OCPEG Organisation

1 EJC H2 Biology T1W3 Organisation of Prok and Euk Genomes I Organisation of Prokaryotic and Eukaryotic Genomes I 1. Introduction An organism’s genome holds the blueprint of all the information necessary for it to survive and reproduce. You have learnt previously in the topic of DNA and Genomics how genes are made of DNA, where a specific DNA sequence determines the function of a gene. You have also understood the central dogma of life involving the processes of transcription of DNA into RNA, and translation of mRNA into proteins. Each of these steps within the central dogma is controlled by specif ic sequence elements within the gene, making them functional and regulated in their expression. Much of the gene structure of eukaryotes and prokaryotes is broadly similar. However, there are k ey differences in the genome organisation between eukaryotes and prokaryotes which reflect their divergent transcription and translation machinery. It is important to understand the structure/ organisation of both the prokaryotic and eukaryotic genomes a s a foundation to understanding gene expression, regulation and function, as well as appreciate the difference between prokaryotic and eukaryotic genomes. This lecture series encompass 3 parts. In Part 1, you will first learn the difference s in the organisation of both prokary otic and eukaryotic genomes. Part 2 explains how both genomes are controlled/ regulated, and Part 3 covers the topic of cancer. 2. Learning Outcomes 2 (d) Describe the structure and organisation of viral, prokaryotic and eukaryotic genomes (including DNA/RNA, single -/double-stranded, number of nucleotides, packing of DNA, linearity/circularity and presence/absence of introns) (Some parts covered in JC1 Biology). 2 (h) Describe the structure and function of non -coding DNA in eukaryotes (i.e. portions that do not encode protein or RNA, including introns, centromeres, telomeres, promoters, enhancers and silencers) (knowledge of transposons, satellite DNA, pseudo-genes and duplication of segments is not required) 3. References Campbell, N.A. and Reece, J.B. (2008). Biology, 8th edition. Pearson.

2 EJC H2 Biology T1W3 Organisation of Prok and Euk Genomes I 4. Organisation of Lecture Content 1. Introduction 1 2. Learning Outcomes 1 3. References 1 4. Organisation of Lecture Content 2 5. Comparison of the structure and organisation of Prokaryotic and Eukaryotic genomes Table 1: Comparing structure of Prokaryotic and Eukaryotic Genomes 3 Table 2: Comparing organisation of Prokaryotic and Eukaryotic Genomes 6 6. Organisation of the Eukaryotic Genome A. Non-coding DNA sequences 7 B. Typical Features of the Eukaryotic Gene 8 C. Non-coding DNA sequences with Important Functions i. Promoters 9 ii. Introns 10 iii. Terminators iv. Enhancers and Silencers 13 D. Important features of the Eukaryotic chromosome made up on non-coding DNA i. Centromeres 15 ii. Telomeres 16

3 EJC H2 Biology T1W3 Organisation of Prok and Euk Genomes I 5. Comparison of the Structure and Organization of Prokaryotic and Eukaryotic Genomes The term Genome refers to the complete set of genetic material in a particular cellular component. The tables 1 and 2 below compare the key structures and organisation of both the prokaryotic and eukaryotic genomes. Recall that you have learnt some information about the Eukaryotic Genome in the topic of DNA and Genomics, as well as the Prokaryotic Genome in the topic of Genetics of Bacteria (covered under LO2d). Table 1: Structure of Genome Feature Prokaryotic genome Eukaryotic genome Location in cell Nucleoid region, non membrane- bound (prokaryotic cells lack nuclear envelope and nucleus) Nucleus, surrounded by nuclear envelope Size 105-107 base pairs 107-1011 base pairs Number of genes 4,500 25,000 Molecule Double Helix DNA Appearance One chromosome, referred to as monoploid Generally a single, circular molecule More than one chromosome, usually in diploid or higher ploidy levels (two or more sets of chromosomes) Multiple, linear molecules Number of origins of replication (per chromosome) One Multiple Importance: To increase the efficiency of replication due to larger genome size Presence of Telomeres No telomeres in prokaryotic chromosomes as DNA is circular Telomeres present at both ends of the linear chromosome supercoiling

4 EJC H2 Biology T1W3 Organisation of Prok and Euk Genomes I Presense of Centromeres No centromere present Centromere present Association with proteins Naked DNA, insignificant amounts Yes – large amounts e.g. histones (octamer), scaffold proteins Level of DNA packing/coiling Lower degree of condensation: (A) Unfolded chromosome from E. coli has a diameter of 430µm. (B) DNA is folded into chromosomal looped domains by protein-DNA associations. Six domains are shown, but actual number is about 50. (C) Supercoiling cause further compaction, such that it fills an area of about 1 µm. Higher degree of condensation: (A) DNA double helix is associated with proteins called histones. DNA molecules are negatively- charged, histones are positively-charged (due to high proportion of positively-charged amino acids Lys and Arg). DNA thus is held around histones by electrostatic interactions (ionic bonds). Most of DNA is wound around octamers of 8 histone proteins (2 molecules of each histone: H2A, H2B, H2 and H4) to form nucleosomes. The width of a nucleosome is approximately 10 nm (thus also known as the 10nm fibre). Remainder of DNA, called linker DNA, joins adjacent nucleosomes. B C D Supercoiling Formation of looped domains (Looping occurs around histone-like proteins) Looped domains Circular chromosomal DNA (DNA double helix) DNA double helix Histones Linker DNA (“string”) Nucleosome (“bead”) Nucleosomes (10-nm fiber) - Euchromatin Nucleosome Protein scaffold 30-nm fiber - Heterochromatin Looped domains (300-nm fiber) Metaphase chromosome A

5 EJC H2 Biology T1W3 Organisation of Prok and Euk Genomes I Note: The nucleosome is usually considered the basic unit of chromosomal packing. (B) The 10-nm fibre coils around itself to form a 30 nm chromatin fiber (or solenoid), with the help of a fifth type of histone, histone H1. (C) The 30-nm chromatin fibre forms loops called looped domains (a 300-nm fibre) when associated with scaffold proteins (non- histone proteins). (D) Supercoiling present. The loops further coil and fold to produce characteristic metaphase chromosome in a dividing cell.

6 EJC H2 Biology T1W3 Organisation of Prok and Euk Genomes I Table 2: Organisation of Genome Feature Prokaryotic genome Eukaryotic genome Location of Functionally-related Genes on Chromosomes Genes that encode proteins for the same metabolic pathway are grouped together in a single operon. Eg. Lac Operon Genes that encode functionally related proteins are usually located on different chromosomes. Non-coding regions (between and within genes) Not common – typically less than 15% Common – about 98% Control by Promoter Promoter present A single promoter controls the structural genes grouped in an operon. Promoter present Each gene is under the control of its own individual promoter (as well as termination sequence and other control sequences). Presence of introns Typically absent Introns present Introns are interspersed between exons Presence of enhancers or silencers Rarely present Present Extrachromosomal DNA (Plasmids) May be presen