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A young lad cries out while his skull is firmly held, a large thumb pressing into his cheek as his father's mighty hand grasps him by the neck. That scene from Abraham's Sacrifice appears in the Uffizi Gallery, creating distress through Caravaggio's harrowing portrayal of the suffering child from the scriptural account. It appears as if Abraham, instructed by God to kill his offspring, could break his neck with a solitary twist. However Abraham's chosen method involves the metallic grey blade he grips in his other hand, prepared to slit the boy's neck. One certain aspect remains – whoever modeled as the sacrifice for this breathtaking piece displayed remarkable expressive ability. Within exists not just fear, surprise and pleading in his shadowed eyes but also deep grief that a protector could abandon him so utterly.

The artist took a familiar scriptural tale and transformed it so vibrant and visceral that its terrors appeared to happen directly in front of you

Standing in front of the painting, observers recognize this as a real face, an precise record of a adolescent subject, because the identical boy – identifiable by his tousled hair and nearly black pupils – features in two additional works by Caravaggio. In every instance, that highly expressive visage dominates the composition. In Youth With a Ram, he peers mischievously from the darkness while holding a lamb. In Victorious Cupid, he grins with a hardness learned on Rome's streets, his black plumed appendages sinister, a unclothed child running chaos in a well-to-do residence.

Amor Vincit Omnia, presently exhibited at a London museum, represents one of the most embarrassing artworks ever created. Observers feel completely disoriented gazing at it. Cupid, whose arrows inspire people with often painful desire, is shown as a extremely tangible, brightly illuminated unclothed form, straddling overturned items that include musical instruments, a musical manuscript, metal armour and an builder's T-square. This heap of items resembles, deliberately, the geometric and architectural gear strewn across the ground in the German master's print Melencolia I – except here, the gloomy disorder is caused by this smirking deity and the turmoil he can unleash.

"Love sees not with the vision, but with the soul, / And thus is feathered Love depicted sightless," penned Shakespeare, shortly before this work was produced around the early 1600s. But Caravaggio's Cupid is not unseeing. He stares straight at you. That face – sardonic and ruddy-faced, looking with brazen confidence as he poses unclothed – is the same one that screams in fear in The Sacrifice of Isaac.

As the Italian master painted his three portrayals of the same distinctive-looking youth in Rome at the start of the seventeenth century, he was the highly acclaimed religious painter in a metropolis enflamed by religious renewal. The Sacrifice of Isaac demonstrates why he was sought to decorate churches: he could take a scriptural narrative that had been depicted many times previously and render it so new, so raw and physical that the terror appeared to be occurring immediately before the spectator.

Yet there was another aspect to the artist, evident as soon as he came in Rome in the winter that concluded the sixteenth century, as a artist in his initial 20s with no mentor or supporter in the city, only skill and boldness. The majority of the works with which he caught the sacred metropolis's attention were everything but devout. That could be the absolute earliest resides in London's art museum. A youth opens his red lips in a yell of pain: while stretching out his filthy fingers for a fruit, he has rather been attacked. Boy Bitten By a Lizard is sensuality amid poverty: observers can see Caravaggio's gloomy room mirrored in the cloudy waters of the glass vase.

The adolescent sports a pink blossom in his hair – a emblem of the sex trade in early modern painting. Northern Italian artists such as Tiziano and Jacopo Palma portrayed courtesans grasping flowers and, in a painting destroyed in the second world war but documented through photographs, Caravaggio represented a famous woman prostitute, holding a bouquet to her bosom. The message of all these floral indicators is obvious: intimacy for sale.

How are we to interpret of Caravaggio's sensual depictions of boys – and of one boy in particular? It is a question that has split his interpreters ever since he gained widespread recognition in the twentieth century. The complicated past reality is that the artist was neither the queer hero that, for example, Derek Jarman put on film in his 1986 movie Caravaggio, nor so entirely pious that, as certain art historians unbelievably assert, his Youth Holding Fruit is in fact a portrait of Christ.

His initial works indeed offer explicit sexual suggestions, or even propositions. It's as if the painter, then a destitute young artist, aligned with the city's sex workers, offering himself to survive. In the Uffizi, with this thought in mind, viewers might look to another initial creation, the 1596 masterpiece the god of wine, in which the deity of alcohol stares calmly at the spectator as he begins to untie the dark sash of his robe.

A several years following Bacchus, what could have driven the artist to paint Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was at last growing almost established with prestigious church commissions? This profane pagan deity resurrects the erotic provocations of his initial paintings but in a increasingly intense, uneasy manner. Fifty years later, its hidden meaning seemed obvious: it was a portrait of Caravaggio's lover. A British traveller viewed the painting in about 1649 and was informed its figure has "the physique and countenance of [Caravaggio's|his] owne youth or assistant that laid with him". The identity of this boy was Francesco.

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