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The youthful boy screams as his head is firmly held, a massive thumb digging into his face as his parent's mighty hand grasps him by the throat. That moment from The Sacrifice of Isaac appears in the Uffizi Gallery, evoking distress through the artist's chilling rendition of the tormented youth from the biblical narrative. It appears as if the patriarch, instructed by God to kill his son, could break his neck with a single turn. However Abraham's preferred method involves the silvery grey knife he grips in his other hand, prepared to cut the boy's throat. A certain element stands out – whomever posed as Isaac for this breathtaking work displayed extraordinary expressive skill. Within exists not just fear, shock and begging in his shadowed eyes but additionally profound grief that a protector could betray him so completely.

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

Standing before the painting, viewers recognize this as a actual countenance, an accurate record of a young model, because the same youth – recognizable by his disheveled hair and almost black eyes – appears in two additional paintings by Caravaggio. In each case, that richly expressive visage dominates the composition. In John the Baptist, he peers playfully from the shadows while embracing a ram. In Victorious Cupid, he grins with a toughness acquired on the city's streets, his black feathery wings demonic, a naked adolescent creating chaos in a well-to-do dwelling.

Victorious Cupid, currently displayed at a London museum, constitutes one of the most discomfiting masterpieces ever created. Observers feel completely unsettled looking at it. Cupid, whose darts fill people with frequently painful longing, is shown as a very real, vividly illuminated unclothed form, standing over toppled-over objects that include stringed devices, a musical score, plate armour and an builder's T-square. This pile of items echoes, deliberately, the geometric and construction gear scattered across the floor in Albrecht Dürer's engraving Melancholy – save here, the gloomy mess is created by this smirking deity and the turmoil he can release.

"Affection sees not with the vision, but with the soul, / And thus is feathered Cupid depicted blind," penned the Bard, just before this work was created around 1601. But Caravaggio's Cupid is not blind. He stares straight at the observer. That countenance – sardonic and ruddy-faced, looking with bold assurance as he struts unclothed – is the same one that shrieks in terror in Abraham's Test.

When Michelangelo Merisi da Caravaggio created his three images of the identical unusual-appearing youth in the Eternal City at the dawn of the 17th century, he was the highly celebrated religious painter in a city ignited by Catholic renewal. The Sacrifice of Isaac reveals why he was sought to decorate sanctuaries: he could adopt a biblical story that had been depicted many times before and make it so new, so raw and physical that the terror seemed to be happening directly before the spectator.

However there existed another aspect to the artist, evident as soon as he arrived in Rome in the cold season that concluded the sixteenth century, as a artist in his early twenties with no teacher or supporter in the urban center, only talent and boldness. The majority of the paintings with which he caught the sacred metropolis's attention were everything but devout. What may be the absolute first hangs in London's National Gallery. A youth parts his red mouth in a scream of pain: while stretching out his filthy digits for a fruit, he has rather been bitten. Youth Bitten by a Reptile is eroticism amid poverty: observers can see the painter's dismal room mirrored in the murky waters of the transparent container.

The adolescent sports a pink blossom in his coiffure – a emblem of the sex commerce in early modern art. Venetian painters such as Tiziano and Palma Vecchio portrayed prostitutes grasping flowers and, in a work destroyed in the WWII but known through images, Caravaggio portrayed a famous woman courtesan, holding a posy to her chest. The message of all these botanical indicators is clear: sex for sale.

What are we to interpret of Caravaggio's erotic depictions of boys – and of one boy in particular? It is a inquiry that has divided his interpreters since he gained mega-fame in the twentieth century. The complex past truth is that the painter was not the homosexual hero that, for example, Derek Jarman put on film in his twentieth-century movie about the artist, nor so completely pious that, as certain art historians unbelievably assert, his Boy With a Basket of Fruit is actually a likeness of Christ.

His early works indeed make overt sexual implications, or even propositions. It's as if the painter, then a penniless young artist, aligned with Rome's prostitutes, selling himself to survive. In the Uffizi, with this thought in mind, observers might look to another initial creation, the 1596 masterpiece the god of wine, in which the deity of alcohol stares coolly at the spectator as he begins to undo the dark sash of his robe.

A several years following Bacchus, what could have motivated Caravaggio to paint Amor Vincit Omnia for the art patron Vincenzo Giustiniani, when he was at last becoming nearly established with important ecclesiastical projects? This profane non-Christian deity revives the erotic provocations of his early works but in a increasingly intense, unsettling manner. Half a century afterwards, its hidden meaning seemed obvious: it was a portrait of Caravaggio's lover. A British traveller viewed the painting in about the mid-seventeenth century and was told its figure has "the body & face of [Caravaggio's|his] owne boy or assistant that slept with him". The name of this boy was Francesco.

The artist had been deceased for about forty annums when this account was documented.