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A young boy cries out as his head is firmly held, a massive thumb digging into his face as his father's powerful hand holds him by the throat. That scene from Abraham's Sacrifice visits the Florentine museum, creating distress through the artist's harrowing rendition of the tormented youth from the scriptural narrative. The painting appears as if the patriarch, instructed by the Divine to sacrifice his son, could break his neck with a single turn. Yet the father's chosen approach involves the metallic grey blade he holds in his remaining hand, ready to slit the boy's throat. A certain element remains – whoever posed as the sacrifice for this astonishing piece displayed extraordinary expressive ability. Within exists not only fear, shock and begging in his darkened gaze but additionally deep sorrow that a protector could abandon him so completely.

He adopted a well-known scriptural tale and made it so fresh and visceral that its terrors seemed to unfold right in front of the viewer

Standing in front of the painting, viewers recognize this as a actual countenance, an accurate record of a young subject, because the identical boy – identifiable by his disheveled hair and nearly dark pupils – features in several other paintings by the master. In each instance, that richly expressive face commands the scene. In Youth With a Ram, he peers mischievously from the shadows while embracing a lamb. In Amor Vincit Omnia, he smirks with a hardness learned on the city's alleys, his dark plumed wings sinister, a unclothed adolescent creating riot in a affluent residence.

Amor Vincit Omnia, currently displayed at a London gallery, constitutes one of the most discomfiting artworks ever created. Observers feel totally disoriented looking at it. Cupid, whose arrows fill people with often painful longing, is shown as a very tangible, vividly lit unclothed form, standing over overturned items that comprise stringed instruments, a music score, metal armor and an builder's T-square. This pile of possessions resembles, deliberately, the geometric and architectural gear strewn across the ground in Albrecht Dürer's engraving Melancholy – save here, the gloomy disorder is created by this smirking deity and the mayhem he can unleash.

"Affection looks not with the eyes, but with the mind, / And therefore is feathered Love depicted blind," wrote Shakespeare, just prior to this work was produced around the early 1600s. But Caravaggio's Cupid is not blind. He stares directly at the observer. That countenance – sardonic and rosy-faced, staring with brazen confidence as he poses unclothed – is the identical one that screams in terror in Abraham's Test.

As Michelangelo Merisi da Caravaggio painted his three portrayals of the same unusual-appearing kid in Rome at the start of the seventeenth century, he was the highly celebrated sacred painter in a metropolis ignited by religious renewal. The Sacrifice of Isaac reveals why he was commissioned to decorate sanctuaries: he could take a biblical story that had been portrayed many occasions previously and render it so fresh, so raw and physical that the horror appeared to be happening immediately in front of you.

However there was another side to the artist, apparent as soon as he arrived in Rome in the winter that concluded the sixteenth century, as a painter in his early 20s with no mentor or patron in the urban center, just skill and audacity. Most of the paintings with which he captured the holy metropolis's eye were anything but devout. What may be the absolute first hangs in London's National Gallery. A young man parts his crimson mouth in a scream of agony: while stretching out his filthy digits for a fruit, he has instead been bitten. Youth Bitten by a Reptile is sensuality amid squalor: observers can see the painter's dismal room reflected in the cloudy liquid of the glass container.

The adolescent sports a pink blossom in his coiffure – a symbol of the erotic trade in early modern painting. Venetian painters such as Titian and Jacopo Palma depicted prostitutes holding flowers and, in a work destroyed in the second world war but known through images, Caravaggio represented a renowned woman courtesan, clutching a bouquet to her bosom. The meaning of all these botanical signifiers is obvious: intimacy for sale.

How are we to make of Caravaggio's erotic portrayals of boys – and of one adolescent in particular? It is a inquiry that has split his commentators ever since he achieved widespread recognition in the 1980s. The complicated past reality is that the painter was not the queer hero that, for example, the filmmaker presented on screen in his twentieth-century film about the artist, nor so entirely devout that, as some artistic scholars unbelievably claim, his Boy With a Basket of Fruit is actually a likeness of Christ.

His early works do make explicit sexual suggestions, or including offers. It's as if the painter, then a destitute youthful creator, identified with Rome's sex workers, offering himself to live. In the Florentine gallery, with this idea in consideration, viewers might turn to an additional initial creation, the 1596 masterpiece Bacchus, in which the deity of alcohol stares coolly at the spectator as he starts to undo the black ribbon of his robe.

A several years following Bacchus, what could have motivated the artist to paint Amor Vincit Omnia for the art collector Vincenzo Giustiniani, when he was finally becoming almost respectable with prestigious ecclesiastical commissions? This unholy pagan god resurrects the erotic provocations of his early works but in a more powerful, uneasy way. Half a century afterwards, its hidden meaning seemed obvious: it was a representation of Caravaggio's companion. A English visitor viewed Victorious Cupid in about the mid-seventeenth century and was informed its subject has "the body & face of [Caravaggio's|his] owne youth or assistant that laid with him". The name of this boy was Cecco.

The artist had been deceased for about 40 annums when this story was recorded.