Prokaryotic and eukaryotic gene structures

Organization of genome in Prokaryotes:
The term prokaryote means “primitive nucleus”. Cell in prokaryotes have no nucleus. The prokaryotic chromosome is dispersed within the cell and is not enclosed by a separate membrane. Much of the information about the structure of DNA comes from studies of prokaryotes, because they are less complex than eukaryotes. Prokaryotes are monoploids they have only one set of genes (one copy of the genome). In most viruses and prokaryotes, the single set of genes is stored in a single chromosome (single molecule either RNA or DNA).
Organization of genome in Prokaryotes:
The term prokaryote means “primitive nucleus”. Cell in prokaryotes have no nucleus. The prokaryotic chromosome is dispersed within the cell and is not enclosed by a separate membrane. Much of the information about the structure of DNA comes from studies of prokaryotes, because they are less complex than eukaryotes. Prokaryotes are monoploids they have only one set of genes (one copy of the genome). In most viruses and prokaryotes, the single set of genes is stored in a single chromosome (single molecule either RNA or DNA). Organization of genome in Prokaryotes:
The term prokaryote means “primitive nucleus”. Cell in prokaryotes have no nucleus. The prokaryotic chromosome is dispersed within the cell and is not enclosed by a separate membrane. Much of the information about the structure of DNA comes from studies of prokaryotes, because they are less complex than eukaryotes. Prokaryotes are monoploids they have only one set of genes (one copy of the genome). In most viruses and prokaryotes, the single set of genes is stored in a single chromosome (single molecule either RNA or DNA).

1. PRESENTED BY M. TUSHARA Ph. D (Ag) – I Year, Dept. of GPBR

2. WHAT IS A GENE ?

3. WHAT IS A CHROMOSOME ? A chromosome is a long DNA molecule with part or all of the genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones to condense the DNA molecule to maintain its integrity.

4. PROKARYOTIC VS EUKARYOTIC CHROMOSOMES

5. GENOME IN PROKARYOTES The term prokaryote means “primitive nucleus” . Cell in prokaryotes have no nucleus. The prokaryotic chromosome is dispersed within the cell and is not enclosed by a separate membrane. Much of the information about the structure of DNA comes from studies of prokaryotes, because they are less complex than eukaryotes. Prokaryotes are monoploids they have only one set of genes (one copy of the genome). The bacterial genome is confined to the nucleoid , which is more or less compact structure without any membrane. The constituents of membrane-free nucleoid are DNA ( ~ 60%), RNA ( ~ 30%) and Protein ( ~ 10%). In addition to the DNA in nucleoids, they have an extra circular DNA called plasmid . nucleoid

6. ORGANIZATION OF DNA IN PROKARYOTES In general, bacterial DNA ranges from 1100 µ m to 1400 µ m in length. A long DNA molecule is greatly folded into loops (40-50). The DNA chain in a loop is coiled on itself to produce supercoilings called chromosomal domain . Supercoils are induced in the loops by DNA gyrase .

7. DNA BINDING PROTEINS The loops in E.coli are bound by some mechanism that may involve proteins and or RNA but the mechanism is not clearly understood. In E. coli , a number of proteins have been isolated which have some similarities with the eukaryotic chromosomal proteins. These proteins are HU, IHF (Integration host factor). H1 (H-NS) and P. It is suspected that HU is involved in the nucleoid condensation. The protein H1 probably has effects on gene expression.

8. EUKARYOTIC CHROMOSOME Eukaryotic chromosome structure  refers to the levels of packaging from the raw  DNA  molecules to the chromosomal structures seen during metaphase in mitosis or meiosis. Chromosomes contain long strands of DNA containing genetic information. The components of eukaryotic chromosome are DNA , RNA , histone , and non-histone proteins , metallic ions , etc. Proteins: Two types of proteins, i.e., histone and non-histone proteins are found associated with DNA in chromosome. Histones (H1, H2A, H2B, H3 & H4) are rich in basic amino acids arginine and lysine. H1, H2A, H2B are rich in lysine whereas H3 & H4 are arginine rich . Histone proteins are highly conserved among eukaryotic cells.

9. ORGANIZATION OF DNA IN EUKARYOTIC CHROMOSOMES Nucleosome Solenoid model is a scientific model which explains the organization of DNA and associated proteins in the chromosome. The model was proposed by Roger Kornberg in 1974 and is the most accepted model of chromatin organization. In eukaryotes, DNA is tightly bound to an equal mass of histones, which serve to form a repeating array of DNA-protein particles, called nucleosomes . If it was stretched out, the DNA double-helix in each human chromosome would form very thin thread, about  6 feet (2 meters) long . Histones play a crucial role in packing this very long DNA molecule in an orderly way (i.e., nucleosome) in nucleus of only a few micrometers in diameter.

10. Nucleosome solenoid model

11. HETEROCHROMATIN VS EUCHROMATIN

12. TELOMERE Telomeres  are the region of DNA at the end of the linear eukaryotic chromosome that are required for the replication and stability of the chromosome. The ends of broken chromosomes are sticky, whereas the normal ends are not sticky. CENTROMERE The region where two sister chromatids of a chromosome appear to be joined or “held together” during mitotic metaphase is called Centromere. Within the centromere region, most species have several locations where spindle fibers attach, and these sites consist of DNA as well as protein. The actual location where the attachment occurs is called the kinetochore and is composed of both DNA and protein. The DNA sequence within these regions is called CEN DNA . Typically, CEN DNA is about 120 base pairs long and consists of several sub-domains, CDE-I, CDE-II and CDE-III.

13. GENE STRUCTURE Genes are made of DNA, where the particular DNA sequence determines the function of the gene. A gene is transcribed (copied) from DNA into RNA , which can either be non-coding ( ncRNA ) with a direct function, or an intermediate messenger ( mRNA ) that is then translated into protein. Each of these steps is controlled by specific sequence elements, or regions, within the gene. These regions may be as short as a few base pairs , up to many thousands of base pairs long.

14. Common gene structure features in prokaryotes and eukaryotes

15. PROKARYOTIC VS EUKARYOTIC GENE STRUCTURES

16. GENE STRUCTURE IN PROKARYOTES A transcription unit is that stretch of DNA that is transcribed into a single RNA molecule. A typical transcription unit has. A promoter at its beginning A start point A coding region and A terminator sequence at its end I n case of prokaryotes, genes encoding the enzymes for a single biosynthetic pathway are usually clustered together into a single regulatory unit called operon . Each operon functions as a single transcription unit.

17. BACTERIAL PROMOTER

18. LAC OPERON The  lac  operon consists of 3  structural genes , and a  promoter , a  terminator ,  regulator , and an  operator . The three structural genes are:  lacZ ,  lacY , and  lacA . LacZ:  It encodes the enzyme β-galactosidase which converts lactose into allolactose (isomeric form) and also breaks a β- galactoside (lactose) into glucose and galactose LacY : It encodes the enzyme galactoside permease. It is transporter protein which facilitates the entry of lactose into cell LacA :  It encodes the enzyme β- galactoside transacetylase. It modify toxic galactoside by transferring an acetyl group from acetyl-CoA to β- galactosides and remove out of cell. Regulatory gene  include Lac I along with Promoter and Operator sequence. Regulatory gene regulate transcription of structural gene. Lac I:  It encodes Repressor protein. The repressor protein binds to operator near promotor. Promoter:  It is the binding site for RNA polymerase. Operator:  It is the binding site for repressor protein.

19. IN THE ABSENCE OF LACTOSE

20. IN THE PRESENCE OF LACTOSE

21. EUKARYOTIC GENE STRUCTURE

22. EUKARYOTIC PROMOTER Eukaryotic promoters are defined as regions that can support transcription at normal efficiency and with proper control. The promoters for RNA polymerase II usually have the following modules or functional sequences. Initiator : It is the region that contains startpoint . It is recognized by RNA polymerase II. The choice of startpoint seems to depend on the location of TATA box. TATA Box: It is a consensus sequence of 8 bases TATAAAAA, having only A.T base pairs and is the only consensus sequence that occupies a fixed position in the promoter at -25. It is usually surrounded by a G.C rich sequence. CAAT Box: This is sequence is located ~ 80 bp upstream of the start point, has the consensus sequence GGCCAATCT and it increases promoter strength. GC Box: It has the consensus sequence GGGCGG, is usually located at -90 and may be present in several copies in a promoter.

23. POST TRANSCRIPTIONAL MODIFICATIONS

24. ALTERNATIVE SPLICING