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The young boy cries out while his head is forcefully held, a large digit digging into his cheek as his father's powerful hand grasps him by the throat. This scene from The Sacrifice of Isaac appears in the Uffizi Gallery, creating unease through Caravaggio's chilling portrayal of the tormented child from the scriptural narrative. The painting seems as if the patriarch, commanded by God to sacrifice his son, could break his spinal column with a single turn. Yet the father's preferred method involves the silvery grey knife he holds in his remaining hand, prepared to slit Isaac's throat. A certain aspect remains – whoever modeled as Isaac for this breathtaking work displayed extraordinary acting ability. There exists not only fear, shock and pleading in his darkened gaze but also deep sorrow that a protector could abandon him so utterly.

The artist adopted a well-known scriptural tale and transformed it so fresh and visceral that its horrors seemed to unfold right in front of the viewer

Standing before the artwork, viewers identify this as a actual face, an precise record of a young subject, because the same boy – recognizable by his tousled hair and almost black pupils – features in several additional works by Caravaggio. In each case, that richly expressive face dominates the composition. In Youth With a Ram, he peers mischievously from the shadows while holding a ram. In Victorious Cupid, he grins with a hardness learned on the city's alleys, his black plumed appendages sinister, a unclothed adolescent running chaos in a affluent dwelling.

Victorious Cupid, presently displayed at a British gallery, constitutes one of the most embarrassing masterpieces ever painted. Observers feel totally disoriented looking at it. Cupid, whose arrows fill people with often painful desire, is portrayed as a very real, vividly illuminated nude form, straddling toppled-over items that comprise stringed devices, a musical manuscript, plate armor and an builder's ruler. This heap of items resembles, deliberately, the geometric and architectural equipment scattered across the ground in the German master's engraving Melancholy – save here, the gloomy disorder is created by this grinning deity and the turmoil he can release.

"Love looks not with the vision, but with the mind, / And thus is winged Cupid depicted sightless," wrote Shakespeare, shortly before this painting was created around the early 1600s. But the painter's god is not blind. He stares directly at you. That face – ironic and ruddy-cheeked, looking with bold assurance as he struts unclothed – is the same one that shrieks in fear in Abraham's Test.

As the Italian master painted his multiple portrayals of the same unusual-looking kid in the Eternal City at the start of the seventeenth century, he was the most acclaimed religious painter in a metropolis ignited by religious renewal. Abraham's Offering reveals why he was sought to adorn sanctuaries: he could adopt a scriptural story that had been depicted many occasions before and render it so fresh, so raw and visceral that the horror seemed to be occurring immediately in front of the spectator.

However there existed another side to Caravaggio, evident as quickly as he came in Rome in the winter that ended the sixteenth century, as a artist in his early 20s with no mentor or supporter in the city, only skill and boldness. The majority of the paintings with which he captured the holy city's eye were anything but devout. That may be the absolute first hangs in the UK's art museum. A young man parts his red mouth in a scream of agony: while stretching out his dirty digits for a fruit, he has rather been bitten. Youth Bitten by a Reptile is eroticism amid squalor: observers can discern Caravaggio's dismal room mirrored in the cloudy liquid of the glass vase.

The boy wears a rose-colored blossom in his hair – a symbol of the erotic commerce in Renaissance art. Northern Italian painters such as Tiziano and Palma Vecchio depicted prostitutes holding blooms and, in a work lost in the WWII but known through photographs, the master portrayed a famous female courtesan, clutching a posy to her chest. The message of all these botanical indicators is clear: sex for sale.

How are we to make of the artist's erotic depictions of boys – and of a particular adolescent in particular? It is a question that has divided his interpreters since he gained mega-fame in the 1980s. The complicated historical truth is that the artist was not the homosexual icon that, for instance, Derek Jarman put on film in his 1986 movie Caravaggio, nor so entirely devout that, as some art historians unbelievably claim, his Boy With a Basket of Fruit is in fact a likeness of Christ.

His initial works indeed offer explicit sexual suggestions, or even propositions. It's as if Caravaggio, then a penniless young artist, aligned with Rome's sex workers, selling himself to survive. In the Uffizi, with this idea in mind, viewers might look to an additional initial work, the 1596 masterpiece Bacchus, in which the god of wine gazes coolly at the spectator as he begins to untie the dark ribbon of his robe.

A several annums following Bacchus, what could have motivated the artist to paint Amor Vincit Omnia for the artistic collector the nobleman, when he was finally growing almost established with prestigious ecclesiastical commissions? This profane pagan god revives the sexual provocations of his initial works but in a more intense, uneasy way. Fifty years later, its hidden meaning seemed obvious: it was a portrait of the painter's lover. A English traveller saw the painting in about the mid-seventeenth century and was told its subject has "the physique and countenance of [Caravaggio's|his] own boy or servant that laid with him". The name of this adolescent was Cecco.

The artist had been dead for about 40 annums when this account was recorded.