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The youthful lad screams as his head is forcefully held, a large digit pressing into his face as his parent's mighty hand holds him by the neck. This scene from Abraham's Sacrifice visits the Uffizi Gallery, creating unease through the artist's harrowing portrayal of the suffering youth from the scriptural account. It appears as if the patriarch, instructed by God to sacrifice his offspring, could break his spinal column with a single twist. Yet the father's chosen method involves the silvery grey knife he grips in his remaining hand, ready to cut Isaac's neck. One definite aspect stands out – whomever posed as the sacrifice for this breathtaking piece demonstrated extraordinary acting skill. Within exists not only fear, shock and pleading in his shadowed gaze but also deep sorrow that a protector could abandon him so utterly.

The artist adopted a well-known biblical story and transformed it so vibrant and raw that its horrors appeared to unfold directly in front of the viewer

Viewing before the artwork, viewers recognize this as a actual countenance, an precise depiction of a young subject, because the same youth – recognizable by his disheveled locks and nearly black eyes – features in two additional works by Caravaggio. In each instance, that richly emotional face dominates the composition. In Youth With a Ram, he gazes playfully from the shadows while holding a lamb. In Amor Vincit Omnia, he grins with a hardness acquired on Rome's alleys, his dark plumed wings sinister, a unclothed child creating chaos in a affluent dwelling.

Amor Vincit Omnia, currently exhibited at a British museum, constitutes one of the most embarrassing masterpieces ever created. Observers feel totally unsettled looking at it. Cupid, whose arrows inspire people with often painful desire, is shown as a very tangible, vividly illuminated unclothed figure, straddling toppled-over items that include musical devices, a musical score, metal armor and an architect's ruler. This heap of items resembles, deliberately, the mathematical and construction gear scattered across the ground in Albrecht Dürer's engraving Melancholy – save here, the melancholic disorder is caused by this smirking deity and the mayhem he can release.

"Affection looks not with the eyes, but with the mind, / And thus is winged Cupid depicted blind," wrote the Bard, shortly before this work was produced around the early 1600s. But the painter's Cupid is not blind. He gazes straight at the observer. That countenance – ironic and ruddy-cheeked, looking with bold assurance as he struts naked – is the same one that shrieks in fear in Abraham's Test.

As the Italian master created his three portrayals of the identical distinctive-appearing kid in Rome at the dawn of the seventeenth century, he was the highly acclaimed sacred artist in a metropolis ignited by religious revival. Abraham's Offering demonstrates why he was sought to adorn churches: he could take a biblical story that had been depicted many times before and render it so new, so raw and physical that the horror appeared to be happening directly before the spectator.

Yet there was another aspect to the artist, apparent as quickly as he arrived in Rome in the cold season that ended 1592, as a artist in his initial 20s with no teacher or patron in the city, just talent and audacity. The majority of the paintings with which he captured the sacred metropolis's eye were everything but holy. What could be the absolute first hangs in the UK's art museum. A young man parts his red lips in a scream of pain: while reaching out his dirty fingers for a cherry, he has rather been bitten. Boy Bitten By a Lizard is sensuality amid poverty: observers can see Caravaggio's dismal chamber mirrored in the murky liquid of the glass container.

The boy sports a pink blossom in his coiffure – a symbol of the sex trade in early modern art. Northern Italian painters such as Tiziano and Palma Vecchio depicted prostitutes grasping blooms and, in a painting lost in the WWII but known through photographs, the master represented a renowned female prostitute, holding a posy to her bosom. The message of all these floral signifiers is clear: intimacy for sale.

What are we to make of Caravaggio's erotic depictions of boys – and of one boy in particular? It is a inquiry that has divided his interpreters ever since he achieved widespread recognition in the twentieth century. The complicated historical reality is that the painter was neither the homosexual hero that, for example, Derek Jarman put on screen in his 1986 film about the artist, nor so entirely pious that, as certain artistic scholars unbelievably assert, his Youth Holding Fruit is actually a portrait of Christ.

His early paintings do make overt erotic implications, or even offers. It's as if the painter, then a destitute young artist, aligned with the city's sex workers, selling himself to live. In the Uffizi, with this thought in mind, observers might turn to an additional initial work, the 1596 masterwork Bacchus, in which the god of wine gazes calmly at the spectator as he starts to untie the black sash of his garment.

A few annums following Bacchus, what could have motivated Caravaggio to paint Amor Vincit Omnia for the artistic collector Vincenzo Giustiniani, when he was finally growing almost respectable with important church projects? This profane pagan deity revives the sexual challenges of his initial paintings but in a increasingly intense, uneasy manner. Half a century afterwards, its secret seemed obvious: it was a representation of Caravaggio's lover. A English visitor viewed Victorious Cupid in about the mid-seventeenth century and was told its figure has "the physique and countenance of [Caravaggio's|his] owne boy or assistant that laid with him". The name of this adolescent was Francesco.

The painter had been deceased for about 40 annums when this account was documented.