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The young boy cries out as his skull is firmly gripped, a massive digit pressing into his face as his father's mighty palm holds him by the throat. This scene from The Sacrifice of Isaac appears in the Uffizi Gallery, creating distress through Caravaggio's chilling portrayal of the suffering youth from the biblical narrative. The painting appears as if Abraham, instructed by the Divine to sacrifice his son, could break his neck with a solitary twist. However the father's chosen approach involves the silvery steel blade he holds in his remaining hand, ready to cut the boy's throat. One certain element stands out – whoever posed as the sacrifice for this astonishing piece displayed extraordinary expressive ability. There exists not just fear, surprise and begging in his darkened gaze but also profound sorrow that a guardian could abandon him so utterly.

The artist took a familiar scriptural tale and transformed it so vibrant and raw that its horrors appeared to unfold directly in view of you

Viewing in front of the painting, viewers recognize this as a real countenance, an precise record of a adolescent subject, because the same boy – recognizable by his tousled hair and almost dark eyes – appears in several other paintings by Caravaggio. In each case, that richly emotional face commands the composition. In Youth With a Ram, he gazes playfully from the darkness while embracing a ram. In Amor Vincit Omnia, he grins with a toughness learned on the city's alleys, his dark plumed wings demonic, a naked child running riot in a well-to-do dwelling.

Amor Vincit Omnia, presently displayed at a British gallery, constitutes one of the most embarrassing artworks ever created. Observers feel completely unsettled looking at it. Cupid, whose arrows fill people with often agonizing longing, is portrayed as a very real, vividly illuminated nude figure, straddling toppled-over items that comprise musical instruments, a music score, plate armor and an builder's T-square. This pile of possessions echoes, intentionally, the geometric and construction equipment scattered across the floor in the German master's print Melancholy – save here, the melancholic mess is caused by this grinning Cupid and the turmoil he can release.

"Love looks not with the vision, but with the soul, / And thus is winged Cupid depicted blind," wrote Shakespeare, shortly before this work was created around the early 1600s. But Caravaggio's god is not blind. He stares directly at the observer. That face – sardonic and ruddy-cheeked, staring with brazen assurance as he struts unclothed – is the same one that screams in terror in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio created his three images of the same distinctive-looking kid in the Eternal City at the start of the 17th century, he was the most acclaimed religious painter in a metropolis ignited by Catholic revival. Abraham's Offering reveals why he was commissioned to decorate churches: he could take a biblical narrative that had been portrayed many occasions before and render it so fresh, so raw and visceral that the terror appeared to be occurring directly before the spectator.

However there existed another side to the artist, evident as quickly as he arrived in Rome in the winter that concluded 1592, as a artist in his early 20s with no teacher or patron in the urban center, just talent and audacity. The majority of the paintings with which he captured the holy city's eye were everything but holy. That could be the very earliest resides in the UK's art museum. A young man parts his red mouth in a scream of pain: while stretching out his dirty digits for a cherry, he has instead been attacked. Youth Bitten by a Reptile is sensuality amid squalor: observers can see Caravaggio's gloomy chamber mirrored in the murky liquid of the glass container.

The boy sports a pink flower in his coiffure – a emblem of the erotic trade in Renaissance art. Venetian artists such as Tiziano and Jacopo Palma portrayed courtesans holding blooms and, in a painting destroyed in the second world war but documented through images, Caravaggio represented a renowned female courtesan, clutching a bouquet to her bosom. The message of all these floral indicators is clear: sex for sale.

What are we to interpret of the artist's sensual portrayals of youths – and of one boy in specific? It is a inquiry that has divided his interpreters since he achieved mega-fame in the 1980s. The complex past truth is that the painter was neither the homosexual icon that, for instance, the filmmaker presented on screen in his 1986 film Caravaggio, nor so completely pious that, as some artistic historians improbably claim, his Boy With a Basket of Fruit is in fact a likeness of Jesus.

His early works indeed offer explicit erotic suggestions, or even offers. It's as if Caravaggio, then a destitute youthful creator, aligned with the city's sex workers, selling himself to live. In the Uffizi, with this thought in consideration, observers might look to another early work, the 1596 masterwork the god of wine, in which the god of alcohol stares coolly at you as he starts to untie the black sash of his robe.

A few annums following Bacchus, what could have driven the artist to create Victorious Cupid for the art patron Vincenzo Giustiniani, when he was finally growing almost established with important ecclesiastical commissions? This profane non-Christian god revives the sexual challenges of his initial works but in a increasingly intense, unsettling manner. Half a century afterwards, its hidden meaning seemed obvious: it was a portrait of the painter's lover. A British visitor saw Victorious Cupid in about 1649 and was told its subject has "the physique and countenance of [Caravaggio's|his] own boy or assistant that slept with him". The identity of this adolescent was Francesco.

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