Caravaggio. In every instance, that richly expressive visage commands the composition. In Youth With a Ram, he gazes mischievously from the shadows while holding a lamb. In Victorious Cupid, he grins with a toughness acquired on Rome's streets, his dark plumed appendages demonic, a unclothed adolescent running chaos in a affluent residence.

Victorious Cupid, presently displayed at a British museum, represents one of the most discomfiting artworks ever painted. Observers feel completely unsettled looking at it. Cupid, whose arrows fill people with often painful longing, is shown as a very tangible, vividly illuminated nude form, standing over overturned objects that comprise musical devices, a musical score, plate armour and an builder's ruler. This heap of items resembles, deliberately, the geometric and construction equipment strewn across the ground in the German master's print Melancholy – save here, the melancholic disorder is caused by this grinning deity and the turmoil he can unleash.

"Affection looks not with the eyes, but with the mind, / And thus is winged Love painted sightless," penned Shakespeare, shortly prior to this painting was created around the early 1600s. But the painter's god is not unseeing. He gazes directly at the observer. That face – ironic and ruddy-faced, looking with bold assurance as he poses unclothed – is the same one that screams in fear in Abraham's Test.

As the Italian master created his three images of the identical unusual-looking youth in the Eternal City at the start of the 17th century, he was the highly celebrated religious artist in a city ignited by religious revival. Abraham's Offering reveals why he was commissioned to decorate sanctuaries: he could adopt a biblical narrative that had been depicted many occasions before and render it so new, so raw and physical that the horror appeared to be happening immediately in front of you.

Yet there was another side to Caravaggio, evident as soon as he arrived in Rome in the winter that concluded 1592, as a painter in his initial 20s with no mentor or supporter in the urban center, just skill and audacity. The majority of the paintings with which he caught the sacred city's attention were everything but devout. What could be the absolute first resides in London's National Gallery. A young man parts his crimson mouth in a yell of pain: 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 discern Caravaggio's dismal chamber mirrored in the murky liquid of the glass vase.

The boy sports a rose-colored blossom in his coiffure – a symbol of the sex trade in Renaissance art. Venetian painters such as Titian and Jacopo Palma portrayed prostitutes grasping flowers and, in a painting destroyed in the second world war but known through photographs, the master portrayed a renowned woman prostitute, clutching a bouquet to her chest. The message of all these floral signifiers is obvious: sex for purchase.

What are we to make of Caravaggio's erotic depictions of youths – and of a particular boy in particular? It is a question that has divided his commentators ever since he achieved mega-fame in the twentieth century. The complex historical reality is that the artist was not the queer hero that, for example, Derek Jarman put on screen in his twentieth-century film Caravaggio, nor so entirely devout that, as certain art historians improbably assert, his Boy With a Basket of Fruit is actually a likeness of Jesus.

His early paintings indeed make explicit sexual suggestions, or even offers. It's as if the painter, then a destitute youthful artist, identified with the city's prostitutes, selling himself to live. In the Uffizi, with this thought in consideration, observers might turn to another initial work, the sixteenth-century masterpiece the god of wine, in which the deity of wine gazes coolly at the spectator as he begins to undo the dark ribbon of his garment.

A few years after the wine deity, what could have motivated the artist to create Amor Vincit Omnia for the art patron the nobleman, when he was finally growing almost respectable with important ecclesiastical projects? This unholy pagan god revives the erotic provocations of his initial paintings but in a more powerful, uneasy way. Half a century later, its hidden meaning seemed clear: it was a representation of the painter's lover. A English visitor viewed Victorious Cupid in about the mid-seventeenth century and was informed its subject has "the physique and countenance of [Caravaggio's|his] owne boy or servant that slept with him". The name of this adolescent was Cecco.

The painter had been dead for about 40 years when this story was recorded.