Metabolism Proteins


 Metabolism Proteins Background

Protein metabolism represents various biochemical processes responsible for the synthesis of proteins and amino acids (anabolic), as well as the breakdown of proteins by catabolism. The steps of protein synthesis include transcription, translation and post-translational modification. During transcription, RNA polymerase transcribes the coding region of the DNA in the cell, producing an RNA sequence, particularly messenger RNA (mRNA). The mRNA sequence contains a codon: 3 nucleotide long segment encoding a particular amino acid. Ribosomes translate codons into their respective amino acids. In humans, non-essential amino acids are synthesized by intermediates in the main metabolic pathway, such as the citric acid cycle. Essential amino acids must be consumed and made in other organisms. Amino acids are joined by peptide bonds to form a polypeptide chain. The polypeptide chain then undergoes post-translational modification and is sometimes linked to other polypeptide chains to form a fully functional protein. Dietary proteins are first broken down into individual amino acids by various enzymes and hydrochloric acid present in the gastrointestinal tract. These amino acids are further broken down into alpha-keto acids, which can be recycled in the body to produce energy and produce glucose or fat or other amino acids. Proteins can be referred to as enzymatic breakdown of peptidases or can be broken down by denaturation. Proteins are denatured under ambient conditions and cannot produce proteins. Protein anabolism is the process by which proteins are formed from amino acids. It relies on five processes: amino acid synthesis, transcription, translation, post-translational modification and protein folding. Proteins are made from amino acids. In humans, some amino acids can be synthesized using existing intermediates. These amino acids are referred to as non-essential amino acids. Essential amino acids require intermediates that are not found in the human body. These intermediates must be ingested, mainly feeding other organisms.

Protein metabolism via Environmental Changes

pH

Cellular proteins are maintained at a relatively constant pH to prevent changes in the protonation state of the amino acids. If the pH drops, some of the amino acids in the polypeptide chain can be protonated if the pka of its R group is above the new pH. Protonation can change the charge of these R groups. If the pH is raised, some of the amino acids in the chain can be deprotonated (if the pka of the R group is below the new pH). This also changed the cost of the R group. Since many amino acids interact with other amino acids based on electrostatic attraction, changing the charge can disrupt these interactions. Loss of these interactions alters the structure of the protein, but most importantly it alters protein function, which can be beneficial or harmful. Significant changes in pH can even destroy many of the interactions produced by amino acids and denature (expand) proteins.

Temperature

As the ambient temperature increases, the molecules move faster. Hydrogen bonding and hydrophobic interactions are important stabilizing forces in proteins. If the temperature rises and the molecules containing these interactions move too fast, the interaction can be compromised or even destroyed. At high temperatures, these interactions cannot be formed and functional proteins are denatured. However, it depends on two factors; the type of protein used and the amount of heat applied. The amount of heat applied determines whether this change in protein is permanent or can be converted back to its original form.

References:

1. Djikaev, Y. S.; et al. Temperature effects on the nucleation mechanism of protein folding and on the barrierless thermal denaturation of a native protein. Physical Chemistry Chemical Physics. 2008,10 (41): 6281.

2. Taylor A. Aminopeptidases: structure and function. FASEB Journal. 1993, 7 (2): 290–298.