All living things have a genetic molecule In prokaryotes and eukaryotes: DNA –Even in viruses, genetic material is DNA or RNA –Directs day to day operations of the cell –Provides instructions for making a new individual –passed on to daughter cells during cell division Eubacteria and Archaea differ in genome structure –Focus is on Eubacteria 1

Chromosome Organization Most bacteria genomes are single, covalently closed, circular DNA molecule –Others may have a linear molecule or several pieces DNA is negatively supercoiled –DNA is slightly underwound –Underwinding carried out by DNA gyrases –Makes separation of strands easier during transcription Supercoiling creates twisted loops –A section of supercoiled DNA is a domain –About 50 domains estimated to exist 2

3 Packaging of E. coli DNA Note arrows: one shows where the DNA has been “nicked”, relaxing the supercoiling. The other points to a supercoiled region. That supercoiling can be relaxed in ONE PLACE means that the DNA is constrained in places.

What’s in the DNA Genes. Lots of genes. –Many eukaryotes have non-coding DNA = junk –Up to 90% or more of DNA is junk in eukaryotes –Relatively little spacer DNA between genes in prokaryotes –Some Archaea have introns, otherwise, no. 4

Bacteria have transposons A bacterial genome has a dozen or so –“jumping genes”, pieces of DNA that copy themselves DNA either cuts out, inserts elsewhere or Copies itself and copy inserts elsewhere –Simple: Insertion sequences; Code for transposase and repressor –Composite transposons Insertion sequences which flank other DNA Typically antibiotic resistance genes 5

6 Plasmids Plasmids: small, circular, independently replicating pieces of DNA with useful, not essential info. –1% to 10% of genome Types of plasmids –Fertility, –resistance, –catabolic, –bacteriocin, –virulence, –tumor-inducing, and –cryptic

7 About plasmids-1 Fertility plasmid: genes to make a sex pilus; replicates, and a copy is passed to another cell. Resistance plasmid: genes that make the cell resistant to antibiotics, heavy metals. Catabolic plasmid: example, tol plasmid with genes for breaking down and using toluene, an organic solvent. micr302/transfer.html

8 About plasmids-2 Bacteriocin plasmid: codes for bacteriocins, proteins that kill related bacteria. Virulence plasmid: has genes needed for the bacterium to infect the host. Tumor-inducing plasmid: The Ti plasmid found in Agrobacterium tumefaciens. Codes for plant growth hormones. When the bacterium infects the plant cell, the plasmid is passed to the plant cell and the genes are expressed, causing local overgrowth of plant tissue = gall. Very useful plasmid for cloning genes into plants. Cryptic: who knows?

9 DNA replication figures Because of requirement for 5’to 3’ synthesis, lagging strand must repeatedly top and start; needs an RNA primer each time.

10 When you’re small, you need to be stingy and quick Look for many ways that bacteria can save energy and respond quickly to changes in environment. E. coli needs 30 minutes to replicate its DNA, but only 20 minutes to divide into two. How? It gets a head start.

11 Sigma subunit recognizes promoter region of DNA

12 Sense, antisense Compare the sense strand of the DNA to the mRNA. Note that mRNA synthesis will be 5’ to 3’ and antiparallel.

13 The Process of Transcription-2 RNA synthesis continues (Elongation), only one DNA strand (template) is transcribed. RNA nucleotides, complementary to bases on DNA strand, are connected to make mRNA Termination: must be a stop sign, right? –In bacteria, hairpin loop followed by run of U’s in the RNA. Of course, the DNA must code for complementary bases and a run of A’s. See next. Most common. OR –Termination factor “rho”. Enzyme. Forces RNA polymerase off the DNA.

14 Termination of Transcription in Bacteria The hairpin loop destabilizes the interactions between the DNA, mRNA, and polymerase; U-A basepairs are very weak, and the complex falls apart.

15 Transcription in prokaryotes As mRNA is made, it is ready to use. Info from more than one gene is typically found on one mRNA molecule. Simpler process than in eukaryotes –no introns to remove –no cap or poly-A tail –no nuclear membrane to transport through Transcription is expensive: each NTP leaves behind 2 Pi; like spending 2 ATP for every base used.

16 Simultaneous transcription and translation No processing, no nucleus; mRNA already where the ribosomes are, so they get started quickly.