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The youthful boy cries out while his head is forcefully held, a large digit pressing into his cheek as his father's powerful hand holds him by the throat. This scene from The Sacrifice of Isaac appears in the Uffizi Gallery, creating unease through Caravaggio's harrowing rendition of the tormented youth from the scriptural account. It seems as if the patriarch, commanded by God to sacrifice his son, could break his spinal column with a solitary twist. However Abraham's preferred method involves the metallic steel blade he grips in his other hand, prepared to slit the boy's neck. A certain element remains – whoever modeled as the sacrifice for this astonishing work demonstrated remarkable expressive ability. Within exists not only fear, surprise and begging in his darkened eyes but also profound sorrow that a guardian could abandon him so utterly.

He took a well-known scriptural story and transformed it so fresh and raw that its horrors appeared to unfold right in view of you

Viewing before the painting, viewers identify this as a real countenance, an accurate depiction of a adolescent model, because the identical boy – recognizable by his tousled locks and nearly dark eyes – appears in several additional paintings by Caravaggio. In every case, that richly emotional face dominates the composition. In John the Baptist, he peers mischievously from the shadows while embracing a ram. In Victorious Cupid, he smirks with a hardness acquired on the city's alleys, his black plumed appendages sinister, a unclothed adolescent creating chaos in a affluent residence.

Victorious Cupid, currently exhibited at a London gallery, represents one of the most discomfiting masterpieces ever painted. Observers feel completely unsettled looking at it. The god of love, whose arrows inspire people with often painful longing, is shown as a extremely tangible, brightly illuminated unclothed figure, straddling overturned objects that comprise musical instruments, a music manuscript, plate armour and an architect's T-square. This heap of possessions resembles, deliberately, the geometric and construction equipment strewn across the ground in Albrecht Dürer's engraving Melancholy – except in this case, the gloomy disorder is caused by this smirking Cupid and the turmoil he can release.

"Love sees not with the vision, but with the soul, / And therefore is winged Love depicted sightless," penned the Bard, just prior to this work was produced around 1601. But the painter's Cupid is not unseeing. He gazes straight at the observer. That face – ironic and rosy-cheeked, looking with brazen assurance as he poses unclothed – is the same one that shrieks in fear in The Sacrifice of Isaac.

When the Italian master painted his multiple images of the same distinctive-appearing kid in the Eternal City at the start of the 17th century, he was the highly acclaimed religious painter in a city ignited by religious revival. The Sacrifice of Isaac demonstrates why he was commissioned to decorate churches: he could adopt a biblical story that had been depicted many occasions previously and render it so fresh, so unfiltered and physical that the terror seemed to be occurring immediately before the spectator.

However there was another aspect to the artist, apparent as soon as he arrived in the capital in the winter that ended the sixteenth century, as a painter in his initial twenties with no teacher or patron in the urban center, just talent and boldness. The majority of the works with which he caught the holy city's eye were anything but holy. What may be the absolute earliest resides in the UK's art museum. A young man parts his crimson lips in a scream of pain: while reaching out his dirty digits for a fruit, he has rather been bitten. Youth Bitten by a Reptile is eroticism amid squalor: viewers can discern Caravaggio's dismal chamber mirrored in the cloudy waters of the glass vase.

The boy sports a pink flower in his hair – a symbol of the erotic trade in early modern art. Northern Italian painters such as Tiziano and Palma Vecchio depicted courtesans grasping flowers and, in a work destroyed in the WWII but documented through photographs, Caravaggio represented a renowned woman prostitute, holding a bouquet to her chest. The meaning of all these floral signifiers is clear: sex for purchase.

How are we to make of the artist'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 widespread recognition in the twentieth century. The complex historical truth is that the artist was not the homosexual hero that, for instance, the filmmaker put on screen in his 1986 film Caravaggio, nor so entirely pious that, as certain artistic historians improbably claim, his Youth Holding Fruit is in fact a portrait of Jesus.

His initial works do make overt sexual suggestions, or including propositions. It's as if Caravaggio, then a destitute young artist, identified with the city's sex workers, offering himself to survive. In the Uffizi, with this idea in mind, viewers might turn to an additional initial creation, the 1596 masterwork the god of wine, in which the god of wine stares coolly at the spectator as he starts to undo the dark sash of his robe.

A few years following the wine deity, what could have motivated Caravaggio to paint Victorious Cupid for the artistic collector the nobleman, when he was finally growing almost established with prestigious ecclesiastical projects? This profane non-Christian god resurrects the erotic provocations of his initial works but in a increasingly intense, uneasy way. Fifty years later, its hidden meaning seemed clear: it was a portrait of Caravaggio's lover. A British traveller saw Victorious Cupid in about 1649 and was told its figure has "the physique and countenance of [Caravaggio's|his] own youth or assistant that laid with him". The name of this boy was Cecco.

The artist had been deceased for about forty annums when this account was documented.