So, first let's assume you digest your protein into the usable building blocks: amino acids. Excess dietary amino acids cannot be stored for future use, nor are they excreted unused. Instead, they are converted to common metabolic intermediates that can be either oxidized by the citric acid cycle or used to form glucose or fat. The excess nitrogen liberated by the metabolic degradation of amino acids is excreted in the form of urea via the urea cycle.

Some gets converted to glucose, some gets used for energy by feeding into metabolic pathways for glucose or fatty acids at various points.

From: http://carbsanity.blogspot.com/2010/06/protein-for-energy.html

FWIW, the "excess" part that you're thinking about being excreted in the urine is the nitrogen in the form of urea. Nitrogen balance limits protein, but I've seen the ceiling on what constitutes too much at least 250g and likely more.

Excess protein will be converted into glucose, so that your body can use it for fuel. The process is called gluconeogenesis. If your body doesn't need to use the fuel, it will store it, like anything else. This is why calories are still calories, no matter what format they come in.

The glucose created from the conversion of protein is not likely to be stored as fat via de novo lipogenesis (nor is consumed carbohydrate). The glucose will be stored as glycogen in either the muscles or liver OR burned up. The only time its converted to fat is when liver and muscle stores are maxed out AND too much glucose is present to be burned off (highly unlikely on a paleo diet with activity). Fat gain is directly related to having high glucose in the blood AND fat. The more glucose present the less fat burned and the more fat (if present) stored. Fat storage is directly correlated to the presence of glucose in the blood stream.

Fat can not be directly converted to glycogen as the metabolic pathway does not exist. The glycerol backbone of fat CAN be converted to glucose through a pyruvate pathway, but it is highly inefficient, produces minimal glucose and only occurs when blood/liver glycogen are depleted and the brain is not keto adapted. Therefore the amount of fat converted to glycogen is negligible.

This link explains the possible 3 outcomes protein can have inside a human.http://themedicalbiochemistrypage.org/amino-acid-metabolism.html

What it really comes down to is what is consumed WITH excess protein, whether or not glycogen stores are full, and whether or not muscles are in growth mode.

The fate of excess protein is different in a fasted state than a fed state, a depleted glycogen state, a keto-genic state, a starvation state, a high glucose state, etc.

Li Z, Treyzon L, Chen S, Yan E, Thames G, Carpenter CL. Protein-enriched meal replacements do not adversely affect liver, kidney or bone density: an outpatient randomized controlled trial. Nutr J 2011;9(1):72. http://www.nutritionj.com/content/pd...-2891-9-72.pdf

BACKGROUND: There is concern that recommending protein-enriched meal replacements as part of a weight management program could lead to changes in biomarkers of liver or renal function and reductions in bone density. This study was designed as a placebo-controlled clinical trial utilizing two isocaloric meal plans utilizing either a high protein-enriched (HP) or a standard protein (SP) meal replacement in an outpatient weight loss program. Subjects/methods: 100 obese men and women over 30 years of age with a body mass index (BMI) between 27 to 40 kg/m2 were randomized to one of two isocaloric weight loss meal plans 1). HP group: providing 2.2 g protein/kg of lean body mass (LBM)/day or 2). SP group: providing 1.1 g protein/kg LBM/day. Meal replacement (MR) was used twice daily (one meal, one snack) for 3 months and then once a day for 9 months. Body weight, lipid profiles, liver function, renal function and bone density were measured at baseline and 12 months.

CONCLUSIONS: These studies demonstrate that protein-enriched meals replacements as compared to standard meal replacements recommended for weight management do not have adverse effects on routine measures of liver function, renal function or bone density at one year.

Excess nitrogen from the breakdown of protein will constantly stress out the kidneys. Yes, the carbon portion of the amino acid will be stored or used but the excess nitrogenous waste products slowly damage the nephrons (kidney functioning units) over many decades of life. Take the ever growing group of individuals (millions) that have diabetes and hypertension and the risks for shorter term kidney damage skyrockets.

See renovatingyourmind.com later today (4/4/13) on this specific topic and other subjects that will blow your mind.