Protein formation

1. Protein formation • The genes in DNA encode protein molecules, which are the "workhorses" of the cell, carrying out all the functions necessary for life. • Expressing a gene means manufacturing its corresponding protein, and this multilayered process has two major steps.

2. Transcription • In the first step, the information in DNA is transferred to a messenger RNA (mRNA) molecule through a process called transcription. • During transcription, the DNA of a gene serves as a template for complementary base-pairing, and an enzyme called RNA polymerase II catalyzes the formation of a pre-mRNA molecule, which is then processed to form mature mRNA. • The resulting mRNA is a single-stranded copy of the gene, which next must be translated into a protein molecule.

4. Transcription • The mRNA is "read" according to the genetic code, which relates the DNA sequence to the amino acid sequence in proteins. • Each group of three bases in mRNA constitutes a codon, and each codon specifies a particular amino acid (hence, it is a triplet code). • The mRNA sequence is thus used as a template to assemble—in order—the chain of amino acids that form a protein.

6. The codons are written 5' to 3', as they appear in the mRNA. AUG is an initiation codon; UAA, UAG, and UGA are termination (stop) codons.

7. Genome and Proteome • A genome is the complete genetic sequence of an organism; the blueprint for the cellular proteome. Genome consists of nucleic acids and DNA. It stays stable throughout our lives except mutations. • Since DNA is the code, or blueprint, for the construction of cellular proteins, the proteins that an organism can make are limited to those encoded in their genome. The proteome is the full complement of proteins produced by a particular genome. • A transcriptome is the full range of messenger RNA, or mRNA, molecules expressed by an organism. In contrast with the genome, which is characterized by its stability, the transcriptome actively changes. In fact, an organism's transcriptome varies depending on many factors, including stage of development and environmental conditions.

8. Post Translational Modifications Post-translational modifications are key mechanisms to increase proteomic diversity. While the genome comprises 20-25,000 genes, the proteome is estimated to encompass over 1 million proteins. Changes at the transcriptional and mRNA levels increase the size of the transcriptome relative to the genome, and the myriad of different post-translational modifications exponentially increases the complexity of the proteome relative to both the transcriptome and genome. https://www.lifetechnologies.com/pk/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-post-translational-modification.html

9. Post-Translational Modification of Proteins • The polypeptide chain, the product of translation, undergoes post-translational modification before becoming the final protein product • Allows for the extension of functions of the protein by undergoing different processes • Addition of functional groups • Glycosylation (addition of carbohydrates) • Acetylation (addition of acetyl group) • Methylation (addition of methyl group) • Sulfation (addition of sulfate group to a tyrosine) • Change of the chemical nature of the amino acids • Change of the overall structure • Removal of the amino end of the protein • Phosphorylation • Activates or inactivates proteins https://www.premedhq.com/post-translational-modification-of-proteins

10. Characteristics of Post-translational Modifications • The process is enzyme mediated,. • It can occur at any stage. • This can be reversible depending on the nature of the modification. For example, the activities of kinases and phosphatases in which one enzyme adds a phosphate group to a protein while the other removes the phosphate group through hydrolysis. This reversible enzymatic activity often acts as an “on-off switch” for the biological activity of the protein. http://www.fastbleep.com/biology-notes/40/116/1090

11. Phosphorylation Phosphorylation is the addition of a phosphate (PO4) group to a serine, tyrosine or threonine residue in a peptide chain, though it can occur on other residues in prokaryotes. The addition or removal of a phosphate group can alter protein conformation (and therefore function) by locally altering the charge and hydrophobicity where it is added. It plays an important role in regulating many important cellular processes such as cell cycle, growth, apoptosis (programmed cell death) and signal transduction pathways. For example, in signalling, kinase cascades are turned on or off by reversible phosphorylation either by addition or removal of a phosphate group. http://www.fastbleep.com/biology-notes/40/116/1090

12. Ubiquitination The addition of ubiquitin (an 8kDa polypeptide consisting of 76 amino acid residues) linked to an amine group of lysine in target protein via its C-terminal glycine. Poly-ubiquitinated proteins are targeted for destruction which leads to component recycling and the release of ubiquitin. http://www.fastbleep.com/biology-notes/40/116/1090

13. Cellular post-translational modifications This schematic figure shows the location and role of a selection of some of the most important 200 types of post-translational modification (PTM). PTMs are found on all types of protein, from nuclear transcription factors to metabolic enzymes, structural proteins and plasma-membrane receptors. PTMs affect the physicochemical properties of proteins, which provides a mechanism for the dynamic regulation of molecular self-assembly and catalytic processes through the reversible molecular recognition of proteins, nucleic acids, metabolites, carbohydrates and phospholipids. Ac, acetyl group; GPI, glycosylphosphatidylinositol; Me, methyl group; P, phosphoryl group; Ub, ubiquitin. http://www.nature.com/nrm/journal/v7/n6/fig_tab/nrm1939_F1.html

14. Activation of p53 and cellular response Stress signals converge on p53 and activate various protein kinases and/or acetyltransferases, which phosphorylate or acetylate p53, respectively. These post-translational modifications generally result in stabilization and activation of p53 in the nucleus, where p53 interacts with sequence-specific DNA binding sites of its target genes. The transcriptional activation leads to diverse cellular responses such as apoptosis, cell-cycle arrest or DNA repair. When p53 is no longer needed, it is targeted for ubiquitylation by MDM2 and moved out of the nucleus to be degraded by the 26S proteasome. p53 can also act outside of the nucleus to induce apoptosis by binding with anti-apoptotic proteins such as BCL2. http://www.nature.com/nrc/journal/v4/n10/fig_tab/nrc1455_F1.html