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A youthful boy cries out as his skull is firmly gripped, a massive thumb pressing into his cheek as his father's mighty hand holds him by the neck. This scene from The Sacrifice of Isaac appears in the Florentine museum, creating distress through the artist's harrowing portrayal of the suffering youth from the scriptural narrative. The painting seems as if Abraham, instructed by the Divine to kill his offspring, could break his neck with a single turn. Yet Abraham's chosen method involves the metallic grey knife he holds in his remaining hand, prepared to cut the boy's throat. A certain element stands out – whoever posed as Isaac for this astonishing work demonstrated extraordinary acting skill. There exists not just fear, shock and begging in his shadowed eyes but additionally deep sorrow that a protector could betray him so completely.

The artist took a familiar biblical story and transformed it so fresh and raw that its horrors seemed to unfold right in front of you

Standing in front of the painting, observers recognize this as a real countenance, an accurate depiction of a young model, because the same youth – recognizable by his tousled hair and nearly dark eyes – features in several additional paintings by the master. In each instance, that richly expressive face commands the scene. In John the Baptist, he peers mischievously from the shadows while holding a ram. In Victorious Cupid, he grins with a toughness learned on Rome's alleys, his black plumed appendages sinister, a unclothed adolescent creating chaos in a affluent residence.

Amor Vincit Omnia, presently exhibited at a British museum, represents one of the most embarrassing masterpieces ever created. Observers feel completely unsettled gazing at it. Cupid, whose darts fill people with often agonizing desire, is shown as a very real, brightly illuminated unclothed form, straddling overturned objects that include musical instruments, a musical score, plate armor and an builder's T-square. This heap of items resembles, deliberately, the geometric and construction gear strewn across the ground in the German master's engraving Melancholy – save in this case, the gloomy disorder is created by this smirking deity and the turmoil he can unleash.

"Affection looks not with the vision, but with the mind, / And thus is winged Love depicted blind," wrote the Bard, just prior to this painting was created around 1601. But the painter's Cupid is not blind. He gazes straight at you. That face – ironic and ruddy-cheeked, staring with bold assurance as he poses unclothed – is the same one that screams in fear in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio created his multiple portrayals of the identical distinctive-looking kid in Rome at the dawn of the 17th century, he was the most celebrated sacred artist in a metropolis ignited by Catholic revival. Abraham's Offering demonstrates why he was sought to adorn sanctuaries: he could adopt a scriptural narrative that had been depicted many occasions previously and render it so new, so raw and physical that the terror appeared to be happening immediately in front of the spectator.

However there was a different aspect to Caravaggio, apparent as soon as he came in Rome in the cold season that ended 1592, as a artist in his early 20s with no teacher or supporter in the urban center, only talent and audacity. The majority of the paintings with which he captured the holy metropolis's eye were anything but holy. What may be the very earliest resides in the UK's art museum. A youth opens his red lips in a scream of agony: while reaching out his filthy fingers for a cherry, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid poverty: viewers can see Caravaggio's dismal chamber mirrored in the murky waters of the transparent container.

The boy sports a rose-colored flower in his coiffure – a symbol of the erotic commerce in early modern art. Venetian painters such as Tiziano and Jacopo Palma depicted courtesans holding flowers and, in a painting destroyed in the second world war but documented through images, the master portrayed a renowned woman prostitute, clutching a posy to her bosom. The message of all these botanical signifiers is clear: sex for purchase.

What are we to make of the artist's erotic portrayals of boys – and of a particular adolescent in particular? It is a inquiry that has divided his interpreters since he gained widespread recognition in the twentieth century. The complex past truth is that the artist was neither the homosexual hero that, for example, the filmmaker presented on film in his 1986 film about the artist, nor so entirely devout that, as some art historians improbably claim, his Youth Holding Fruit is actually a likeness of Jesus.

His early paintings indeed offer explicit erotic suggestions, or including propositions. It's as if the painter, then a penniless young artist, aligned with Rome's prostitutes, offering himself to survive. In the Florentine gallery, with this thought in mind, viewers might look to another early work, the 1596 masterwork the god of wine, in which the deity of alcohol gazes coolly at you as he starts to undo the dark ribbon of his garment.

A several annums after Bacchus, what could have motivated the artist to create Amor Vincit Omnia for the art collector the nobleman, when he was at last becoming nearly established with important ecclesiastical projects? This profane pagan god resurrects the sexual challenges of his initial paintings but in a increasingly intense, unsettling way. Fifty years afterwards, its hidden meaning seemed clear: it was a portrait of the painter's lover. A British traveller saw the painting in about 1649 and was told its subject has "the body & face of [Caravaggio's|his] owne youth or assistant that laid with him". The identity of this adolescent was Cecco.

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