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The young lad screams while his skull is forcefully gripped, a large digit pressing into his cheek as his parent's mighty palm holds him by the neck. That scene from Abraham's Sacrifice appears in the Uffizi Gallery, evoking unease through the artist's harrowing rendition of the suffering youth from the biblical narrative. It appears as if Abraham, instructed by God to kill his son, could break his spinal column with a solitary twist. Yet the father's preferred approach involves the metallic grey knife he holds in his other hand, prepared to cut the boy's neck. A certain element stands out – whomever posed as the sacrifice for this breathtaking work demonstrated extraordinary acting skill. There exists not only dread, surprise and begging in his darkened gaze but also profound sorrow that a protector could abandon him so completely.

He took a familiar biblical story and made it so vibrant and visceral that its terrors seemed to unfold right in view of the viewer

Viewing before the painting, observers recognize this as a real face, an accurate record of a young subject, because the same youth – identifiable by his disheveled hair and almost dark eyes – appears in two additional paintings by the master. In each case, that highly expressive face commands the scene. In John the Baptist, he gazes mischievously from the darkness while holding a lamb. In Amor Vincit Omnia, he smirks with a toughness learned on Rome's alleys, his dark feathery wings demonic, a naked child running riot in a well-to-do dwelling.

Victorious Cupid, currently exhibited at a London gallery, represents one of the most embarrassing artworks ever painted. Viewers feel totally unsettled looking at it. The god of love, whose darts fill people with often agonizing longing, is portrayed as a very tangible, brightly illuminated nude form, straddling toppled-over items that comprise musical devices, a musical manuscript, plate armor and an architect's T-square. This heap of possessions echoes, intentionally, the mathematical and architectural equipment scattered across the floor in the German master's print Melancholy – except in this case, the gloomy mess is caused by this grinning Cupid and the turmoil he can unleash.

"Love sees not with the eyes, but with the soul, / And thus is winged Cupid painted blind," penned Shakespeare, just prior to this work was created around the early 1600s. But the painter's Cupid is not unseeing. He gazes straight at the observer. That countenance – sardonic and ruddy-faced, staring with brazen assurance as he struts naked – is the identical one that screams in fear in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio created his multiple portrayals of the same distinctive-appearing kid in the Eternal City at the dawn of the seventeenth century, he was the most acclaimed religious painter in a city ignited by Catholic revival. Abraham's Offering reveals why he was sought to decorate churches: he could adopt a biblical narrative that had been depicted numerous occasions previously and make it so fresh, so unfiltered and visceral that the horror seemed to be occurring immediately in front of the spectator.

Yet there was a different aspect to Caravaggio, apparent as quickly as he arrived in Rome in the winter that concluded the sixteenth century, as a painter in his early 20s with no teacher or supporter in the city, just talent and boldness. Most of the works with which he caught the holy city's eye were everything but holy. That may be the very first hangs in the UK's art museum. A young man opens his red mouth in a yell of pain: while stretching out his filthy fingers for a fruit, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid squalor: viewers can discern Caravaggio's dismal chamber reflected in the murky liquid of the glass vase.

The adolescent sports a pink blossom in his hair – a emblem of the erotic trade in Renaissance art. Venetian artists such as Titian and Palma Vecchio portrayed courtesans grasping blooms and, in a painting lost in the second world war but known through photographs, Caravaggio portrayed a famous woman prostitute, holding a bouquet to her chest. The meaning of all these floral signifiers is clear: sex for purchase.

How are we to make of the artist's sensual depictions of youths – and of one boy in specific? It is a inquiry that has divided his interpreters ever since he gained mega-fame in the twentieth century. The complex past reality is that the artist was neither the homosexual hero that, for example, Derek Jarman presented on screen in his twentieth-century movie Caravaggio, nor so entirely pious that, as certain art historians unbelievably assert, his Boy With a Basket of Fruit is in fact a likeness of Christ.

His initial paintings do offer explicit erotic implications, or even propositions. It's as if Caravaggio, then a destitute young artist, aligned with Rome's sex workers, selling himself to live. In the Uffizi, with this thought in mind, viewers might turn to an additional initial creation, the 1596 masterpiece Bacchus, in which the god of alcohol gazes calmly at you as he starts to untie the dark ribbon of his robe.

A several years following Bacchus, what could have driven the artist to create Victorious Cupid for the artistic patron the nobleman, when he was finally growing almost respectable with important ecclesiastical projects? This profane non-Christian deity revives the erotic challenges of his early works 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 traveller 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 Francesco.

The painter had been deceased for about 40 years when this story was documented.