Molecular Genetics of Bacteria

1. Molecular Genetics of Bacteria • DNA contains info for making entire cell. • info contained in segments called genes • each gene codes for a protein (many are enzymes) • different enzymes carry out different reactions. • lots of different enzymes, lots of genes needed, long DNA molecule • Types of bacteria differ from one another because their DNA is different. • DNA is information in molecular form.

2. Information is coded into the molecule Other 3 bases are Guanine, cytosine, and thymine. These 2 phosphate groups are lost (to provide energy) when nucleotides are joined together, sugar of one to phosphate of next. The coded information is in the order of the 4 bases.

3. DNA structure Double-stranded molecule. A always pairs with T C always pairs with G H-bonds between the bases help hold the two strands together. (rungs) “Backbone”: alternating sugar and phosphate groups. D = deoxyribose (sugar) P = phosphate

4. Double helix Helix: spiral. Two strands that bind to each other and twist. Because of “base pairing”, if you know the sequence of one strand, you automatically know the sequence of the other. Long thin molecule: if as thick as spaghetti, a bacterial DNA molecule would stretch from here to Bono

5. DNA replication Complementary base-pairing allows for a mechanism for 1 DNA molecule to be copied to produce two identical molecules. Because each new double-stranded molecule is made of one old strand and one new strand, this is called “semi-conservative” replication. The same genetic information thus appears in both new daughter cells.

6. How long and thin? How many genes? • Bacteria are all different. E. coli: • An operon is a group of genes used together at the same time. An average size operon is 4000 bp • Total genome size of E.coli is about 4,000,000 bp • E. coli has over 4,000 genes One gene http://www.sciencebuddies.org/mentoring/plugin_bac_diversity_bacteria_and_dna.jpg

7. Not just for storage, but for use • A cell doesn’t just store its genetic information, it uses it. • Some genes are needed all the time. • Other genes are not; they are turned on and off as needed to save energy • Genes code for proteins • Proteins are made at the ribosomes • How to get a copy of the information to the ribosomes? (DNA is too big and bulky)

8. Transcription • A copy of 1 or more genes is made • The copy is in the form of RNA (mRNA), a much smaller nucleic acid in which is coded the information from one or more genes. • The mRNA is complementary to one of the 2 strands of the DNA (if the DNA strand has T, the RNA has A. • The process of making the mRNA copy of a portion of the DNA is known as transcription. • At the beginning of each gene (or group of genes) there is a sequence of DNA recognized by enzymes that make mRNA. This sequence is called the promoter.

9. RNA has differences 1) DNA is double stranded, but RNA is single stranded. 2) RNA contains ribose instead of deoxyribose 3) RNA contains uracil instead of thymine. www.layevangelism.com/.../ deoxyribose.htmhttp://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/images/uracil.gif

10. Translation • Translation is protein synthesis, the actual making of proteins by the ribosomes using the information in a mRNA molecule. • The actual decoding is done by small RNAs called transfer RNAs (tRNA) that read the code in the mRNA and bring the correct amino acid to be used in the protein. • Review the definition of “primary structure” of a protein • The genetic code is read as 3 bases in a row. Each combination of 3 bases indicates a particular amino acid • Because the DNA of bacteria is in the cytoplasm, not within a nucleus, mRNA is used even before it’s done.

11. Bacterial ribosomes • Ribosomes have 2 subunits, a large and a small • Large subunit: 50 S • 33 polypeptides, 5S RNA, 23 S RNA • Small subunit: 30 S • 21 polypeptides, 16S RNA • Ribosome structure and differences between prokaryotes and eukaryotes are important. • Prokaryotic ribosomes are 70S; eukaryotic are 80S • Differences are the basis for success of many antibiotics • S is Svedberg unit, how fast a particle travels during centrifugation. Affected by both mass and shape.

12. The Genetic Code-2 http://www.biology.arizona.edu/molecular_bio/problem_sets/nucleic_acids/graphics/gencode.gif

13. tRNA: the decoder a.a. attaches here anticodon http://www.designeduniverse.com/articles/Nobel_Prize/trna.jpg

14. Simultaneous transcription and translation • No processing, no nucleus; mRNA already where the ribosomes are, so they get started quickly. http://opbs.okstate.edu/~petracek/Chapter%2027%20Figures/Fig%2027-30.GIF

15. Plasmids • Plasmids: small, circular, independently replicating pieces of DNA with useful, not essential info • Types of plasmids • Fertility, • resistance, • catabolic, • bacteriocin, • virulence, • tumor-inducing, and • cryptic http://www.estrellamountain.edu/faculty/farabee/biobk/14_1.jpg

16. 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. www.science.siu.edu/.../ micr302/transfer.html

17. 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?

18. Gene transfer • Ways that bacteria can acquire new genetic info • Transformation • Taking up of “naked DNA” from solution • Transduction • Transfer of DNA one to cell to another by a virus • Conjugation • “Mating”: transfer of DNA from one bacterium to another by direct contact.

19. Conjugation: bacterial sex • If sex is the exchange of genetic material, this is as close as bacteria get. Conjugation is widespread and does NOT require bacteria to be closely related. • Bacteria attach by means of a sex pilus, hold each other close, and DNA is transferred. • Plasmids other than F plasmids, such as resistance plasmids, can also be exchanged, leading to antibiotic-resistant bacteria.

20. DNA of a cell can be altered • Mutations • Any change in the DNA that can be passed on • Copying mistakes, radiation, chemicals can be causes • Most mutations harmful, but sometimes can help • New DNA becoming permanent • DNA from transformation, transduction, or conjugation becomes permanent part of cell’s DNA. • Some viruses can insert their DNA into the cell’s DNA and hang out indefinitely • These provide new genetic information.