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
Q
Viral Structure
A
- 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
Q
Phage Therapy Advantages
A
- 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
Q
Phage Therapy Disadvantages
A
- 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
Q
CRISPR - Cas9
A
- 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
Q
CRISPR - biofilm
A
- 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
Q
Four Chains of Infection
A
- Organism (virulence factor)
- Reservoir (where you find the microbe multiplying but may not be infecting): humans/animal/water/environment
- Transmission: modes of transmission discussed above
- Susceptible host: enter through portal of entry and depends on immunocompetence of host
31
Q
Epidemiology Vocabulary
A
- 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
Q
HIV
A
- 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
Q
HIV progression to AIDS
A
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
Q
Taxonomy
A
- Classification of Organisms
- Microscopy - physical properties
- Enzymology - how they got and used energy
- Molecular biology - how close their gene sequences are
35
Q
Phylogeny
A
- classification of organisms by evolutionary relatedness
- 16S RNA
