"and yet he felt like he was nailed down and stretched out..."
See in text (Chapter II)
Kafka alludes to two different Biblical images: first, the apple Adam and Eve eat in the Garden of Eden (this fruit is never explicitly named, but is commonly depicted as an apple); and second, to the crucifixion, as Gregor is "nailed down" in the same way that Christ was nailed to the Cross. Kafka uses this image to liken Gregor to a martyr who is nailed to the Cross so that his family might have a better life.
"the clock tower struck the third hour of the morning..."
See in text (Chapter III)
In Part II, Kafka used the image of Gregor being "nailed down" by the apple his father threw at him to allude to Christ's crucifixion. Here, he alludes to the hour of Christ's death (three o'clock) to further equate Gregor with the martyr and to suggest that he's sacrificing himself in order so that his family might have a better life.