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The youthful lad cries out while his head is firmly held, a massive thumb digging into his cheek as his father's powerful palm holds him by the throat. This scene from Abraham's Sacrifice appears in the Uffizi Gallery, evoking unease through Caravaggio's harrowing rendition of the tormented child from the scriptural account. It seems as if Abraham, instructed by God to sacrifice his son, could snap his neck with a single twist. Yet Abraham's chosen method involves the metallic grey blade he holds in his remaining palm, prepared to slit Isaac's neck. One definite element stands out – whomever modeled as the sacrifice for this astonishing piece demonstrated extraordinary acting skill. There exists not only fear, surprise and begging in his shadowed gaze but also profound sorrow that a protector could abandon him so completely.

He adopted a well-known biblical tale and transformed it so vibrant and visceral that its horrors appeared to unfold directly in front of the viewer

Standing in front of the artwork, observers identify this as a real countenance, an accurate record of a adolescent model, because the identical boy – identifiable by his tousled locks and nearly dark pupils – appears in two other paintings by Caravaggio. In every instance, that richly expressive face dominates the scene. In John the Baptist, he gazes mischievously from the darkness while holding a lamb. In Amor Vincit Omnia, he grins with a toughness acquired on Rome's streets, his black feathery appendages sinister, a naked child running riot in a well-to-do residence.

Victorious Cupid, currently displayed at a British museum, represents one of the most discomfiting masterpieces ever created. Observers feel completely disoriented looking at it. The god of love, whose darts fill people with often painful desire, is portrayed as a extremely real, brightly illuminated nude form, straddling overturned objects that comprise musical instruments, a musical manuscript, plate armor and an builder's T-square. This pile of possessions resembles, intentionally, the geometric and construction equipment scattered across the floor in the German master's print Melancholy – except here, the melancholic mess is caused by this smirking deity and the turmoil he can unleash.

"Affection sees not with the vision, but with the soul, / And therefore is winged Love painted blind," wrote Shakespeare, shortly prior to this work was produced around 1601. But Caravaggio's Cupid is not blind. He gazes straight at you. That face – ironic and ruddy-faced, looking with bold confidence as he struts unclothed – is the same one that shrieks in fear in Abraham's Test.

As Michelangelo Merisi da Caravaggio painted his multiple portrayals of the identical distinctive-looking youth in the Eternal City at the start of the seventeenth century, he was the highly celebrated sacred artist in a metropolis ignited by religious renewal. The Sacrifice of Isaac demonstrates why he was sought to adorn sanctuaries: he could adopt a biblical narrative that had been depicted numerous times before and make it so fresh, so unfiltered and physical that the horror appeared to be occurring directly in front of you.

Yet there existed another aspect to the artist, evident as quickly as he arrived in the capital in the winter that concluded 1592, as a painter in his initial 20s with no mentor or patron in the city, just skill and audacity. Most of the works with which he captured the sacred city's attention were anything but holy. That could be the very first hangs in the UK's art museum. A young man opens his crimson mouth in a scream of pain: while stretching out his dirty digits for a cherry, he has rather been bitten. Youth Bitten by a Reptile is eroticism amid poverty: observers can discern Caravaggio's gloomy room reflected in the murky waters of the transparent vase.

The boy wears a pink blossom in his hair – a emblem of the sex commerce in Renaissance painting. Venetian artists such as Tiziano and Palma Vecchio portrayed prostitutes holding blooms and, in a work lost in the second world war but documented through photographs, Caravaggio portrayed a renowned woman courtesan, holding a bouquet to her chest. The message of all these floral indicators is obvious: sex for sale.

How are we to make of Caravaggio's erotic depictions of boys – and of a particular boy in particular? It is a question that has split his interpreters ever since he achieved mega-fame in the twentieth century. The complicated historical reality is that the painter was neither the queer icon that, for example, the filmmaker presented on film in his twentieth-century film about the artist, nor so completely pious that, as certain art scholars improbably claim, his Boy With a Basket of Fruit is in fact a likeness of Jesus.

His early works do make explicit erotic implications, or even propositions. It's as if the painter, then a destitute young artist, aligned with Rome's prostitutes, offering himself to survive. In the Uffizi, with this thought in consideration, viewers might look to another initial work, the 1596 masterwork the god of wine, in which the god of alcohol gazes coolly at the spectator as he starts to undo the dark sash of his garment.

A few annums following Bacchus, what could have driven Caravaggio to create Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was at last growing almost established with prestigious ecclesiastical projects? This unholy pagan deity revives the erotic challenges of his initial works but in a increasingly intense, uneasy way. Half a century later, its hidden meaning seemed obvious: it was a portrait of the painter's companion. A British visitor saw the painting in about 1649 and was informed its subject has "the body & face of [Caravaggio's|his] own youth or servant that slept with him". The name of this adolescent was Cecco.

The painter had been dead for about 40 annums when this story was documented.