This part of the brain controls the signals that we process, and decides which part of the brain we need for a task. In those that have anxiety, it is highly and possibly over active. If we sense a threat, our amygdala directs traffic in the brain to the parts that have learned how to respond to threats. If it senses a calm situation, it directs traffic in our brain to the higher cognitive centers.
"When we experience an amygdala hijack, the emotional part of the brain – the amygdala – overrides the thinking part of the brain – the neocortex – in response to a perceived threat. Depending on the degree of hijack, your ability to reason and think logically is compromised. Your working memory will become less efficient and your blood pressure, adrenaline and hormone levels rise. It can take 3 to 4 hours for it to clear your system…
While an overactive amygdala serves a useful purpose when faced with a genuine physical threat (when emotions and reactions are crucial), it can cause problems when faced with an emotional threat."
http://northofneutral.wordpress.com/2013/05/01/beware-of-amygdala-hijacks/