EJC OCPEG Control

1 EJC H2 Biology T1W3 Control of Prok and Euk Genomes I Control of Prokaryotic and Eukaryotic Genomes I I 1. Introduction If you extract the genome from two different cells of an organism and analyse them, you will find that they are identical. They contain the same number and type of genes. We know that the expressed proteins determine the specific function of the individual different cells. By extrapolation, this means that if all the genes were expressed into functional protein s in each cell , there should be no difference in how these two c ells should look or function. How then do both cells have distinct characteristics and specific functions? We will look at the concept of gene regulation to derive the answer in part 2 of our lecture series. In order to understand the gene regulation mech anisms in both the eukaryotic and prokaryotic genomes (with the focus on eukaryotic genome control as outlined in LO2j), a clear understanding of the mechanisms of gene expression in both must be first learnt. Thus, a snapshot of the overarching structure of this lecture series is as such: 1. Brief overview of gene expression in Prokaryotes and Eukaryotes 2. The various stages of gene expression in Eukaryotes and the associated gene regulation mechanisms involved (covered in greater detail). 3. The various stages of gene expression in Prokaryotes and the associated gene regulation mechanisms involved (covered in less detail). 4. A summary table comparing the control of Prokaryotic and Eukaryotic Genomes (to consolidate understanding and as a side-by-side reference) 2. Learning Outcomes 2 (j) Explain how differential (i.e. spatial and temporal) gene expression in eukaryotes can be regulated at different levels: i. chromatin level (histone modification and DNA methylation) ii. transcriptional level (control elements, such as promoters, silencers and enhancers, and proteins, such as transcription factors and repressors) iii. post-transcriptional level (processing of pre -mRNA in terms of splicing, polyadenylation and 5’ capping) iv. translational level (half-life of RNA and initiation of translation) post-translational level (biochemical modification and protein degradation) 3. References Campbell, N.A. and Reece, J.B. (2008). Biology, 8th edition. Pearson.

2 EJC H2 Biology T1W3 Control of Prok and Euk Genomes I 4. Organisation of Lecture Content Introduction 1 2. Learning Outcomes 1 3. References 1 4. Organisation of Lecture Content 2 5. Introduction to Gene Regulation 4 6. Brief Overview of Transcription and Translation in Prokaryotes and Eukaryotes 7 7. Eukaryotic Gene Expression and Regulation 8 A. At the Genome Level 8 A1 Chromatin Modification 8 A1.1 Chromatin remodelling complex 9 A1.2 DNA Methylation 10 A1.3 Acetylation/Deacetylation of Histones 11 A2 Gene Amplification 12 B. At the Transcription Level 12 B1 Promoter 13 B2 Enhancers and Silencers 14 B2.1 Increasing Transcription Frequency: Enhancers + Activator 14 B2.2 Decreasing Transcription Frequency: Silencers + Repressor 16 C. At the Post - Transcription Level 18 C1 Addition of the 5’ 7-methylguanosine cap 19 C2 Splicing of pre-mRNA 20 C3 Polyadenylation – addition of a poly-A tail to the 3’ end of mRNA 21 D. At the Translational Level 21 D1 mRNA stability / Half-life 21 D2 Binding of small ribosomal subunit 22 D3 Initiation Factors 22 E. At the Post- Translational Level 22 E1 Proteolytic Cleavage and Activation 23

3 EJC H2 Biology T1W3 Control of Prok and Euk Genomes I E2 Chemical Modification 23 E3 Protein Degradation 23 8. Prokaryotic Gene Expression and Regulation 25 A. At the Transcriptional Level 25 A1 Promoter 25 A2 Sigma factor 27 A3 Operon (Covered under Genetics of Bacteria) 28 B. At the Post- Transcriptional level 29 C. At the Translational level 29 C1 mRNA stability / Half-life 29 C2 Binding of small ribosomal subunit 30 C3 Initiation Factors 31 D. At the Post-Translational level 31 9. Table Comparing Control of Gene Expression in Prokaryotes and Eukaryotes 32

4 EJC H2 Biology T1W3 Control of Prok and Euk Genomes I 5. 4 Gene Regulation Gene expression refers to the transcription of a gene to synthesize a functional RNA and/or protein product. Gene regulation in all organisms including prokaryotes and eukaryotes is crucial. This means that prokaryotes and eukaryotes must regulate which genes are expressed and how high/ low the frequency of their expression must be at any given time. The control of gene expres sion/ gene regulation thus refers to the regulation of the amount and timing of appearance of the functional gene product. Question: Why is it important to control gene expression?  Control of gene expression is important due to several reasons. o Some genes are expressed in all the cells all the time. These genes are said to be constitutively expressed.  These are essential genes that code for proteins responsible for metabolic functions (e.g. respiration) common to all cells. o A cell must be responsive to changes in the environment. They therefore must have the ability to continuously turn genes on and off in response to circumstances and demands.  E.g. The lac operon, in which some enzymes involved in lactose metabolism are expressed by E Coli only in the presence of lactose and absence of glucose. o Cellular differentiation: Different cell types need to synthesize different sets of proteins in order to be specialized ( having specific stru ctures and functions).  Although all cells within a multicellular organism have the same genome ( as they were derived from a single zygote), they have specific functions. This is because they express different genes at a specific time during development (temporal) or within a specific tissue (spatial), resulting in different proteins produced.  This spatial and temporal regulation is called differential gene expression. Notes to self

5 EJC H2 Biology T1W3 Control of Prok and Euk Genomes I  Regulation of gene expression can occur at the following levels: o Genome o Transcriptional o Post- transcriptional (RNA processing applies to Eukaryotes only) o Translational (Eukaryotes only) o Post- translational (Eukaryotes only)  Each of these key stages r epresents a potential control point where the expression of a particular gene can be regulated i.e. increased or decreased expression. Hence, not every stage needs to be activated during regulation.  Figure 2 shows a schematic diagram of the main levels of gene expression and potential regulation points, using a eukaryotic cell as an example. Figure 1. Differential Gene Expression in individual cells of an organism. At any given point in time, the type of genes and quantity of gene products expressed in each cell type differs. Note: Gene C is likely an essential or “housekeeping gene” as it is expressed in all cell types shown. Notes to self Notes to self

6 EJC H2 Biology T1W3 Control of Prok and Euk Genomes I Figure 2. Five key stages at which eukaryotic gene expression can be regulated Genomic Control: - Alter the extent of condensation of DNA to promote or prevent transcription Transcriptional Con