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The young boy cries out as his head is firmly held, a massive digit digging into his face as his parent's mighty hand grasps him by the neck. That moment from The Sacrifice of Isaac visits the Uffizi Gallery, evoking unease through the artist's harrowing portrayal of the suffering youth from the scriptural account. The painting appears as if Abraham, instructed by God to sacrifice his son, could snap his spinal column with a single twist. Yet Abraham's chosen method involves the metallic steel blade he grips in his other hand, ready to cut the boy's neck. A certain aspect remains – whoever modeled as the sacrifice for this astonishing piece demonstrated remarkable acting ability. Within exists not only fear, shock and pleading in his shadowed gaze but also deep sorrow that a guardian could abandon him so utterly.

He took a familiar scriptural tale and transformed it so vibrant and raw that its terrors appeared to unfold right in front of you

Standing in front of the artwork, observers recognize this as a real countenance, an precise depiction of a young subject, because the identical boy – identifiable by his tousled locks and nearly black pupils – appears in several additional works by Caravaggio. In each case, that highly emotional visage commands the composition. In John the Baptist, he peers playfully from the shadows while holding a ram. In Amor Vincit Omnia, he grins with a hardness acquired on the city's alleys, his dark plumed appendages demonic, a unclothed adolescent running riot in a affluent dwelling.

Victorious Cupid, currently displayed at a British museum, represents one of the most embarrassing artworks ever painted. Viewers feel completely disoriented gazing at it. Cupid, whose arrows fill people with often agonizing desire, is portrayed as a very real, vividly lit unclothed figure, standing over overturned items that include musical instruments, a music manuscript, metal armor and an builder's T-square. This pile of items resembles, deliberately, the geometric and architectural gear strewn across the ground in the German master's print Melencolia I – save in this case, the gloomy mess is created by this grinning deity and the turmoil he can unleash.

"Affection sees not with the eyes, but with the mind, / And thus is feathered Love painted blind," wrote the Bard, just before this painting was created around the early 1600s. But the painter's god is not unseeing. He stares directly at the observer. That face – sardonic and rosy-cheeked, looking with brazen assurance as he struts unclothed – is the identical one that screams in terror in Abraham's Test.

As the Italian master created his three images of the same distinctive-looking kid in the Eternal City at the dawn of the 17th century, he was the most acclaimed sacred painter in a city ignited by Catholic renewal. The Sacrifice of Isaac demonstrates why he was commissioned to adorn sanctuaries: he could adopt a biblical story that had been depicted numerous occasions previously and make it so new, so unfiltered and visceral that the terror seemed to be happening directly before the spectator.

However there existed a different aspect to Caravaggio, apparent 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 patron in the city, just skill and audacity. The majority of the works with which he captured the sacred city's eye were anything but holy. What could be the very first resides in the UK's art museum. A youth opens his red lips in a yell of pain: while stretching out his dirty digits for a cherry, he has rather been bitten. Youth Bitten by a Reptile is sensuality amid squalor: viewers can see Caravaggio's dismal chamber reflected in the murky waters of the glass vase.

The adolescent wears a pink blossom in his coiffure – a emblem of the sex trade in Renaissance art. Northern Italian artists such as Tiziano and Jacopo Palma portrayed prostitutes holding blooms and, in a work destroyed in the WWII but known through photographs, Caravaggio portrayed a renowned female courtesan, clutching a posy to her bosom. The meaning of all these floral signifiers is obvious: sex for purchase.

How are we to make of Caravaggio's sensual depictions of boys – and of a particular adolescent in particular? It is a inquiry that has split his interpreters ever since he achieved widespread recognition in the twentieth century. The complex historical reality is that the artist was neither the queer hero that, for instance, Derek Jarman put on screen in his twentieth-century movie about the artist, nor so entirely pious that, as some art historians improbably assert, his Youth Holding Fruit is in fact a portrait of Jesus.

His initial works indeed offer explicit erotic implications, or even offers. It's as if Caravaggio, then a destitute youthful creator, identified with the city's prostitutes, offering himself to survive. In the Florentine gallery, with this idea in consideration, observers might look to an additional early work, the sixteenth-century masterpiece the god of wine, in which the deity of wine stares coolly at you as he starts to undo the black sash of his robe.

A several annums after Bacchus, what could have driven Caravaggio to paint Amor Vincit Omnia for the artistic collector the nobleman, when he was finally growing nearly established with prestigious church projects? This profane pagan god resurrects the erotic provocations of his early works but in a increasingly intense, unsettling manner. Fifty years afterwards, its secret seemed obvious: it was a portrait of the painter's companion. A British visitor viewed Victorious Cupid in about the mid-seventeenth century and was informed its subject has "the body & face of [Caravaggio's|his] own youth or assistant that laid with him". The name of this adolescent was Cecco.

The painter had been deceased for about 40 years when this account was documented.