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The youthful boy cries out as his skull is firmly held, a large digit digging into his cheek as his father's mighty palm grasps him by the throat. That scene from Abraham's Sacrifice appears in the Florentine museum, creating distress through Caravaggio's harrowing portrayal of the tormented youth from the biblical narrative. It appears as if the patriarch, instructed by God to kill his offspring, could snap his neck with a solitary turn. However Abraham's chosen method involves the metallic grey knife he holds in his remaining hand, ready to slit the boy's throat. A definite element remains – whomever posed as Isaac for this breathtaking piece displayed remarkable expressive ability. There exists not just fear, shock and pleading in his darkened gaze but additionally profound sorrow that a guardian could abandon him so utterly.

He took a familiar biblical tale and made it so vibrant and visceral that its horrors seemed to happen directly in front of the viewer

Standing in front of the artwork, observers recognize this as a real face, an precise depiction of a young subject, because the same boy – identifiable by his tousled hair and nearly dark pupils – appears in several additional paintings by the master. In every instance, that richly expressive visage dominates the scene. In Youth With a Ram, he peers playfully from the darkness while holding a lamb. In Amor Vincit Omnia, he grins with a hardness acquired on the city's alleys, his dark feathery wings demonic, a naked child running chaos in a well-to-do residence.

Amor Vincit Omnia, currently displayed at a British gallery, constitutes one of the most discomfiting masterpieces ever created. Observers feel totally disoriented gazing at it. The god of love, whose arrows inspire people with often painful longing, is portrayed as a very tangible, vividly illuminated unclothed figure, standing over toppled-over objects that comprise stringed instruments, a musical score, metal armour and an architect's T-square. This heap of possessions resembles, intentionally, the mathematical and construction equipment scattered across the ground in the German master's engraving Melencolia I – save here, the melancholic mess is caused by this grinning deity and the turmoil he can unleash.

"Love sees not with the vision, but with the mind, / And therefore is winged Love depicted blind," penned Shakespeare, just before this work was produced around 1601. But the painter's Cupid is not unseeing. He gazes straight at you. That countenance – ironic and ruddy-faced, looking with brazen confidence as he poses unclothed – is the identical one that screams in fear in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio created his three portrayals of the identical unusual-looking kid in Rome at the start of the 17th century, he was the highly celebrated religious painter in a metropolis enflamed by religious revival. Abraham's Offering reveals why he was commissioned to adorn sanctuaries: he could take a biblical narrative that had been portrayed many times previously and make it so new, so unfiltered and physical that the terror seemed to be happening directly before the spectator.

Yet there existed a different aspect to the artist, evident as quickly as he arrived in the capital in the cold season that concluded the sixteenth century, as a artist in his early twenties with no mentor or patron in the city, only skill and audacity. The majority of the paintings with which he caught the holy city's eye were everything but devout. What could be the absolute earliest resides in London's art museum. A young man opens his crimson mouth in a yell of pain: while reaching out his filthy digits for a fruit, he has instead been bitten. Youth Bitten by a Reptile is sensuality amid poverty: observers can see Caravaggio's gloomy chamber reflected in the murky waters of the transparent container.

The adolescent wears a pink blossom in his coiffure – a symbol of the sex commerce in early modern art. Northern Italian painters such as Titian and Palma Vecchio portrayed courtesans holding flowers and, in a work destroyed in the second world war but documented through photographs, the master represented a famous female courtesan, holding a bouquet to her chest. The meaning of all these botanical signifiers is obvious: sex for purchase.

What are we to make of Caravaggio's sensual portrayals of boys – and of one adolescent in specific? It is a question that has split his interpreters since he achieved widespread recognition in the twentieth century. The complicated past truth is that the artist was not the queer icon that, for example, the filmmaker put on screen in his twentieth-century film about the artist, nor so entirely pious that, as certain art historians improbably assert, his Youth Holding Fruit is in fact a portrait of Christ.

His early paintings do make overt erotic implications, or including offers. It's as if Caravaggio, then a penniless young creator, identified with Rome's prostitutes, offering himself to survive. In the Uffizi, with this thought in consideration, observers might turn to another early work, the 1596 masterwork the god of wine, in which the god of wine stares coolly at you as he begins to undo the black sash of his garment.

A several annums after Bacchus, what could have driven the artist to paint Victorious Cupid for the art patron Vincenzo Giustiniani, when he was finally becoming almost established with prestigious church commissions? This profane non-Christian deity resurrects the sexual provocations of his early works but in a increasingly intense, unsettling way. Half a century afterwards, its hidden meaning seemed obvious: it was a representation of the painter's companion. A English visitor saw Victorious Cupid in about the mid-seventeenth century and was informed its figure has "the body & face of [Caravaggio's|his] owne boy or assistant that slept with him". The name of this boy was Cecco.

The artist had been dead for about 40 annums when this story was documented.