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The young lad cries out as his skull is forcefully held, a large digit digging into his face as his father's mighty hand holds him by the neck. That scene from Abraham's Sacrifice visits the Uffizi Gallery, creating distress through the artist's harrowing rendition of the suffering child from the biblical narrative. The painting seems as if Abraham, commanded by God to sacrifice his son, could snap his spinal column with a single turn. Yet Abraham's chosen method involves the silvery grey blade he holds in his other hand, prepared to cut Isaac's neck. A definite aspect remains – whoever modeled as the sacrifice for this astonishing work demonstrated extraordinary expressive ability. There exists not only fear, surprise and begging in his shadowed eyes but also deep sorrow that a protector could abandon him so completely.

He took a familiar scriptural story and transformed it so fresh and visceral that its terrors appeared to happen right in view of you

Viewing in front of the painting, observers recognize this as a actual countenance, an precise depiction of a young subject, because the same youth – identifiable by his disheveled hair and almost dark pupils – appears in two other works by Caravaggio. In every case, that highly expressive visage dominates the scene. In Youth With a Ram, he gazes mischievously from the shadows while holding a ram. In Amor Vincit Omnia, he smirks with a hardness acquired on Rome's alleys, his black feathery appendages sinister, a unclothed adolescent running chaos in a affluent residence.

Victorious Cupid, presently exhibited at a London museum, constitutes one of the most embarrassing artworks ever created. Observers feel completely unsettled gazing at it. The god of love, whose darts inspire people with often agonizing desire, is portrayed as a very tangible, vividly lit nude figure, straddling overturned items that comprise stringed devices, a music score, plate armour and an builder's T-square. This heap of possessions resembles, intentionally, the mathematical and architectural equipment strewn across the ground in Albrecht Dürer's print Melancholy – except in this case, the melancholic mess is caused by this grinning Cupid and the turmoil he can release.

"Affection sees not with the vision, but with the soul, / And thus is winged Love depicted blind," penned Shakespeare, shortly prior to this painting was produced around the early 1600s. But the painter's god is not blind. He gazes directly at the observer. That countenance – ironic and rosy-cheeked, looking with brazen confidence as he struts naked – is the same one that screams in terror in The Sacrifice of Isaac.

When the Italian master created his multiple portrayals of the identical unusual-looking kid in Rome at the start of the seventeenth century, he was the highly acclaimed religious artist in a metropolis enflamed by Catholic renewal. Abraham's Offering reveals why he was sought to adorn sanctuaries: he could take a biblical story that had been portrayed numerous times before and make it so fresh, so raw and physical that the horror appeared to be happening immediately in front of you.

Yet there existed a different aspect to Caravaggio, apparent as quickly as he arrived in Rome in the cold season that concluded the sixteenth century, as a artist in his early twenties with no mentor or supporter in the city, just talent and audacity. The majority of the paintings with which he captured the holy city's attention were everything but holy. What could be the very first resides in the UK's art museum. A young man opens his crimson mouth in a yell of agony: while stretching out his dirty digits for a fruit, he has instead been bitten. Youth Bitten by a Reptile is eroticism amid poverty: observers can discern Caravaggio's dismal room reflected in the murky waters of the glass vase.

The boy sports a rose-colored blossom in his coiffure – a emblem of the sex trade in Renaissance painting. Northern Italian painters such as Tiziano and Palma Vecchio depicted courtesans grasping blooms and, in a work lost in the second world war but known through photographs, Caravaggio represented a famous woman prostitute, clutching a posy to her chest. The message of all these botanical signifiers is clear: intimacy for purchase.

What are we to make of Caravaggio's erotic depictions of boys – and of a particular boy in specific? It is a question that has divided his commentators since he achieved mega-fame in the 1980s. The complex historical reality is that the artist was neither the queer hero that, for instance, the filmmaker put on film in his twentieth-century movie Caravaggio, nor so entirely pious that, as some art scholars improbably claim, his Boy With a Basket of Fruit is in fact a likeness of Jesus.

His initial paintings do make overt sexual implications, or including offers. It's as if Caravaggio, then a penniless youthful 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 masterpiece the god of wine, in which the deity of alcohol stares calmly at the spectator as he starts to untie the black ribbon of his robe.

A few annums following Bacchus, what could have motivated the artist to paint Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was finally becoming almost respectable with prestigious church commissions? This profane pagan god revives the erotic challenges of his initial paintings but in a more intense, uneasy manner. Half a century later, its hidden meaning seemed obvious: it was a portrait of Caravaggio's companion. A British visitor viewed Victorious Cupid in about the mid-seventeenth century and was told its figure has "the physique and countenance of [Caravaggio's|his] own boy or assistant that slept with him". The name of this boy was Francesco.

The artist had been dead for about 40 years when this story was documented.