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A young lad cries out as his head is forcefully gripped, a large thumb pressing into his cheek as his parent's mighty palm holds him by the throat. This scene from The Sacrifice of Isaac visits the Uffizi Gallery, evoking distress through the artist's chilling portrayal of the suffering child from the biblical account. It seems as if Abraham, instructed by God to sacrifice his offspring, could break his spinal column with a solitary turn. However the father's preferred method involves the metallic grey blade he grips in his other palm, ready to cut the boy's neck. A definite element stands out – whomever posed as the sacrifice for this breathtaking piece displayed extraordinary expressive ability. Within exists not only dread, surprise and begging in his shadowed gaze but also deep grief that a protector could betray him so utterly.

The artist adopted a well-known biblical story and made it so fresh and raw that its horrors appeared to unfold right in view of you

Standing in front of the artwork, observers recognize this as a real face, an accurate record of a young subject, because the identical boy – recognizable by his disheveled locks and nearly black eyes – appears in two additional works by Caravaggio. In each instance, that richly expressive face dominates the composition. 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 sinister, a unclothed child running riot in a affluent dwelling.

Victorious Cupid, currently exhibited at a British museum, represents one of the most discomfiting masterpieces ever painted. Observers feel totally unsettled gazing at it. Cupid, whose darts inspire people with frequently painful desire, is shown as a extremely tangible, brightly illuminated unclothed form, standing over toppled-over items that include stringed instruments, a musical manuscript, metal armour and an architect's ruler. This pile of items echoes, intentionally, the geometric and architectural equipment scattered across the ground in the German master's engraving Melancholy – save here, the melancholic disorder is created by this grinning deity and the mayhem he can unleash.

"Affection sees not with the eyes, but with the soul, / And thus is feathered Love depicted sightless," wrote the Bard, just before this painting was created around 1601. But Caravaggio's Cupid is not blind. He stares directly at you. That countenance – ironic and ruddy-faced, looking with bold confidence as he poses unclothed – is the identical one that screams in fear in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio painted his multiple images of the identical distinctive-looking youth in Rome at the dawn of the 17th century, he was the most acclaimed religious artist in a metropolis ignited by religious revival. Abraham's Offering reveals why he was sought to adorn sanctuaries: he could take a biblical story that had been depicted many times before and make it so new, so unfiltered and visceral that the terror seemed to be occurring immediately before the spectator.

Yet there existed a different aspect to Caravaggio, evident as soon as he arrived in the capital in the cold season that ended the sixteenth century, as a artist in his early twenties with no teacher or patron in the city, just talent and boldness. The majority of the works with which he captured the sacred metropolis's eye were everything but devout. That could be the very earliest hangs in the UK's National Gallery. A youth opens his red mouth in a scream of agony: while stretching out his filthy fingers for a cherry, he has rather been attacked. Youth Bitten by a Reptile is sensuality amid squalor: viewers can see the painter's dismal room mirrored in the cloudy waters of the transparent vase.

The boy sports a rose-colored blossom in his hair – a emblem of the sex trade in Renaissance art. Northern Italian artists such as Tiziano and Jacopo Palma depicted prostitutes holding flowers and, in a painting destroyed in the WWII but documented through images, Caravaggio represented a famous female courtesan, clutching a bouquet to her chest. The message of all these botanical signifiers is obvious: sex for purchase.

What are we to interpret of the artist's sensual portrayals of boys – and of a particular boy in particular? It is a inquiry that has split his interpreters ever since he achieved mega-fame in the 1980s. The complicated historical truth is that the painter was not the queer hero that, for example, Derek Jarman presented on screen in his twentieth-century film about the artist, nor so entirely pious that, as certain art scholars unbelievably claim, his Youth Holding Fruit is in fact a likeness of Christ.

His early works do make explicit sexual suggestions, or including propositions. It's as if Caravaggio, then a penniless young creator, aligned with the city's sex workers, selling himself to live. In the Uffizi, with this thought in mind, observers might turn to another early work, the 1596 masterpiece Bacchus, in which the god of wine gazes calmly at you as he begins to untie the dark sash of his robe.

A several years following the wine deity, what could have motivated Caravaggio to paint Victorious Cupid for the art patron the nobleman, when he was finally becoming nearly respectable with prestigious ecclesiastical projects? This unholy non-Christian god revives the sexual challenges of his initial works but in a increasingly intense, unsettling way. Half a century later, its secret seemed obvious: it was a portrait of the painter's lover. A English traveller viewed Victorious Cupid in about 1649 and was informed its figure has "the body & face of [Caravaggio's|his] owne boy or servant that slept with him". The identity of this boy was Cecco.

The artist had been dead for about forty annums when this story was recorded.