1. Chapter- 6: Gene Regulations Regulation of gene expression (or gene regulation) includes the processes that cells and viruses use to regulate the way that the information in genes is turned into gene products.cellsvirusesgenesgene products Although a functional gene product may be an RNA or a protein, the majority of known mechanisms regulate protein coding genes. RNAprotein Any step of the gene's expression may be modulated, from DNA-RNA transcription to the post-translational modification of a protein.gene's expressiontranscription post-translational modification

2. Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility and adaptability of an organism by allowing the cell to express protein when needed.viruses prokaryoteseukaryotes organism The first discovered example of a gene regulation system was the lac operon, discovered by Jacques Monod, in which protein involved in lactose metabolism are expressed by E. coli only in the presence of lactose and absence of glucose.lac operonJacques MonodlactoseE. coli

3. Regulated stages of gene expression Any step of gene expression may be modulated, from the DNA-RNA transcription step to post-translational modification of a protein.transcriptionpost-translational modification The following is a list of stages where gene expression is regulated, the most extensively utilised point is Transcription Initiation: Chromatin domains Transcription Post-transcriptional modification RNA transport Translation mRNA degradation

4. Modification of DNA Chemical Methylation of DNAMethylation of DNA is a common method of gene silencing. DNA is typically methylated by methyltransferase enzymes on cytosine nucleotides in a CpG dinucleotide sequence (also called "CpG islands" when densely clustered).CpG islands

5. Regulation of transcription Regulation of transcription controls when transcription occurs and how much RNA is created. Transcription of a gene by RNA polymerase can be regulated by at least five mechanisms:RNA polymerase 1. Specificity factors alter the specificity of RNA polymerase for a given promoter or set of promoters, making it more or less likely to bind to them (i.e., sigma factors used in prokaryotic transcription).Specificity factorspromotersigma factorsprokaryotic transcription 2. Repressors2. Repressors bind to non-coding sequences on the DNA strand that are close to or overlapping the promoter region, impeding RNA polymerase's progress along the strand, thus impeding the expression of the gene.

6. 3. General transcription factors3. General transcription factors position RNA polymerase at the start of a protein-coding sequence and then release the polymerase to transcribe the mRNA. 4. Activators4. Activators enhance the interaction between RNA polymerase and a particular promoter, encouraging the expression of the gene. Activators do this by increasing the attraction of RNA polymerase for the promoter, through interactions with subunits of the RNA polymerase or indirectly by changing the structure of the DNA.promoter 5. Enhancers5. Enhancers are sites on the DNA helix that are bound to by activators in order to loop the DNA bringing a specific promoter to the initiation complex.

7. Post-transcriptional regulation After the DNA is transcribed and mRNA is formed, there must be some sort of regulation on how much the mRNA is translated into proteins. Cells do this by modulating the capping, splicing, addition of a Poly(A) Tail, the sequence-specific nuclear export rates, and, in several contexts, sequestration of the RNA transcript. These processes occur in eukaryotes but not in prokaryotes. This modulation is a result of a protein or transcript that, in turn, is regulated and may have an affinity for certain sequences.

8. Regulation of translation The translation of mRNA can also be controlled by a number of mechanisms, mostly at the level of initiation. Recruitment of the small ribosomal subunit can indeed be modulated by mRNA secondary structure, antisense RNA binding, or protein binding. In both prokaryotes and eukaryotes, a large number of RNA binding proteins exist, which often are directed to their target sequence by the secondary structure of the transcript, which may change depending on certain conditions, such as temperature or presence of a ligand (aptamer). Some transcripts act as ribozymes and self-regulate their expression.ribozymes

9. GENE REGULATION Virtually every cell in your body contains a complete set of genes But they are not all turned on in every tissue Each cell in your body expresses only a small subset of genes at any time During development different cells express different sets of genes in a precisely regulated fashion

10. GENE REGULATION Gene regulation occurs at the level of transcription or production of mRNA A given cell transcribes only a specific set of genes and not others Insulin is made by pancreatic cells

11. CENTRAL DOGMA Genetic information always goes from DNA to RNA to protein Gene regulation has been well studied in E. coli When a bacterial cell encounters a potential food source it will manufacture the enzymes necessary to metabolize that food

12. Gene Regulation In addition to sugars like glucose and lactose E. coli cells also require amino acids One essential aa is tryptophan. When E. coli is swimming in tryptophan (milk & poultry) it will absorb the amino acids from the media When tryptophan is not present in the media then the cell must manufacture its’ own amino acids

13. Trp Operon E. coli uses several proteins encoded by a cluster of 5 genes to manufacture the amino acid tryptophan All 5 genes are transcribed together as a unit called an operon, which produces a single long piece of mRNA for all the genes RNA polymerase binds to a promoter located at the beginning of the first gene and proceeds down the DNA transcribing the genes in sequence

15. GENE REGULATION In addition to amino acids, E. coli cells also metabolize sugars in their environment In 1959 Jacques Monod and Fracois Jacob looked at the ability of E. coli cells to digest the sugar lactose

16. GENE REGULATION In the presence of the sugar lactose, E. coli makes an enzyme called beta galactosidase Beta galactosidase breaks down the sugar lactose so the E. coli can digest it for food It is the LAC Z gene in E coli that codes for the enzyme beta galactosidase

17. Lac Z Gene The tryptophane gene is turned on when there is no tryptophan in the media That is when the cell wants to make its’ own tryptophan E. coli cells can not make the sugar lactose They can only have lactose when it is present in their environment Then they turn on genes to beak down lactose

18. GENE REGULATION The E. coli bacteria only needs beta galactosidase if there is lactose in the environment to digest There is no point in making the enzyme if there is no lactose sugar to break down It is the combination of the promoter and the DNA that regulate when a gene will be transcribed

19. GENE REGULATION This combination of a promoter and a gene is called an OPERON Operon is a cluster of genes encoding related enzymes that are regulated together

20. GENE REGULATION Operon consists of A promoter site where RNA polyerase binds and begins transcribing the message A region that makes a repressor Repressor sits on the DNA at a spot between the promoter and the gene to be transcribed This site is called the operator

22. LAC Z GENE E. coli regulate the production of Beta Galactocidase by using a regulatory protein called a repressor The repressor binds to the lac Z gene at a site between the promotor and the start of the coding sequence The site the repressor binds to is called the operator

24. LAC Z GENE Normally the repressor sits on the operator repressing transcription of the lac Z gene In the presence of lactose the repressor binds to the sugar and this allows the polymerase to move down the lac Z gene

25. LAC Z GENE This results in the production of beta galactosidase which breaks down the sugar When there is no sugar left the repressor will return to its spot on the chromosome and stop the transcription of the lac Z gene

28. GENE REGULATION In eukaryotic organisms like ourselves there are several methods of regulating protein production Most regulatory sequences are found upstream from the promoter Genes are controlled by regulatory elements in the promoter region that act like one/off switches or dimmer switches

29. GENE REGULATION Specific transcription factors bind to these regulatory elements and regulate transcription Regulatory elements may be tissue specific and will activate their gene only in one kind of tissue Sometimes the expression of a gene requires the function of two or more different regulatory elements

30. INTRONS AND EXONS Eukaryotic DNA differs from prokaryotic DNA it that the coding sequences along the gene are interspersed with noncoding sequences The coding sequences are called EXONS The non coding sequences are called INTRONS

31. INTRONS AND EXONS After the initial transcript is produced the introns are spliced out to form the completed message ready for translation Introns can be very large and numerous, so some genes are much bigger than the final processed mRNA

32. INTRONS AND EXONS Muscular dystrophy DMD gene is about 2.5 million base pairs long Has more than 70 introns The final mRNA is only about 17,000 base pairs long

33. RNA Splicing Provides a point where the expression of a gene can be controlled Exons can be spliced together in different ways This allows a variety of different polypeptides to be assembled from the same gene Alternate splicing is common in insects and vertebrates, where 2 or 3 different proteins are produced from one gene