Background The Thread of Life. Susan Aldridge. Chapter 2 Molecular Biology of the Cell. Alberts et al. Garland Press Suggested further reading Protein molecules as computational elements in living cells. D. Bray. Nature. 1995 Jul 27;376(6538):307-12. Signaling complexes: biophysical constraints on intracellular communication. D. Bray. Annu Rev Biophys Biomol Struct. 1998;27:59-75. Metabolic modeling of microbial strains in silico. Ms W. Covert, et al. Trends in Biochemical Sciences Vol.26 ( 2001). 179-186. Modelling cellular behaviour. D. Endy & R. Brent. Nature(2001) 409: 391- 395.
A - Introduction to Proteins / Translation The primary structure is defined as the sequence of amino acids in the protein. This is determined by and is co-linear to the sequence of bases (triplet codons) in the gene *. 5---CTCAGCGTTACCAT---3 3---GAGTCGCAATGGTA---5 5---CUCAGCGUUACCAU---3 N---Leu-Ser-Val-Thr---C DNA RNA PROTEIN transcription translation * - this is not strictly true in most eukaryotic genomes
Structure of Genes In Eukaryotic Organisms hnRNA heterogeneous nuclear RNA RNA splicing Transcription mRNA
hnRNA heterogeneous nuclear RNA RNA splicing Transcription mRNA Introns Structure of Genes In Eukaryotic Organisms Exons
Structure of Genes In Eukaryotic Organisms hnRNA heterogeneous nuclear RNA RNA splicing Transcription mRNA Alternative RNA splicing
Structure of Genes In Eukaryotic Organisms hnRNA heterogeneous nuclear RNA RNA splicing Transcription mRNA Control Elements
Structure of Genes In Eukaryotic Organisms Coding sequence can be discontinuous and the gene can be composed of many introns and exons. The control regions (= operators) can be spread over a large region of DNA and exert action-at-a-distance. There can be many different regulators acting on a single gene i.e. more signal integration than in bacteria. Alternate splicing can give rise to more than one protein product from a single gene. Predicting genes (introns, exons and proper splicing) is very challenging. Because the control elements can be spread over a large segment of DNA, predicting the important sites and their effects on gene expression are not very feasible at this time.
Schematic Illustration of Transcription The nucleotides in an mRNA are joined together to form a complementary copy of the DNA sequence.
Translation Note that many ribosomes can read one message like beads on a string generating many polypeptide chains simultaneously. Translation is the synthesis of a polypeptide (protein) chain using the mRNA template. Note the mRNA has directionality and is read from the 5end towards the 3end. The 5end is defined at the DNA level by the promoter but this does not define the translation start. The translation start sets the register or reading frame for the message. The end is determined by the presence of a STOP codon (in the correct reading frame).
Schematic Illustration of Translation Protein Synthesis involves specialized RNA molecules called transfer RNA or tRNA.
The translation start is dependent on: 1) a sequence motif called a ribosome binding site (rbs) 2) an AUG start codon 5-10 bp downstream from the rbs Translation Start Position 3end of 16S rRNA 3AU //-5 UCCUCA |||||| 5-NNNNNNNAGGAGU-N 5-10 -AUG-//-3 mRNA rbs start
In bacteria a single mRNA molecule can code for several proteins. Such messages are said to be polycistronic. Since the message for all genes in such a transcript are present at the same concentration (they are on the same molecule), one might predict that translation levels will be the same for all the genes. This is not the case: translation efficiency can vary for the different messages within a transcript. Gene 1 Gene 2 Gene 3 Gene 4 Promoter (Start) Terminator (Stop) mRNA DNA 4 genes, 1 message