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Proteins exhibit a diverse array of roles, including serving as receptors, signaling molecules, structural elements, enzymes, components for intracellular transport, frameworks for the extracellular matrix, ion transporters, ion channels, and even facilitators of oxygen and carbon dioxide transport such as hemoglobin. Moreover, proteins contribute to essential bodily structures such as collagen fibers in bones, tendons, and cartilage, and muscle proteins within muscle fibers. In addition to these critical functions, proteins can also be harnessed as a source of metabolic energy. Around 10 to 15 percent of the total energy supply is derived from the breakdown of amino acids, considerably less than lipids (20 to 35 percent) and carbohydrates (45 to 65 percent).
Proteins are made up of long chains of amino acids. The terminology varies from peptide for a short amino acid chain to polypeptide for a chain of about 50 amino acids, and finally, protein for a longer chain than a polypeptide (Figure 44). This hierarchical classification reflects the diverse sizes and functions of these fundamental building blocks in biological systems.
During the process of protein synthesis, the shape of the protein evolves sequentially. Initially, it takes the form of a linear sequence of amino acids, known as the primary structure. Subsequent interactions between neighboring amino acids lead to the folding of the linear chain into various shapes, which constitutes the secondary structure or alpha-helix. Further folding, facilitated by interactions among the amino acids in their new positions, results in the intricate three-dimensional structure referred to as the tertiary structure. For most proteins, the tertiary structure represents their final conformation. However, in some instances, multiple polypeptide chains come together to form a functional protein, creating what is known as the quaternary structure (Figure 45). For example, insulin consists of two polypeptide chains, whereas hemoglobin comprises four polypeptide chains.
Figure 45 | Levels of Structural Organization of Protein | 62 1) Primary Structure : the linear structure of amino acids in the polypeptide chain 2) Secondary Structure : hydrogen bonds between peptide group chains in an alpha helix or beta 3) Tertiary Structure : three-dimensional structure of alpha helices and beta helices folded 4) Quaternary Structure : three-dimensional structure of multiple polypeptides and how they fit together
Essential and Non-essential Amino Acids
While 20 diverse amino acids are found in nature, certain types can be generated within the body and are classified as nonessential amino acids. For instance, glutamine arises through the combination of glutamate and ammonia. On the other hand, specific amino acids must be acquired from the diet due to their inability to be produced within the body. These are categorized as essential amino acids. A prime example is histidine, which the body cannot synthesize and thus needs to be obtained from dietary sources. Other amino acids that fall under the essential category include isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.
Deamination and Transamination
Approximately 60 percent of amino acids undergo conversion into carbohydrates for energy utilization. This metabolic transformation is orchestrated through two interconnected processes related to amino acids: deamination and transamination. Deamination, as its name implies, involves the removal of the amino group from an amino acid. The remaining structure of the amino acid then serves as an intermediary molecule within either the glycolytic pathway or the Krebs cycle. For instance, alanine, an amino acid, is converted into pyruvate by shedding its amino group, which is subsequently converted into ammonia and ultimately transformed into a less harmful substance, urea. In cases where the amino group from alanine is detached and transferred to α-ketoglutarate to form glutamate, another amino acid, this mechanism is termed transamination. In transamination, one of the reactants is an amino acid, and the other is a keto acid. The amino group (NH2) of one molecule is substituted for the keto group (=O) of another molecule. Transamination plays a pivotal role in the synthesis of nonessential amino acids 63.
An amino acid is typically transformed into significant metabolic intermediates, which can be further converted into glucose or subjected to oxidation through aerobic pathways. Amino acids that undergo degradation leading to acetyl CoA are classified as ketogenic because they serve as precursors for ketone bodies. Conversely, amino acids contributing to glucose synthesis or progressing through the Krebs cycle are termed glucogenic.
Urea Cycle
Urea constitutes a substantial portion of the nitrogenous waste, encompassing 80 to 90 percent of nitrogen-containing compounds excreted in urine. Its synthesis occurs in the liver, followed by secretion into the bloodstream and elimination through the kidneys via urine. Notably, sweat glands also expel a minor quantity of urea during physical exertion.
Most of the amino acids are utilized in protein synthesis, producing relatively scant free amino acids within cells. In cases of amino acid surplus, the body lacks the capacity and mechanisms for their storage. Consequently, they are converted into glucose or ketones or are subject to decomposition. Amino acid degradation predominantly occurs in the liver, especially in the presence of protein excess. The breakdown of amino acids yields hydrocarbons and nitrogenous waste. Adding a hydrogen atom converts the amino group into ammonia (NH3). Under acidic conditions, when ammonia captures an electron, it becomes an ammonium ion (NH4+). Stringent regulation of ammonia levels is imperative because it can cross the blood-brain barrier, potentially endangering the central nervous system. The urea cycle orchestrates the processing of the amino group, facilitating its elimination from the body. The liver is the principal site for the complete urea cycle, a series of biochemical reactions that convert NH4+ into urea 64.
Nitrogen Balance
When dietary nitrogen intake matches the quantity excreted, the individual achieves a state of nitrogen balance. Negative nitrogen balance can arise during illness or injury, while positive nitrogen balance might occur due to heightened protein consumption or conditions hindering nitrogenous waste removal 65. For example, young children who receive sufficient protein frequently maintain a positive nitrogen balance.
This page titled 1.6.3: Protein Metabolism was last modified on Wed, 19 Aug 2026 01:43:06 GMT and is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Chaya Gopalan (Consortium of Academic and Research Libraries in Illinois (CARLI)) .
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