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The youthful boy cries out while his head is forcefully held, a large thumb pressing into his face as his parent's powerful palm grasps him by the throat. That scene from Abraham's Sacrifice visits the Uffizi Gallery, creating unease through Caravaggio's chilling rendition of the tormented youth from the scriptural narrative. The painting seems as if Abraham, instructed by God to kill his offspring, could snap his neck with a solitary turn. Yet the father's preferred approach involves the metallic steel blade he holds in his other palm, prepared to cut Isaac's throat. One definite element stands out – whoever posed as the sacrifice for this astonishing work displayed extraordinary expressive skill. Within exists not just fear, shock and begging in his darkened eyes but also profound sorrow that a guardian could betray him so utterly.

The artist took a familiar scriptural story and transformed it so vibrant and visceral that its horrors seemed to happen right in front of the viewer

Viewing before the painting, viewers recognize this as a real countenance, an accurate depiction of a young model, because the identical youth – recognizable by his disheveled locks and almost dark eyes – appears in several other paintings by Caravaggio. In every case, that highly expressive face commands the scene. In Youth With a Ram, he gazes mischievously from the darkness while embracing a lamb. In Amor Vincit Omnia, he grins with a toughness acquired on Rome's alleys, his dark feathery wings sinister, a naked adolescent running riot in a affluent residence.

Victorious Cupid, currently exhibited at a London museum, constitutes one of the most embarrassing masterpieces ever created. Viewers feel totally unsettled gazing at it. The god of love, whose darts inspire people with frequently agonizing longing, is portrayed as a very real, brightly lit nude figure, straddling overturned objects that comprise musical instruments, a music score, plate armour and an architect's T-square. This pile of possessions resembles, intentionally, the mathematical and construction equipment strewn across the floor in the German master's print Melencolia I – except here, the melancholic disorder is caused by this smirking deity and the turmoil he can unleash.

"Affection looks not with the eyes, but with the soul, / And therefore is feathered Cupid painted blind," wrote Shakespeare, shortly before this painting was produced around 1601. But the painter's Cupid is not blind. He stares straight at the observer. That face – sardonic and ruddy-faced, staring with brazen confidence as he struts naked – is the identical one that shrieks in fear in Abraham's Test.

When Michelangelo Merisi da Caravaggio painted his three images of the identical distinctive-looking youth in the Eternal City at the start of the seventeenth century, he was the highly acclaimed sacred artist in a metropolis enflamed by religious revival. Abraham's Offering demonstrates why he was sought to adorn sanctuaries: he could adopt a scriptural story that had been depicted numerous times before and make it so new, so raw and physical that the terror seemed to be occurring immediately before you.

However there existed a different side to the artist, apparent as soon as he arrived in Rome in the cold season that ended the sixteenth century, as a artist in his early 20s with no mentor or patron in the city, only skill and audacity. Most of the paintings with which he caught the sacred city's attention were anything but holy. What may be the absolute first resides in the UK's art museum. A young man parts his red mouth in a scream of pain: while stretching out his dirty fingers for a fruit, he has instead been bitten. Boy Bitten By a Lizard is eroticism amid squalor: viewers can see Caravaggio's dismal chamber reflected in the cloudy liquid of the glass container.

The boy sports a pink flower in his coiffure – a symbol of the sex commerce in early modern art. Northern Italian artists such as Tiziano and Jacopo Palma depicted prostitutes grasping flowers and, in a painting destroyed in the second world war but known through images, Caravaggio represented a renowned female courtesan, holding a bouquet to her chest. The message of all these floral signifiers is clear: intimacy for sale.

What are we to interpret of the artist's erotic depictions of boys – and of one boy in specific? It is a question that has divided his interpreters since he gained mega-fame in the 1980s. The complicated historical truth is that the artist was neither the queer icon that, for instance, the filmmaker presented on screen in his 1986 film Caravaggio, nor so entirely pious that, as certain artistic historians unbelievably claim, his Boy With a Basket of Fruit is in fact a portrait of Jesus.

His initial paintings indeed offer explicit sexual implications, or including offers. It's as if the painter, then a penniless young artist, identified with Rome's sex workers, offering himself to survive. In the Uffizi, with this idea in mind, viewers might look to another initial creation, the sixteenth-century masterpiece the god of wine, in which the deity of wine gazes coolly at you as he begins to untie the black sash of his garment.

A several annums after the wine deity, what could have driven the artist to paint Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was finally becoming nearly respectable with important church commissions? This unholy pagan deity resurrects the erotic challenges of his initial works but in a more powerful, unsettling manner. Half a century later, its hidden meaning seemed obvious: it was a representation of the painter's companion. A English traveller saw Victorious Cupid in about 1649 and was informed its subject has "the physique and countenance of [Caravaggio's|his] own youth or assistant that slept with him". The identity of this adolescent was Cecco.

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