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A youthful lad screams while his head is firmly held, a massive thumb digging into his face as his parent's powerful hand holds him by the throat. This scene from Abraham's Sacrifice appears in the Uffizi Gallery, evoking distress through the artist's chilling portrayal of the tormented youth from the scriptural narrative. It seems as if Abraham, commanded by the Divine to kill his offspring, could break his spinal column with a solitary turn. Yet the father's chosen method involves the silvery grey blade he holds in his remaining palm, ready to slit the boy's throat. One certain element stands out – whoever posed as Isaac for this breathtaking work demonstrated extraordinary acting skill. Within exists not just fear, shock and pleading in his shadowed gaze but additionally deep sorrow that a guardian could betray him so completely.

The artist adopted a well-known scriptural story and transformed it so vibrant and visceral that its horrors appeared to happen directly in front of the viewer

Viewing in front of the artwork, viewers recognize this as a actual countenance, an accurate depiction of a adolescent model, because the identical boy – identifiable by his tousled hair and nearly black pupils – features in several other paintings by Caravaggio. In every case, that richly emotional visage dominates the scene. In John the Baptist, he peers playfully from the darkness while holding a lamb. In Amor Vincit Omnia, he smirks with a toughness acquired on the city's streets, his dark plumed wings sinister, a naked adolescent running riot in a well-to-do dwelling.

Victorious Cupid, currently exhibited at a London museum, constitutes one of the most embarrassing masterpieces ever created. Viewers feel completely disoriented gazing at it. The god of love, whose arrows inspire people with often painful desire, is shown as a extremely real, vividly illuminated unclothed form, straddling overturned objects that comprise musical instruments, a music manuscript, plate armour and an builder's T-square. This heap of items resembles, intentionally, the geometric and construction equipment strewn across the floor in the German master's engraving Melancholy – except in this case, the melancholic disorder is created by this grinning deity and the turmoil he can unleash.

"Love looks not with the eyes, but with the soul, / And thus is feathered Love painted sightless," penned the Bard, shortly before this work was produced around the early 1600s. But Caravaggio's Cupid is not unseeing. He stares straight at you. That countenance – ironic and ruddy-faced, looking with brazen assurance as he struts unclothed – is the same one that screams in terror in The Sacrifice of Isaac.

When the Italian master created his multiple images of the same distinctive-looking youth in Rome at the start of the seventeenth century, he was the highly celebrated sacred painter in a city enflamed by religious revival. Abraham's Offering demonstrates why he was sought to decorate sanctuaries: he could take a scriptural narrative that had been portrayed many times previously and make it so new, so raw and physical that the horror appeared to be occurring directly before the spectator.

Yet there existed another side to the artist, evident as soon as he arrived in Rome in the winter that ended the sixteenth century, as a painter in his initial twenties with no mentor or patron in the city, only talent and audacity. Most of the works with which he caught the holy metropolis's eye were anything but holy. What may be the very first resides in the UK's National Gallery. A youth parts his crimson mouth in a yell of pain: while reaching out his filthy fingers for a cherry, he has rather been bitten. Boy Bitten By a Lizard is eroticism amid poverty: viewers can discern the painter's gloomy room mirrored in the cloudy liquid of the transparent vase.

The boy wears a pink flower in his hair – a emblem of the erotic commerce in early modern art. Northern Italian painters such as Titian and Jacopo Palma portrayed prostitutes grasping flowers and, in a painting destroyed in the second world war but documented through photographs, Caravaggio represented a renowned female courtesan, clutching a posy to her bosom. The message of all these floral signifiers is obvious: intimacy for purchase.

What are we to make of the artist's erotic depictions of boys – and of a particular boy in particular? It is a question that has split his interpreters since he gained mega-fame in the twentieth century. The complicated past reality is that the painter was neither the homosexual hero that, for example, the filmmaker presented on film in his 1986 movie Caravaggio, nor so completely pious that, as some artistic historians unbelievably assert, his Boy With a Basket of Fruit is in fact a portrait of Christ.

His early works indeed make explicit erotic implications, or including offers. It's as if the painter, then a destitute youthful artist, identified with Rome's prostitutes, offering himself to live. In the Uffizi, with this idea in consideration, observers might turn to another early creation, the 1596 masterwork Bacchus, in which the deity of alcohol gazes calmly at you as he starts to undo the black ribbon of his robe.

A several years after Bacchus, what could have motivated the artist to paint Victorious Cupid for the artistic collector the nobleman, when he was at last becoming almost respectable with prestigious church projects? This profane non-Christian deity resurrects the erotic challenges of his initial works but in a increasingly powerful, unsettling manner. Fifty years afterwards, its secret seemed clear: it was a portrait of Caravaggio's lover. A English traveller saw Victorious Cupid in about the mid-seventeenth century and was informed its subject has "the body & face of [Caravaggio's|his] own youth or servant that slept with him". The identity of this boy was Francesco.

The painter had been dead for about forty years when this story was recorded.