Midterm 2 Flashcards
1
Q
Antibiotics against bacterial transcription/translation
A
- rifamycin: binds to RNA polymerase
- streptomycin: inhibits peptide initiation and elongation
2
Q
Inducible Operon
A
- turned on by substrate
- usually off
- catabolic operons: breaks down nutrients (lac operon)
3
Q
Repressible Operon
A
- turned off by product synthesized
- usually on
- anabolic operons: enzymes required to synthesize an amino acid stop when no longer needed to be produced (arg operon)
4
Q
Structure of Operon
A
- regulator: gene encoding for repressor protein (on/off switch)
- control locus: promoter locus (binds RNA polymerase) and operator locus (binds the repressor)
- structural locus: actual gene transcribed
5
Q
lac operon
A
- lactose metabolism in e.coli (not e.coli’s first nutrient - glucose is first)
- can be induced on a spectrum
- lactose concentration removes repressor and allows transcription
6
Q
arg operon
A
- regulates arginine synthesis
- excess nutrient binds to repressor and activates it
7
Q
Causes and effects of mutations
A
- causes: spontaneous (random changes arising from error - fluctuation test) or induced (exposure to known mutagens - ames test)
- effects (positive or negative) - mutations are permanent, mainly harmful - can still provide adaptive advantages like antibacterial resistance
8
Q
Ames test
A
- screens mutagenic/carcinogenic compounds
- organism: salmonella typhimurium mutant -> lost the ability to synthesize histidine. (mutation is susceptible to back mutation)
- mutant plated on media with minimal histidine (one sample has mutagen and the other is normal)
- high number of revertant (reverts back to natural) means exposed chemical is mutagenic
9
Q
Fluctuation test
A
- tests for randomly occuring mutation (mutations don’t need to occur by selective agent)
- organism: streptomycin-sensitive organisms
- one sample is cultured in large flask of medium and another is inoculated in 100 tubes of medium
- large flask ~ approximately same number of restant colonies on each plane (always mixing allows even spread of antibiotic resistance)
- inoculated 100 tubes: number of resistant colonies varies widely from plate to plate
10
Q
Horizontal Gene Transfer
A
- movement of any genes between organisms
- G/C content: if there is a large genomic island that is different from core genome and is flanked by direct repeats indicate HGT
11
Q
Transformation Experiment - mice
A
- Fredrick Griffith (1928)
- organism - streptococcus pneumoniae
- four mice injected with rough strain (nonvirulent), smooth strain (virulent), heat-killed smooth strain, and rough strain inoculated with heat killed smooth strain
- shows that bacteria can take up something to become virulent
12
Q
Transformation Experiment - bacteria
A
- Avery & McCarthy (1941)
- Demonstration that DNA is genetic material
- s. pneumoniae is naturally competent (which is rare) - able to take up DNA from environment
13
Q
Gram-positive DNA transformation
A
- dsDNA enters transformasome (DNA binding protein + pore)
- DNA is sucked inside and nuclease makes it ssDNA
- ssDNA is taken by RecA for homologous recombination
14
Q
Gram-negative DNA transformation
A
- pilus binds to dsDNA
- dsDNA becomes ssDNA in periplasm
- other steps are similar to gram positive transformation (RecA recruits ssDNA to homologous site)
15
Q
Bacteria competency
A
- naturally competent
- artificially: induced by electroporation or calcium chloride
- acquired: reponse to signals
16
Q
Conjugation experiment - bacteria
A
- lederberg and tatum (1946)
- e.coli nutritional mutatants
17
Q
Conjugation experiment - cell to cell contact
A
- U-shaped tube with glass filter only for DNA
18
Q
HFR
A
- f-plasmid integrates into the chromosome rather than having f-plasmid free forming like normal
- hfr cell brings parts of chromosome into recipient cell
- recipient cell can’t become donor under hfr because the chromosome transfer is incomplete (could be missing gene necessary for conjugation)
19
Q
Transposable Elements
A
- DNA moving within organism genome
- surrounded by repeats
- replicative: gene can be replicated in orignal and target
- conservative: gene only enters target - not in both spots
20
Q
Generalized Transduction
A
- pure bacterial DNA is integrated in a bacteriophage capside
- same generation transfer of bacterial DNA
- lytic stage
21
Q
Specialized Transduction
A
- lysogenic first: phage is integrated into DNA and will replicate
- when environmental stress occurs, changes into lytic phase
- phage genome excised incorrectly so transduced bacteria isn’t pure
22
Q
How to determine evolutionary history/ what is a good biological clock?
A
- need a gene/protein that all organisms have
- is highly conserved with a slow mutation rate
- functionally constant
- e.g 16S rRNA
23
Q
3 domains of life
A
- Carl Woese
- Archaea, Bacteria, Eukarya
24
Q
Phylogenetic trees - key terms
A
- root - initial ancestor
- node - ancestor relating branch of the tree
- monophyletic clade - all from the same ancestor
25
Viral Structure
* viroid - genome/nucleic acid
* virion - capsid (protein layer) + viroid
* sheath and tail fibers (bacteriophage)
* membrane (developed from previous host cells which aid in protection, binding, and entry)
* Symmetrical viral structure: isosahedral and filamentous
* Asymmetrical viral structure: membrane viruses
26
Phage Therapy Advantages
- Specific targeting only certain bacterial species
- Replicate at site of infection to amplify effects
- Active against antibiotic resistant bacteria
- Phages can evolve to overcome bacterial resistant mechanisms (******************************phage-host arms race******************************)
27
Phage Therapy Disadvantages
- development of phage resistance (****************************************phage-host arms race****************************************)
- development of phage neutralizing bacteria
- not accessible to intracellular pathogens
- can transfer toxin genes that make bacteria more pathogenic by inducing lytic phase
- bacteria can also use ************************************************restriction endonuclease************************************************ to cleave unprotected phage DNA that renders it inactive. they may also have methylated (limits transcription) recognition sites so phage DNA can’t integrate.
28
CRISPR - Cas9
* originally inherent to bacteria - primative adaptive immune system
* Clustered Regularly Interspaced Short Palindromic Repeats
* repeats and spacers which don't code for anything but it is near gene coding of proteins for cleavage - Cas9
* finds specific PAM sequence and cuts upstream
29
CRISPR - biofilm
* WT lysogenized strain showed no biofilm formation. Cas gene deleted strain showed biofilm formation (crystal violet stain). Reintroduced Cas gene strain showed restoration of antibiofilm phenotype.
* This ensures that phage produced by lysogen bacteria isn’t contained within a biofilm and can’t kill the rest of the community.
30
Four Chains of Infection
1. Organism (virulence factor)
2. Reservoir (where you find the microbe multiplying but may not be infecting): humans/animal/water/environment
3. Transmission: modes of transmission discussed above
4. Susceptible host: enter through portal of entry and depends on immunocompetence of host
31
Epidemiology Vocabulary
- Prevalence: proportion of cases in a population at a given time and place
- Incidence rates: number of new cases of disease per susceptible people (excludes those already sick) per year
- Morbidity rate: incidence of all diseases in a population
- Mortality rates: number of deaths per number of cases of dease in an area
32
HIV
- HIV is a special RNA virus
- retrovirus: uses reverse transcriptase to copy RNA genome into DNA and insert viral DNA into host genome → life-long infection
- viral genome is surrounded by capsid as well as envelope with a protein layer → protein fit well into CD 4 receptor proteins
-
33
HIV progression to AIDS
CD-4 t-cells decreases as time of infection increases
- Opportunistic disease often are the cause of death for individuals with AIDS as they take advantage of the weakened immune system
- Not all individuals with HIV progress to AIDS as there are therapies that keep CD-4 T-cell counts high
34
Taxonomy
* Classification of Organisms
* Microscopy - physical properties
* Enzymology - how they got and used energy
* Molecular biology - how close their gene sequences are
35
Phylogeny
* classification of organisms by evolutionary relatedness
* 16S RNA
