The Basics of Molecular Biology Tutorial on Comparative Genomics part II NSF DBI-1515704

A Starting Point You know what a gene looks like and where it falls on a chromosome from part I. Genes themselves don’t do anything. They need to be “expressed”.

The Central Dogma of Molecular Biology Expression is the conversion of the information in a gene from DNA to protein, which carries out the chemical functions of a cell. DNA is first converted to mRNA in a process called transcription. mRNA is then converted to protein in a process called translation. In addition to the chemical sequence of a protein, the amount of protein that is produced (concentration) is also critical to its function. The image at right is from Dhorspool at en.wikipedia, CC BY-SA 3.0, https://commons.wikimedia.org/w/inde x.php?curid=15183788.

Transcription Transcription is the process of producing mRNA from the DNA-based gene. mRNA is chemically similar to DNA, but is single stranded. mRNA production in eukaryotes can be tightly regulated by transcription factors. mRNAs are processed to remove introns, the non-coding bits of the gene, and to add a 5’ cap and a 3’ long poly-A tail. The figure on the left shows the assembly of transcriptional regulators on a gene (from http://mol- biol4masters.masters.grkraj.org/html/Gene_Expression_II5B- Mechanism_of_Transcription.htm). The image on the right shows the process of mRNA maturation to read the mRNA for translation (taken from http://www.biology-pages.info/T/Transcription.html).

Translation Translation is the process by which the information in an mRNA sequence is converted to the information in a protein sequence. Proteins are also polymers, made up of individual amino acids (there are 20 of these). An enzyme called a ribosome (that is a mix of RNA and protein molecules) produces protein molecules from mRNA molecules with the use of additional molecules called tRNAs that provide the “translation” between informational languages according to the genetic code (next slide). The image at right shows a ribosome using tRNAs to produce a protein (with amino acid balls) from an mRNA. The image was taken from http://www.bio.miami.edu/dana/250/250S S10_9print.html.

The Genetic Code The genetic code represents the translation from the 4 character mRNA language of A, C, G, U(T) and the 20 character protein language. It is a triplet code, meaning groups of 3 contiguous nucleotides encode an amino acid. There is redundancy in the code, as there are 64 codons to represent 20 amino acids plus a stop signal. The genetic code is different in different organisms, but the most standard code is shown at right, taken from https://upload.wikimedia.org/wiki pedia/commons/thumb/d/d6/Gen eticCode21-version-2.svg/2000px- GeneticCode21-version-2.svg.png.

Protein structure determines protein function Proteins are made up of domains, sets of sequence that fold independently. There are a limited number of domains that function together as proteins. Each domain orients a specific set of residues in a specific way, so as to enable the protein to function. An example of an SH2 domain is shown below. This domain binds proteins and peptides that contain phosphotyrosine or tyrosine and functions in signal transduction (which will be explained two slides forward).

What are protein functions? Protein function really boils down to chemistry. Some proteins bind to other proteins or other molecules. This can, for example, facilitate the interaction of bound molecules or conversely sequester them. Some proteins (enzymes) catalyze reactions (chemical transformations). Some proteins are involved in the transport of other molecules, for example transporting ions from one side of a membrane to another.

Proteins function as part of metabolic and signaling pathways Proteins don’t really function in isolation but act together with other proteins in a couple key ways. What is metabolism? Metabolism is the set of chemical transformation involved in obtaining energy and biological building blocks and breaking down other compounds. It involves collections of enzymes, frequently working in tandem in what is called a pathway. What is signaling? Signal transduction is the process of relaying information from outside a cell or from the cytoplasm to the nucleus, spurring transcription of other genes. This frequently involves cascades of binding and phosphorylation/dephosphorylation. Examples of metabolic and signaling pathways taken from the KEGG database are shown at left and below, respectively.