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A youthful boy screams while his skull is firmly held, a massive digit pressing into his cheek as his father's powerful palm holds him by the neck. That moment from Abraham's Sacrifice appears in the Florentine museum, creating unease through the artist's harrowing portrayal of the tormented child from the biblical account. It seems as if the patriarch, instructed by the Divine to sacrifice his offspring, could break his spinal column with a single turn. Yet the father's chosen method involves the metallic steel blade he holds in his other hand, prepared to cut Isaac's neck. One definite aspect stands out – whomever modeled as the sacrifice for this breathtaking piece demonstrated extraordinary acting skill. Within exists not just dread, surprise and begging in his darkened eyes but also profound grief that a protector could abandon him so utterly.

The artist adopted a familiar biblical story and transformed it so vibrant and raw that its horrors appeared to unfold directly in front of you

Standing in front of the painting, observers identify this as a actual face, an accurate depiction of a adolescent model, because the identical boy – identifiable by his disheveled locks and nearly black eyes – appears in several other paintings by the master. In every instance, that richly expressive visage commands the composition. In John the Baptist, he gazes mischievously from the darkness while embracing a lamb. In Victorious Cupid, he grins with a toughness acquired on the city's alleys, his black feathery wings sinister, a unclothed child running riot in a well-to-do dwelling.

Victorious Cupid, presently displayed at a London gallery, constitutes one of the most discomfiting masterpieces ever painted. Observers feel completely unsettled gazing at it. The god of love, whose arrows inspire people with often painful desire, is shown as a extremely tangible, vividly illuminated nude form, standing over overturned items that include musical devices, a musical manuscript, plate armor and an builder's T-square. This pile of possessions resembles, deliberately, the geometric and construction gear strewn across the ground in the German master's print Melencolia I – save in this case, the melancholic mess is caused by this smirking Cupid and the mayhem he can release.

"Love looks not with the vision, but with the soul, / And thus is winged Love painted sightless," wrote the Bard, just prior to this painting was created around the early 1600s. But the painter's Cupid is not blind. He stares directly at you. That countenance – ironic and ruddy-faced, staring with brazen confidence as he poses unclothed – is the same one that screams in fear in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio created his three portrayals of the same distinctive-appearing youth in the Eternal City at the start of the 17th century, he was the highly acclaimed religious artist in a city ignited by Catholic renewal. Abraham's Offering demonstrates why he was commissioned to decorate churches: he could adopt a biblical narrative that had been depicted many times previously and make it so new, so unfiltered and visceral that the horror appeared to be occurring immediately before you.

Yet there existed another aspect to Caravaggio, evident as quickly as he arrived in Rome in the winter that ended the sixteenth century, as a artist in his early 20s with no mentor or supporter in the city, only talent and boldness. Most of the works with which he captured the holy city's eye were anything but holy. That may be the absolute first hangs in the UK's National Gallery. A youth opens his red lips in a scream of agony: while stretching out his dirty digits for a fruit, he has instead been attacked. Boy Bitten By a Lizard is sensuality amid poverty: observers can see the painter's dismal chamber mirrored in the cloudy liquid of the transparent vase.

The boy wears a pink flower in his hair – a symbol of the sex commerce in early modern painting. Venetian artists such as Titian and Jacopo Palma depicted prostitutes grasping blooms and, in a work destroyed in the second world war but documented through images, the master portrayed a renowned female prostitute, holding a bouquet to her bosom. The meaning of all these floral signifiers is obvious: intimacy for purchase.

What are we to make of Caravaggio's erotic portrayals of youths – and of a particular adolescent in particular? It is a inquiry that has split his commentators ever since he achieved widespread recognition in the twentieth century. The complicated historical truth is that the painter was not the queer hero that, for example, Derek Jarman presented on screen in his 1986 film about the artist, nor so completely pious that, as some art scholars improbably claim, his Youth Holding Fruit is in fact a portrait of Christ.

His initial works do offer explicit sexual implications, or including offers. It's as if Caravaggio, then a destitute youthful artist, aligned with Rome's prostitutes, offering himself to live. In the Florentine gallery, with this thought in mind, viewers might turn to another early work, the sixteenth-century masterwork Bacchus, in which the deity of alcohol gazes coolly at the spectator as he starts to undo the dark sash of his garment.

A few years after Bacchus, what could have motivated Caravaggio to create Amor Vincit Omnia for the art collector Vincenzo Giustiniani, when he was at last growing nearly respectable with important church commissions? This unholy pagan deity resurrects the erotic challenges of his early works but in a more powerful, uneasy manner. Half a century later, its hidden meaning seemed clear: it was a representation of the painter's companion. A English visitor saw the painting in about the mid-seventeenth century and was told its subject has "the body & face of [Caravaggio's|his] own youth or assistant that laid with him". The identity of this adolescent was Francesco.

The artist had been dead for about 40 years when this account was recorded.