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A youthful boy screams while his head is forcefully gripped, a massive thumb pressing into his cheek as his parent's mighty palm grasps him by the throat. This moment from The Sacrifice of Isaac appears in the Florentine museum, creating distress through the artist's harrowing portrayal of the tormented youth from the scriptural narrative. It appears as if the patriarch, commanded by God to kill his offspring, could break his spinal column with a solitary twist. However Abraham's preferred method involves the metallic grey blade he holds in his remaining hand, ready to slit Isaac's neck. A definite element remains – whomever posed as the sacrifice for this breathtaking piece displayed extraordinary expressive ability. Within exists not only dread, shock and begging in his shadowed eyes but additionally profound sorrow that a guardian could abandon him so completely.

The artist took a well-known scriptural tale and made it so fresh and raw that its terrors seemed to unfold right in front of the viewer

Standing before the painting, viewers identify this as a real face, an precise depiction of a adolescent subject, because the identical youth – identifiable by his disheveled locks and almost dark pupils – features in two other works by the master. In each instance, that highly expressive visage commands the scene. In Youth With a Ram, he gazes mischievously from the shadows while holding a ram. In Victorious Cupid, he smirks with a hardness acquired on Rome's alleys, his dark plumed wings sinister, a naked adolescent running riot in a affluent residence.

Amor Vincit Omnia, presently displayed at a London gallery, represents one of the most discomfiting artworks ever created. Viewers feel totally unsettled gazing at it. Cupid, whose darts fill people with frequently agonizing longing, is portrayed as a extremely real, brightly illuminated unclothed form, straddling toppled-over items that comprise musical devices, a music score, plate armour and an architect's ruler. This pile of possessions echoes, intentionally, the mathematical and construction gear scattered across the floor in the German master's engraving Melencolia I – except in this case, the gloomy mess is created by this grinning Cupid and the turmoil he can unleash.

"Love sees not with the eyes, but with the mind, / And therefore is winged Love painted sightless," penned Shakespeare, just prior to this painting was created around the early 1600s. But the painter's Cupid is not unseeing. He gazes straight at you. That countenance – sardonic and ruddy-cheeked, staring with brazen assurance as he poses unclothed – is the same one that screams in terror in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio created his three portrayals of the identical distinctive-looking youth in Rome at the start of the 17th century, he was the highly celebrated sacred painter in a city enflamed by religious revival. Abraham's Offering demonstrates why he was commissioned to adorn sanctuaries: he could adopt a biblical story that had been portrayed numerous occasions previously and render it so new, so unfiltered and visceral that the horror appeared to be occurring directly in front of you.

However there existed another side to the artist, evident as quickly as he arrived in the capital in the cold season that ended the sixteenth century, as a painter in his early 20s with no teacher or patron in the urban center, just talent and boldness. The majority of the works with which he captured the holy city's eye were everything but holy. What could be the very first hangs in the UK's National Gallery. A young man parts his crimson mouth in a scream of agony: while reaching out his dirty fingers for a cherry, he has instead been bitten. Youth Bitten by a Reptile is sensuality amid poverty: viewers can see the painter's dismal chamber reflected in the cloudy waters of the glass container.

The adolescent sports a rose-colored blossom in his coiffure – a symbol of the sex trade in early modern painting. Northern Italian artists such as Titian and Palma Vecchio depicted prostitutes grasping flowers and, in a work destroyed in the second world war but documented through photographs, Caravaggio represented a famous female prostitute, holding a posy to her bosom. The message of all these floral signifiers is clear: sex for sale.

How are we to interpret of the artist's erotic portrayals of boys – and of one boy in particular? It is a question that has split his commentators since he achieved mega-fame in the twentieth century. The complicated past reality is that the painter was neither the homosexual icon that, for instance, the filmmaker presented on film in his twentieth-century movie about the artist, nor so completely pious that, as some artistic scholars improbably assert, his Youth Holding Fruit is in fact a portrait of Jesus.

His early works indeed offer overt erotic suggestions, or even offers. It's as if Caravaggio, then a penniless young creator, aligned with the city's prostitutes, offering himself to live. In the Uffizi, with this idea in mind, observers might turn to an additional early creation, the 1596 masterwork Bacchus, in which the deity of wine stares coolly at the spectator as he starts to undo the black ribbon of his robe.

A few years following Bacchus, what could have driven Caravaggio to paint Victorious Cupid for the artistic collector Vincenzo Giustiniani, when he was at last becoming nearly established with prestigious ecclesiastical commissions? This profane pagan deity revives the sexual challenges of his early paintings but in a more intense, uneasy manner. Fifty years afterwards, its secret seemed obvious: it was a representation of the painter's lover. A English traveller viewed the painting in about the mid-seventeenth century and was informed its figure has "the physique and countenance of [Caravaggio's|his] owne youth or assistant that laid with him". The identity of this adolescent was Francesco.

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