Week 2
What is the difference between an acute, chronic and latent viral infection? Which one is most likely to spread when the host is asymptomatic?
Acute-comes on suddenly then goes away, short infectious virions Chronic- Long infectious virions after no more symptoms Latent- temperate virus where DNA becomes part of your chromosome and can be reactivated
Scientists were unable to culture bacterium X from a soil sample even though DNA sequence data indicated that the bacterium was present. Why?
Bacterium X has complex nutritional requirements. Bacterium X can only grow in the presence of certain other bacterial species. Lab techs placed the culture plates at the wrong temperature.
Why are microbes generally more resistant to antibiotics and disinfectants when growing in a biofilm?
Can work as community in biofilms, work together
What is the difference between an enveloped and non-enveloped virus? What is the envelope composed of and where do viruses obtain an envelope?
Enveloped virus contains extra lipid bilayer obtained from host cell
What is EPS? What does it do?
Extra polymeric substance created by planktonic, creates biofilm, allows microbes to live in biofilm together
What does the term "planktonic" mean?
Free roaming bacteria in nature that creates biofilms
What is an example of a human disease caused by reactivation of a latent virus?
Scarlet fever
What is the difference between lytic and temperate phages?
Temperate phage can go into latent state- where viral genome is inserted into host cell genome and both host and viral genomes are replicated
Why are viruses usually specific for a single cell type and/or single host species?
The virus binds to specific receptors on host cell
What does the term "generation time" mean? How can the total number of cells in a population be calculated if the generation time is known? (What is the formula and can you use it?)
Time it takes for bacterial population to double N0(# of cells at time beginning) x 2^n(# of generations-# of doublings) = Nt(# of cells at end)
Why are there relatively few antiviral drugs (as opposed to antibacterial drugs)?
Viruses have no cell wall, no ribosomes and therefore do not have protein synthesis, use host ribosomes and nutrients
lac operon
a gene system whose operator gene and three structural genes control lactose metabolism in E. coli, only turned on when glucose is not available
phase induction
a prophage is excised and enters lytic cycle
proton motive force
energy formed by electrochemical gradient established by electron transport chain
oxidative phosphorylation
energy of proton motive force drive the reaction
repressible
enzyme who's synthesis can be turned off in certain conditions
constitutive
enzymes synthesized constantly; ex enzymes of glycolysis
inducible
enzymes that are synthesized when needed
How are viruses classified?
genome structure (type of nucleic acid and strandedness) and hosts they infect
The protein receptor molecules on a host cell to which viruses attach by their spikes are
glycoproteins
facultative anaerobes
grow better if O2 is present but can also grow w/o it, use aerobic respiration if O2 is available
complex
have nucleocapsid head, tail spikes and tail
precursor
intermediate of catabolism that exit "deconstruction line" of breakdown process when cells use glucose to make amino acids; carbon skeletons
What are the phases of the growth curve? What is happening during each phase? How might bacterial growth in pure culture be different than growth in a natural setting?
lag- transcribing and translating bacterial genes, no division exponential growth/log- division, towards end is production of endospores Stationary- decrease nutrients and space increase waste, endospore production, some bacteria producing antibiotics, net 0=cells are dividing at the rate they are dying Death phase/prolonged decline- bacteria not able to recycle any more nutrients, waste buildup
amphipathic
like soap; A molecule that has both a hydrophilic region and a hydrophobic region.
transition step
links glycolysis to the TCA cycle.
4 biological macromolecules necessary for cellular structures
lipids, carbohydrates, proteins and nucleic acids
If bacterial cell is growing slowly because of nutrient limitation, then a _____ infection is more likely to occur
lysogenic
ATP
main energy of cells, ribose, adenine, and 3 phosphate groups; produced by adding inorganic phosphate group to ADP
sandwiched between the nucleocapsid and the envelope in enveloped viruses is the..
matrixes protein
Soap generally does not destroy all microbes but it aids in their
mechanical removal
terminal electron acceptor
molecule with high affinity (wants electrons), O2
energy source
molecules with low electron affinity (wants to give up electrons), glucose
Is there a cure for prion disease?
no
Chemoorganotrophs
obtain energy by degrading organic compounds to make other organic compounds. take potential energy of chemical bonds to create other ones. dependent on photosynthetic organisms; use substrate-level phosphorylation and oxidative phosphorylation to make ATP
What is an example of a way in which microbes can cooperate in a biofilm?
one microbe might break down polysaccharides while another microbe uses the waste as energy
generalized transduction
result of packaging errors during assembly stage of phage replication
photophosphorylation
use sun's energy and an electron transport chain to create proton motive force
Latent infection
viral infection in which viral genome is present but not active, so new viral particles are not being produced
Lytic infection
viral infection of host cell with subsequent production of more viral particles and lysis of cell
transcription
RNA polymerase enzyme synthesizes single-stranded RNA molecule from DNA template; 5' to 3' direction
temperate phage
bacteriophage that can either become integrated into the host cell DNA as a prophage or direct a productive infection that leads to cell lysis
Lysogen
bacterium that carries phage DNA (prophage) integrated into its genome
Glutaraldehyde
because of toxicity of this sterilant, treated items must be thoroughly rinsed with sterile water before use
translation
decoding information carried in mRNA to synthesize specified protein; requires mRNA, ribosomes and tRNA
elongation of translation
empty tRNAs leave ribosome via E-site, peptide bond formed between amino acids on adjacent tRNAs, tRNAs carrying amino acids occupy A-site and P-site of ribosome
substrate-level phosphorylation
energy release in exergonic reaction is used to add phosphate to ADP
Describe the structure of the SARS-CoV-2 virus. In basic terms, how does it replicate?
genetic instructions to make millions of copies of itself, infected cell reads RNA and translates into many kinds of virus proteins
What is a chemoorganoheterotroph? A photoautotroph?
get energy from organic compounds, Able to create own energy by sun
3 central metabolic pathways that oxidize glucose to CO2
glycolysis, pentose phosphate pathway, and Krebs cycle
What is the difference between an acidophile and a neutrophile? Which one would grow in a jar of pickles?
most microbes are neutrophils (pH 5-8); acidophils, not a lot of microbes can live in it therefore
TCA cycle
oxidizes 2 acetyl groups from transition step and releases two precursor metabolites, two CO2 and 2 ATP
mRNA
temporary copy of DNA, composed of nucleotides, cells decode mRNA into amino acids, 3 nucleotides (codon) to one amino acid
promoter
the DNA sequence to which RNA polymerase binds and initiates transcription
what processes are required for production of virus particles in a host cell?
translation of viral genes, transcription of viral genes, replication of viral genome
signal transduction
transmission of info form outside to inside of cell, allows cells to monitor and react to environmental conditions
formaldehyde
used to kill bacteria and inactivate viruses in vaccines; also used to preserve biological specimens
retrovirus
uses revers transcriptase to make DNA copy form its RNA genome like HIV
cellular respiration
uses the reducing power of NADH and FADH2 generated in glycolysis, the transition step, and the TCA cycle to synthesize ATP
photosynthetic organisms
using energy of sunlight, synthesis organic compounds from CO2. Convert kinetic energy of photons to potential energy of chemical bonds
productive infection
viral infection in which more viral particles are produced
filamentous phages
-single stranded DNA phages that look like long fibers, cause infections but process doesn't kill host cell- 1. Phage attaches to the F pilus of a bacterial cell and injects its single-stranded DNA 2. Phage DNA replicates; phage capsomeres are synthesized and embedded in the host membrane 3. split and have two carrier cells -M13 phage is useful in certain recombinant DNA procedures
Two types of transduction
1. generalized 2. specialized
catabolism of glucose steps
1. oxidizing glucose molecules to generate ATP, reducing power and precursor metabolites; accomplished in series of reactions called central metabolic pathways 2. transferring electrons carried by NADH and FADH2 to terminal electron acceptor, done by cellular respiration or fermentation
Why would an infection involving a biofilm be difficult to treat? Why might the microorganisms be difficult to identify?
Infection could be causes by more than one microorganism present in biofilm, some species cannot be cultured
Why does the research described in "An Irresistible Newcomer" represent a breakthrough discovery?
New way to grow bacterial and new antibiotic
Can viroids infect humans? Where do viroids cause significant disease?
No, are infectious for plants
When a bacterium is in a state of lysogenic conversion, why does it express a different protein(s)---often a toxin? What does this mean for the pathogenicity of the bacterium?
Phenotype is changed by lysogenic phase,
What factors could influence growth rate in vivo? (in the body)
Presence of competing microorganisms host immune system host genetics
elongation of RNA transcript
RNA polymerase denatures DNA exposing new region so elongation can continue and single-stranded RNA molecule is synthesized
obligate aerobes
absolute requirement of O2, use O2 in aerobic respiration
An antiviral drug that binds to a viral spike protein would directly prevent:
attachment
fastidious organisms
bacteria that require growth factors and specific nutrients
halophile
bacteria that require high concentration of salt
obligate anaerobes
cannot grow if O2 is present, killed by O2,
nucleocapsid
capsid- protein coat made up of subunits called capsomeres and nucleic acid
What are two enzymes that obligate aerobes and facultative anaerobes make that protect the cells from reaction oxygen species (ROS)?
catalase and superoxide dismutase
fermentation
cells break down glucose via glycolysis and use pyruvate or derivative as terminal electron acceptor, ATP generated comes from substrate-level phosphorylation during glycolysis
glycolysis
central metabolic pathway that splits glucose and oxidizes it to form molecules of pyruvate
Lysogenic conversion
change in properties of bacterium conferred by prophage
psychrophile
cold arctic regions
What is a way in which microbes can compete in a biofilm?
compete for space and nutrients, some might produce antibiotics
Virion
complete virus in its inert non-replicating form viral particle
thermophile
compost heat
Why is salt a good preservative?
creates a lot of dissolved solute outside of cell so water will flow from in to out of the cell causing cytoplasmic membrane to pull away from cell wall (plasmolysis)
mesophile
human body
If microorganism has temperature optimum close to boiling point of water, is it considered a
hyperthemophile extremophile
aerotolerant anaerobes/obligate fermenters
indifferent to O2, use fermentation
viroid
infectious agents of plants that consists only of RNA, lacks capsid
Prion
infectious protein that causes neurodegenerative disease
What directs corporation of phage DNA into bacterial chromosome
integrase
Viroids are known to infect:
plants
antigenic variation
process by which routine changes occur in a microbial surface antigen
specialized transduction
produces defective phage particles, transfers phage DNA and adjacent host genes, results form errors in excision of the prophage
lytic or virulent phages are ______ infections
productive; exit host at end of infection cycle by lysing cell
endergonic reaction
products have more free energy than starting compounds, requires input of energy
nuclease
protein in T4 lytic cycle that degrades bacterial DNA
chaperones
proteins that fold polypeptides so they become functional
psychrotroph
refrigeration
Enzymes are grouped according to type of _____ that controls their ____
regulation synthesis
microaerophiles
require small amounts of O2
autotroph
requires only carbon dioxide as sole carbon source
metabolic pathway
series of chemical reactions that converts a starting compound to an end product; linear, branched or cyclical
lysogenic conversion
some pathogenic bacteria produce toxins that are encoded on prophage DNA
How do viruses attach to cells?
spike proteins
exergonic reaction
starting compounds have more free energy than products; energy is released
electron carriers
step between energy source and terminal electron acceptor; NAD+/NADH NADP+/NADPH FAD/FADH2
Ribosome
string amino acids together to make polypeptide
reduced/hydrogenation
substance that gains electrons (addition of hydrogen atom)
Oxidized/dehydrogenation
substance that loses electrons (removal of hydrogen atom)
Why organisms use fermentation
suitable inorganic terminal electron acceptor is not available; they lack electron transport chain
antigenic shift
two different strains of a segmented virus enter the same cell, reassortment of the gene segments occur
phase variation
the routine switching on and off of certain genes
In contrast to phage replication, eukaryotic viruses...
the whole protein is encapsulated by the cell
A bacterial species was isolated from the middle of a compost pile where the temperature was 55-65oC. The group that best describes this microorganism would be:
thermophile
tRNA
transfer RNA; type of RNA that carries amino acids to the ribosome, has anticodon
2 major microorganism groups found on skin
transient- from environment, stay on skin for short time, # reduced by hand washing resident(microbiota)- associated with sweat and sebaceous glands, not removed easily
What is the human "phageome"? How is this distinct from the virome?
virome- collection of all viruses in and on human body Phageome- collection of all phages that infect bacterial cells vs. Viruses- that infect host cells
Icosahedral
virus shape, 20 flat triangles arranged like soccer ball
helical
virus shape, appear cylindrical, spiral staircase
Bacteriophage/ phage
virus that infects bacteria