(USMLE topics) Biochemistry of proteins, protein digestion, role of the liver, protein synthesis, amino acid metabolism (deamination, urea cycle), connections between aminoacid metabolic pathways and glucose metabolism.

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Proteins are responsible for nearly all bodily and cellular functions: from structural proteins in bones; contractile proteins in muscles; transport proteins in blood plasma; to hormones, antibodies, cell receptors, ion channels, and enzymes that catalyze almost every chemical reactions in biological systems.
Proteins are polymers of amino-acids linked together by peptide bonds. An amino-acid consists of an amino group, a carboxyl group, and a unique side chain, connected to a central carbon, the α-carbon. Instead of being an extended chain of amino-acids, a protein usually folds into a three-dimensional conformation that is critical for its functions. The structure forms as a result of interactions between the side chains of amino-acids, and is thus dictated by the amino-acid sequence.
Of the 20 amino-acids that make up proteins, nearly half are essential, meaning the body cannot synthesize them and must get them from the diet. Animal proteins are usually considered high-quality, complete proteins, because they have similar amino-acid composition as human proteins, and can thus provide all the required amino-acids, but a combination of a variety of plant foods may also do the job.
Proteins in foods are digested in the stomach and small intestine, by the action of stomach acid, which denatures proteins, and several enzymes that hydrolyze peptide bonds. Together they break down proteins into individual amino acids, which are then absorbed into the bloodstream and transported to the liver. The liver uses these amino-acids to synthesize new proteins, most of which are plasma proteins. The liver also distributes free amino-acids to other tissues, for synthesis of tissue-specific proteins. Proteins are synthesized based on genetic information of the cell, using the genetic code, and regulatory signals. Each cell has a characteristic collection of proteins, specific to its functions.
Body proteins are constantly renewed. Older proteins are broken down into free amino-acids, which are recycled, they combine with dietary amino-acids to make new proteins.
Unlike carbohydrates and lipids, proteins cannot be stored for later use. Once the cellular requirement for proteins is met, excess amino-acids are degraded and used for energy, or converted into glucose or fatty acids. Use of amino-acids for energy production also occurs when there is energy shortage, such as during prolonged exercise or extended fasting.
Since there are no nitrogenous compounds in the energy production pathways, the first step in amino-acid degradation is the removal of the amino group, by deamination or transamination, to produce keto-acids. Some amino-acids can be directly deaminated, while others must transfer their amino group to α-ketoglutarate to form glutamate, which is then deaminated to recycle α-ketoglutarate.
Depending on their side chains, keto-acids from different amino-acids may enter the metabolic cycles at different points. They may be converted to pyruvate, acetyl-CoA, or one of the intermediates of the citric acid cycle. Some of these reactions are reversible. When amino-acids are in short supply, citric acid intermediates can be aminated to create new amino-acids for protein synthesis.
Deamination produces ammonia, which is toxic if accumulated. The liver converts ammonia to urea to be excreted in urine. Extreme diets that are excessively high in proteins may overwhelm the kidneys with nitrogenous waste and cause renal damage.

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