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A youthful lad screams as his skull is firmly held, a large thumb pressing into his cheek as his parent's mighty palm grasps him by the throat. This scene from The Sacrifice of Isaac visits the Uffizi Gallery, creating distress through Caravaggio's chilling portrayal of the suffering youth from the scriptural narrative. The painting appears as if the patriarch, instructed by God to sacrifice his son, could break his spinal column with a solitary turn. Yet Abraham's chosen approach involves the metallic steel blade he grips in his remaining hand, ready to slit Isaac's neck. One certain element stands out – whoever posed as Isaac for this breathtaking piece demonstrated extraordinary acting skill. There exists not only fear, surprise and begging in his darkened gaze but also profound grief that a guardian could betray him so completely.

He adopted a familiar biblical story and made it so fresh and raw that its terrors seemed to happen right in view of the viewer

Standing in front of the artwork, observers identify this as a actual countenance, an precise record of a adolescent subject, because the identical youth – identifiable by his tousled locks and nearly dark pupils – features in two other paintings by the master. In every case, that richly expressive face dominates the scene. In John the Baptist, he peers playfully from the darkness while embracing a ram. In Victorious Cupid, he smirks with a hardness learned on the city's streets, his dark feathery wings sinister, a naked child creating chaos in a well-to-do dwelling.

Amor Vincit Omnia, currently displayed at a British museum, represents one of the most discomfiting masterpieces ever created. Observers feel totally unsettled gazing at it. Cupid, whose arrows inspire people with often agonizing longing, is portrayed as a very tangible, vividly lit nude figure, standing over toppled-over objects that include stringed instruments, a music score, plate armor and an builder's ruler. This pile of possessions echoes, deliberately, the mathematical and architectural equipment strewn across the ground in Albrecht Dürer's print Melencolia I – save in this case, the gloomy disorder is created by this smirking deity and the mayhem he can unleash.

"Love sees not with the eyes, but with the soul, / And therefore is feathered Cupid depicted sightless," wrote the Bard, just before this painting was produced around the early 1600s. But Caravaggio's Cupid is not blind. He stares directly at the observer. That face – ironic and ruddy-cheeked, staring with brazen assurance as he struts naked – is the identical one that shrieks in fear in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio painted his three images of the identical distinctive-appearing kid in Rome at the start of the seventeenth century, he was the highly acclaimed religious artist in a city ignited by religious renewal. The Sacrifice of Isaac demonstrates why he was commissioned to decorate sanctuaries: he could take a biblical story that had been depicted many times before and make it so fresh, so unfiltered and physical that the terror seemed to be happening directly in front of you.

Yet there was a different side to Caravaggio, evident as soon as he came in the capital in the winter that concluded 1592, as a painter in his initial twenties with no mentor or patron in the city, just talent and boldness. Most of the paintings with which he caught the holy metropolis's attention were anything but devout. What could be the very earliest hangs in the UK's art museum. A young man opens his red lips in a scream of pain: while stretching out his dirty fingers for a cherry, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid squalor: observers can see the painter's dismal chamber mirrored in the cloudy waters of the transparent vase.

The boy wears a pink flower in his coiffure – a emblem of the sex trade in Renaissance painting. Northern Italian artists such as Tiziano and Palma Vecchio depicted courtesans grasping blooms and, in a work destroyed in the second world war but known through photographs, Caravaggio portrayed a renowned woman courtesan, clutching a posy to her bosom. The meaning of all these botanical signifiers is obvious: sex for purchase.

What are we to make of the artist's sensual portrayals of boys – and of one boy in specific? It is a inquiry that has divided his commentators since he gained mega-fame in the twentieth century. The complicated past reality is that the artist was not the queer icon that, for instance, Derek Jarman presented on screen in his twentieth-century movie about the artist, nor so completely pious that, as some artistic historians unbelievably assert, his Boy With a Basket of Fruit is in fact a likeness of Christ.

His initial works do make explicit erotic implications, or even propositions. It's as if Caravaggio, then a penniless youthful artist, identified with the city's sex workers, selling himself to live. In the Uffizi, with this idea in consideration, observers might look to an additional initial work, the sixteenth-century masterwork the god of wine, in which the god of wine stares coolly at the spectator as he starts to untie the dark ribbon of his robe.

A few years after Bacchus, what could have motivated Caravaggio to paint Amor Vincit Omnia for the artistic patron the nobleman, when he was finally growing almost established with prestigious ecclesiastical projects? This unholy pagan deity resurrects the sexual challenges of his initial works but in a more intense, unsettling manner. Fifty years later, its hidden meaning seemed clear: it was a portrait of Caravaggio's lover. A British visitor viewed Victorious Cupid in about 1649 and was informed its subject has "the body & face of [Caravaggio's|his] owne boy or servant that laid with him". The identity of this boy was Francesco.

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