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A young lad screams while his skull is forcefully gripped, a massive digit pressing into his face as his father's powerful hand holds him by the throat. This scene from The Sacrifice of Isaac appears in the Uffizi Gallery, evoking distress through the artist's harrowing rendition of the tormented youth from the biblical narrative. It seems as if the patriarch, commanded by the Divine to kill his offspring, could break his spinal column with a solitary twist. Yet Abraham's preferred method involves the silvery steel knife he grips in his remaining palm, ready to slit the boy's throat. A certain aspect remains – whomever modeled as Isaac for this astonishing piece displayed remarkable expressive skill. There exists not just dread, surprise and pleading in his shadowed eyes but also profound sorrow that a protector could abandon him so utterly.

He adopted a familiar scriptural story and made it so fresh and visceral that its terrors appeared to unfold directly in view of you

Standing in front of the painting, observers identify this as a actual face, an accurate depiction of a adolescent subject, because the same boy – identifiable by his tousled hair and nearly black pupils – features in several other works by Caravaggio. In every instance, that highly emotional visage dominates the scene. In John the Baptist, he gazes mischievously from the shadows while embracing a ram. In Amor Vincit Omnia, he smirks with a hardness learned on Rome's streets, his dark plumed wings demonic, a unclothed child running chaos in a well-to-do dwelling.

Amor Vincit Omnia, presently exhibited at a London gallery, represents one of the most discomfiting masterpieces ever created. Viewers feel completely unsettled gazing at it. The god of love, whose arrows fill people with frequently painful longing, is shown as a extremely tangible, vividly illuminated nude form, straddling overturned items that comprise stringed instruments, a music manuscript, metal armor and an architect's T-square. This heap of items echoes, intentionally, the geometric and architectural equipment scattered across the floor in the German master's print Melencolia I – save in this case, the gloomy mess is created by this grinning Cupid and the mayhem he can release.

"Love looks not with the vision, but with the mind, / And thus is winged Love painted blind," penned Shakespeare, shortly before this painting was produced around 1601. But the painter's god is not blind. He stares directly at the observer. That countenance – ironic and rosy-cheeked, staring with brazen assurance as he poses naked – is the same one that shrieks in terror in The Sacrifice of Isaac.

When the Italian master created his three images of the identical unusual-appearing youth in Rome at the dawn of the 17th century, he was the highly celebrated religious painter in a city ignited by Catholic revival. Abraham's Offering reveals why he was sought to decorate churches: he could adopt a scriptural narrative that had been depicted numerous occasions before and make it so new, so unfiltered and visceral that the terror seemed to be occurring immediately in front of the spectator.

Yet there existed a different side to Caravaggio, evident as quickly as he came in the capital in the cold season that ended 1592, as a painter in his early 20s with no teacher or supporter in the urban center, just skill and audacity. The majority of the works with which he caught the sacred city's eye were everything but holy. That could be the very first hangs in the UK's National Gallery. A young man parts his red mouth in a scream of agony: while stretching out his dirty fingers for a fruit, he has instead been bitten. Youth Bitten by a Reptile is sensuality amid poverty: viewers can discern Caravaggio's dismal chamber reflected in the cloudy waters of the transparent vase.

The boy wears a rose-colored blossom in his coiffure – a emblem of the sex trade in early modern art. Northern Italian artists such as Titian and Jacopo Palma portrayed prostitutes holding flowers and, in a painting destroyed in the second world war but documented through images, Caravaggio portrayed a famous female prostitute, holding a posy to her chest. The message of all these floral signifiers is obvious: sex for sale.

What are we to interpret of the artist's erotic portrayals of youths – and of a particular adolescent in particular? It is a inquiry that has divided his commentators since he gained widespread recognition in the 1980s. The complex historical truth is that the painter was neither the queer icon that, for example, Derek Jarman put on film in his twentieth-century movie Caravaggio, nor so completely pious that, as certain artistic historians improbably claim, his Boy With a Basket of Fruit is actually a portrait of Christ.

His initial works indeed make explicit sexual suggestions, or including offers. It's as if the painter, then a penniless youthful creator, aligned with Rome's sex workers, selling himself to survive. In the Florentine gallery, with this idea in mind, observers might turn to an additional early work, the 1596 masterpiece the god of wine, in which the god of wine stares calmly at the spectator as he starts to untie the dark ribbon of his garment.

A few years following Bacchus, what could have motivated the artist to paint Amor Vincit Omnia for the artistic collector the nobleman, when he was at last becoming almost respectable with prestigious church commissions? This unholy pagan deity revives the erotic provocations of his initial paintings but in a increasingly intense, uneasy manner. Half a century afterwards, its hidden meaning seemed obvious: it was a representation of the painter's lover. A British traveller viewed Victorious Cupid in about the mid-seventeenth century and was informed its figure has "the physique and countenance of [Caravaggio's|his] owne boy or servant that slept with him". The identity of this boy was Cecco.

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