Protein metabolism

Protein metabolism denotes the various biochemical processes responsible for the synthesis of proteins and amino acids (anabolism), and the breakdown of proteins by catabolism.*Complexes that are italicized are enzymes. Protein metabolism denotes the various biochemical processes responsible for the synthesis of proteins and amino acids (anabolism), and the breakdown of proteins by catabolism. The steps of protein synthesis include transcription, translation, and post translational modifications. During transcription, RNA polymerase transcribes a coding region of the DNA in a cell producing a sequence of RNA, specifically messenger RNA (mRNA). This mRNA sequence contains codons: 3 nucleotide long segments that code for a specific amino acid. Ribosomes translate the codons to their respective amino acids. In humans, non-essential amino acids are synthesized from intermediates in major metabolic pathways such as the Citric Acid Cycle. Essential amino acids must be consumed and are made in other organisms. The amino acids are joined by peptide bonds making a polypeptide chain. This polypeptide chain then goes through post translational modifications and is sometimes joined with other polypeptide chains to form a fully functional protein. Dietary proteins are first broken down to individual amino acids by various enzymes and hydrochloric acid present in the gastrointestinal tract. These amino acids are further broken down to α-keto acids which can be recycled in the body for generation of energy, and production of glucose or fat or other amino acids. Proteins can be broken down by enzymes known as peptidases or can break down as a result of denaturation. Proteins can denature in environmental conditions the protein is not made for. Protein anabolism is the process by which protein are formed from amino acids. It relies on five processes: amino acid synthesis, transcription, translation, post translational modifications, and protein folding. Proteins are made from amino acids. In humans, some amino acids can be synthesized using already existing intermediates. These amino acids are known as non-essential amino acids. Essential amino acids require intermediates not present in the human body. These intermediates must be ingested, mostly from eating other organisms.   In transcription, RNA polymerase reads a DNA strand and produces an mRNA strand that can be further translated. In order to initiate transcription, the DNA segment that is to be transcribed must be accessible (i.e. it cannot be tightly packed). Once the DNA segment is accessible, the RNA polymerase can begin to transcribe the coding DNA strand by pairing RNA nucleotides to the template DNA strand. During the initial transcription phase, the RNA polymerase searches for a promoter region on the DNA template strand. Once the RNA polymerase binds to this region, it begins to “read” the template DNA strand in the 3’ to 5’ direction. RNA polymerase attaches RNA bases complementary to the template DNA strand (Uracil will be used instead of Thymine). The new nucleotide bases are bonded to each other covalently. The new bases eventually dissociate from the DNA bases but stay linked to each other, forming a new mRNA strand. This mRNA strand is synthesized in the 5’ to 3’ direction. Once the RNA reaches a terminator sequence, it dissociates from the DNA template strand and terminates the mRNA sequence as well. Transcription is regulated in the cell via transcription factors. Transcription factors are proteins that bind to regulatory sequences in the DNA strand such as promoter regions or operator regions. Proteins bound to these regions can either directly halt or allow RNA polymerase to read the DNA strand or can signal other proteins to halt or allow RNA polymerase reading. During translation, ribosomes convert a sequence of mRNA (messenger RNA) to an amino acid sequence. Each 3-base-pair-long segment of mRNA is a codon which corresponds to one amino acid or stop signal. Amino acids can have multiple codons that correspond to them. Ribosomes do not directly attach amino acids to mRNA codons. They must utilize tRNAs (transfer RNAs) as well. Transfer RNAs can bind to amino acids and contain an anticodon which can hydrogen bind to an mRNA codon. The process of bind an amino acid to a tRNA is known as tRNA charging. Here, the enzyme aminoacyl-tRNA-synthetase catalyzes two reactions. In the first one, it attaches an AMP molecule (cleaved from ATP) to the amino acid. The second reaction cleaves the aminoacyl-AMP producing the energy to join the amino acid to the tRNA molecule. Ribosomes have two subunits, one large and one small. These subunits surround the mRNA strand. The larger subunit contains three binding sites: A (aminoacyl), P (peptidyl), and E (exit). After translational initiation (which is different in prokaryotes and eukaryotes), the ribosome enters the elongation period which follows a repetitive cycle. First a tRNA with the correct amino acid enters the A site. The ribosome transfers the peptide from the tRNA in the P site to the new amino acid on the tRNA in the A site. The tRNA from the P site will be shifted into the E site where it will be ejected. This continually occurs until the ribosome reaches a stop codon or receives a signal to stop. A peptide bond forms between the amino acid attached to the tRNA in the P site and the amino acid attached to a tRNA in the A site. The formation of a peptide bond requires an input of energy. The two reacting molecules are the alpha amino group of one amino acid and the alpha carboxyl group of the other amino acids. A by-product of this bond formation is the release of water (the amino group donates a proton while the carboxyl group donates a hydroxyl). Translation can be downregulated by miRNAs (microRNAs). These RNA strands can cleave mRNA strands they are complementary to and will thus stop translation. Translation can also be regulated via helper proteins. For example, a protein called eukaryotic initiation factor-2 (eIF-2) can bind to the smaller subunit of the ribosome, starting translation. When elF-2 is phosphorylated, it cannot bind to the ribosome and translation is halted.