Exam 4 Flashcards
What do repressors do?
Block RNA polymerase from binding. Bind a DNA sequence called an operator, when bound, expression is off
Where is the operator located?
Overlapping or downstream of promoter
Differentiate between inducible and repressible promoters (different terminology from operon)
Promoters controlled by repressors can be inducible (adding signal molecule results in expression) or repressible (adding signal molecule results in repression -> as seen with app/co repressors)
What do activators do?
Help RNA polymerase bind to DNA. Bind upstream of promoter, when bound, expression is on
Differentiate between cis-regulatory elements and trans regulatory elements
CREs are regions of noncoding DNA which regulate transcription of neighboring genes.
TRES are genes that regulate the expression of distant genes
How is the Lac operon controlled by glucose
low glucose causes adenylyl cyclase to make cAMP, which binds to the CAP/CRP protein to activate the operon
How is the Lac operon controlled by lactose
lactose is converted to allolactose that inactivates the Lac repressor (LacI)
Describe how biosynthesis of tryptophan is affected by the presence of tryptophan
Tryptophan binds to and activates a repressor which binds to an operator and prevents synthesis
What is attenuation in regards to the trp operon?
Attenuation is a way to finely tune regulation by controlling when the mRNA from the trp gene is processed intro protein
In the attenuation of the trp operon, what happens when levels of trp are low and more needs to be synthesized?
When levels of trp are low, the ribosome translating the mRNA gets stuck at a pair of trp codons, allowing regions 2 and 3 to pair with each other and RNA P to continue synthesizing the mRNA
anti-termination signal
In the attenuation of the trp operon, what happens when levels of trp high and none is needed?
When levels of trp are high, the ribosome continues past the region with the trp codons, blocking region 2 and causing regions 3 and 4 to pair with each other and RNA P to stop making the mRNA.
termination signal
What does quorum sensing allow?
Quorom sensing allows cells to respond to cell density by producing their own regulatory signal
What does bioluminescence require?
Oxygen, the luciferase enzyme, and lots of ATP
What are autoinducers?
Chemical signal molecules produced by quorum sensing bacteria. Increase in concentration as a function of cell density. The detection of a minimum threshold of autoinducers leads to an alteration in gene expression.
What are the usual autoinducers in the case of gram-negative (bioluminescene)? Gram-positive?
Gram-negative- AHLs (acyl-homoserine lactones)
Gram-positive- peptides
Describe how Quorum sensing works for bioluminescence.
The bacteria sends out AHLs to its environment. If it receives some back, it produces light and more AHL. LuxR is an activator that binds to AHL and DNA allowing RNA polymerase to synthesize Luxl (which produces more AHL) and genes necessary for light production.
Describe a two-component regulatory system. What does it allow and what does it consist of?
A basic stimulus-response coupling mechanism that allows organisms to sense and respond to changes in many different environmental conditions. Consists of an external sensor protein and an internal response regulator protein.
How does a two-component regulatory system work?
The signal interacts with the sensor and causes a conformational change. The sensor phosphorylates the regulator protein and converts regulator to active form.
Describe how the location of a regulator binding on a gene affects its role.
If a regulator binds upstream of a gene it is an activator, if it binds downstream it is a repressor. Can have different roles for different genes.
Describe flagella. What are the two types?
Flagella are rigid and can only rotate clockwise or rotate counterclockwise. They can be either polar (single flagella) or peritrichous (many flagella).
Describe how a polar flagella works when rotated counterclockwise vs clockwise.
The flagella is straight (straight line) when rotated counterclockwise allowing the bacterium to move forward
The flagella is distorted (wiggly line) when rotated clockwise leading to random tumbling
Describe how a peritrichous flagella works when rotated counterclockwise vs clockwise.
Form a polar bundle when rotated counterclockwise leading to forward movement
Point in all directions when rotated clockwise leading to random tumbling
Describe how flagella work when in the context of an attractant or a repellant
Attractant
- External sensors relay signals through methylation cascade into proteins that control the direction of rotation by phosphorylation
- –Still have to tumble to sense conditions, extend counterclockwise run if conditions are improving
Repellant
-Tumble more frequently until they find a direction where the levels of repellant are lowering
Describe Mutualism
benefits both
Describe Syntrophy
chemical relationship, metabolic interaction
Describe Commensalism
one benefits, other is unaffected (most of human microbiome)
Describe Parasitism
one benefits, one is harmed
Describe Antagonism
one is harmed, other is unaffected
Describe Competition
both are harmed
What are the potential benefits of symbiosis?
Protection, access to new habitats, recognition aids, nutrition
What are ruminants?
Herbivorous mammals with four-chambered stomachs that eat plant matter (insoluble polysaccharides) with help from microbes.
Describe what bacteria do in ruminants. What are the major types?
Bacteria provide volatile fatty acids through unfavorable reactions that are powered through the removal of hydrogen gas (converted to methane/CO2)
Bacteria are mostly Firmicutes (G+ fermentation), then Euryarchaeota (methanogens), then Bacteroidetes
What is the human gut biome like?
Fecal is mostly firmicutes and bacteroidets, then proteobacteria (coliform). E coli is less than 1% (we think it represents more because it is easy to culture and is used as an indicator for fecal matter)
Varies with diet, antibiotics, age, exercise
What is the skin microbiome like?
Mostly gram positive. Staphylococcus, Micrococcus, Corynebacterium, Propionibacterium. Nutrient sources are the sebaceous and sweat glands, dry areas have much lower densities.
What is the Respiratory Tract microbiome like? (excluding mouth)
Mouth, throat, trachea, bronchi, lungs.
Mucus membranes form barriers to bacteria; they are antibacterial (let macrophage in) and can slough off to remove bacteria.
The lower respiratory tract (trachea, bronchi, lungs) should not have bacteria, microbes in these sites would be harmful. (Kep tout with barrier defenses: alive, movement of air, mucus, ciliated cells.
What is the mouth microbiome like?
Mouth: nutrient-rich, stable pH and temperature, colonies can adhere to the tongue/gums/teeth. Dental plaque is a biofilm created when tooth enamel is colonized by bacteria such as streptococcus mutant, S. ssanguis, and the anaerobic actinomycetes.
What is the gastrointestinal tract microbiome like?
Esophagus, stomach, small intestine, large intestine
Bacteria change throughout the intestinal tract
O2 levels drop.
We don’t want bacteria in our small intestine, because that is where we absorb food. The Duodenum has few bacteria due to stomach acids, bile, pancreatic secretions.
We can’t eat the food that made it to our large intestine, so we let the bacteria break it down. Mostly just remove moisture, population is anaerobes, bacteria that can digest the complex macromolecules left over and we get extra food out of that.
How is the gut of a newborn populated with bacteria?
Sterile gut of newborn is quickly populated by bacteria from adults and milk
If breast-fed, Bifidobacterium is dominant due to the presence of an amino disaccharide in the milk
Define Virulence
ability to cause disease and how aggressive that disease may be
What type of bacteria are associated with obesity and which with leanness?
Obesity is linked to Firmicutes and leanness to Bacteroidetes
Describe Virulence factors
Allow the organism to obtain nutrients the body does not normally make available
Ex: pathogens make molecules that have a higher affinity for iron that the host’s (free iron is usually very low)
Describe endotoxins (characteristics)
Causes fever, inflammation
Low lethality, weak immunogenicity
Heat stable
Similar structure for all G-
Lipid A
What is the structure of endotoxins?
component of the cell membrane of gram negative bacteria, all have a core of lipid A
How do endotoxins act?
Reacts with proteins in the bloodstream → we overreact → septic shock (low concentrations of endotoxin our reaction is helpful, high concentrations our reaction hurts us) -> fever/inflammation
Define cytokines
substances secreted by certain cells of the immune system, cell signaling
Define pyrogens
substances that produce fever when they react with cytokines
Describe exotoxins (characteristics)
Specific effects based on targeting of receptors
Lethal/strong immunogenicity
Heat labile
Spread throughout the body
Vary widely (each species is different)
Protein
Which type of bacteria produce exotoxins?
Gram +
How are endotoxins/exotoxins produced?
endotoxins are released when the cell dies or reproduces
exotoxins are secreted
Where do enterotoxins work?
gut
Where do cytotoxins act?
cells
Describe AB toxins
A subunit is enzyme that produces toxin, B subunit targets cells
Can permanently attach a ADP to an interior enzyme that turns it on or off forever
Describe superantigens
Toxic shock by overstimulating immune system
Link antigen presenting cells will many different B cells → overproduction of cytokines
What can inactivate toxins? What are they called then?
All toxins can be inactivated by formalin
Then called toxoid, used in vaccines
What is antigenic variation?
External proteins such as fimbriae, pipi, and flagella help the bacteria adhere and colonize
Antigenic variation among populations allow the bacteria to evade the immune system
Immune system selects for those that are not recognized
What are some human factors that contribute to infectious disease?
domestication of animals, travel, overuse of antibiotics/fungals/virals, overcrowding, hygiene + living conditions, technology (legionnaires and air conditioners), moving into new areas (lyme), foods and shipping, mass food production, cultural factors (burial practices → prions)
Describe how most pathogens are opportunists
take advantage of changes, good bacteria in the wrong place
