Genomes
What is a genome?
The total of all inherited genetic material (DNA, and for some viruses, RNA) in the cell (includes all chromosomes and plasmids).
What does an activator protein do?
Helps RNA polymerase find promoter sequences that are difficult to "see".
What does RNA polymerase do?
It scans the DNA looking for a "start" sequence, which indicates the presence of a gene (aka promoter sequences), and then fall off the DNA at the "stop" sequences (indicates end of gene).
What "reads" mRNA and produces proteins?
Ribosomes.
How much of the DNA in bacteria is non-coding?
How much of the DNA in humans is non-coding?
Bacteria - less than 15%.
Humans - 95%.
What does a repressor protein do?
Binds and blocks promoter sequence.
Vibrio fisheri is a microorganism found in the light producing organ of the bob tail squid that helps it to hide from predators. Suppose the bob tail squids main predator, the monk seal, is swimming above the squid on the prowl for its next meal. What will the squid do to avoid being eaten?
Produce a cloud of ink to camouflage itself.
What detail about bacteria allows translation to begin while transcription is still underway, making the process of building proteins occur more quickly and efficiently?
The lack of a nucleus.
For prokaryotes, but not eukaryotes, the size of the genome is directly related to the number of genes, and, hence, the number of ______.
Functions.
What is the "central dogma" of molecular biology?
DNA -> (transcription) -> mRNA -> (translation) -> protein
Pseudomonas aeruginosa is a pathogenic bacteria found in the lungs of people with cystic fibrosis. This bacteria uses quorum sensing to determine when to start producing toxins (higher population density = start producing toxins). Suppose you are a microbiologist looking to combat this pathogen. What function would you target to prevent this pathogen from infecting people?
It's ability to quorum sense. If we block quorum sensing, then we can minimize biofilms and minimize infections.
Another possible answer: Assuming that the pathogen has plasmids that code for the toxin and biofilm production, you could target either of these plasmids, and it should prevent infection.
What organism holds the record for the largest genome?
A Japanese flowering pant called Paris japonica.
What key feature distinguishes a plasmid from a chromosome?
Plasmids are not essential for basic cell functions.
Why does a cell make decisions about whether to make specific proteins?
(Hint: 3 answers)
1. Save energy.
2. Timing (certain proteins only needed at specific times for specific functions).
3. Developmental or location specific reasons.
Staphylococcus aureus is the bacteria that causes a range of infections from pneumonia to skin infections to food poisoning. This bacteria forms biofilms in its host and will switch to producing toxins once its population density has hit a certain concentration (Grow to a high number while hidden in a biofilm, then break out and invade). What process/function is Staphylococcus aureus using to determine when to stop forming the biofilm and start producing toxin?
Quorum sensing.
What type of fish in finding nemo appears when Marlin and Dory are in the deep sea/aphotic zone of the ocean (It has a light attached to its head). What is it called when an organism is able to produce its own light?
1. Angler fish.
2. Bioluminescence.
Yersinia pestis, the bacteria known for causing the plague, has a nucleoid (circular DNA) and three plasmids: pPCP1, pFra, and pMT. pPCP1 encodes for a plasminogen-activating protease, which is essential for virulence via a subcutaneous [under the skin] route. On the other hand the pFra and pMT plasmids encode for a capsular protein that has antiphagocytic activity as well as encodes for phospholipase D, which is crucial for survival in the flea gut. Suppose an unethical scientist wanted to make a strain of Yersinia pestis that was missing the pPCP1 plasmid and release a bunch of fleas infected with it into the wild. What would happen?
References:
(https://www.medicalbiochemist.com/2019/03/mcq-yersinia-pestis-pasteurella.html)
Luckily for the microbiologist, their strain will not cause disease (however, they most likely won't be able to continue with their experiments anymore).
Why is a Vibrio cholerae infection deemed an acute infection?
Vibrio cholerae uses quorum sensing to determine when to STOP making its biofilm and toxins. This happens when the cell concentration is high. Therefore, it is an acute infection because the bacteria enter the host, reproduce rapidly, and leave after a limited period of time (~6 months).
Someone with anemia is infected by Corynebacterium diphtheriae, the bacteria responsible for causing diphtheria. The diphtheria toxin is encoded by the dtx gene, and its function is to break open host cells to release iron for the pathogen when iron concentrations are low. Would you expect the gene to be expressed? Why or why not?
No, because the person with anemia should be taking iron supplements, which would increase the concentration of iron in the body. This would mean that the dtx gene would not end up being expressed.
Bacillus anthracis is the bacteria that causes anthrax. It has two plasmids, one that encodes for the enzymes needed to make a capsule and one that encodes for toxins. What happens if the cell is missing one or both plasmids?
It doesn't cause disease, but the cell is still able to grow and divide.