for something like the alert box showing you can use ajax to parse data also without changing the DOM every time also. The most taxing part of running your 2 requests every second and inserting new html each time is the DOM refresh ( not page reload) when the new html is inserted.
As an example you could have a hidden element that is an alert flag. Running your ajax and testing the returned data only, vs indiscriminate and unnecessary replacement of html is a lot more efficient.
On my alert flag I have a clcik handler that would make another request to see the messages, or a hover dropdown element that gets populated with them or whatever UI desired
I'll use JSON as example
{"hasMessages": 1, "pointsChange":0,"newPointsAmount": 330}
now run ajax to pull data, but not change html unless necessary
$.getJSON( url, function(data){
if( data.hasMessages){
$('#messageFlag').text( data.hasMessages).show()
}
if(data.pointsChange){
$('#points').text( newPointsAmount);
}
});