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A youthful lad cries out as his skull is forcefully gripped, a large digit digging into his face as his father's mighty hand grasps him by the neck. That scene from The Sacrifice of Isaac visits the Uffizi Gallery, creating distress through Caravaggio's chilling rendition of the tormented youth from the biblical account. It appears as if Abraham, commanded by the Divine to kill his offspring, could break his neck with a single twist. Yet Abraham's preferred approach involves the silvery grey knife he grips in his other palm, ready to cut the boy's throat. One definite element remains – whoever posed as Isaac for this astonishing piece displayed extraordinary expressive ability. Within exists not just dread, surprise and pleading in his shadowed gaze but also deep grief that a protector could betray him so utterly.

He adopted a well-known scriptural tale and transformed it so vibrant and raw that its horrors appeared to unfold right in front of the viewer

Standing before the painting, viewers recognize this as a real countenance, an precise record of a young model, because the identical youth – recognizable by his disheveled hair and nearly black pupils – appears in several other works by the master. In each case, that highly expressive visage dominates the composition. In Youth With a Ram, he peers playfully from the darkness while holding a ram. In Victorious Cupid, he smirks with a hardness acquired on Rome's streets, his black feathery wings demonic, a unclothed adolescent creating chaos in a affluent residence.

Amor Vincit Omnia, currently exhibited at a British museum, constitutes one of the most discomfiting masterpieces ever created. Viewers feel completely unsettled gazing at it. The god of love, whose arrows inspire people with frequently painful longing, is shown as a extremely real, brightly illuminated unclothed form, standing over overturned items that include musical instruments, a musical manuscript, plate armor and an architect's ruler. This heap of possessions resembles, deliberately, the mathematical and architectural gear scattered across the floor in Albrecht Dürer's engraving Melencolia I – save here, the melancholic mess is caused by this grinning Cupid and the turmoil he can unleash.

"Love looks not with the eyes, but with the soul, / And therefore is winged Love depicted sightless," wrote the Bard, shortly before this painting was produced around the early 1600s. But Caravaggio's god is not blind. He stares directly at the observer. That face – sardonic and ruddy-faced, looking with brazen confidence as he poses unclothed – is the identical one that shrieks in terror in Abraham's Test.

When the Italian master painted his multiple portrayals of the identical distinctive-appearing youth in Rome at the start of the 17th century, he was the most celebrated religious painter in a city enflamed by Catholic revival. The Sacrifice of Isaac demonstrates why he was sought to adorn sanctuaries: he could adopt a biblical story that had been portrayed many times previously and make it so fresh, so raw and visceral that the horror seemed to be happening immediately in front of the spectator.

However there was a different side to Caravaggio, evident as quickly as he came in Rome in the cold season that ended the sixteenth century, as a painter in his early 20s with no teacher or supporter in the city, just talent and audacity. The majority of the paintings with which he caught the sacred metropolis's eye were everything but devout. That could be the very earliest hangs in the UK's National Gallery. A young man opens his red mouth in a yell of agony: while reaching out his dirty fingers for a fruit, he has rather been attacked. Youth Bitten by a Reptile is eroticism amid poverty: viewers can see the painter's gloomy room reflected in the cloudy liquid of the transparent vase.

The boy sports a rose-colored flower in his hair – a emblem of the sex trade in Renaissance painting. Northern Italian painters such as Titian and Jacopo Palma depicted prostitutes holding blooms and, in a painting lost in the second world war but documented through images, Caravaggio portrayed a renowned female courtesan, clutching a posy to her bosom. The meaning of all these botanical indicators is obvious: intimacy for sale.

What are we to interpret of Caravaggio's sensual depictions of youths – and of a particular boy in particular? It is a inquiry that has split his commentators ever since he achieved mega-fame in the 1980s. The complex past reality is that the artist was not the homosexual hero that, for example, the filmmaker presented on screen in his 1986 movie Caravaggio, nor so entirely pious that, as some artistic historians improbably claim, his Youth Holding Fruit is in fact a likeness of Christ.

His initial works do offer explicit sexual implications, or even propositions. It's as if the painter, then a penniless young artist, aligned with the city's prostitutes, offering himself to survive. In the Florentine gallery, with this idea in mind, viewers might look to an additional early work, the 1596 masterpiece Bacchus, in which the deity of alcohol stares coolly at you as he starts to untie the dark sash of his garment.

A few annums following the wine deity, what could have motivated Caravaggio to paint Victorious Cupid for the artistic patron the nobleman, when he was at last growing almost respectable with important church commissions? This unholy non-Christian god resurrects the erotic challenges of his early works but in a more powerful, uneasy way. Half a century later, its secret seemed clear: it was a representation of the painter's lover. A English visitor saw the painting in about 1649 and was informed its figure has "the body & face of [Caravaggio's|his] owne youth or assistant that slept with him". The identity of this boy was Cecco.

The painter had been dead for about forty annums when this story was documented.