DeYoung and Gray (2009) wrote a review on the neuroscience of the Big Five traits in The Cambridge handbook of personality.

The two relevant paragraphs on conscientiousness:

When considering research on the biological basis of the various impulsivity-related traits, one must bear in mind that most are related to multiple Big Five dimensions. Zuckerman (2005) noted that many studies have found Impulsive Sensation-Seeking and similar traits to be associated with high levels of dopaminergic function and low levels of serotonergic function. However, he argued that dopamine is associated with the approach tendencies reflected in these traits, whereas low serotonin is related to the absence of control or restraint. Involvement of serotonin in control and restraint is consistent with findings that serotonin is associated with Conscientiousness (Manuck, Flory, McCaffery et al. 1998, Rosenberg, Templeton, Feigin et al. 2006).

Another biological factor that may be related to Conscientiousness is glucose metabolism. Glucose represents the basic energy source for the brain, and a number of studies indicate that blood-glucose is depleted by acts of self-control and that the extent of this depletion predicts failures of self-control (Gailliot, Baumeister, DeWall et al. 2007; Gailliot and Baumeister 2007). Further, a self-report measure of trait self-control, which correlates highly with Conscientiousness, similarly predicts failures of self-control (Gailliot, Schmeichel and Baumeister 2006; Tangney, Baumeister and Boone 2004). Perhaps individuals whose metabolism provides their brains with an ample and steady supply of glucose are likely to be higher in Conscientiousness. If individual differences in glucose metabolism prove to be involved in Conscientiousness, one will also want to know what brain systems are consuming glucose to fuel acts of self-control. The prefrontal cortex seems likely to be involved, given its central role in planning and voluntary control of behaviour, and given that its consumption of glucose appears relatively high (Gailliot and Baumeister 2007). An fMRI study (Brown, Manuck, Flory and Hariri 2006) showed that brain activity inventral prefrontal cortex during a response inhibition task was negatively associated with a questionnaire measure of impulsivity that is strongly negatively correlated with Conscientiousness (Whiteside and Lynam 2001).

It seems like high levels of serotonin and blood-glucose are associated with high levels of some specific facets of conscientiousness.