Unit 3 Lecture 10/28

Quarum Sensing – the ability of certain kinds of bacteria to change their gene expression or their phenotype at different population densities
Penotype – the genes that something expresses; set of genes that are expressed; can change your phenotype for example, tanning; set of ch. that you actually see in an organism
Genotype – the set of traits that they have DNA/genes and genetic information for
* Many bacteria have genes that are not always on/expressed under some conditions
Ex) Some bacteria commit suicide at high population densities = “quarum sensing”
S. pneumonia = genes for signal, receptor are both always on; at high population densities the signaling molecules attach to the receptor on the bacteria itself and the bacterial gene expression for bacteria cell lyses from the inside is expressed (Lyt A) gene
When all receptors have signal bound to them, Lyt A gene is expressed and kills the bacterium from the inside out
Pseudomonas aeruginosa = at high population densities makes a biofilm made out of ramnolipids, pyocyanin; made at high population densities
Genes for signal and receptor are always on; when all receptors have signal (Homoserine Lactone) molecule bound to them; genes that are expressed are rhamnolipids and pyocyanin genes for biofilm
Genes for HSL signal molecule and receptor are always on
Signaling molecule sticking to receptor causes expression of the ramnolipid gene and pyocyanin gene
This is a common soil and water bacterium; catheters can introduce pseudomonas aeruginosa and its biofilm to the human body
Vibrio fischer = gm -; expresses a gene called luciferase at high population densities  blue green light; uses same signaling molecule as pseudomona aeruginosa (HSL) gene for signal molecule and receptor are always on
When all signaling molecules are attached to receptors on bacteria then luciferase gene is expressed; makes bacteria glow somewhat blue/green
Has a symbiotic relationship with a squid called Eurympmna Scolopes
The squid is nocturnal and a predator to small animals and also is prey for larger animals; off the coast at Hawaii; the squid emitting this kind of light has the same glow as the moon does on the ocean; is able to glow and cancel its own shadow because it has an organ in its head called the “light organ” that is specifically colonized with these bacteria (vibrio fischer)
“Light organ” in the head is volonized w/ Vibrio Fischeri allows high population density of Vibrio Fischeri to express liciferase
Lecture Review
A) OriC site – bacteria have circular chromosomes; at OriC site this is where DNA replication begins on the chromosome; has a whole bunch of A and T because they only have 2 hydrogen bonds between them and not 3 like G and C
DNA has to be unwound before it can be replicated; at OriC site, locally the DNA has to be unwound; only small portion is unwound and unzipped
DNA A binds to the OriC site; and recruits DNA helicase which unwinds the DNA at the OriC site
B) Primase – kind of RNA polymerase is going to synthesize swatch of RNA complementary to bit of DNA – this will allow DNA polymerase enzyme to attach to the strand of DNA, and start copying it
To keep DNA strands separate, single-strand binding protein attaches to unzipped strands to prevent re-annealing
c. DNA polymerase attaches to the RNA primer, synthesizes DNA
i. DNA polymerase synthesizes new DNA complementary to the template strand moving in 5’  3’ direction
ii. DNA polymerase enzyme is going to bring in bases that are complementary to the bases on the single strand of DNA (template strand) and match them up and hook the bases together using a sugar phosphate backbone
iii. This enzyme can only move/travel in a 5’ to a 3’ direction
1. This is an issue since the DNA strands are antiparalell
d. One strand synthesized continuously, but opposite strand has to be synthesized in pieces – it is not synthesized continuously
i. Okazaki fragments on lagging strand
ii. The fragments have to be patched together by DNA Ligase who’s only job is to patch the copied of the lagging strand fragments together
e. DNA replication enzyme sets are moving in opposite directions around the circular chromosome meet at the terminus site, DNA replication stops here
f. Interlocked circles that we got from our complete round of DNA replication have to be uninterlocked/detached
i. Done by 2 enzymes:
1. DNA gyrase
2. Topoisomerase IV
4. Repair to errors in DNA replication
a. Spontaneous mutation rate about 1 mutant base pair per 10 billion base pairs copied
i. Size of bacteria genomes
b. Mismatch repair system
i. Find mismatched bases
iii. Methylated DNA is older
How many mutant bacteria are there in a colony of 1 billion E. coli?
1. Protection of bacterial chromosome from degredation
a. Methylation of adenines and cytosines
b. Restriction enzymes

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