"Mentally challeneged" is a fairly broad term. I will assume you are asking about learning disabilities. Learning disabilities can have an organic cause or they can be a matter of inattention. Take Down Syndrome for example, a chromosomal problem exists in which the person has too many copies of chromosome 21. This organic cause can have definite impacts on the ability to learn. Mild to moderate mental impairment may be present.
Attention Deficit Hyperactivity Disorder or ADHD, on the other hand is a problem that is rooted in a biologic basis, but bouts of inattention are the driving force in some children (and adults) that interfere with some forms of learning. Hyperactivity also contributes because if the child can't sit still for an extended period of time, they might have difficulty learning some things. ADHD children can learn, and some are very smart, but they can't pay attention long enough to hear their lessons.
Even with todays developments in brain studies it is difficult to say in absolute clear terms the difference between a 'healthy' brain and a brain that belongs to a mentally challenged person. Mentally challenged -- this class is a wide one and could be of genetic, social or cognitive impairments. Being a complex organ that is not only culturally controlled but also chemically and electrically, the changes in the brain are found not always in the morphological structure or cortical areas, but in the nature of neural firings.
A mentally challenged person is one suffering from a condition of subnormal intellectual and social development. IQ of such a person ranks significantly below average person. Also the person is less competent in social functioning as compared to to persons of same age group and cultural background.
A person may become mentally challenged due to many diverse causes. Generally condition of most such persons results from a combination of such factors, that none of which could have produce the condition by itself. The contributing factors include things like poverty, poor physical health, malnutrition, insufficient educational advancement, and basic mental capacity.
In a few cases the condition of a mentally challenged person may result from a single cause that may be genetic or environmental. The genetic causes include the presence of an extra chromosome or an abnormal chromosome in the cells.
Environmental causes may occur before, during, or after birth of the mentally challenged person. For example it can be caused by improper mental development of he affected person due to mother catching some types of diseases or encountering other health problems during pregnancy. Premature birth, injury during birth, or failure of new born baby to breathe properly may also cause improper development or damage to the brain resulting in the person becoming mentally challenged. During childhood brain may be damaged by causes such as as brain infection, head injury, prolonged high fever, swallowing or breathing poisonous substances.